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# Children's Brain Tumor Network

Accelerating childhood brain tumor research to faster cures

## Sitemaps

- [XML Sitemap](https://cbtn.org/sitemap.xml): Contains all public & indexable URLs for this website.

## Posts

- [News](https://cbtn.org/news/)
- [Tracking Tumor Evolution to Advance Pediatric Brain Tumor Research](https://cbtn.org/tracking-tumor-evolution-to-advance-pediatric-brain-tumor-research/) - The new CBTN Curated | GFAC Post Mortem helps close a gap by giving researchers a longitudinal view of pediatric brain tumors across the full disease journey.
- [CBTN Curated | LGG-BRAF Brings Research-Ready Precision to Pediatric Cancer Discovery](https://cbtn.org/cbtn-curated-lgg-braf-brings-research-ready-precision-to-pediatric-cancer-discovery/) - The Children’s Brain Tumor Network (CBTN) is working to change pediatric research barriers with a first-of-its-kind low-grade glioma (LGG) data product.
- [Elora J. Khan Foundation Joins CBTN as its Newest Champion](https://cbtn.org/elora-j-khan-foundation-joins-cbtn-as-its-newest-champion/) - Children’s Brain Tumor Network (CBTN) announces its newest Champion, Elora J. Khan Foundation.
- [Breaking Silos, Accelerating Discovery: The Power of Connected Radiation Therapy Data](https://cbtn.org/breaking-silos-accelerating-discovery-the-power-of-connected-radiation-therapy-data/) - Pediatric brain tumor research depends on collaboration. Hospitals worldwide contribute patient data, tumor samples, and clinical expertise to help researchers better understand these complex diseases. Yet even in highly collaborative environments, the data behind that work has often remained difficult to connect. Different types of information live in different systems. Genomic data, clinical records, imaging, - August 9, 2026
- [Bridge To A Cure Integrates with the Children’s Brain Tumor Network to Expand the Power of Collaborative, Data-Driven Discovery](https://cbtn.org/btacintegration/) - Philadelphia, PA — April 2, 2026 — The Children’s Brain Tumor Network (CBTN) today announced the integration of Bridge To A Cure Foundation into its global research network, uniting a decade of philanthropic leadership with one of the world’s most powerful engines for collaborative pediatric brain tumor discovery. The announcement comes as Bridge To A
- [Children’s Brain Tumor Network Names Tatiana Patton as New Director of Operations](https://cbtn.org/childrens-brain-tumor-network-names-tatiana-patton-as-new-director-of-operations/) - The Children’s Brain Tumor Network (CBTN) has announced the appointment of Tatiana Patton, MS, as its new Director of Operations. Patton will lead the organization’s operational strategy and infrastructure to support collaborative, efficient research on a global scale, accelerating progress toward improved outcomes for children with brain tumors. As Director of Operations, Patton’s work advances
- [United We Cure: A Clearer Vision for Pediatric Brain Tumor Research](https://cbtn.org/united-we-cure-a-clearer-vision-for-pediatric-brain-tumor-research/) - Progress in pediatric brain tumor research doesn’t happen in isolation. It happens when data, expertise, and purpose are aligned—and when institutions move forward together. Connection creates focus. Focus accelerates discovery. And discovery saves lives. That belief has guided the Children’s Brain Tumor Network from the start. What’s changed is the scale, strength, and maturity of
- [Children’s Brain Tumor Network to Empower National Expansion of Pediatric Data Sharing Through ARPA-H Pediatric Care eXpansion (PCX)](https://cbtn.org/childrens-brain-tumor-network-to-empower-national-expansion-of-pediatric-data-sharing-through-arpa-h-pediatric-care-expansion-pcx/) - The Children’s Brain Tumor Network (CBTN) today announced its participation in the Pediatric Care eXpansion (PCX) program, a $50 million national initiative launched by the Advanced Research Projects Agency for Health (ARPA-H) to improve health outcomes for children with complex diseases, beginning with pediatric brain cancer, the leading cause of disease-related death among children in
- [CBTN Announces Appointment of Dr. David Kram to Strengthen Tissue Donation Leadership](https://cbtn.org/cbtn-announces-appointment-of-dr-david-kram-to-strengthen-tissue-donation-leadership/) - Children’s Brain Tumor Network (CBTN) announces that David Kram, MD, MCR, FAAP, will serve in a new leadership capacity supporting Gift from a Child (GFAC), a CBTN partner advancing pediatric brain tumor research through patient legacy tissue donation. Dr. Kram, a respected clinician at the University of North Carolina, is a longstanding advocate for post-mortem
- [Blazing A New Path: CBTN Scientists Publish Groundbreaking Research in Nature Communications](https://cbtn.org/blazing-a-new-path-cbtn-scientists-publish-groundbreaking-research-in-nature-communications/) - The Children's Brain Tumor Network (CBTN), a visionary initiative dedicated to accelerating research to improve outcomes for children with brain tumors, recently achieved a significant milestone. A research paper by Dr. Anahita Fathi Kazerooni, Dr. Adam Kraya, and other colleagues, published in the prestigious Nature Communications Journal, sheds new light on the complexities of pediatric low-grade
- [Hassenfeld Children’s Hospital at NYU Langone Joins the Children’s Brain Tumor Network to Accelerate Pediatric Research](https://cbtn.org/hassenfeld-childrens-hospital-at-nyu-langone-joins-the-childrens-brain-tumor-network-to-accelerate-pediatric-research/) - This press release was distributed on April 10, 2025, via PRNewswire. PHILADELPHIA, April 10, 2025 ⎯ Children’s Brain Tumor Network (CBTN) welcomes Hassenfeld Children’s Hospital at NYU Langone as a new member institution. Dr. Jessica Clymer, director of the pediatric neuro-oncology program at Hassenfeld Children’s Hospital, will serve as CBTN principal investigator. “My team and I at Hassenfeld Children’s Hospital are thrilled to collaborate with
- [CBTN Scientists’ Discovery Brings New Hope to Children with Brain Tumors](https://cbtn.org/cbtn-scientists-discovery-brings-new-hope-to-children-with-brain-tumors/) - Treating childhood brain tumors, especially aggressive ones like high-grade gliomas (HGG), has long been a major challenge. But scientists from the Children’s Brain Tumor Network (CBTN) are bringing new hope through innovative research and a fresh approach to understanding these diseases. Looking at Tumors in a New Way Dr. Ammar Naqvi, a lead bioinformatics scientist
- [Children’s Brain Tumor Network Names Dr. John Prensner as New Scientific Co-Chair](https://cbtn.org/childrens-brain-tumor-network-names-dr-john-prensner-as-new-scientific-co-chair/) - This press release was distributed on November 5, 2025, via PRNewswire. The Children’s Brain Tumor Network (CBTN) announced the appointment of John Prensner, MD, PhD, as its new scientific co-chair. A pediatric neuro-oncologist and physician-scientist at the Chad Carr Pediatric Brain Tumor Center at the University of Michigan, Dr. Prensner combines clinical care with leading-edge genomics and RNA
- [Celebrating CBTN Women Behind the Science: Ximena Cuellar](https://cbtn.org/celebrating-cbtn-women-behind-the-science-ximena-cuellar/) - The fight against childhood brain tumors is complex and multifaceted, demanding dedication not only from doctors and researchers in the lab but also from a team of equally vital individuals working behind the curtain where science happens. At the Children’s Brain Tumor Network (CBTN), we recognize that progress wouldn't be possible without the tireless efforts
- [Celebrating CBTN Women Behind the Science: Gerri Trooskin](https://cbtn.org/celebrating-cbtn-women-behind-the-science-gerri-trooskin/) - While researchers rightly take center stage after significant scientific breakthroughs, a dedicated group of people behind the scenes also play critical roles in the Children’s Brain Tumor Network (CBTN) success. These unsung heroes – the masterminds behind legal, research, fundraising, project management, and relationship-building empower these scientists to focus on their groundbreaking work. This February
- [Celebrating CBTN Women Behind the Science: Tatiana Patton](https://cbtn.org/celebrating-cbtn-women-behind-the-science-tatiana-patton/) - The fight against pediatric brain tumors requires a dedicated army of researchers, clinicians, and support staff. That’s only half the story, however. Behind the scenes, unseen heroes empower these researchers to focus on science. This blog, part of our February Women in Science Month series to honor just a few of these invaluable people, shines
- [The Carson Leslie Foundation Joins the Children's Brain Tumor Network To Drive Data-Driven Progress Toward Cures](https://cbtn.org/the-carson-leslie-foundation-joins-the-childrens-brain-tumor-network-to-drive-data-driven-progress-toward-cures/) - The fight against pediatric brain cancer is a marathon, not a sprint: every advancement and every new partnership fuels our journey toward a future free from these devastating diseases. Today, the Children's Brain Tumor Network (CBTN) announces a deepened alliance in the search for cures and treatments for deadly pediatric diseases. Since 2021, the Carson Leslie
- [Innovative Tool Protects Patient Privacy in Pediatric Brain Tumor Data](https://cbtn.org/innovative-tool-protects-patient-privacy-in-pediatric-brain-tumor-data/) - Progress in any field requires dedication, time, and effort, and this is especially true in pediatric brain tumor research. Recently, a project led by Dr’s Ariana M. Familiar and Ali Nabavizadeh at the Children’s Brain Tumor Network (CBTN) published an article in the American Journal of Neuroradiology (AJNR) Imaging Publication about the development of a new tool
- [A Legacy of Love, Lifted by Community](https://cbtn.org/a-legacy-of-love-lifted-by-community/) - Infinite Love for Kids Fighting Cancer (Infinite Love) has long been a champion for children and families facing the unimaginable. Among its earliest and most passionate partners are Susan Funck and her daughter, Hannah Duffy. When Hannah was diagnosed with brain cancer at just 13 years old, she made a choice not to retreat.
- [Breaking Down Barriers to Transform Pediatric Brain Tumor Research](https://cbtn.org/breaking-down-barriers-to-transform-pediatric-brain-tumor-research/) - When it comes to childhood brain tumor research, the idea of collaboration is not just an idealistic concept; it's quickly becoming a lifeline. Doctors and scientists who study children's brain tumors often work on their own. This means they keep their important information private, which slows down the search for new treatments. However, a new
- [Where Hope Lives](https://cbtn.org/where-hope-lives/) - On a quiet street, a porch light glows against the evening sky. Inside, a research coordinator makes one last check before tomorrow’s clinical trial update. On the sidewalk outside, the word HOPE glows in bright chalk—left by a child home from a scan with good news. As night deepens, a scientist across town bends over
- [RADIANT and the Rise of the Patient Voice in Healthcare](https://cbtn.org/radiant-and-the-rise-of-the-patient-voice-in-healthcare/) - “No matter how much technology we bring into the system, healthcare is a human enterprise.” — Adam Resnick, PhD, Co-Executive Director of the Center for Data-Driven Discovery in Biomedicine (D3b) at Children’s Hospital of Philadelphia For too long, medicine has happened to patients. Families have contributed data, enrolled in studies, and endured treatments, yet discoveries often remain locked
- [Finding Meaning in the Middle Miles: What Jena Lilly’s Marathon Taught Her About Endurance and Purpose](https://cbtn.org/finding-meaning-in-the-middle-miles-what-jena-lillys-marathon-taught-her-about-endurance-and-purpose/) - “Never doubt that a small group of thoughtful, committed citizens can change the world. Indeed, it is the only thing that ever has.” — Margaret Mead This quote has long resonated with Jena Lilly, reflecting the quiet power she sees daily in her work and advocacy. And when Jena crossed the finish line of her first marathon
- [Crisis for Kids: The Looming Threat to Childhood Cancer Research](https://cbtn.org/crisis-for-kids-the-looming-threat-to-childhood-cancer-research/) - We are moving into a world where the whispers of hope for children facing cancer seem to be growing fainter. A world where the relentless pursuit of cures slows, and the bright promise of a healthier future dims. And while the federal government's efforts to restructure the vast and complex American health research system may

## Pages

- [Home](https://cbtn.org/) - We’re Changing How Science Is Done Because Kids Can’t Wait. CBTN doesn’t wait for change—we drive it, turning global collaboration into faster discovery and better futures for children.
- [Brand Assets](https://cbtn.org/brand-tools/) - Unified Voices. Stronger Impact. Find everything you need to represent our shared mission with clarity and consistency. Logos Show your partnership with confidence using the official CBTN logo in approved formats. DOWNLOAD ASSETS VIEW ASSETS Download (.jpg) Download (.pdf) Download (.png) Download (.svg) Download (.ai) Download (.jpg) Download (.pdf) Download (.png) Download (.svg) Download (.ai) Download
- [Platforms](https://cbtn.org/research/platforms/) - Empowering Discovery Through Data Access CBTN Research Resources for Pediatric Brain Tumor DiscoveryData, Specimens, Imaging, and Preclinical Models CBTN provides researchers with one of the most comprehensive pediatric brain tumor research resources available, including Pediatric Brain Tumor Atlas (PBTA) clinical data, multiomic datasets, imaging data, preclinical models, and thousands of high-quality biospecimens spanning diverse tumor
- [Platforms](https://cbtn.org/research/platforms-2/) - Empowering Discovery Through Data Access CBTN Research Resources for Pediatric Brain Tumor DiscoveryData, Specimens, Imaging, and Preclinical Models CBTN provides researchers with one of the most comprehensive pediatric brain tumor research resources available, including Pediatric Brain Tumor Atlas (PBTA) clinical data, multiomic datasets, imaging data, preclinical models, and thousands of high-quality biospecimens spanning diverse tumor
- [Video Tutorials](https://cbtn.org/help-center/video-tutorials/) - CBTN Data User Video Tutorials The Children’s Brain Tumor Network (CBTN) tutorials are designed to help researchers navigate the tools, platforms, and workflows used to access and analyze CBTN genomic and clinical data within the Gabriella Miller Kids First Data Resource Center Portal. Here, researchers can securely explore, access, and analyze harmonized pediatric cancer data
- [Help Center](https://cbtn.org/help-center/) - SCIENTIFIC RESOURCES HELP CENTER Welcome to the CBTN Help Center This information hub is designed to help researchers, clinicians, and collaborators access and use CBTN data, tools, and resources across the network’s vast ecosystem. Together, these resources help transform shared knowledge into faster discovery and greater impact for children facing a brain tumor diagnosis.
- [Data Security](https://cbtn.org/help-center/data-security/) - DATA SECURITY HOW CBTN PROTECTS PARTICIPANT PRIVACY The Children’s Brain Tumor Network (CBTN) is committed to advancing pediatric brain tumor research while protecting the privacy, dignity, and trust of the children and families who make this work possible. CBTN data and research resources, including genomic data, biospecimens, models, and imaging, are made available through controlled-access
- [Tissue Donation](https://cbtn.org/network/tissue-donation/) - Turning Love into Legacy Gift from a Child (GFAC) is a family-centered initiative that honors one of the most courageous decisions a family can make: choosing to donate a child’s brain tumor tissue to advance research after death. Through its partnership with CBTN, GFAC makes tissue donation possible across most pediatric hospitals in the U.S.
- [Network](https://cbtn.org/network/) - Unified Pursuit of Breakthroughs Uniting Institutions, Innovators, and Advocates to Transform Pediatric Brain Tumor Research. CBTN brings together hospitals, families, industry, and government to create an open-science ecosystem where shared data accelerates discovery, drives new treatments, and delivers hope worldwide. MEMBER INSTITUTIONS Worldwide Collaboration Advancing Hope CBTN is a world leader in open science, powered
- [Publications](https://cbtn.org/publications/) - Critical Discoveries
- [About](https://cbtn.org/about-us/) - Unlocking Answers. Accelerating Cures.Brain tumors take more young lives than any other disease in the U.S. and many other countries, yet progress has remained too slow for decades. CBTN was created to change that. Since 2011, we’ve built the world’s largest open-access ecosystem of pediatric brain tumor data, tools, and expertise, removing barriers and accelerating
- [FAQs](https://cbtn.org/faqs/) - FAQsAnswers in Brief Sample CollectionClinical Data CollectionMolecular Data Generation & CollectionPost-mortem CollectionThe CBTN Study: How to ParticipatePatient Information & TreatmentCBTN ResearchCBTN PartnershipsCBTN Future Directions Sample Collection How is CBTN different from other biobanks? CBTN turns donated tissue and biospecimens into a powerful, global research engine. Instead of limiting access, we make the world’s largest collection
- [Sign Up](https://cbtn.org/sign-up/) - Sign Up Name(Required) First Last Email(Required) Role(Required)Your RoleResearcherClinicianFamily MemberFoundationGovernmentOtherTitle(Required)Organization(Required)Topics of Interest Research & Data Releases Events & Investigator Meetings Funding & Collaboration Opportunities Family & Advocacy Impact Policy & Industry News Tools & Platforms Updates Deselect All Submit
- [Submit a Project](https://cbtn.org/submit-a-project/) - Submit a Project Contact InformationName(Required) First Last Email(Required) PhoneProject DetailsProject ID(Required)Project Title(Required)Project Description - Lay Summary(Required)Project Status(Required) Active Complete Project Type(Required) Data Specimen Was a GFAC Tissue Donation used?(Required) No Yes Lead Researcher(Required)Enter Full NameLead Researcher Email(Required) Enter email address of lead researcherLead Institution(Required)Enter Institution NameResearch TeamEnter Research team member names Submit Project
- [Member Institutions](https://cbtn.org/network/member-institutions/) - Worldwide Collaboration Advancing Hope CBTN is a world leader in open science,powered by the strength of its member institutions. When the most innovative research hospitals unite, we don’t just accelerate discovery—we amplify its impact on a worldwide scale. By contributing biospecimens, medical data, and clinical expertise, member institutions fuel a collaborative research ecosystem that is
- [Difference](https://cbtn.org/about-us/difference/) - Smarter Science, Stronger Outcomes M3 Approach For decades, one of the most significant obstacles to curing pediatric brain tumors has been fragmentation—research happening in isolation, data trapped in silos, and a lack of unified strategy. These diseases are too complex and funding far too limited for stopgap solutions. At CBTN, we realized it’s time to
- [Industry](https://cbtn.org/network/industry/) - From Data to Discovery CBTN partners with leading technology and pharmaceutical companies to translate research into real-world therapies. Our work with forward-thinking biotech and pharmaceutical companies ensures that biospecimens and data are used across discovery, development, and clinical trials, bringing new therapies to children faster. Pharmaceutical Collaborators CBTN’s collaboration is vital to pharmaceutical companies’ drug
- [Government](https://cbtn.org/network/government/) - National Vision, Global Impact Government CBTN progress is made possible in part through strong partnerships with U.S. federal agencies committed to transforming childhood cancer research. Key partners include: National Institutes of Health (NIH) A central collaborator advancing open-science initiatives that accelerate pediatric brain tumor research. Gabriella Miller Kids First Data Resource Center Provides researchers open
- [Leadership](https://cbtn.org/about-us/leadership/) - Bold Leadership with Global Impact.CBTN is more than a consortium—it’s a global force for change. Driven by urgency, united by purpose, and powered by collaboration, CBTN is advancing the frontier of pediatric brain tumor research with unprecedented speed and coordination. Operations are led from the Center for Data Driven Discovery in Biomedicine (D3b) at Children’s
- [Scientific Projects](https://cbtn.org/projects/) - Bold Science for Brighter Futures
- [Innovation](https://cbtn.org/research/innovation/) - Advancing Care Through Data-Driven Innovation Two Goals. One Network. Infinite Impact. Every child deserves a future free from the threat of deadly disease. By uniting global research with advanced technology, CBTN is closing the gap between scientific discovery and clinical care. We’re focused on two priorities: accelerating the path from laboratory insight to treatment, and
- [Research](https://cbtn.org/research/) - Fueling the Science Driving Discovery Advancing Discovery Through Research, Technology, and Shared Resources CBTN unites groundbreaking research projects, powerful data platforms, and accessible resources to accelerate innovation, improve patient outcomes, and empower scientists worldwide to uncover new therapies for pediatric brain tumors. 1Projects That AccelerateCBTN is driving discovery through the M3 Approach and the development
- [Membership](https://cbtn.org/membership/) - Membership Institution Inquiry Your InformationName(Required) First Last Email(Required) Phone(Required)Institution DetailsInstitution Name(Required)Institutional Lab, Center, or Division, if applicableInstitution Location(Required) Street Address City State / Province / Region ZIP / Postal Code AfghanistanAlbaniaAlgeriaAmerican SamoaAndorraAngolaAnguillaAntarcticaAntigua and BarbudaArgentinaArmeniaArubaAustraliaAustriaAzerbaijanBahamasBahrainBangladeshBarbadosBelarusBelgiumBelizeBeninBermudaBhutanBoliviaBonaire, Sint Eustatius and SabaBosnia and HerzegovinaBotswanaBouvet IslandBrazilBritish Indian Ocean TerritoryBrunei DarussalamBulgariaBurkina FasoBurundiCabo VerdeCambodiaCameroonCanadaCayman IslandsCentral African RepublicChadChileChinaChristmas IslandCocos IslandsColombiaComorosCongoCongo, Democratic Republic of
- [Foundations](https://cbtn.org/network/foundations-families/) - Progress Fueled by Purpose CBTN’s mission is driven by those who refuse to accept the status quo. Foundations and family-led initiatives are not just supporters—they are also strategic partners shaping the future of pediatric brain tumor research. From strengthening infrastructure and advancing technology to funding bold science and expanding awareness, CBTN philanthropic partners are embedded
- [Story](https://cbtn.org/about-us/story/) - Driving Bold Discovery for Kids Unlocking Answers. Accelerating Cures. Brain tumors take more young lives than any other disease in the U.S. and many other countries, yet progress has remained too slow for decades. CBTN was created to change that. Since 2011, we’ve built the world’s largest open-access ecosystem of pediatric brain tumor data, tools,
- [Submit a Publication](https://cbtn.org/submit-a-publication/) - Submit a Publication Contact InformationName First Last Email(Required) PhonePublication DetailsPublication Title(Required)Journal(Required)Publication Date PubID / PubMedidPublication Abstract(Required)Authors(Required)Link to Publication(Required) FundersAcknowledgements Submit Publication
- [Privacy Policies](https://cbtn.org/privacy-policies/) - Disclaimers, Terms & Conditions, and Privacy Policy The Children’s Brain Tumor Network (“CBTN” or “we”) has created this privacy policy to demonstrate its commitment to privacy and transparency of practices. This privacy policy explains the CBTN’s information-gathering and dissemination practices for the Children’s Brain Tumor Network’s website (the “services”). By accessing the services, you consent
- [Request Specimens](https://cbtn.org/request-specimens/) - Request Specimens Project InformationFor New Projects: Is this a data project, specimen project, or both? Note, if you are looking for pre-clinical models, please select "Specimens".Project Type * Data Specimens Your InformationName(Required) First Last Email(Required) Phone(Required)Institution DetailsInstitution Name(Required)Institution Role / Title(Required) First Last Institutional Lab, Center, or Division, if applicableInstitution Location(Required) Street Address City State
- [testtest6](https://cbtn.org/testtest6/)
- [testtest5](https://cbtn.org/testtest5/) - Resources
- [testtest](https://cbtn.org/testtest4/) - Resources
- [TESTTEST](https://cbtn.org/testtest/) - Resources
- [Protect Kids](https://cbtn.org/protect-kids/) - Protect Kids: Support the Gabriella Kids First Research Act (S. 1624) More than 225,000 children are impacted each year due to cancer and congenital disorders. Many will have severe consequences and sadly will not make it through the year. Helping kids is a moral imperative.The Gabriella Miller Kids First Research Act is crucial to address
- [Progress Report](https://cbtn.org/progress-report/) - WELCOME Reflecting on everything we accomplished in 2024, a powerful question arises: How can CBTN be Champions for Children? Like a title-winning team, our progress in conquering pediatric brain tumors is built on collaboration, innovation, and unwavering dedication. We at CBTN are grateful to champion this vital effort. Thank you for being part of our
- [PedSNO](https://cbtn.org/pedsno/) - Discover Research Innovation, Powered by a Child's Gift Join us at PedSNO 2025 Connect with the innovators at Gift from a Child and the Children’s Brain Tumor Network (CBTN). Elevate pediatric care through a collaborative, technology-driven approach made possible through a child’s gift. Join our leading-edge coalition to: 1Unlock clinical and genomic data, robust biospecimens,
- [ISPNO](https://cbtn.org/ispno/) - SCIENCE IS ATEAM SPORTJOIN CBTN AT ISPNO 2024 When we all work together, kids win Connect with the world’s premier pediatric neuro-oncology all-stars at the ISPNO conference! Passionate about scoring big on behalf of children battling brain tumors? Get on the Children’s Brain Tumor Network (CBTN) roster and you’ll help drive a determined force at
- [Education: CBTN SUMMIT](https://cbtn.org/education-cbtn-summit/) - OCTOBER 9-11, 2024 ARLINGTON, VA Wisdom gained. Cures await. We loved having you in class. Thanks for participating in the 2024 CBTN Summit education track. We hope you feel empowered to take newfound knowledge and uplevel your research. To keep the momentum going, view your class recordings below and download your certificate to celebrate your
- [Comms Request](https://cbtn.org/comms-request/) - About YouName(Required) First Last Department(Required)Email(Required) PhoneRequestCommunications Need(Required)What do you intend to accomplish with this communication?(Required)Do you have a format in mind? Please describe.(Required)What outcomes do you envision?(Required)Primary Audience Researcher Foundation Clinician Patient Other Secondary Audience Researcher Foundation Clinician Patient Other Program CBTN Kids First INCLUDE D3b CHOP Other If you’d like to have a communication
- [Collaboration Central](https://cbtn.org/collaboration-central/) - Collaboration Central CBTN thrives through collaboration. Whether you’re a returning investigator, new to the network, or exploring how to get involved, this page is your central resource for current opportunities. CONTACT CBTNVISIT CBTNSEE METRICS Working Groups CBTN working groups bring together researchers with shared interests to accelerate discovery through regular, focused collaboration. These investigator-led groups
- [CBTN SUMMIT SPONSORSHIP](https://cbtn.org/cbtn-summit-sponsorship/) - OCTOBER 9-11 , 2024 ARLINGTON, VA SPONSORSHIP OPPORTUNITIES MenuCBTN SUMMITAGENDASPONSORSHIPABSTRACTVISIT CBTN.ORG THE VISIONARE YOU READY TO UNITE FOR CURES? The 2024 CBTN Summit isn’t your typical conference. It’s a coalition of brilliant minds—the brightest stars in STEM—coming together to ignite a revolution in pediatric cancer research. For three action-packed days, we spark groundbreaking discussions, foster
- [CBTN SUMMIT AGENDA](https://cbtn.org/cbtn-summit-agenda/) - OCTOBER 9-11, 2024 ARLINGTON, VA CBTN 2024 SUMMIT AGENDA AI and machine learning are transforming scientific research and patient care, marking a pivotal moment in innovation. Discover how CBTN’s network of brilliant minds is pioneering collaborative strategies that accelerate discovery and explore groundbreaking advancements in healthcare and scientific discovery. MenuCBTN SUMMITAGENDASPONSORSHIPABSTRACTVISIT CBTN.ORG CBTN Scientific Summit
- [CBTN SUMMIT ABSTRACTS](https://cbtn.org/cbtn-summit-abstracts/) - OCTOBER 9-11, 2024 ARLINGTON, VA MenuCBTN SUMMITAGENDASPONSORSHIPABSTRACTVISIT CBTN.ORG ABSTRACT SUBMISSION You’re Invited Present your research at the 2024 CBTN Summit poster session. For full submission guidelines, download here. SUBMIT AN ABSTRACT Poster sessionThe CBTN Summit Poster Session features an array of distinguished researchers, clinicians, and thought leaders from across the globe. Researchers have ample networking
- [CBTN SUMMIT](https://cbtn.org/cbtn-summit/) - OCTOBER 9-11, 2024 ARLINGTON, VA THE CBTN SUMMIT ISN’T JUST A CONFERENCE, IT’S A CATALYST FOR BREAKTHROUGHS. The brightest minds in science and technology come together at the 2024 CBTN Summit for a powerful purpose: Uniting minds to unlock cures for childhood brain tumors. Uncover the momentum happening at the Children’s Brain Tumor Network (CBTN)
- [CBTN Metrics 2025](https://cbtn.org/cbtn-metrics-2025/) - Metrics Welcome to the Children’s Brain Tumor Network Metrics Dashboard. In this edition, You can explore specimen and data metrics, and stay informed about the latest CBTN resources. We’re dedicated to supporting members of the clinical, research, and patient communities. If you have suggestions for content you’d like to see on this dashboard, please reach
- [CBTN Metrics](https://cbtn.org/cbtn-metrics/) - Metrics Welcome to the Children’s Brain Tumor Network Metrics Dashboard. In this edition, You can explore specimen and data metrics, and stay informed about the latest CBTN resources. We’re dedicated to supporting members of the clinical, research, and patient communities. If you have suggestions for content you’d like to see on this dashboard, please reach
- [PBTA](https://cbtn.org/research/pbta/) - PBTA
- [Cutout-1](https://cbtn.org/cutout-1/) - Test Content CBTN unites groundbreaking research projects, powerful data platforms, and accessible resources to accelerate innovation, improve patient outcomes, and empower scientists worldwide to uncover new therapies for pediatric brain tumors. Test Content CBTN unites groundbreaking research projects, powerful data platforms, and accessible resources to accelerate innovation, improve patient outcomes, and empower scientists worldwide to
- [PIXELWAVE 5](https://cbtn.org/pixelwave-5/) - Get the Latest news, articles, and resources sent to your inbox. SUBSCRIBE ABOUT NETWORK RESEARCH NEWS DONATE Stay Informed Sign up to keep pace with our progress and customize your content. Name(Required) First Last Email(Required) Role(Required)Your RoleResearcherClinicianFamily MemberFoundationGovernmentOtherTitle(Required)Organization(Required)Topics of Interest Research & Data Releases Events & Investigator Meetings Funding & Collaboration Opportunities Family & Advocacy
- [PIXELWAVE 3](https://cbtn.org/pixelwave-3/) - Get the Latest News news, articles, and resources, sent to your inbox. SUBSCRIBE ABOUT NETWORK RESEARCH NEWS
- [Our Mission](https://cbtn.org/mission/)
- [Our Approach](https://cbtn.org/approach/)
- [CBTN Metrics 2025b](https://cbtn.org/cbtn-metrics-2025b/)
- [Home](https://cbtn.org/home-2/)

## Institutions

- [Beijing Tiantan Hospital Neurosurgery Center](https://cbtn.org/institution/beijing-tiantan-hospital-neurosurgery-center/) - As China’s most renowned neurosurgical hospital, Beijing Tiantan Hospital Neurosurgery Center (BTHNC) provides children access to unrivaled neurological expertise. Each year, its surgeons perform up to 700 operations to treat the full spectrum of brain and spinal tumors in children. BTHNC is recognized not only for its volume and precision, but also for its leadership
- [Ann & Robert H. Lurie Children’s Hospital of Chicago](https://cbtn.org/institution/ann-robert-h-lurie-childrens-hospital-of-chicago/) - Innovation and collaboration define care for children with brain tumors at Lurie Children’s. Its Brain Tumor Center has pioneered advanced treatments such as proton therapy while connecting families to a wide range of clinical trials. Weekly, a multidisciplinary Brain Tumor Board reviews patient cases to ensure that every child benefits from the combined expertise of
- [Children’s National Hospital](https://cbtn.org/institution/childrens-national-hospital/) - Innovation defines the Brain Tumor Institute at Children’s National. Its experts have pioneered molecularly targeted therapies, vaccines, T-cell immunotherapies, and less invasive surgical techniques, reshaping how pediatric brain tumors are treated worldwide. Each year, the institute evaluates more than 100 new patients, delivering comprehensive care backed by leading-edge research. Children’s National is also recognized among
- [China National Genebank](https://cbtn.org/institution/china-national-genebank/) - The China National GeneBank (CNGB) in Shenzhen, operated by BGI-Research, is China’s first national gene bank and a global leader in conserving, digitizing, and applying genetic resources. As a public, nonprofit platform, CNGB champions the idea that genetic resources should be shared for the benefit of all. Through CBTN, CNGB brings this vision to pediatric
- [Seattle Children's Hospital](https://cbtn.org/institution/seattle-childrens-hospital/) - Seattle Children’s Hospital hosts the largest pediatric brain tumor program in the Northwestern U.S. and is internationally recognized for its expertise in CNS tumors. It has been ranked among the nation’s best children’s hospitals for more than 25 years, and its Cancer and Blood Disorders Center has been a top pediatric oncology program for over
- [UCSF Benioff Children's Hospital](https://cbtn.org/institution/ucsf-benioff-childrens-hospital/) - The Pediatric Brain Tumor Center at UCSF Benioff Children’s Hospital treats more than 100 children each year and connects families to innovative trials through the Pacific Pediatric Neuro-Oncology Consortium (PNOC). Its researchers are advancing new ways to deliver therapies across the blood-brain barrier, including convection-enhanced delivery and ultrasound, while also leading immunotherapy trials for aggressive
- [UC Santa Cruz Treehouse Childhood Cancer Initiative](https://cbtn.org/institution/uc-santa-cruz-treehouse-childhood-cancer-initiative/) - The Treehouse Childhood Cancer Initiative is a champion for open data sharing, ensuring that discoveries move swiftly from analysis to the clinic. Through this approach, it contributes to CBTN’s vision of accelerating precision medicine and expanding treatment options for children with cancer. Treehouse also harnesses large-scale genomic data from both pediatric and adult cancers to
- [UPMC Children's Hospital of Pittsburgh](https://cbtn.org/institution/upmc-childrens-hospital-of-pittsburgh/) - The Neuro-Oncology Program at UPMC Children’s Hospital is a national leader in developing new treatments for pediatric brain and nervous system cancers. Patients gain access to leading-edge clinical trials for brain and spine tumors, supported by research across hematology, oncology, and neuro-oncology. Led by experts such as Dr. Ian Pollack, the team’s high-grade glioma studies
- [Weill Cornell Medicine](https://cbtn.org/institution/weill-cornell-medicine/) - As a driving force in pediatric neuro-oncology, Weill Cornell Medicine partners with other CBTN institutions to unite science and care for children with brain tumors. Its Clinical Neuro-Oncology Program treats hundreds of patients each year, connecting them to advanced therapies and innovative clinical trials. By integrating developmental biology, immunotherapy, precision medicine, and novel drug delivery
- [Nicklaus Children's Hospital](https://cbtn.org/institution/nicklaus-childrens-hospital/) - Nicklaus Children’s Hospital is South Florida’s leading pediatric referral center, caring for nearly 70% of the region’s children. Its Centers of Excellence in cancer, neuroscience, orthopedics, and heart care are supported by a state-of-the-art surgical tower and robust transfer and transport programs that save nearly 5,000 lives each year. As home to the Southeast’s most
- [University of Iowa Stead Family Children’s Hospital](https://cbtn.org/institution/university-of-iowa-stead-family-childrens-hospital/) - The University of Iowa Stead Family Children’s Hospital is the state’s only comprehensive children’s hospital, offering services that span general wellness, trauma, surgery, chronic conditions, and developmental disabilities, providing comprehensive pediatric care for families across Iowa. As part of an academic medical center, the hospital drives research into childhood diseases and trains the next generation
- [University Children's Hospital Zürich](https://cbtn.org/institution/university-childrens-hospital-zurich/) - The University Children’s Hospital Zurich is the largest pediatric hospital in Switzerland and one of Europe’s leading centers for pediatric care and research. Its Oncology Department, part of the Comprehensive Cancer Center Zürich, collaborates with ETH Zurich to advance discovery and innovation. With deep expertise in clinical trials and international consultations, the team is shaping
- [UNC Chapel Hill - North Carolina Children's Hospital](https://cbtn.org/institution/unc-chapel-hill-north-carolina-childrens-hospital/) - As both a care provider and a research hub, UNC Children’s Hospital integrates academic medicine with a commitment to families, advancing discovery, education, and treatment in alignment with CBTN’s mission to improve outcomes for children. UNC Children’s brings together nearly 200 physician faculty from the UNC School of Medicine, spanning 50 programs across 20 clinical
- [Texas Children's Hospital](https://cbtn.org/institution/texas-childrens-hospital/) - Texas Children’s Hospital in Houston is one of the nation’s largest and most distinguished pediatric centers, consistently ranked among the top children’s hospitals in the U.S. As the primary pediatric teaching hospital of Baylor College of Medicine and a cornerstone of the Texas Medical Center, it combines world-class clinical care with leading education and research.
- [Sydney Children’s Hospital, Randwick](https://cbtn.org/institution/sydney-childrens-hospital-randwick/) - The Kids Cancer Centre (KCC) at Sydney Children’s Hospital, Randwick cares for children with cancer and blood disorders across New South Wales, Australia, and the Asia-Pacific region. By bridging research and care, the Kids Cancer Centre strengthens CBTN’s mission to accelerate progress and bring new hope to children worldwide. Through its Early Phase Clinical Trials
- [St. Louis Children's Hospital](https://cbtn.org/institution/st-louis-childrens-hospital/) - St. Louis Children’s Hospital (SLCH), founded in 1879 and affiliated with Washington University School of Medicine, is a nationally ranked pediatric center with 258 beds and Magnet® designation for nursing excellence. Its Pediatric Neuro-Oncology Center provides comprehensive care for brain and spinal cord tumors, offering advanced technologies such as intra-operative MRI and proton beam radiation.
- [Orlando Health Arnold Palmer Hospital for Children](https://cbtn.org/institution/orlando-health-arnold-palmer-hospital-for-children/) - For more than 30 years, Orlando Health Arnold Palmer Hospital for Children has delivered expert, compassionate care to families across Central Florida and beyond. Home to the region’s only pediatric Level One Trauma Center and Emergency Department, the hospital combines advanced technology with a team dedicated to putting children’s health first. Through this commitment, it
- [Michigan Medicine C.S. Mott Children’s Hospital](https://cbtn.org/institution/michigan-medicine-c-s-mott-childrens-hospital/) - C.S. Mott Children’s Hospital is a leader in treating relapsed and resistant cancers, running Michigan’s largest pipeline of Phase 1 trials and one of the nation’s most advanced gene sequencing programs to deliver personalized therapies. It also operates the state’s largest pediatric bone marrow transplant and cellular therapy programs. The Chad Carr Pediatric Brain Tumor
- [Meyer Children's Hospital](https://cbtn.org/institution/meyer-childrens-hospital/) - Integrated with the University of Florence, Meyer Children’s Hospital combines advanced care, research, and training to serve children across Italy and beyond. With 250 beds and expertise spanning all pediatric medical and surgical specialties, Meyer stands as a national referral center within the Italian health system. Meyer strengthens the shared global mission of CBTN to
- [Maria Fareri Children’s Hospital at Westchester Medical Center](https://cbtn.org/institution/maria-fareri-childrens-hospital-at-westchester-medical-center/) - As a partner in CBTN’s mission to drive discovery and improve outcomes for children, Maria Fareri Children’s Hospital in Valhalla, NY, delivers advanced pediatric care through the Hudson Valley’s only Level I pediatric trauma and burn center and its only Level IV NICU. The hospital offers expertise across various specialties, including neurology and oncology. Committed
- [Lucile Packard Children's Hospital Stanford](https://cbtn.org/institution/lucile-packard-childrens-hospital-stanford/) - Lucile Packard Children’s Hospital Stanford, housed within Stanford Children’s Health, is nationally ranked for excellence in pediatrics and obstetrics. Its Pediatric Neuro-Oncology Program brings together a multidisciplinary team using advanced, minimally invasive techniques, including ROSA™ robotic-assisted surgery. The hospital leads more than a dozen brain tumor clinical trials. By uniting expert care with groundbreaking research,
- [Joseph M. Sanzari Children’s Hospital at Hackensack University Medical Center](https://cbtn.org/institution/joseph-m-sanzari-childrens-hospital-at-hackensack-university-medical-center/) - Advancing the CBTN mission, Hackensack Meridian Children’s Health brings world-class care and discovery to children with brain and spinal cord tumors. Its Pediatric Neuro-Oncology Program combines cutting-edge research and clinical trials with comprehensive treatment delivered by a multidisciplinary team of specialists. The hospital is home to New Jersey’s only nationally ranked pediatric cancer program, placed
- [Johns Hopkins Medicine](https://cbtn.org/institution/johns-hopkins-medicine/) - Johns Hopkins Medicine, based in Baltimore, unites the Johns Hopkins University School of Medicine with a broad network of hospitals, research institutes, and care facilities. With six hospitals, dozens of patient care centers, and global partnerships, Johns Hopkins delivers care and drives discovery at a scale few can match. As part of CBTN, Johns Hopkins
- [Johns Hopkins All Children's Hospital](https://cbtn.org/institution/johns-hopkins-all-childrens-hospital/) - Johns Hopkins All Children’s Hospital delivers personalized care for children with brain and spinal tumors, using precision medicine to guide treatments based on each tumor’s genetic and molecular profile. Advanced neuro-imaging and complex surgical expertise are paired with a focus on preserving motor skills, vision, hearing, and cognition. Backed by the Cancer & Blood Disorders
- [Intermountain Primary Children's Hospital](https://cbtn.org/institution/intermountain-primary-childrens-hospital/) - Intermountain Primary Children’s Hospital is a nationally ranked leader in pediatric care and the only Level I Pediatric Trauma Center in the Intermountain West. As the teaching hospital for the University of Utah, it serves families across one of the largest geographic areas in the U.S. With a strong focus on research and innovation, the
- [Hudson Institute of Medical Research](https://cbtn.org/institution/hudson-institute-of-medical-research/) - At the Hudson Institute in Melbourne, science is always moving toward solutions. From discoveries in inflammation and cancer to breakthroughs in reproductive and child health, Hudson’s researchers are shaping the future of care. The Hudson Monash Paediatric Precision Medicine Program zeroes in on childhood brain cancers and solid tumors, translating laboratory insights into new, targeted
- [Hassenfeld Children's Hospital at NYU Langone](https://cbtn.org/institution/hassenfeld-childrens-hospital-at-nyu-langone/) - By combining breadth of care with a commitment to discovery, Hassenfeld Children’s Hospital contributes to CBTN’s mission of improving outcomes for children everywhere. With over 400 physicians, Hassenfeld offers a comprehensive range of services to patients in the New York City region, from routine treatments to highly complex interventions. Beyond clinical excellence, the hospital advances
- [Doernbecher Children’s Hospital](https://cbtn.org/institution/doernbecher-childrens-hospital/) - The Pediatric Neuro-Oncology Program at OHSU Doernbecher Children’s Hospital is nationally recognized for excellence in cancer and neurosurgery and stands as a leading center on the West Coast. As part of the Pacific Pediatric Neuro-Oncology Consortium (PNOC), the program helps drive forward new therapies for children with brain and spinal cord tumors. Care is delivered
- [Dayton Children’s Hospital](https://cbtn.org/institution/dayton-childrens-hospital/) - Dayton Children’s Hospital serves more than 280,000 patients each year, with its neurosurgery team performing over 200 complex procedures annually—some offered at only a few centers nationwide. Through partnerships with Miami Valley Hospital, Wright State University, and Premier Health, Dayton Children’s connects patients to cutting-edge neuroscience research and advanced treatments, advancing the CBTN mission to
- [Children’s Hospital of Philadelphia](https://cbtn.org/institution/childrens-hospital-of-philadelphia/) - The Children’s Hospital of Philadelphia (CHOP) is a global leader in pediatric brain tumor research and care, and the Operations Center home for the Children’s Brain Tumor Network. CHOP houses the world’s largest pediatric brain and CNS tumor biorepository, fueling discovery on a global scale. With one of the largest pediatric neuro-oncology teams in the
- [Children's of Alabama](https://cbtn.org/institution/childrens-of-alabama/) - Through its scale, expertise, and commitment to discovery, Children’s of Alabama strengthens the CBTN mission to accelerate cures and deliver better outcomes. Children’s of Alabama is the only medical center in the state dedicated solely to pediatric care, and it stands among the largest pediatric medical facilities in the U.S. As the teaching hospital for
- [Children's Healthcare of Atlanta](https://cbtn.org/institution/childrens-healthcare-of-atlanta/) - The Aflac Cancer and Blood Disorders Center at Children’s Healthcare of Atlanta is one of the nation’s largest pediatric brain tumor programs, caring for more than 750 children each year. Its specialists provide comprehensive treatment that includes advanced neurosurgery, radiation, chemotherapy, stem cell transplantation, and clinical trials for resistant or relapsed cancers. Researchers at Aflac
- [Wake Forest Baptist Health](https://cbtn.org/institution/wake-forest-baptist-health/) - Known for top-ranked programs in pediatrics, cancer, cardiology, transplants, and specialized care, Atrium Health delivers innovation and compassion at scale. Through Wake Forest School of Medicine, the system’s academic core, Atrium advances experiential medical education, biomedical discovery, and new medical technologies. By combining expansive clinical reach with research leadership, Atrium Health contributes to CBTN’s mission
- [Akron Children's Hospital](https://cbtn.org/institution/akron-childrens-hospital/) - Akron Children’s Hospital provides care to more than one million patients each year across its network. Its certified oncology team treats a range of childhood cancers and blood disorders, caring for approximately eight newly diagnosed cancer patients each month. As a member of the Children’s Oncology Group (COG) and one of the few pediatric programs

## Partners

- [Ollie's Orchestra](https://cbtn.org/partner/ollies-orchestra/) - Ollie’s Orchestra channels love, art, and advocacy into research. As a Champion, it amplifies CBTN’s mission to transform individual stories into collective power and lasting change.
- [Elora J. Khan Foundation](https://cbtn.org/partner/elora-j-khan-foundation/) - Elora J. Khan Foundation is a family-founded nonprofit dedicated to honoring Elora’s life by supporting children and families impacted by pediatric brain tumors
- [Winning With Wyatt](https://cbtn.org/partner/winning-with-wyatt/) - Winning With Wyatt supports pediatric brain and spinal tumor research at leading medical institutions, including Lurie Children’s in Chicago. The foundation is dedicated to fundraising, building awareness about the impact brain and spinal tumors have on children, and advocating for more advanced treatment. Winning With Wyatt was established after a child, family, and community experienced
- [Children's Brain Tumor Foundation](https://cbtn.org/partner/childrens-brain-tumor-foundation/) - CBTF was among the first philanthropic partners to invest in CBTN, helping to lay the groundwork for its open-science model. Its continued support reflects a long-term commitment to advancing research infrastructure, improving access to shared data, and ensuring that families and patients remain at the heart of progress.
- [Bridge To A Cure Foundation](https://cbtn.org/partner/bridge-to-a-cure-foundation/) - Bridge To A Cure is driving systemic change in childhood cancer research by demanding shared infrastructure, collaboration, and accountability. Their partnership supports CBTN’s role as a unifying force in pediatric brain tumor research, building the data and operational backbone needed to accelerate discovery and translate patient contributions into cures.
- [Carson Leslie Foundation & CureMEdullo](https://cbtn.org/partner/carson-leslie-foundation-curemedullo/) - Born from Carson’s legacy, the foundation fuels innovation in medulloblastoma and pediatric brain tumor research. Its investment in targeted data generation and precision medicine reflects a shared commitment to turning patient stories into actionable discoveries.
- [Dragon Master Initiative](https://cbtn.org/partner/dragon-master-initiative/) - Dragon Master Initiative has been a catalyst for open science from CBTN’s earliest days, helping build the data-sharing ecosystem that now powers discovery globally. Its leadership in advocating for shared infrastructure has shaped CBTN’s trajectory, ensuring data is collected, harmonized, and made accessible to the entire research community.
- [Head for the Cure Foundation](https://cbtn.org/partner/head-for-the-cure-foundation/) - Head for the Cure mobilizes communities nationwide to support research and awareness. Its sustained support strengthens CBTN’s site infrastructure and expands the network’s reach, ensuring more patients and families can contribute to and benefit from open science.
- [Infinite Love for Kids Fighting Cancer Foundation](https://cbtn.org/partner/infinite-love-for-kids-fighting-cancer-foundation/) - Infinite Love channels the power of community into research infrastructure. Its annual Tutu Trot, which draws over 1,000 runners and raises more than $100,000 each year, is a cornerstone of its commitment to CBTN. This sustained investment directly supports the backbone systems that enable data generation and sharing at scale, ensuring that patient contributions become
- [Lilabean Foundation](https://cbtn.org/partner/lilabean-foundation/) - The Lilabean Foundation has been one of CBTN’s most deeply engaged partners, providing multiyear, catalytic funding for core infrastructure. Its CBTN investments enable more precise and scalable preclinical research. The Lilabean also has supported Project Accelerate, equipping the research community to move faster. Its commitment reflects a strategic, long-term vision to transform how research is
- [Making Headway Foundation](https://cbtn.org/partner/making-headway-foundation/) - Making Headway blends family support with strategic investment in research infrastructure. Its partnership helped integrate NYU site data and biobanking into CBTN, ensuring families and patients are part of the global research engine.
- [McKenna Claire Foundation](https://cbtn.org/partner/mckenna-claire-foundation/) - Driven by McKenna’s legacy, the foundation channels community energy into high-impact research. Its sustained support strengthens CBTN’s collaborative infrastructure and ensures that data generated from patient contributions drives real progress.
- [Musella Foundation for Brain Tumor Research & Information, Inc.](https://cbtn.org/partner/musella-foundation-for-brain-tumor-research-information-inc/) - The Musella Foundation focuses on high-risk cancers such as DMG and glioblastoma while championing data sharing that serves patients across their lifespan. Its partnership reinforces CBTN’s ability to integrate pediatric data into broader research ecosystems and drive innovation for all patients.
- [Pediatric Brain Tumor Foundation](https://cbtn.org/partner/pediatric-brain-tumor-foundation/) - As the largest patient advocacy funder dedicated to childhood brain tumors, PBTF has been a CBTN partner for more than a decade. Guided by its Care. Cure. Thrive. mission, PBTF’s investment has sustained the infrastructure that underpins CBTN’s global impact. Its commitment strengthens open science, ensuring that every child’s story contributes to meaningful discovery and
- [Rally Foundation](https://cbtn.org/partner/rally-foundation/) - The Rally Foundation empowers communities to fund transformative pediatric cancer research through collaboration-first philanthropy. Its partnership with CBTN focuses on advancing collaborative initiatives that strengthen shared infrastructure, accelerate data-driven discovery, and expand access to research resources across institutions.
- [Rally for Reid Foundation](https://cbtn.org/partner/rally-for-reid-foundation/) - Created in Reid’s honor, the foundation channels advocacy into lasting infrastructure. Its support expands CBTN’s network reach, including efforts to bring Iowa into the consortium, strengthening national collaboration.
- [Raymond A. Wood Foundation](https://cbtn.org/partner/raymond-a-wood-foundation/) - Dedicated to children with craniopharyngioma, RAWF ensures rare tumor types are represented in global datasets. Its support expands CBTN’s data ecosystem and reflects a commitment to inclusive, infrastructure-driven progress.
- [Robert Connor Dawes Foundation](https://cbtn.org/partner/robert-connor-dawes-foundation/) - RCD Foundation is building shared data infrastructure across Australia, extending CBTN’s impact globally. Its investment strengthens international collaboration and long-term architecture for open data.
- [Swifty Foundation](https://cbtn.org/partner/swifty-foundation/) - The Swifty Foundation has fundamentally changed pediatric brain tumor research through its leadership of Gift from a Child, the national postmortem tissue donation initiative. Its partnership with CBTN has created the backbone of the largest postmortem pediatric brain tumor collection in the world, embedding GFAC within the network’s infrastructure to ensure these contributions are not
- [Tommy Strong Foundation](https://cbtn.org/partner/tommy-strong-foundation/) - Tommy Strong’s support advances CBTN’s tumoroid modeling and medulloblastoma classifier initiatives, critical building blocks for precision research and targeted therapies.
- [The Ross K. MacNeill Foundation](https://cbtn.org/partner/the-ross-k-macneill-foundation/) - The mission of The Ross K. MacNeill Foundation is to end pediatric brain cancer by funding research that will rapidly develop innovative, nontoxic therapies to put to end the devastating diagnosis of pediatric brain cancer.
- [Smashing Walnuts](https://cbtn.org/partner/smashing-walnuts/) - Founded by Ellyn Miller in honor of her daughter Gabriella, Smashing Walnuts’ advocacy was instrumental in establishing the Gabriella Miller Kids First Pediatric Research program, home of the CBTN PBTA dataset. Its ongoing partnership underscores the power of advocacy to catalyze infrastructure change and accelerate discovery.
- [Pied Piper Foundation](https://cbtn.org/partner/pied-piper-foundation/) - Pied Piper’s commitment reflects their focus on ependymoma and rare tumors, as well as their support for preclinical and data infrastructure to make future trials more precise and impactful. Its partnership with CBTN strengthens the research pathways that bring better treatments to children faster.
- [Lauren's First and Goal](https://cbtn.org/partner/laurens-first-and-goal/) - Lauren’s First and Goal channels broad community energy into research. Its project support for low-grade glioma strengthens CBTN’s infrastructure to advance disease-specific precision science.
- [Kortney Rose Foundation](https://cbtn.org/partner/kortney-rose-foundation/) - Among CBTN’s earliest funders, Kortney Rose Foundation helped build core infrastructure to support DIPG research and data sharing. Its legacy funding ensures that work continues, keeping rare and aggressive tumors represented in global datasets.

## Projects

- [Diversity, Equity, and Inclusion: Translation of Informed Consent Forms](https://cbtn.org/projects/diversity-equity-and-inclusion-translation-of-informed-consent-forms/) - In collaboration with the Children’s Brain Tumor Network and the Pacific Pediatric Neuro-Oncology Consortium, Cassie Kline, MD, MAS, and Angela Waanders, MD, MPH, lead the Diversity, Equity, and Inclusion Working Group. The mission is to work together to end inequalities for pediatric neuro-oncology by improving access to care for our patients, broadening diversity within our
- [Discovering Novel Epigenetic Dependencies in Pediatric High-grade Glioma](https://cbtn.org/projects/discovering-novel-epigenetic-dependencies-in-pediatric-high-grade-glioma/) - Primary resistance to chemotherapy is a major challenge in treating brain tumors today. Finding novel and specific tumor dependencies is therefore essential for effective drug development and improving patient outcomes. High-grade gliomas (HGG) are the most aggressive brain tumors in children and young adults. They are uniformly fatal despite multimodal treatment strategies combining surgery, radiation
- [Cell Ecosystem and Signaling Pathways of Primary and Metastatic Pediatric Posterior Fossa Ependymoma](https://cbtn.org/projects/cell-ecosystem-and-signaling-pathways-of-primary-and-metastatic-pediatric-posterior-fossa-ependymoma/) - Ependymomas constitute nearly one third of the central nervous system neoplasms among children aged < 3 years1. The disease remains a significant therapeutic challenge, with a 5-year overall survival rate < 55 % among this age group2 and no available chemotherapy of proven efficacy. The breadth of therapies is constrained by the current limited knowledge
- [Biomarker Identification for Neurofibromatosis Type 2 Background](https://cbtn.org/projects/biomarker-identification-for-neurofibromatosis-type-2-background/) - NF2 is a tumor suppressor disorder that leads to the formation of many tumors throughout the lifetime of a patient. Tumors associated with NF2 include schwannomas, meningiomas, and ependymomas. In the treatment of cancer, biomarkers, or substances found in the body that indicate the presence of cancer, are essential to track disease progression and response
- [Developing a Novel Tumor Model to Screen for New Therapies for Spinal Ependymoma](https://cbtn.org/projects/developing-a-novel-tumor-model-to-screen-for-new-therapies-for-spinal-ependymoma/) - Spinal ependymomas (SEs) are rare tumors of the central nervous system that currently have limited treatment options and poor outcomes for advanced cases. Unfortunately, SEs do not respond well to radiation therapy or chemotherapy and almost half of patients will experience tumor recurrence. Because these tumors are rare, there are few tumor models and limited
- [Gene Expression Analysis Platform Evaluation for FFPE Specimen Material-Based Studies](https://cbtn.org/projects/gene-expression-analysis-platform-evaluation-for-ffpe-specimen-material-based-studies/) - Understanding pediatric brain cancers and developing new treatments requires constant innovation. In this project, researchers have developed a new technology for the analysis of tumor RNA, particularly mRNA, the strands of RNA that carry messages through a cell. This new method is called the HTG EdgeSeq technology pipeline for mRNA and/or miRNA profiling. HTG technology
- [Whole Genome Sequencing and RNA Sequencing of the CBTN Bank for the Pediatric Brain Tumor Atlas](https://cbtn.org/projects/whole-genome-sequencing-and-rna-sequencing-of-the-cbtn-bank-for-the-pediatric-brain-tumor-atlas/) - Information about the genetic underpinnings of pediatric brain cancers is necessary for tumor identification, testing, and treatment. In an effort to expand genetic understanding, The Children’s Brain Tumor Network collection of biospecimens approximately 1650 subsamples from the CBTN BioBank have undergone Whole Genome Sequencing and RNA sequencing. This is the largest collection of such data
- [Integrative Functional Genomics of Recurrent Childhood Medulloblastoma](https://cbtn.org/projects/integrative-functional-genomics-of-recurrent-childhood-medulloblastoma/) - Medulloblastoma (MB), the most common malignant brain tumor in children, often confers a poor prognosis, especially for patients who have cancer relapse. Tumor relapse is among the most powerful predictors of prognosis despite therapeutic intervention and clinical trial enrollment in patients with MB. Little is known about the molecular genetics of MB relapse and although
- [DIPG and Other Primary Pediatric Brain Tumors](https://cbtn.org/projects/dipg-and-other-primary-pediatric-brain-tumors/) - Gene expression, the process by which the genetic information is used to direct production of proteins in the body, is crucial in understanding the similarities and differences across tumor types and across same-type tumor mutations. Beginning with gliomas with H3K27M mutations, researchers will investigate genes related to the immune system and their possible role in
- [Molecular Characterization of Pediatric Brain Tumor Subjects and Trios within the Pediatric Brain Tumor Atlas](https://cbtn.org/projects/molecular-characterization-of-pediatric-brain-tumor-subjects-and-trios-within-the-pediatric-brain-tumor-atlas/) - We have not yet discovered why the vast majority of children develop brain cancer, and researchers are always looking for ways to advance their research to answer this question. As part of the launch of the Kids First DRC in 2017, principal investigators within CBTN collaborated to provide an initial cohort of ~1000 WGS/RNAseq tumor/normal
- [Immune Receptor Recombinations in Childhood Brain](https://cbtn.org/projects/immune-receptor-recombinations-in-childhood-brain/)
- [CDC42 RHOJ Interaction Inhibitors for the Treatment of Neurofibromatosis](https://cbtn.org/projects/cdc42-rhoj-interaction-inhibitors-for-the-treatment-of-neurofibromatosis/) - Neurofibromatosis type 2, a disorder driven by Merlin mutation, can cause significant life long issues such as permanent hearing loss. While recent advances have identified the drug selumetinib as a promising therapy for these tumors, this drug can induce serious side effects that reduce compliance and tolerance. This is a particular problem as NF2 patients
- [Comparison of RNA-Binding Protein Expressions in Pediatric and Adult Glioblastoma](https://cbtn.org/projects/comparison-of-rna-binding-protein-expressions-in-pediatric-and-adult-glioblastoma/) - We will select RNA-binding protein genes of interest and check their expression levels in RNA-seq data.
- [MI-ONCOSEQ DMG Study](https://cbtn.org/projects/mi-oncoseq-dmg-study/) - The University of Michigan established the Michigan Oncology Sequencing Center (MI-ONCOSEQ) to use high throughput DNA sequencing technologies to advance the goals of precision cancer medicine. An “integrative sequencing approach” carried out in a CLIA-certified laboratory is utilized to provide a comprehensive landscape of the genetic alterations in individual tumor specimens for the purpose of
- [Functional Dependency Mapping in Paediatric Brain Cancers](https://cbtn.org/projects/functional-dependency-mapping-in-paediatric-brain-cancers/) - Brain tumours are the most common form of solid tumours in children and can have lasting physical impacts beyond childhood. A common form of pediatric brain tumor is a pediatric high grade glioma (pHGG). Recent research has highlighted that pediatric high grade gliomas (pHGGs), are composed of subgroups that are distinct from their adult counterparts
- [Identification of Novel Therapeutic Approaches for pHGGs](https://cbtn.org/projects/identification-of-novel-therapeutic-approaches-for-phggs/) - Gliomas are the most common central nervous system (CNS) tumors in children and adolescents, and they display a particularly broad range of clinical behaviors. Unfortunately, during the last decades there have been no advances in the prognosis of these tumors and therapeutic strategies have changed very little. Pediatric high-grade glioma (pHGG) is a devastating form
- [Leveraging Existing Pediatric Low-Grade Tumor Specimens, Clinical and Imaging Outcome Data, and Artificial Intelligence Innovations to Develop Integrated Biomarkers of Response for Children With Low-Grade Glioma](https://cbtn.org/projects/leveraging-existing-pediatric-low-grade-tumor-specimens-clinical-and-imaging-outcome-data-and-artificial-intelligence-innovations-to-develop-integrated-biomarkers-of-response-for-children-with-low-gr/) - The overall hypothesis is that by using state of the art molecular profiling and artificial intelligence (AI) methods, we will develop imaging biomarkers that predict underlying subtype and response to therapies for pediatric low grade glioma (pLGG). The knowledge gap that will be addressed is our current limited understanding of integrated imaging and molecular characteristics;
- [Analyze the Relationship Between the Expression of Specific Genes and the Prognosis in Pediatric Gliomas](https://cbtn.org/projects/analyze-the-relationship-between-the-expression-of-specific-genes-and-the-prognosis-in-pediatric-gliomas/) - The protein encoded by SETD1A (SET Domain Containing 1A, Histone Lysine Methyltransferase) is a component of a histone methyltransferase (HMT) complex that produces mono-, di-, and trimethylated histone H3 at Lys4. Literatures have found that SETD1A is required for survival of acute myeloid leukemia (AML) cells. H3K4me3 levels positively correlate with WHO grade malignancy in
- [Genetic Vulnerabilities in Supratentorial and Infratentorial Pediatric High-grade Gliomas](https://cbtn.org/projects/genetic-vulnerabilities-in-supratentorial-and-infratentorial-pediatric-high-grade-gliomas/) - Gliomas are the most common central nervous system (CNS) tumors in children and adolescents, and they display a particularly broad range of clinical behavior. The impact of CNS tumors on infant mortality is very important. During the last decades there have been no advances in the prognosis of these tumors, while therapeutic strategies have changed
- [Pediatric Meningiomas](https://cbtn.org/projects/pediatric-meningiomas/)
- [Non-coding Genetic Events in Medulloblastoma and Ependymoma](https://cbtn.org/projects/non-coding-genetic-events-in-medulloblastoma-and-ependymoma/) - Transposable elements (TEs) are sequences of DNA that can change their position within a genome. Researchers working on this project hypothesize that TEs have a role in genomic evolution of high grade gliomas (HGGs). Researchers also hypothesize that transposition events are key in the development of other pediatric brain cancers, including medulloblastomas and ependymomas. Pediatric
- [Aberrant Splicing Candidates as Potential Neoantigen Expression in High-grade Glioma](https://cbtn.org/projects/aberrant-splicing-candidates-as-potential-neoantigen-expression-in-high-grade-glioma/) - Patients with high grade gliomas (HGG) face considerable treatment challenges. Comprehensive genetic and immune system research is needed to find new therapeutic options. One form of therapy that is promising for HGG patients is CAR T cell therapy. CAR T cell therapy is a type of treatment in which a patient's T cells, a type
- [Health Disparities of Pediatric Brain Tumors](https://cbtn.org/projects/health-disparities-of-pediatric-brain-tumors/) - Brain tumors are the leading cause of cancer related death in children. While significant advances have been made in subgrouping tumors of the same diagnosis based on molecular findings, little is known about the differences of tumor biology and the clinical outcomes among racial/ethnic populations. Previous work involving the direct implantation of pediatric brain tumor
- [Proteomic Analysis of CBTN Cell Lines](https://cbtn.org/projects/proteomic-analysis-of-cbtn-cell-lines/) - Scientists at Children’s Medical Research Institute are analyzing tens of thousands of examples of all types of cancer from all over the world to develop a library of information to advance scientific discovery and enhance clinical treatment worldwide. This database will mean doctors can effectively narrow down the best type of currently available treatment to
- [Investigating Disease Mechanism In Adamantinomatous Craniopharyngioma Using New Cell Line Models](https://cbtn.org/projects/investigating-disease-mechanism-in-adamantinomatous-craniopharyngioma-using-new-cell-line-models/) - Adamantiomatious craniopharyngioma (ACP) is an intracranial tumor that is histologically benign, but the clinical manifestation of the disease can have profound effects due to the location of the tumor. Current understanding of the disease pathology is limited and there are no targeted drug therapeutics for the disease. The lack of reliable cell line models for
- [Defining the Global Impact of Somatic Structural Variation on the Transcriptome of Human Pediatric Brain Cancers](https://cbtn.org/projects/defining-the-global-impact-of-somatic-structural-variation-on-the-transcriptome-of-human-pediatric-brain-cancers/) - Somatic structural variants (SSVs) are mutations arising in tumors that involve large segments of DNA in somatic cells, cells of the body that are not eggs or sperm. Researchers seek to identify genes for which the presence of nearby SSV regions is associated with altered expression. Altered expression may involve gene fusions, gene disruption, and
- [Oncolytic Virus to Potentiate Immune-checkpoint Blockade in Immunologically Cold Pediatric Brain Tumors](https://cbtn.org/projects/oncolytic-virus-to-potentiate-immune-checkpoint-blockade-in-immunologically-cold-pediatric-brain-tumors/) - Some common viruses (e.g. measles, poliovirus) preferentially infect and kill tumor cells. This fact was discovered at the beginning of the 20th century. However, it was not until recently that this approach was recognized as an immunotherapy. It has been shown that viruses have the ability to stimulate an immune response in solid tumors with
- [Exploring the Possible Role of Mutations in MTOR pathway Genes in the Pathogenesis of DNET Tumors](https://cbtn.org/projects/exploring-the-possible-role-of-mutations-in-mtor-pathway-genes-in-the-pathogenesis-of-dnet-tumors/) - Recent tissue-based research suggests that overactivation of the mTOR pathway, central to the regulation of metabolism, growth, proliferation, and survival, could be a driver in the development of various diseases and malformations in children including DNET tumors. Using samples from the CBTN BioBank, researchers will conduct studies into the hyperactivation of the mTOR pathway and
- [Cross-disease Variant Lookup in CBTN](https://cbtn.org/projects/cross-disease-variant-lookup-in-cbtn/) - This project aims at identifying variants in the CBTN germline DNA whole genome sequencing data that are reported and/or found in other diseases, esp. birth defects and rare Mendelian disorders, hoping to explain/reveal shared genetics between pediatric cancer and rare diseases.
- [CBTN Cell Lines High-Throughput Drug Screening Study (NCATS)](https://cbtn.org/projects/cbtn-cell-lines-high-throughput-drug-screening-study-ncats/) - While the understanding of pediatric brain cancers has grown over time, there are still very limited options for targeted treatments. One reason for this is the inefficiency of current analysis methods and a lack of centralization of such data for rare pediatric brain tumors. Here, researchers propose a collaborative effort with the National Center For
- [Comprehensive Molecular Profiling of Pediatric Meningioma](https://cbtn.org/projects/comprehensive-molecular-profiling-of-pediatric-meningioma/) - Meningiomas are the most common tumors occurring in the brain and spine. Pediatric meningiomas, however, are extremely rare tumors and are often of the most aggressive form. Furthermore, a majority of these tumors are associated with a well-described genetic disorder, neurofibromatosis type 2 (NF2). The mechanisms involved in NF2 driven meningiomas is well described, but
- [Investigating Biomarker for Treatment Respondors and Non-respondors in PDX Model Experiment](https://cbtn.org/projects/investigating-biomarker-for-treatment-respondors-and-non-respondors-in-pdx-model-experiment/) - Children with high-grade glioma, diffuse intrinsic pontine glioma, rhabdoid brain tumors, and certain other types of brain tumors experience a low likelihood of survival even with the maximum available therapy. The standard therapies for pediatric brain tumors, including surgery, intensive chemotherapy, and radiation therapy are often toxic for patients, therefore there is a strong need
- [Comprehensive Molecular Profiling of Pediatric Diffuse Astrocytomas: Independent Validation of Proteomic Analysis](https://cbtn.org/projects/comprehensive-molecular-profiling-of-pediatric-diffuse-astrocytomas-independent-validation-of-proteomic-analysis/) - Brain tumors are the most common cause of pediatric cancer-related death in the United States, and glial tumors (astrocytomas, oligodendrogliomas, etc.) are the most common class of pediatric brain tumors. Adult low-grade diffuse astrocytomas nearly always transform into deadly, high grade glioblastomas, while pediatric tumors of the same kind are much less likely to do
- [A Highly-Usable and Fully-Comprehensive Proteogenomic Method Leveraging the Breadth of Genetic Variation for Oncogenic and/or Therapeutic Novel Protein Discovery](https://cbtn.org/projects/a-highly-usable-and-fully-comprehensive-proteogenomic-method-leveraging-the-breadth-of-genetic-variation-for-oncogenic-and-or-therapeutic-novel-protein-discovery/) - The development of many cancers is known to be driven by genetic rearrangements. Many of these genetic rearrangements can be caused by transposons, DNA sequences that can change position and move to other positions within the genome. In previous studies, one of these genes, human piggyBac transposable element derived 5 (PGBD5), was examined for its
- [Microglial Mosaicism in BRAFV600E Glioma Development](https://cbtn.org/projects/microglial-mosaicism-in-brafv600e-glioma-development/) - Pediatric Low Grade Gliomas (pLGG) are the most common brain tumor in children and BRAFV600E is a mutation found in up to 20% of pLGG cases. This mutation is associated with a poor prognosis. In the majority of cases, factors leading to progression and malignant transformation are unknown. There is growing evidence of the existence
- [Discover New Therapeutics for DIPG using a Systems-Based Approach](https://cbtn.org/projects/discover-new-therapeutics-for-dipg-using-a-systems-based-approach/) - Diffuse intrinsic pontine glioma (DIPG) is an aggressive type of brainstem cancer that targets young children. Complete surgical removal is not possible, and chemotherapy and radiotherapy are currently only effective in controlling pain and discomfort. New therapies are greatly needed to combat the poor prognosis of this cancer but they can not be developed without
- [Descriptive "Pharmacogenomics Analysis" of the CBTN PBTA Cohort](https://cbtn.org/projects/descriptive-pharmacogenomics-analysis-of-the-cbtn-pbta-cohort/) - Outcomes for pediatric cancer patients have improved over the last few decades due to advancements in treatments, including those for pediatric brain tumors. However, side effects can still have negative effects on patients long after treatment is complete, and some research focus has shifted to combating these effects. One emerging field to address this issue
- [Comparison of CBTN Patient Data with Molecularly-Defined Stem Cell Models of Pediatric Brain Tumors](https://cbtn.org/projects/comparison-of-cbtn-patient-data-with-molecularly-defined-stem-cell-models-of-pediatric-brain-tumors/) - Preclinical models are a common way for researchers to study tumor types as well as test diagnostics and therapies. Researchers are currently developing various models of malignant pediatric tumors such as medulloblastoma, malignant glioma, diffuse intrinsic pontine gliomas (DIPG) and choroid plexus carcinomas. The focus of this research is on the signaling pathways of MYC
- [Landscape of Tumor-infiltrating T-Cell Repertoire of Pediatric Brain Tumors](https://cbtn.org/projects/landscape-of-tumor-infiltrating-t-cell-repertoire-of-pediatric-brain-tumors/) - The cellular immune system, mediated by specialized cells called T-cells, is responsible for detecting and combating microorganisms that may cause disease such as bacteria and viruses. T-cell receptors (TCRs) are highly specialized receptors on the outside of cells. Knowledge of TCRs can characterize the T-cell immune status in patients. The ability to assess T-cell-mediated immunity
- [Genomic Analysis of Oligodendrogliomas Across Pediatrics, Adolescents and Adults](https://cbtn.org/projects/genomic-analysis-of-oligodendrogliomas-across-the-pediatrics-adolescents-and-adults/) - Oligodendroglioma is a malignant brain cancer that develops from specialized nervous cells called oligodendrocytes. Oligodendroglioma is one of the more common types of glioma (which also includes glioblastoma multiforme and astrocytoma) that can affect people of all ages. Rarely, families with multiple affected members have been reported, suggesting that a predisposition for oligodendroglioma can be
- [Children's Brain Tumor Network Pediatric Brain Tumor Proteomics Pilot](https://cbtn.org/projects/childrens-brain-tumor-network-pediatric-brain-tumor-proteomics-pilot/) - Pediatric brain tumors are the leading cause of disease related death in children. Major factors contributing to treatment failures for children with brain tumors include: i) the lack of comprehensive molecular description of the disease and an associated dearth of integration of the tumors’ biological signatures at gene, protein and RNA levels; ii) paucity of
- [Comprehensive Genomic and Immune Signature Profiling of Ependymoma and Diffuse Intrinsic Pontine Glioma](https://cbtn.org/projects/comprehensive-genomic-and-immune-signature-profiling-of-ependymoma-and-diffuse-intrinsic-pontine-glioma/) - Brain tumors are the most common form of pediatric tumor, and while advancements have been made in treating a variety of tumor types, the need for comprehensive research into all pediatric brain tumors is great. Certain subtypes of ependymoma are associated with poor outcomes for patients as well as with diffuse intrinsic pontine glioma (DIPG)
- [Pediatric Brain Tumor miRNA Profiling for the Cohort of Children’s Brain Tumor Network Specimens](https://cbtn.org/projects/pediatric-brain-tumor-mirna-profiling-for-the-cohort-of-childrens-brain-tumor-network-specimens/) - The leading cause of disease related death in children is pediatric brain tumors. Surgery remains the main form of treatment for such tumors, however many brain tumors are unable to be fully removed with surgery. There are many factors that could lead to new and more effective therapies, including greater understanding of tumor genetics, comprehensive
- [Project Hope: High-Grade Glioma-Omics in Pediatric and AYA](https://cbtn.org/projects/project-hope-high-grade-glioma-omics-in-pediatric-and-aya/) - High grade gliomas affect patients across age groups, and this project seeks to better understand high grade gliomas as they affect pediatric, adolescent, and young adult populations. The goal of this project is to generate single cell sequencing data of cancer cells, immune cells and non-immune microenvironment in pediatric and adolescent and young adult high-grade
- [Alternative Splicing in CBTN Data](https://cbtn.org/projects/alternative-splicing-in-cbtn-data/) - Alternative splicing of RNA is the process that changes information from genes into proteins that can be used by a cell. Alternative splicing plays a critical role in the regulation of gene expression and protein diversity found within a cell, and understanding its function across pediatric tumors could lead to the identification of new therapeutic
- [Immunotherapeutically-targeting IDO1 in Pediatric High-grade Glioma](https://cbtn.org/projects/immunotherapeutically-targeting-ido1-in-pediatric-high-grade-glioma/) - Cancer Immunotherapy is a therapy which uses the patient’s own immune system to destroy tumors. This strategy is considered particularly promising for patients with high-grade pediatric brain cancer, whose survival rate is currently 10-15% despite use of aggressive surgical and radiation treatments. Immune cells are capable of the destruction of glioblastoma (GBM), but research into
- [Telomere Maintenance Across Multiple Brain Tumors](https://cbtn.org/projects/telomere-maintenance-across-multiple-brain-tumors/) - To keep Chromosomes bundled, telomeres act as caps on the ends of DNA strands. As cells divide, telomeres get shorter causing cell aging and death. It has been demonstrated that the dramatic shortening of telomeres could lead to the ability for cancer to continually grow and divide such as neuroblastoma. In this study, researchers seek
- [In Silico Neo-antigen Detection in High-grade Pediatric Brain Tumors Utilizing RNA-seq and WGS](https://cbtn.org/projects/in-silico-neo-antigen-detection-in-high-grade-pediatric-brain-tumors-utilizing-rna-seq-and-wgs/) - Immunotherapy, therapy that uses a patient’s own immune system to attack a tumor, is a promising form of therapy for high grade tumors such as high grade glioma, diffuse intrinsic pontine glioma (DIPG), atypical teratoid rhabdoid tumors (ATRT), and medulloblastoma. In these cases, there does not seem to be genetic targets for therapy, but rather
- [Choroid Plexus Tumor (CPT) Therapies Based on Patient-derived Cell Culture Resources](https://cbtn.org/projects/choroid-plexus-tumor-cpt-therapies-based-on-patient-derived-cell-culture-resources/) - Choroid plexus tumors (CPT) are rare tumors. Around 80% of choroid plexus carcinoma (CPC) arise in children and account for 10-15% of all CPTs. Clinically, this group of tumors tends to cause hydrocephalus and increased intracranial pressure. Surgical removal is considered to be the most effective treatment for CPCs and chemotherapy contributes to long-term survival,
- [Fusion Analysis in CBTN RNAseq Data](https://cbtn.org/projects/fusion-analysis-in-cbtn-rnaseq-data/) - Gene fusions occur when two formally independent genes merge to create a new gene. These gene fusions also result in fusion proteins, proteins that may otherwise not be made by the cell. Gene fusions and their fusion proteins have been shown to play a role in the development of cancers, including pediatric brain cancers. Researchers
- [Genetic Polymorphisms and Neuro-Cognitive Outcomes in Pediatric Brain Tumor Survivors](https://cbtn.org/projects/genetic-polymorphisms-and-neuro-cognitive-outcomes-in-pediatric-brain-tumor-survivors/) - Within specific pediatric brain tumor types, there can be various genetic mutations that could have effects on the ongoing neurological health of pediatric brain cancer survivors. These genetic differences are referred to as genetic polymorphisms. Combining genetic data from the Pediatric Brain Tumor Atlas with measures of cognitive, emotional, social and behavioral functioning of pediatric
- [Treehouse Childhood Cancer Initiative: Identification of Therapeutic Leads for Individual Pediatric Cancer Patients via Cancer Analysis](https://cbtn.org/projects/treehouse-childhood-cancer-initiative-identification-of-therapeutic-leads-for-individual-pediatric-cancer-patients-via-cancer-analysis/) - The information stored in DNA dictates how cells make proteins and other molecules. Cancer alters this gene expression, resulting in tumors. Oncogenes, genes with the potential to cause cancer, can be utilized in the treatment of cancer itself but they must first be identified. Using the Pediatric Brain Tumor Atlas, researchers are comparing data across
- [Advancing DMG Drug Discovery with an Organoid-Based Toolkit](https://cbtn.org/projects/advancing-dmg-drug-discovery-with-an-organoid-based-toolkit/) - The specimens from the Children's Brain Tumor Network (CBTN) are of paramount importance for validating our micro-organoid and multi-organ-on-a-chip modeling systems. The comprehensive clinical and genomic data accompanying these specimens will be pivotal in our assessment of the fidelity with which our organoid model replicates DMG tumors and to help better interpret the correlations between
- [From Data to Treatment: AI-Driven Identification of Molecular Targets and Bio-Inspired Therapeutics for Pediatric Glioma](https://cbtn.org/projects/from-data-to-treatment-ai-driven-identification-of-molecular-targets-and-bio-inspired-therapeutics-for-pediatric-glioma/) - Pediatric gliomas, including high-risk tumors like diffuse midline glioma (DMG/DIPG) and diffuse leptomeningeal glioneuronal tumor (DLGNT), remain some of the most challenging childhood cancers to treat. Despite advances in research, effective therapies are still limited, and survival rates for aggressive forms remain poor. Our study aims to leverage artificial intelligence (AI) and multi-omics analysis to
- [Bayer NTRK Fusion Project](https://cbtn.org/projects/bayer-ntrk-fusion-project/) - TRK fusions are rare genetic changes that occur in a wide range of tumors, including pediatric brain tumors. Drugs that specifically block these fusions (TRK inhibitors) have demonstrated remarkable activity, but little is known about the natural history of brain tumors with TRK fusions. Here we will analyze the cohort of patients with TRK fusion
- [Analysis of outcomes in recently treated subjects with DIPG](https://cbtn.org/projects/analysis-of-outcomes-in-recently-treated-subjects-with-dipg/) - The CBTN data will be used to compare outcome of patients with DIPG after standard treatment using radiation to outcome after treatment with a new viral immunotherapy, DNX-2401 plus radiation.
- [Multi-Tensor Decompositions for Personalized Pediatric Glioma Diagnostics and Prognostics](https://cbtn.org/projects/multi-tensor-decompositions-for-personalized-pediatric-glioma-diagnostics-and-prognostics/) - Eigengene, Inc., requests access to the tumor and normal whole-genome sequencing data from high- and low-grade pediatric glioma patients, as well as the patient-matched clinical data, in order to create personalized diagnostic and prognostic tests for pediatric gliomas. Eigengene develops powerful universal algorithms, and, by applying these algorithms to cancer genomic data, finds signatures that
- [Integrative analysis of childhood cancers](https://cbtn.org/projects/integrative-analysis-of-childhood-cancers/) - We will apply integrative analysis of data types to find potential novel drug targets and matching of therapeutics.
- [Project Hope, High-Grade Glioma-Omics in Pediatric and AYA](https://cbtn.org/projects/project-hope-high-grade-glioma-omics-in-pediatric-and-aya-2/) - High grade gliomas affect patients across age groups, and this project seeks to better understand high grade gliomas as they affect pediatric, adolescent, and young adult populations. The goal of this project is to generate single cell sequencing data of cancer cells, immune cells and non-immune microenvironment in pediatric and adolescent and young adult high-grade
- [Clinical and molecular characterization of rare and newly defined brain tumor entities Including CNS sarcomas, BCOR altered tumors, astroblastomas/MN-1 altered tumors. PLAG1 altered tumors and histologically ambiguous/unclassifiable brain tumors](https://cbtn.org/projects/clinical-and-molecular-characterization-of-rare-and-newly-defined-brain-tumor-entities-including-cns-sarcomas-bcor-altered-tumors-astroblastomas-mn-1-altered-tumors-plag1-altered-tumors-and-histolo/) - The outlook of childhood brain tumors is very different across different brain cancer types. Certain brain tumors can be very rare. Due to the rarity of certain tumor types, very few studies have been completed thereby explaining our lack of understanding of the biological behavior and best treatment approaches. Recent genetic studies demonstrated that these
- [Development of Cancer Immunoprevention in a High-Risk Population of CMMRD: Characterization of Frameshift Neoantigens in Mismatch Repair Deficient Individuals](https://cbtn.org/projects/development-of-cancer-immunoprevention-in-a-high-risk-population-of-cmmrd-characterization-of-frameshift-neoantigens-in-mismatch-repair-deficient-individuals/) - The Constitutional Mismatch Repair Deficiency syndrome (CMMRD) is an inherited disease passed from both mother and father, which results in an extremely high risk of developing multiple cancers including brain (>50%) and gastrointestinal (>40%) tumors, leukemia or lymphoma (>30%), and other types of cancers during childhood. CMMRD is caused by one faulty DNA mismatch repair
- [Profiling non-canonical open reading frames in pediatric brain cancer](https://cbtn.org/projects/profiling-non-canonical-open-reading-frames-in-pediatric-brain-cancer/) - Learning the underlying causes of pediatric brain use statement cancers has the potential to yield long-term benefits for the development of new therapeutic approaches. Our work specifically focuses on the discovery of previously-unknown small proteins (termed microproteins) that may enrich our knowledge of brain cancer biology. In this work, we will be focusing our microprotein
- [The Role of Histone Chaperones in H3.3K27M-altered Pediatric Diffuse Midline Glioma](https://cbtn.org/projects/the-role-of-histone-chaperones-in-h3-3k27m-altered-pediatric-diffuse-midline-glioma/) - Diffuse midline glioma (DMG) is a highly aggressive and lethal brain tumor that occurs in young children between 6-9 years old. The overall survival of children with DMG is only 9-15 months with no curative therapies to date. Our proposed study will establish the identity of H3.3K27M histone chaperone, uncover its role in tumorigenesis and
- [iPC EU Horizon 2020 - Individualized Paediatric Cure: Cloud-based virtual-patient models for precision paediatric oncology](https://cbtn.org/projects/ipc-eu-horizon-2020-individualized-paediatric-cure-cloud-based-virtual-patient-models-for-precision-paediatric-oncology/) - Unsupervised visual anomaly detection methods will be developed on available imagery data (histology images, MR images, radiology images) to detect anomalies (e.g. tumours, metastases) without the need for expertly labeled lesion level data. Research will be performed as part of the iPC EU Horizon 2020 project and PIs PhD study.
- [Mechanism of action and efficacy of ONC201 and ONC206 in DMG preclinical models](https://cbtn.org/projects/mechanism-of-action-and-efficacy-of-onc201-and-onc206-in-dmg-preclinical-models/) - Currently, we have access to a couple of commercially available DIPG cell lines. The large panel of wt and K27M mutant midline glioma lines from CBTN will be particularly important for our project to understand the heterogeneity of response and mechanism of action of ONC201 and ONC206.
- [Molecular and Spatial Insights into Treatment Failure in Pediatric Low-Grade Gliomas](https://cbtn.org/projects/molecular-and-spatial-insights-into-treatment-failure-in-pediatric-low-grade-gliomas/) - Treatment failure is common and a major cause of tumor recurrence, life-long morbidity and increased mortality in children and adolescents with pediatric low-grade glioma (pLGG). Even though most patients with unresectable pLGG fail one or multiple therapies, the genetic and spatial evolution of pediatric LGGs through time and after treatment remains poorly understood. The scarcity
- [Rapid Molecular Central Nervous System Tumor Diagnosis](https://cbtn.org/projects/rapid-molecular-central-nervous-system-tumor-diagnosis/) - Currently, surgeons must make critical decisions about how extensively to remove tumor tissue without having complete information about the tumor type. For some tumors, survival depends on the amount of tumor resected, while for others the risk of aggressive surgical resection does not outweigh benefit of doing so. This project aims to improve the speed
- [Leveraging Deep Learning to Decipher Single-cell Epigenetic Regulation in Diffuse Midline Glioma and Ependymoma](https://cbtn.org/projects/leveraging-deep-learning-to-decipher-single-cell-epigenetic-regulation-in-diffuse-midline-glioma-and-ependymoma/) - Diffuse midline glioma (DMG) is a deadly childhood tumor with no effective treatments. This project seeks to understand the genetic and molecular mechanisms driving its development. Through cutting-edge single-cell analyses and advanced AI models, researchers aim to map the tumor's landscape, identify key regulatory elements, and predict the function of mutations. This knowledge could pave
- [Systems biology integration of single-cell and spatial omics data to dissect tumor and tumor microenvironment interaction map of atypical teratoid rhabdoid tumors.](https://cbtn.org/projects/systems-biology-integration-of-single-cell-and-spatial-omics-data-to-dissect-tumor-and-tumor-microenvironment-interaction-map-of-atypical-teratoid-rhabdoid-tumors/) - Our research aims to explore the biology of Atypical Teratoid Rhabdoid Tumors (ATRT) at an unprecedented level of detail. We intend to obtain human specimens from the Children's Brain Tumor Network (CBTN) to generate the first single cell and spatial omics data for this disease. This could provide critical insights into the tumor's development and
- [The Proteomic Landscape of Low-Grade Glioma (LGG)](https://cbtn.org/projects/the-proteomic-landscape-of-low-grade-glioma-lgg/) - This project will not be possible without the tissue samples from those patients nor without the associated clinical/pathological and follow-up data.
- [Medulloblastoma subgroups stratification using transcriptome and RNA modification landscape](https://cbtn.org/projects/medulloblastoma-subgroups-stratification-using-transcriptome-and-rna-modification-landscape/) - CBTN cohort is comprehensive in encompassing various subgroups of medulloblastoma. Access to patient samples will enable us in efficiently sequencing the native RNA. Clinical information associated with samples that is available with CBTN samples is important in building prototype to successfully delineate subgroups using novel sequencing technology rapidly. Additionally, the genomic and epigenomic datasets previously
- [An immuno-epigenomic approach to identify therapeutic opportunities for Paediatric High-Grade Gliomas](https://cbtn.org/projects/an-immuno-epigenomic-approach-to-identify-therapeutic-opportunities-for-paediatric-high-grade-gliomas/) - We aim to identify more therapeutic opportunities in epigenetic pathways and immunotherapy in combination with radiotherapy. With CBTN, we hope to test the targets in the patient samples at diagnosis and after radiotherapy (autopsy samples) to understand the potential of combinatory treatment with radio therapy.
- [Maternal Microchimerism in Human Brain](https://cbtn.org/projects/maternal-microchimerism-in-human-brain/) - We obtained strikingly positive results for maternal Mc in brain that we have studied from epilepsy patients but we currently have no other condition for comparison.
- [Understanding the effect of mismatch repair deficiency on the alternative lengthening of telomeres](https://cbtn.org/projects/understanding-the-effect-of-mismatch-repair-deficiency-on-the-alternative-lengthening-of-telomeres/) - The project aims at understanding if deactivation of the mismatch repair (MMR) pathway leads to the usage of the alternative lengthening of telomeres (ALT) in high grade gliomas. The impact will be significant as we currently know little about the origin of ALT and therapeutics against this type of tumors are scarse. We expect to
- [Mechanisms of medulloblastoma formation](https://cbtn.org/projects/mechanisms-of-medulloblastoma-formation/) - Medulloblastoma, while highly malignant are rare tumors and access to specimens is limited. In particular when trying to understand differences between subtypes, one needs to have enough specimens representing each subtype for statistical significance.
- [Genetic Susceptibility to Medulloblastoma](https://cbtn.org/projects/genetic-susceptibility-to-medulloblastoma/) - An adequately powered study setting is important for the proposed GWAS to identify novel validated germline variants associated with medulloblastoma. As in such studies, extremely conservative p-value estimates must be used to correct for multiple comparisons. A large sample size is essential to be able to detect variants at a genome-wide significance level of p
- [Genomic Analysis of Oligodendrogilomas across the pediatrics, adolescents and adults](https://cbtn.org/projects/genomic-analysis-of-oligodendrogilomas-across-the-pediatrics-adolescents-and-adults/) - There are no other specimens available in the pediatric arena.
- [Evaluation of immunosignature profile in medulloblastoma](https://cbtn.org/projects/evaluation-of-immunosignature-profile-in-medulloblastoma/) - Whole blood samples will be analyzed in immunosignature assay RNA from tumor tissue will be analyzed by mRNA microarray analysis and next analyzed by institution designedgenomic analysis pipeline. RNA-Seq data will be analyzed by institution designed genomic analysis pipeline.
- [Development of Preclinical Models of Pediatric Ependymoma](https://cbtn.org/projects/development-of-preclinical-models-of-pediatric-ependymoma/) - The incidence of pediatric ependymoma is low. In order to expedite the development of these preclinical models so that they could also be used for preclinical drug development, we are trying to identify as many existing cases as possible. Since CBTTC currently has the largest collection of childhood brain tumor specimens that are available for
- [Center for Pediatric Tumor Cell Atlas](https://cbtn.org/projects/center-for-pediatric-tumor-cell-atlas/) - The proposed project to create the pHGG Diagnosis-Relapse Human Tumor Atlas (HTA) will provide in-depth single cell and whole exome sequencing data for 20 supratentorial HGG specimens at the time of diagnosis and relapse / autopsy, with clinical, pathologic and radiographic correlation.
- [ENPP1 inhibition in models of medulloblastoma](https://cbtn.org/projects/enpp1-inhibition-in-models-of-medulloblastoma/) - We are developing inhibitors of ENPP1 which is the only known checkpoint of innate immunity. Our goal with these samples is to test the effect of ENPP1 inhibitors in an immune organoid based system using medulloblastoma organoids.
- [Personalized therapy for high-risk ependymoma of childhood](https://cbtn.org/projects/personalized-therapy-for-high-risk-ependymoma-of-childhood/) - We are requesting models of childhood ependymoma (both supratentorial and posterior fossa) which propagate in vitro, which are amenable to both chemical and genetic screening. As there is a paucity of ependymoma models that propagate in vitro, these will be extremely valuable to identify potential therapeutic targets which can be developed further. Currently we have
- [Delineating pediatric glioma progression using single-nuclei sequencing](https://cbtn.org/projects/delineating-pediatric-glioma-progression-using-single-nuclei-sequencing/) - The CBTTC consists of 18 international institutions that aims to support transformative research for pediatric brain tumours. More than 2,500 participants have been enrolled by CBTTC to date and over 40,000 biospecimens have been collected and annotated with clinical, pathological, imaging and genomic data. Available biospecimens include flash frozen tumour tissues, FFPE blocks, Blood, CSF,
- [Identifying the cells of origins of brain tumors using somatic mutations](https://cbtn.org/projects/identifying-the-cells-of-origins-of-brain-tumors-using-somatic-mutations/) - The CBTTC has unique access to and a network for obtaining post-mortem samples that are vital for this work. This is because we are most interested in normal brain tissue adjacent to brain tumors, which is usually not preserved or stored. Additionally, the CBTTC has already sequenced many pediatric brain tumors, which could be immediately
- [Targeting regions of converging synteny in pediatric and canine glioma](https://cbtn.org/projects/targeting-regions-of-converging-synteny-in-pediatric-and-canine-glioma/) - CBTTC provided pediatric high-grade glioma data resources and cell lines will be crucial for both of our aims. Specifically, available cell-line and patient WGS and RNA-seq data will be used to identify aneuploidy in conserved synteny regions. Cell-lines will then be subject to low pass WGS to screen for candidate aneuploidy shared with canine glioma
- [Impeding LIN28 function in ATRT](https://cbtn.org/projects/impeding-lin28-function-in-atrt/) - ATRT is a heterogenous disease comprised of multiple subtypes. Our current in vitro work with ATRT has utilized the ATCC provided cell line CHLA-02-ATRT. Without testing our hypothesis in a larger cohort of cell lines, more fully representing the heterogeneity within the disease, any conclusions that can be drawn based on our experiments are severely
- [Investigating the Metabolic Hallmarks of Oligodendroglioma](https://cbtn.org/projects/investigating-the-metabolic-hallmarks-of-oligodendroglioma/) - Oligodendrogliomas, especially those that arise in adolescents, are fairly rare brain tumors. As such, obtaining sufficient numbers of pediatric oligodendroglioma samples from sources other than the CBTTC would be difficult and require years to collect in sufficient numbers if done prospectively. The samples requested from the CBTTC are integral to our efforts to elucidate the
- [Identification of circulating noncoding RNAs and metabolites in cerebrospinal fluid (CSF) in medulloblastoma patients](https://cbtn.org/projects/identification-of-circulating-noncoding-rnas-and-metabolites-in-cerebrospinal-fluid-csf-in-medulloblastoma-patients/) - We tried to secure samples from collaborators and other sources but until today, we have not been successful in securing CSF for our research. Out last resource is to contact CBTTC today and we were asked to submit this proposal for evalutaion. Currently we have secured $100’000 to conduct this study but unfortuantely we can’t
- [Regional Response to ONC201 in Pediatric High-Grade Glioma](https://cbtn.org/projects/regional-response-to-onc201-in-pediatric-high-grade-glioma/) - The pHGG cell lines with annotated molecular and regional information are critical resources to answer our pre-clinical questions.
- [Targeting medulloblastoma by regulating RNA binding proteins](https://cbtn.org/projects/targeting-medulloblastoma-by-regulating-rna-binding-proteins/) - The Schnepp laboratory has experience in studying aggressive solid tumors including neuroblastoma and rhabdomyosarcoma but little experience in studying brain tumors like medulloblastoma. We currently have access to a few established medulloblastoma cell lines (D321, D556, DAOY) and a line derived from a patient treated here at Children’s Healthcare of Atlanta through the Ians Friends
- [Therapeutic targeting of the blood-brain barrier in pediatric malignant brain tumors](https://cbtn.org/projects/therapeutic-targeting-of-the-blood-brain-barrier-in-pediatric-malignant-brain-tumors/) - CBTTC source provides a uniform database of optimized tissue with highly notated data regarding clinical specimens, location, and associated therapies. At the NIH, we do not have a large clinical sample database for translational studies. Thus, use of CBTTC specimens and data will allow us to evaluate BBB restrictions related to treatment response with bioinformatic
- [Genomic Analysis of Chordomas across the pediatrics, adolescents and adults](https://cbtn.org/projects/genomic-analysis-of-chordomas-across-the-pediatrics-adolescents-and-adults/) - There are no other specimens available in the pediatric arena.
- [Investigating disease mechanism in Adamantinomatous Craniopharyngioma using new cell line models.](https://cbtn.org/projects/investigating-disease-mechanism-in-adamantinomatous-craniopharyngioma-using-new-cell-line-models-2/) - The cell lines requested from CBTTC are very important for this project because of the lack of such comparable cell lines from another source. Additionally, the access to matched samples and curated database of clinical, histological, and molecular information associated with these cell lines that is available from the CBTTC is very critical for the
- [The role of genetic factors in ependymoma susceptibility](https://cbtn.org/projects/the-role-of-genetic-factors-in-ependymoma-susceptibility/) - An adequately powered study setting is important for the proposed GWAS to identify novel validated germline variants associated with ependymoma. As in such studies, extremely conservative p-value estimates must be used to correct for multiple comparisons. A large sample size is essential to be able to detect variants at a genome-wide significance level of p
- [Using whole genome bisulfite sequencing to identify novel therapeutic targets in DIPG and ATRT](https://cbtn.org/projects/using-whole-genome-bisulfite-sequencing-to-identify-novel-therapeutic-targets-in-dipg-and-atrt/) - CBTTC has the largest collection of these specimens in the world to our knowledge. Access to CBTTC specimens and data will allow us to propel target discovery and vailidation in these two diseases.
- [Defining the role of the histone 3 (H3.3G34R) mutation in the pathogenesis of pediatric high astrocytoma](https://cbtn.org/projects/defining-the-role-of-the-histone-3-h3-3g34r-mutation-in-the-pathogenesis-of-pediatric-high-astrocytoma/) - The patient derived cell lines will be used to validate the findings from our BioID screen. They will be essential in that they represent an endogenously expressing H3.3G34R mutant line. Further, they will be critical for determining the clinical significance of our findings and for testing potential novel therapeutic approaches.
- [Circular RNAs in Medulloblastoma](https://cbtn.org/projects/circular-rnas-in-medulloblastoma/) - We are requesting medulloblastoma RNA samples from CBTTC as this consortium represents the largest collection of brain tumor material that we are aware. We have already contacted Swedish sources and have received / are in the process of receiving three samples of SHH medulloblastoma tumors. However, in order to obtain robust data on the circular
- [Elucidate potential therapeutic targets in H3.3G34 mutant pHGG cells](https://cbtn.org/projects/elucidate-potential-therapeutic-targets-in-h3-3g34-mutant-phgg-cells/) - Currently, we are only aware one H3.3G34V line. The precious lines you generated are extremely useful for the studies. The biospecimens and patient derived tumor models are greatly useful for the basic and translational research in understanding the mechanism of the disease thus helping develop effective therapeutically method (3). The H3.3G34R cell line will be
- [Elucidating the role of driver mutations in pediatric High Grade Glioma](https://cbtn.org/projects/elucidating-the-role-of-driver-mutations-in-pediatric-high-grade-glioma/) - The CBTTC has a large number of pHGG cell lines and specimens. Additionally both pHGG tumor samples and cell lines have been analyzed in depth providing invaluable data for our projects. Currently, we do not have any human pHGG cell lines in hand and the analysis of human material (cell lines or tissue microarray) nor
- [Molecular and functional characterization of childhood supratentorial ependymoma](https://cbtn.org/projects/molecular-and-functional-characterization-of-childhood-supratentorial-ependymoma/) - I am requesting CBTTC specimens as this provides an opportunity to validate my current findings in a large validation cohort comprising high quality tumor tissue, which comprises patients treated on modern protocols. Considering the rarity of supratentorial ependymoma and the overall difficulties in obtaining the current discovery cohort, this provides an opportunity to validate both
- [Disclosing chromatin accessibility in brain tumor cells after treatment by cracking a 'nucleosomal code'](https://cbtn.org/projects/disclosing-chromatin-accessibility-in-brain-tumor-cells-after-treatment-by-cracking-a-nucleosomal-code/) - The collection of cell lines at the CBTTC will be invaluable to globally investigate the epigenetic alterations of chromatin in response to epigenetic drugs. We are particularly interested to include in our study the pediatric cell lines with wt histone H3 as well as with the common mutations such as K27M or G34R, to help
- [Released Tumor DNA in the CSF for the Diagnosis and Monitoring of Pediatric Brain Tumors](https://cbtn.org/projects/released-tumor-dna-in-the-csf-for-the-diagnosis-and-monitoring-of-pediatric-brain-tumors/) - The CBTTC has a rare collection of medulloblastoma CSF, with matched tumor and blood tissue. For us to perform our assays to detect CSF-tDNA, we ideally will need all three tissues, which is difficult to accrue at any one medical center given the rarity of medulloblastoma. We already have an IRB approved protocol that allows
- [Germline and somatic determinants of paediatric brain tumor evolution](https://cbtn.org/projects/germline-and-somatic-determinants-of-paediatric-brain-tumor-evolution/) - CBTTC samples will be used to increase our cohort of pediatric brain tumors for genomic analysis and functional studies.
- [Elucidating the somatic epigenetic landscape of pediatric meningioma and schwannoma](https://cbtn.org/projects/elucidating-the-somatic-epigenetic-landscape-of-pediatric-meningioma-and-schwannoma/) - Accessing the CBTTC samples will allow an unprecedented epigenetic analysis of pediatric meningiomas. and schwannomas. Using integrative methylation profiling we will conclusively address how pediatric meningiomas and schwannomas are both similar or unique from their adult counterparts. This project can only be completed with the use of CBTTC samples.
- [Interactions between astrocytes and tumor cells are critical for medulloblastoma growth](https://cbtn.org/projects/interactions-between-astrocytes-and-tumor-cells-are-critical-for-medulloblastoma-growth/) - We have been always using primary MB cells isolated from Ptch1 deficient mice. We wish to be able to validate our research findings in human MB, which will pave the road to rapidly translate our findings to clinics. Currently we do not have any MB samples from human patients.
- [Molecular Analysis of the Cellular Ecosystem of Childhood Ependymoma](https://cbtn.org/projects/molecular-analysis-of-the-cellular-ecosystem-of-childhood-ependymoma/) - Although they led to interesting and novel results, our preliminary analyses (Fig. 1) are limited by the lack of longitudinal single-cell expression data of ependymal tumors. Childhood ependymomas are rare tumors (4.6 new cases/year per 100,000 children15). To our knowledge, CBTTC is the only biorepository with a sufficiently large collection of flash-frozen specimens of primary,
- [Exploring the possible role of mutations in MTOR pathway genes in the pathogenesis of DNET tumors.](https://cbtn.org/projects/exploring-the-possible-role-of-mutations-in-mtor-pathway-genes-in-the-pathogenesis-of-dnet-tumors-2/) - The access to the CBTTC samples will allow to investigate the role of DNA mutations in the mTOR pathway genes in the pathogenesis of DNET tumors and to clarify their possible connection with BRAF or FGFR1 alterations. The use of histologically characterized DNET samples will also permit to test if the FGFR2-INA fusion gene, previously
- [Cracking the Histone Code: Characterizing Pediatric Brain Tumor Epigenetics using Cerebrospinal Fluid](https://cbtn.org/projects/cracking-the-histone-code-characterizing-pediatric-brain-tumor-epigenetics-using-cerebrospinal-fluid/) - Matched CSF and tumor tissue protein specimens from children with brain tumors are required to conduct the proposed research. A query of CBTTC database identified 84 subjects with available tumor tissue and CSF and 38 tumor tissue specimens for which our institution has matched CSF on hand (See Harvest Report). To further strengthen our approach
- [GPC2 as an immunotherapeutic target in medulloblastoma and other pediatric brain tumors](https://cbtn.org/projects/gpc2-as-an-immunotherapeutic-target-in-medulloblastoma-and-other-pediatric-brain-tumors/) - CBTTC cell lines are important to this project to provide newly developed cellular brain tumor models to characterize for GPC2 expression and to test the efficacy of this GPC2 directed ADC. Commercially available cell lines will also be used as additional pediatric brain tumor preclinical cellular models.
- [Pediatric brain tumor miRNA profiling for the cohort of Children's Brain Tumor Tissue Consortium specimens](https://cbtn.org/projects/pediatric-brain-tumor-mirna-profiling-for-the-cohort-of-childrens-brain-tumor-tissue-consortium-specimens/) - This project will support the CBTTC vision of open access and collaboration by generating a significant amount of free data for further analysis by brain researchers worldwide, both within and outside of the consortium for pediatric brain tumor miRNA profiling.
- [Oncolytic virus to potentiate immune-checkpoint blockade in immunologically cold brain tumors](https://cbtn.org/projects/oncolytic-virus-to-potentiate-immune-checkpoint-blockade-in-immunologically-cold-brain-tumors/) - We request frozen tumor specimens from all PNOC-005 subjects that have been identified as enrolled on CBTTC with tissue available. We request these specimens to profile them using single-cell genetic and protein assays. Since these subjects have been treated for MB with MV-NIS therapy, these assays will enable us to determine the interactions between MV-NIS
- [CBTTC cell lines high throughput drug screening study](https://cbtn.org/projects/cbttc-cell-lines-high-throughput-drug-screening-study/) - The cell lines will be utilized in the high throughput approach in vitro drug testing. This project will provide extensive in vitro drug response information across multiple pediatric tumor diagnoses providing the pediatric brain tumor cell line drug response atlas.
- [Microglial Mosaicism in BRAFV600E Glioma](https://cbtn.org/projects/microglial-mosaicism-in-brafv600e-glioma/) - Specify why the CBTTC request is important to your project Our proof-of-concept studies in mice, strongly suggest that the presence of somatic mutations in the tumor microenvironment, in our case microglia, contribute to tumor grade. Therefore, we want to test this novel hypothesis in human samples. Since our model is recapitulating a developmental disease, we
- [Identifying tumor cell vulnerabilities in recurrent/progressive human medulloblastomas by single-cell RNA-seq](https://cbtn.org/projects/identifying-tumor-cell-vulnerabilities-in-recurrent-progressive-human-medulloblastomas-by-single-cell-rna-seq/) - The ambition reflected in this proposal is a product of robust collaboration across clinical/laboratory/bioinformatics experts within our team and external collaborators. Since MB is a rare disease, we need to extend our collaboration to centers/consortium with larger number of patients to be able to profile patient-matched recurrent tumors before and after treatment. Moreover, our scRNA-seq
- [Development of the ganglioside GD2 as a biomarker and clinical trial endpoint for childhood cancers](https://cbtn.org/projects/development-of-the-ganglioside-gd2-as-a-biomarker-and-clinical-trial-endpoint-for-childhood-cancers/) - Tumor biomarkers (TB) that are validated surrogate endpoints of a drug's therapeutic effect can improve the accuracy and sensitivity of assessing tumor response in phase 2 trials and could also substantially shorten the time line of phase 3 trials if they are predictive of subsequent relapse or survival. Our goal is to identify and validate
- [Comprehensive molecular analysis of pediatric thalamic tumors](https://cbtn.org/projects/comprehensive-molecular-analysis-of-pediatric-thalamic-tumors/) - Childhood thalamic tumors are rare types of brain cancer that make up about 5% of all brain tumors in children. These tumors usually originate from a type of brain cell called glial cells, and they can be classified as either low grade (less aggressive) or high grade (more aggressive) gliomas based on their appearance under
- [Proteogenomic Identification of Structural Variations](https://cbtn.org/projects/proteogenomic-identification-of-structural-variations/) - We request 10-15 mg of FF tumor tissue for proteomic peptide sequencing for 40 MB tumors RNA-Seq data from the same samples for the construction of custom search databases Germline and Tumor WGS data from the same patients to confirm structural variations and screen out normal variants Blood DNA from 5 subjects for pilot ddPCR
- [Targeting Replicative Stress in Pediatric Brain Tumors with ALT](https://cbtn.org/projects/targeting-replicative-stress-in-pediatric-brain-tumors-with-alt/) - If we are able to detect C-circle DNA with adequate sensitivity/specificity, we would expand this to a larger study and if validated, could consider incorporation to a future trial for patients who are entered on a retrospective (or prospective study) for patients whose tumors are ALT positive.
- [Target identification and modeling of NF1-associated low-grade glioma](https://cbtn.org/projects/target-identification-and-modeling-of-nf1-associated-low-grade-glioma/) - Synodos for NF1: This project aims at a comprehensive molecular and functional characterization of NF1-associated low-grade gliomas in children, to identify cooperating pathomechanisms with loss of NF1 and thereby potential new therapeutic vulnerabilities.
- [Neurocytoma WGS and RNAseq](https://cbtn.org/projects/neurocytoma-wgs-and-rnaseq/) - The specimens selected for this project already have sequencing data generated through other sequencing platforms (BGI/Sidra and NANT). Using these specimens for validation allows for direct comparison between the BGISEQ-500 sequencer and those already utilized by the CBTTC. This will validate an additional sequencing platform for future CBTTC data generation.
- [Exploration of IDO1 as a therapeutic target in pediatric central nervous system tumors](https://cbtn.org/projects/exploration-of-ido1-as-a-therapeutic-target-in-pediatric-central-nervous-system-tumors/) - This proposal aims to determine the level of IDO1 expression in pediatric CNS tumors, specifically focus on low grade glioma, high grade glioma, medulloblastoma and ependymoma.
- [Multi-modal data integration and functional screening to discover druggable targets in pediatric low-grade glioma](https://cbtn.org/projects/multi-modal-data-integration-and-functional-screening-to-discover-druggable-targets-in-pediatric-low-grade-glioma/) - The goal of this project is to validate prior work in fly models that have shown key metabolic players in the development and growth of pediatric low-grade glioma with BRAF mutations. In this project we want to expand this knowledge to translational models available through CBTN such as patient derived cell lines and organoids. This
- [Identification and functional targeting of alternative splice site usage in pediatric high-grade gliomas](https://cbtn.org/projects/identification-and-functional-targeting-of-alternative-splice-site-usage-in-pediatric-high-grade-gliomas/) - This project focuses on understanding how abnormal gene splicing—an essential process that can change how genes are read and how proteins are made—controls the growth of these tumors. By studying these splicing errors, we aim to uncover new therapeutic targets that have never been considered before. Building on our lab’s previous discoveries, we will identify
- [GPC2 CAR T immunotherapy against pediatric central nervous system tumors](https://cbtn.org/projects/gpc2-car-t-immunotherapy-against-pediatric-central-nervous-system-tumors/) - Pediatric brain tumors are the leading cause of cancer death in children and new targeted therapies are urgently needed. Glypican 2 (GPC2) is highly expressed on multiple pediatric central nervous system (CNS) tumors, including embryonal tumors and high-grade gliomas. Our data shows locoregional delivery of GPC2 CAR T cells is safe and effective in preclinical models
- [Genomic evaluation of malignant pediatric cortical tumors](https://cbtn.org/projects/genomic-evaluation-of-malignant-pediatric-cortical-tumors/) - The analysis of high-throughput gene expression will improve standard histologic classification of malignant supratentorial pediatric brain tumors, identify clinically significant genomic alterations, and suggest candidates for targeted therapy.
- [Medulloblastoma High Resolution Genomic Data for the CBTTC Repository](https://cbtn.org/projects/medulloblastoma-high-resolution-genomic-data-for-the-cbttc-repository/) - This project will create the ideal standard for presentation of high resolution genomic data in the consortium. We will identify tumors of the specific histologic diagnoses of Medulloblastoma with matching blood specimens in the repository for whole genome and RNA sequencing. All results will be placed back into the repository for researchers to access and
- [Epigenetic basis of gender differences in pediatric GBM](https://cbtn.org/projects/epigenetic-basis-of-gender-differences-in-pediatric-gbm/) - CBTTC specimen will be collected for RNA-seq and Reduced representation bisulfite sequencing - we will profiling the transcriptome and epigenome. We will then compare these profiles between boys and girls with pediatric GBM to identify lesions that cause the difference in clinical outcomes of these patients.
- [Sequencing of CBTTC Biorepository](https://cbtn.org/projects/sequencing-of-cbttc-biorepository/) - The CBTN was has been provided with a unique opportunity to sequence a large portion, (over 1600 aliquots), of biospecimens by outsource entities. The center constantly evaluates opportunities to expand on the sequencing additional cohorts of samples. Dr. Adam Resnick, together with Dr. Jessica Foster have the opportunity to work with The Translational Genomics Research
- [HTG EdgeSeq system evaluation using CBTTC FFPE research specimens.](https://cbtn.org/projects/htg-edgeseq-system-evaluation-using-cbttc-ffpe-research-specimens/) - FFPE tissue material will be processed by the HTG EdgeSeq technology pipeline for mRNA and/or miRNA profiling.
- [Integrated Genomic Analysis to elucidate the role of PIKC3A and 10q LOH as Unique drivers and cooperating events in pediatric high grade gliomas](https://cbtn.org/projects/integrated-genomic-analysis-to-elucidate-the-role-of-pikc3a-and-10q-loh-as-unique-drivers-and-cooperating-events-in-pediatric-high-grade-gliomas/) - Our analysis suggests that the PTEN/AKT/PIK3CA group represents a fourth distinct molecularly tractable entity that has a prognosis almost as poor as the K27M subset. Moreover, this pathway has not been explored as a stand alone, driver or as cooperating or exclusive events from other known entities of pHGG including the H3 (K27M, G34R/V), BRAF
- [Integrative functional genomics of recurrent childhood medulloblastoma.](https://cbtn.org/projects/integrative-functional-genomics-of-recurrent-childhood-medulloblastoma-2/) - The data and samples will be used to generate and will be used in your research. compare the genomic and transcriptional landscapes in patient-matched primary/relapse MB pairs
- [Choroid Plexus Tumor (CPT) therapies based on patient derived cell culture resources](https://cbtn.org/projects/choroid-plexus-tumor-cpt-therapies-based-on-patient-derived-cell-culture-resources-2/) - CPCs carry a dismissal prognosis and there is limited clinical data available to describe treatment and outcome of CPTs. Further lack of patient cell lines and clinically relevant animal models have impeded in understanding this disease. Cell lines generated from CPC patient specimen ((#7316UP-1356) can greatly aid in delineating this disease both at molecular and
- [BGI Validation Cohort](https://cbtn.org/projects/bgi-validation-cohort/) - The specimens selected for this project already have sequencing data generated through other Illumina based sequencing at other sequencing centers (BGI Americas/Sidra and NANT). Using these specimens for validation allows for direct comparison between the BGISEQ-500 sequencer and those already utilized by the CBTTC. This will validate an additional sequencing platform for future CBTTC data
- [Targeting neurodevelopmental pathways in pediatric high-grade gliomas](https://cbtn.org/projects/targeting-neurodevelopmental-pathways-in-pediatric-high-grade-gliomas/) - Pediatric high-grade gliomas are fast-growing brain tumors that occur in children and adolescents. Unfortunately, no effective therapies are currently available for these patients. Surgery is rarely possible because the tumor cells are in close proximity and tangled up with important healthy brain cells. Recently, researchers have found that the tumor cells act in similar ways
- [Molecular and Functional Characterization of Paediatric Solid Tumours](https://cbtn.org/projects/molecular-and-functional-characterization-of-paediatric-solid-tumours/) - The Childhood Cancer Model Atlas (CCMA) represents a pioneering effort aimed at cultivating pediatric cancer cell lines that faithfully mirror the molecular intricacies of various pediatric malignancies. Spearheaded by the Hudson Institute of Medical Research, this initiative has meticulously developed and characterized over 300 pediatric cancer models, yielding novel therapeutic strategies with clinical significance (Sun
- [Predictive biomarkers of cognitive outcome in children who received radiation therapy](https://cbtn.org/projects/predictive-biomarkers-of-cognitive-outcome-in-children-who-received-radiation-therapy/) - Whole Brain Radiation Therapy (WBRT) is often used to treat brain tumors, but it can cause memory and thinking problems in 40-50% of people who survive long-term. WBRT has been a key treatment for brain tumors that can't be removed by surgery and for cancer that has spread to the brain. However, because it can
- [Neurosurgically-applied chemotherapy for childhood brain tumours arising in the posterior fossa using a biodegradable paste](https://cbtn.org/projects/neurosurgically-applied-chemotherapy-for-childhood-brain-tumours-arising-in-the-posterior-fossa-using-a-biodegradable-paste/) - Medulloblastoma (MB) group 3 and Atypical Teratoid Rhabdoid Tumours (ATRT) represent paediatric brain tumours with a very poor prognosis. Current standard treatment methods are not effective, and we are in need of finding new drug treatments against these tumours. To this end, we have developed a 3D in vitro model which mimics the environment in
- [Epitranscriptomic characterization of pediatric central nervous system tumors](https://cbtn.org/projects/epitranscriptomic-characterization-of-pediatric-central-nervous-system-tumors/) - Cancer cells adopt many ways to control expression of genes that increase growth and invasion of the tumor. High-grade central nervous system (CNS) tumors in pediatric patients are particularly aggressive and many patients do not have curative therapy options. Many of these high-grade tumors are characterized by specific genetic alterations. Following transcription, little is known
- [Evaluating inhibitors of exosomes secretion as pan-treatment for medulloblastoma](https://cbtn.org/projects/evaluating-inhibitors-of-exosomes-secretion-as-pan-treatment-for-medulloblastoma/) - Significance: Medulloblastoma is the most common malignant pediatric brain tumor. Current therapy, developed empirically more than 50 years ago, follows surgical removal with the nonspecific regimen of radiation and chemotherapy. This treatment yields 70-80% long-term survival, but survivors suffer disabling long-term toxicities, including dementia, early strokes, and hearing loss. (1) Patients that survive remain at
- [Overcoming immunotherapy resistance in Group 3 medulloblastoma](https://cbtn.org/projects/overcoming-immunotherapy-resistance-in-group-3-medulloblastoma/) - Brain tumors are the leading cause of cancer-associated deaths in children. Medulloblastoma (MB) is the most common malignant pediatric brain tumor characterized by four major molecular subgroups including WNT, SHH, Group 3 and Group 4. Group 3 medulloblastoma (G3MB), which features MYC amplification or overexpression, exhibits the worst prognosis and highest rate of metastasis. Currently,
- [Assessing glioma gene expression signatures from patient biofluids](https://cbtn.org/projects/assessing-glioma-gene-expression-signatures-from-patient-biofluids/) - We are requesting CBTN specimens because we have not had access to these samples (e.g. CSF from pediatric low grade glioma) in our institutional biobanks.
- [Validation of tumor splice targets](https://cbtn.org/projects/validation-of-tumor-splice-targets/) - Pediatric cancer is the leading cause of disease-related death in children, but few drugs are designed specifically for pediatric tumors, especially those highly resistant to treatment. This research aims to identify and validate tumor-specific targets created by abnormal RNA splicing in pediatric brain tumors, paving the way for new, effective therapeutic strategies to improve outcomes
- [New Treatments for Pediatric Brain Tumors](https://cbtn.org/projects/new-treatments-for-pediatric-brain-tumors/) - Treating high-grade brain tumors in kids is a challenge, and survival rates are low. Over the past twenty years, there has been a surge in the molecular understanding of these gliomas, allowing for a more personalized approach to treatment. Researchers are testing new drugs that target specific molecules in these tumors. But for many children,
- [Developing a Local Delivery System for Group 3 Medulloblastoma](https://cbtn.org/projects/developing-a-local-delivery-system-for-group-3-medulloblastoma/) - The project aims to test novel targeted therapies against Group 3 medulloblastoma in vitro and investigate the impact of local delivery of these agents using a biodegradable hydrogel in the survival of mouse models of the disease.
- [Role of CRK and CRKL in tumor cell migration in pediatric high grade glioma cell lines](https://cbtn.org/projects/role-of-crk-and-crkl-in-tumor-cell-migration-in-pediatric-high-grade-glioma-cell-lines/) - Our research goal is to block the diffuse invasion of brain tumors into neighboring healthy brain tissues, increasing the efficacy of standard care and reducing recurrence. The two proteins that we have studied for the last two decades play critical roles in tumor cell migration in adult brain tumor cells. We will remove the two
- [Development of Blood Plasma cfDNA Assay to Detect the Alternative Lengthening of Telomeres (ALT) Phenotype in Pediatric High-Grade Glioma Patients](https://cbtn.org/projects/development-of-blood-plasma-cfdna-assay-to-detect-the-alternative-lengthening-of-telomeres-alt-phenotype-in-pediatric-high-grade-glioma-patients/) - Telomeres are the protective repeats of DNA sequences and proteins at the ends of chromosomes. (1) Cancer cells rely on the extension and maintenance of telomere length to avoid cell death. (1) About 85-90% of cancers use telomerase to maintain telomere length while 10-15% of cancers utilize the alternative lengthening of telomeres (ALT) mechanism. (2-3) ALT cancers are
- [Antibody-Drug Conjugate for Pediatric Gliomas](https://cbtn.org/projects/antibody-drug-conjugate-for-pediatric-gliomas/) - We are developing new drugs to combat brain cancer with increased effectiveness and reduced side effects. To do this, we are looking to specifically target certain proteins that are more typical of brain cancers and less common outside of tumor cells. This work aims to improve the likelihood of patient recovery as well as reduce
- [Secretion of GD2-CD3 BiTEs from B7H3 CAR T-Cells Enhances their Anti-Tumor Activity in Pediatric High-Grade Gliomas](https://cbtn.org/projects/secretion-of-gd2-cd3-bites-from-b7h3-car-t-cells-enhances-their-anti-tumor-activity-in-pediatric-high-grade-gliomas/) - Brain tumors cause more death and disability than any other pediatric cancer. The past 5 decades have yielded minimal progress in curing the most aggressive brain tumors known as high grade gliomas. Immunotherapy is an exciting and developing approach that harnesses patients’ own immune systems to fight their cancer. Chimeric antigen receptor (CAR) T-cell therapy
- [Examine GFAP-expressing tumor cells](https://cbtn.org/projects/examine-gfap-expressing-tumor-cells/) - We hypothesize that the quiescent GFAP+ tumor cells play a critical role in tumor recurrence. Deletion of this cell population in combination with conventional therapy will prevent tumor recurrence.
- [Development of neoantigen mRNA vaccines for pediatric brain tumors](https://cbtn.org/projects/development-of-neoantigen-mrna-vaccines-for-pediatric-brain-tumors/) - We want to develop neoantigen mRNA vaccines for pediatric brain tumors and translate this new immunotherapy into clinical trials to help these devastating tumors. CBTN specimens will help us identify the effective neoantigen targets for mRNA vaccine development and manufacturing.
- [Differentiation Induction effects of thyroid hormone on tumor cells from atypical teratoid rhabdoid tumor and diffuse midline gliomas](https://cbtn.org/projects/differentiation-induction-effects-of-thyroid-hormone-on-tumor-cells-from-atypical-teratoid-rhabdoid-tumor-and-diffuse-midline-gliomas/) - Brain tumors are the leading cause of cancer-related death in children. Our research has found that tumor cells in certain pediatric brain cancers, such as medulloblastoma, still have the ability to mature into normal nerve cells. When this happens, the tumor cells stop growing. We discovered that thyroid hormone, a natural hormone in the body,
- [Characterizing ATRT subtype evolution](https://cbtn.org/projects/characterizing-atrt-subtype-evolution/) - Central nervous system (CNS) tumors are the leading cause of death by disease in children, and our lab is dedicated to advancing treatments for the most aggressive forms, including Atypical Teratoid Rhabdoid Tumors (ATRTs). This project will pilot single-cell resolution analyses of splicing and transcriptomic profiles in two pairs of longitudinal tumor samples, enabling us
- [Evaluating the Efficacy of ZIKV Oncolytic Virus Killing Efficiency on Tumor Cell Lines](https://cbtn.org/projects/evaluating-the-efficacy-of-zikv-oncolytic-virus-killing-efficiency-on-tumor-cell-lines/) - The neurotropism of Zika virus in the developing brain has led to investigation of its oncolytic potential in many cancers, especially pediatric brain cancers. Childhood brain tumors are among the most difficult to treat and impact thousands of children yearly. We aim to evaluate naturally occurring strains of Zika for their killing capacity and viral
- [Targeting Glioma Oncoproteins with Peptide Centric CAR T Cells](https://cbtn.org/projects/targeting-glioma-oncoproteins-with-peptide-centric-car-t-cells/) - The CBTN has a unique biobank of very well annotated an analyzed pediatric brain tumors. For our project we need tumor samples, knowledge of mutation data and RNA expression data. The CBTN is one of the few places that has this depth and wealth of information available.
- [Tumor Chemo-Sensitivity Assays for therapy and Targeting Cancer Stem-Like Cell in Patients Affected by high grade glioma](https://cbtn.org/projects/tumor-chemo-sensitivity-assays-for-therapy-and-targeting-cancer-stem-like-cell-in-patients-affected-by-high-grade-glioma/) - The access to the CBTTC samples will allow to investigating and define the role of chemotherapy in HGG management. All samples of CBTTC biobank are associated to complete information about patients, therapies and outcome that will be crucial for the significance of our study. Moreover, TCAs can be a powerful tool in HGG therapy and
- [Analyzing circulating tumor DNA in childhood ependymoma CSF](https://cbtn.org/projects/analyzing-circulating-tumor-dna-in-childhood-ependymoma-csf/) - Acquiring specimens from CBTN is critical to obtaining a significant sample size (n≥30) so we can contribute accurate, novel data to the currently limited knowledge on liquid biopsies in ependymomas. We have met during CBTN office hours to discuss the availability of specimens and data, and as a CBTN satellite site we would be grateful
- [Striking brain tumor metabolic vulnerabilities through identification of synthetic lethal pairs](https://cbtn.org/projects/striking-brain-tumor-metabolic-vulnerabilities-through-identification-of-synthetic-lethal-pairs/) - The heterogeneity in patient-specific drug response could be the major obstacle for this proposal, however, by i) increasing the number and the diversity of PDO enrolled in this project, and ii) strictly controlling the experimental culture conditions, the patient genetic background will be excluded from the proposed synthetic lethality screening with the scope to focus
- [CD47 Checkpoint Blockade to treat Choroid Plexus Carcinoma](https://cbtn.org/projects/cd47-checkpoint-blockade-to-treat-choroid-plexus-carcinoma/) - CPC is a rare tumor, and it is hard to find human CPC cell lines to study the effect of different therapies on killing the tumor. We are in the process of purchasing mouse CPC cell lines from RIKEN Cell Bank, Japan, and we will try our anti-CD47 treatment on mouse cell lines. Still, human-derived
- [Novel organoid model generation for transformed gliomas in patients with NF1](https://cbtn.org/projects/novel-organoid-model-generation-for-transformed-gliomas-in-patients-with-nf1/) - Our team is requesting CBTN specimens to help support our efforts in the above stated aim for our project. The Children’s National Hospital Brain Tumor Biorepository currently has one NF-1 cell line which was obtained from Eric Raabe (JHU), as well as several CBTN lines with somatic NF-1 mutations. We have developed the experience and
- [Evaluating immune biomarkers overlapping in tumor and CSF in pediatric brain tumors](https://cbtn.org/projects/evaluating-immune-biomarkers-overlapping-in-tumor-and-csf-in-pediatric-brain-tumors/) - In accessing CBTN specimens, we will be able to map treatment responses in paired tumor and CSF patient samples, validating our preliminary findings using murine tumor compared to human CSF.
- [Establishment of Liquid Biopsy Platforms from longitudinal medulloblastoma patients](https://cbtn.org/projects/establishment-of-liquid-biopsy-platforms-from-longitudinal-medulloblastoma-patients/) - The CBTN samples will greatly expand our ability to validate and establish liquid biopsy platforms for the monitoring of longitudinal medulloblastoma patients and recurrently medulloblastoma patients with longitudinal samples. For many medulloblastoma patients’ serial plasma and cerebral spinal fluid samples are collected. Currently, in our biobank we have 30 medulloblastoma patients with 2 or more
- [Proteomics X01](https://cbtn.org/projects/proteomics-x01/) - This project will generate quantitative proteomics data include post-translational modification data for phospho-, acetyl-, methyl-, and ubiquito- proteomics on at least 406 padiatric brain tumor samples. These cohorts will include craniopharyngioma, medulloblastoma, ependymoma, ATRT and CNS sarcomas. Analysis will be performed in both inter- and intra- histologic diagnosis contexts by teams including bioinformatic support and
- [Investigating somatic mutations in the normal tissues of neurofibromatosis type 1](https://cbtn.org/projects/investigating-somatic-mutations-in-the-normal-tissues-of-neurofibromatosis-type-1/) - To assess the generalizability of our observations, it is essential that we acquire additional normal tissue from other patients with neurofibromatosis type 1. This is very rarely collected, and we have yet to identify any other eligible donors. We have normal brain, brain tumour, blood, skin, and multiple intra-abdominal viscera from a single child but
- [Targeting Cell Surface ALK](https://cbtn.org/projects/targeting-cell-surface-alk/) - Having access to brain tumor cell lines allows us to test our hypothesis, that this ALK-ADC will work in other tumor types, along with NB, if they have cell surface ALK expression. Neuroblastoma is not the only cancer type that expresses ALK on the cell surface and whose patients are in need of better therapies.
- [Understanding molecular and cellular mechanisms and identifying drug targets in human cancers](https://cbtn.org/projects/understanding-molecular-and-cellular-mechanisms-and-identifying-drug-targets-in-human-cancers/) - I have recently been appointed to start-up my laboratory at Deakin University, Geelong, Australia and as a researcher that has worked in the field of cancer, drug discovery and therapeutics, understanding the molecular and cellular mechanisms of cancers and developing new therapies for them has always been an area that I have been passionate about
- [Drug development for pediatric HGG](https://cbtn.org/projects/drug-development-for-pediatric-hgg/) - Tissue microarray – performing immunostaining on multiple cases of pediatric HGG with matching genomic information will resolve the question of most vulnerable population that could benefit from targeted treatment that we are working towards. The advantage of immunostaining is that we will be able to apply our image analysis expertise to extract single-cell level information.
- [T cell Receptor Therapies for pediatric High-Grade Gliomas](https://cbtn.org/projects/t-cell-receptor-therapies-for-pediatric-high-grade-gliomas/) - CBTN Research Resources are invaluable to pediatric HGG research. Patient derived cell lines 7316-158 and 7316-5317 whose diagnosis and subsequent relapse tumors have the H3 G34R mutation. This rare tumor mutation is the focus of our laboratory research. We seek to understand the consequences of the H3 G34R/V mutations that characterize these tumors, in relation
- [Generation of a Tissue Micro Array (TMA) from pediatric brain tumor patients](https://cbtn.org/projects/generation-of-a-tissue-micro-array-tma-from-pediatric-brain-tumor-patients/) - Currently, a comprehensive, robust, and clinically annotated tissue microarray of pediatric DMG specimens does not exist. Our team aims to develop this resource (while also including other pediatric CNS tumor types) and make it globally accessible to both clinicians and researchers. While our first patient cohort included samples 80 pediatric patients with CNS tumor and
- [Identification of hCMV antigens in pediatric brain tumors](https://cbtn.org/projects/identification-of-hcmv-antigens-in-pediatric-brain-tumors/) - The University of Chicago Biorepository has only 5-10 ependymoma specimens available for analysis. Based on previous literature analyzing the presence of hCMV antigens in glioblastoma [5, 8] and the possibility of only 33-40% of specimens expressing CMV antigens [7, 10], we estimate 40 specimens are needed to ensure validity. We are requesting 30 from the
- [Metabolic and proteomic landscapes of DMG and DHG: Navigating uncharted paths for therapeutic discovery](https://cbtn.org/projects/metabolic-and-proteomic-landscapes-of-dmg-and-dhg-navigating-uncharted-paths-for-therapeutic-discovery/) - DMG-K27M and DHG-H3G34 are rare cancers and the number of patient samples in our possession is limited. The CBTN request is crucial as it provides an opportunity to access a substantial number of well-curated DMG-H3K27 and DHG-H3G34 specimens, allowing us to form a representative cohort for our metabolomic profiling. By specifically targeting this rare and
- [Validation of Germline Variants](https://cbtn.org/projects/validation-of-germline-variants/) - This specimen request is connected to CBTTC_D0012, which is a project focusing on identification and characterization of pathogenic germline variation in pediatric brain tumor patients, along with somatic second hits.
- [Proteogenomic characterization of pediatric hematopoietic malignancies](https://cbtn.org/projects/proteogenomic-characterization-of-pediatric-hematopoietic-malignancies/) - Acute myeloid leukemia (AML) is the second most common pediatric hematologic malignancy with approximately 600 new cases per year among patients under 20 years of age. Although AML accounts for only about 20% of leukemias in children, it is responsible for more than half of pediatric leukemia deaths. The prognosis of children with AML has
- [Optical Genome Mapping for the discover of novel structural variants in pediatric brain tumors](https://cbtn.org/projects/optical-genome-mapping-for-the-discover-of-novel-structural-variants-in-pediatric-brain-tumors/) - In our preliminary studies, we have been able to identify a large number of clinically significant SVs in tumor samples obtained from the Children’s National brain tumor biobank. However, these samples to not have WGS and RNA-sequencing data available for comparison. The CBTN samples are critical for our project, as they will allow for a
- [Pharmaco-proteogenomic profiling of pediatric high-grade gliomas](https://cbtn.org/projects/pharmaco-proteogenomic-profiling-of-pediatric-high-grade-gliomas/) - By performing pharmaco-proteogenomic investigations use statement (3 sentences MAX) we aim to couple genomics, proteomics and drug screening in real-time to guide/develop treatment approaches for pediatric high-grade glioma patients. As more tumour samples are analysed, we will gain a greater picture of the biology of these tumours and what influences their growth and survival with
- [Development of CAR-T Cell Therapy for Atypical Teratoid/Rhabdoid Tumors](https://cbtn.org/projects/development-of-car-t-cell-therapy-for-atypical-teratoid-rhabdoid-tumors/) - Our group will be using ATRT cell lines from the CBTN to perform in vitro and in vivo work testing a CAR-T cell approach that targets a cell surface protein, CLDN-6, that is known to be over-expressed in a subset of ATRTs.
- [Evaluating NF2 and Other Tumor Disease Mechanisms](https://cbtn.org/projects/evaluating-nf2-and-other-tumor-disease-mechanisms/) - The objective is to share patient skin derived fibroblasts, induced Schwann cells as well as tumor cells between CBTT and Nationwide Children’s Hospital. Dr. Meyer’s lab will have access to frozen tumor samples as well as tumor cell lines from NF2 patients and patients suffering from other forms of cancer through CBTTC. The samples are
- [Novel platforms for developing therapies for transformed gliomas in patients with NF1](https://cbtn.org/projects/novel-platforms-for-developing-therapies-for-transformed-gliomas-in-patients-with-nf1/) - Our team is requesting CBTN specimens to help support our efforts in the above stated aims for our project. The Children’s National Hospital Brain Tumor Biorepository currently has one NF-1 cell line which was obtained from Eric Raabe (JHU). We have developed the experience and expertise to culture cells for pre-clinical studies. The CBTN samples
- [Establishing a thalamic glioma model](https://cbtn.org/projects/establishing-a-thalamic-glioma-model/) - We are requesting CBTTC cell lines from thalamic glioma patient(s).
- [The role of non-coding RNA in development of pediatric brain tumors](https://cbtn.org/projects/the-role-of-non-coding-rna-in-development-of-pediatric-brain-tumors/) - CBTN plasma samples will expand our cohort from Sheba Medical Center to see if we can correlate the comprehensive list of the lincRNA in plasma to the clinical data of the patient.
- [Drivers of recurrence in PFA ependymoma](https://cbtn.org/projects/drivers-of-recurrence-in-pfa-ependymoma/) - The CBTN specimens will allow us to expand our pilot cohort in this exploratory study which will allow us to increase our ability to identify recurrence specific events. Depending on the number of paired samples available, will use the CBTN cohort as a validation cohort, and it will provide a tremendous ability for us to
- [Profiling the amino acid transporter landscape to inform fluorescent dye development for improved surgical outcome of image-guided intervention in adolescent and young adult glioma patients](https://cbtn.org/projects/profiling-the-amino-acid-transporter-landscape-to-inform-fluorescent-dye-development-for-improved-surgical-outcome-of-image-guided-intervention-in-adolescent-and-young-adult-glioma-patients/) - We specifically request pediatric glioma tissue microarrays (TMAs) from CBTN, because the CBTN is in the unique position to provide such TMAs based on tissue banking of pediatric glioma tissues. We are specifically interested in TMAs that contain pediatric gliomas and medulloblastoma-tissues. Via our co-investigators Drs. Ali Nabavizadeh and Mariarita Santi (contact: Anatomic Pathology; CHOP;
- [CBTN PBTA X01 Data Generation Project](https://cbtn.org/projects/cbtn-pbta-x01-data-generation-project/) - The project's sequencing cohort defines the largest, clinically annotated pediatric brain tumor cohort study to date and seeks to define the intersection of germline and somatic underpinnings of pediatric brain tumors across a shared developmental context of cancer and structural birth defects. Data includes tumor/normal whole genome sequencing pairs with matching RNASeq and paternal and
- [Role of the Immunosuppressive Tumor Microenvironment in Therapeutic Resistance in Pediatric CNS Cancers](https://cbtn.org/projects/role-of-the-immunosuppressive-tumor-microenvironment-in-therapeutic-resistance-in-pediatric-cns-cancers/) - We are requesting these medulloblastoma cell lines so that we can further study MDSC induction by different medulloblastoma cell lines/subgroups.
- [Novel Polyvinyl-alcohol microsphere for Everolimus delivery for Subependymal Giant Cell Astrocytoma](https://cbtn.org/projects/novel-polyvinyl-alcohol-microsphere-for-everolimus-delivery-for-subependymal-giant-cell-astrocytoma/) - The CBTN request is of great importance to test the cytotoxicity of the drug delivery vehicle embedded with the chemotherapeutic agent Everolimus on the specimen (SEGA tumour).
- [Lipid nanoparticles for the treatment of neurofibromatosis type 2](https://cbtn.org/projects/lipid-nanoparticles-for-the-treatment-of-neurofibromatosis-type-2/) - We are requesting NF-2 tissue from CBTN. It will help us engineer a LNP by taking into account the different NF-2 tissue’s tropism.
- [Mitochondria and Cancer Connections](https://cbtn.org/projects/mitochondria-and-cancer-connections/) - Acquisition of the fluorescently labeled CBTN cell line DMG 7316-195++GL GFP, will allow model development for establishment of a zebrafish xenograft, where the tumor can be monitored for its location, migration, size, and proliferation. While osteosarcoma is the focus of this project, the glioma cell line will provide model development and validation opportunities for localization
- [Assessing Activity of Agents Targeting ALT Cancers in Pediatric Brain Tumor Cell Lines](https://cbtn.org/projects/assessing-activity-of-agents-targeting-alt-cancers-in-pediatric-brain-tumor-cell-lines/) - In speaking with CBTN investigators we learned that CBTN has brain tumor cell lines known to be DNA C circle positive. Those are necessary to determine the potential for drugs active against non-CNS ALT cancer patient-derived models to be active against ALT brain tumors. Because of the availability of the cell lines from CBTN these
- [Pediatric Brain Tumor Classification Using Transcriptional Profiles from Low-Cost Nanopore mRNA Sequencing](https://cbtn.org/projects/pediatric-brain-tumor-classification-using-transcriptional-profiles-from-low-cost-nanopore-mrna-sequencing/) - CBTN tissue is crucial for this project, as all pediatric brain tumor specimens are quite rare. While the Lineberger CCC at UNC-Chapel Hill has a tissue repository, it has only recently been amended to include pediatric CNS tumors. Therefore, we simply do not have enough samples internally to investigate this novel diagnostic platform. In addition
- [Identifying Neuro-Glycoproteome Disruption in Congenital Disorders of Glycosylation](https://cbtn.org/projects/identifying-neuro-glycoproteome-disruption-in-congenital-disorders-of-glycosylation/) - I have access to flash frozen cerebellum from a PMM2-CDG individual available at the Children’s Hospital of Philadelphia for glycoproteomic analysis, however, no appropriate control tissue is available. I require control cerebellum tissue to confidently determine changes in glycosite occupancy and glycan structure. I was referred to CBTN by CHOP Pathology who had previously helped
- [High-trhoughput drug screening of adamantinomatous craniopharyngioma primary cell lines](https://cbtn.org/projects/high-trhoughput-drug-screening-of-adamantinomatous-craniopharyngioma-primary-cell-lines/) - We will use craniophanrygioma cell lines to identify new therapeutical approaches.
- [Identification of Novel therapeutics for choroid plexus carcinoma](https://cbtn.org/projects/identification-of-novel-therapeutics-for-choroid-plexus-carcinoma/) - Complementary assays on additional choroid plexus carcinoma cell lines to validate novel therapeutics for choroid plexus carcinoma
- [Proteomic Analysis of Pediatric Craniopharyngiomas](https://cbtn.org/projects/proteomic-analysis-of-pediatric-craniopharyngiomas/) - Pediatric craniopharyngioma is a rare tumor. In order to be able to draw the most robust conclusions from the data, we want to obtain as many samples as possible for analysis. CBTN is the best resource for obtaining high quality samples of rare pediatric brain tumors. Additionally, this study will expand on a prior proteomic
- [Elucidating the ETMR Microenvironment using Next Generation Imaging and Multi-omics Technologies](https://cbtn.org/projects/elucidating-the-etmr-microenvironment-using-next-generation-imaging-and-multi-omics-technologies/) - As there is known diversity in histologic features of ETMR tumors, we feel that it is important to characterize multiple tissue samples using our IMC and MSI techniques to truly define the landscape of the ETMR microenvironment. Due to the rarity of ETMR, there is a paucity of tissue specimens available for research. Therefore, the
- [Pre-clinical Studies for NF2 Schwannomas](https://cbtn.org/projects/pre-clinical-studies-for-nf2-schwannomas/) - NF2 is a rare tumor disorder. NF2 Biosolutions Inc. has entered into an agreement with CBTTC to have NF2 patients donate their tumor tissue. Because we are not affiliated with a clinical department, we do not have access to patient tumors. Therefore the ability for us to develop therapeutics for NF2 schwannomas is dependent on
- [Evaluation of drug vulnerability of NF2 tumor models](https://cbtn.org/projects/evaluation-of-drug-vulnerability-of-nf2-tumor-models/) - NF2 tumors are very rare and understudied tumor around rare pediatric brain tumor research field. There are only very few cell lines in the field derived from specimens from subjects carrying NF2 mutation and they are of limited availability. Using models from CBTN and NF2 Biosolutions is essential for the project.
- [RP58 and SMARCB1 in AT/RT pathogenesis](https://cbtn.org/projects/rp58-and-smarcb1-in-at-rt-pathogenesis/) - Because these tumors are very rare, the CBTN is an invaluable resource for studying these diseases. Cell lines for AT/RT are absolutely critical for research in AT/RT and for this project specifically.
- [Elucidating Heterogeneity of Resistance Across Molecular Subgroups of Pediatric Ependymomas to Inform Future Therapeutics](https://cbtn.org/projects/elucidating-heterogeneity-of-resistance-across-molecular-subgroups-of-pediatric-ependymomas-to-inform-future-therapeutics/) - We are interested in looking at functional differences in resistance between molecular subgroups of ependymomas in order to inform future therapeutics. We would like to study 2-4 cell lines from each of the subgroups most common in children, specifically PF-EPN-A, ST EPN-RELA, ST-EPN-YAP1. Ependymoma tumors are rare in children and ependymoma cell lines are difficult
- [MET alterations in DMGs](https://cbtn.org/projects/met-alterations-in-dmgs/) - Our immediate objective is to identify, characterize, and establish distinct MET SVs, such as GFs and copy gain, as potent precision medicine targets in DMGs.
- [Methylation Profiling of Pediatric Brain Tumors](https://cbtn.org/projects/methylation-profiling-of-pediatric-brain-tumors/) - The CBTN represents an ideal source for the required specimens because: 1) there is a large number of them lending analytic and statistical strength to the classification and correlative analyses, 2) the samples’ clinical annotation will further inform the characterization of cases, particularly those on the edge of clusters, 3) methylation data will be a
- [EXPRESSION OF EAAT2 IN DYSEMBRYOPLASTIC NEUROEPITHELIAL TUMORS (DNT) AND IN ANGIOCENTRIC GLIOMA. ITS POSSIBLE ROLE IN THE PATHOGENESIS OF THE EPILEPSY](https://cbtn.org/projects/expression-of-eaat2-in-dysembryoplastic-neuroepithelial-tumors-dnt-and-in-angiocentric-glioma-its-possible-role-in-the-pathogenesis-of-the-epilepsy/) - Angiocentric glioma is a rare cerebral tumor with about only 110 cases described at the time of this request. The access to the CBTTC samples and the consequent possibility to obtain a critical number of AGs specimens, a tumor for which we have already demonstrated the loss of EAAT2, would be essential to confirm this
- [Investigating the tumorigenesis mechanisms and vulnerabilities of pediatric high-grade gliomas with H3G34R/V](https://cbtn.org/projects/investigating-the-tumorigenesis-mechanisms-and-vulnerabilities-of-pediatric-high-grade-gliomas-with-h3g34r-v/) - We hope to systematically discover more chromatin factors like RACK7 that promote tumor formation in pHGGs and understand their molecular mechanisms.
- [Oncogene-Induced Senescence in RTK-fused Infant High Grade Gliomas](https://cbtn.org/projects/oncogene-induced-senescence-in-rtk-fused-infant-high-grade-gliomas/) - CBTTC/CBTN tissue is crucial for this project, as iHGG is exceedingly rare. The tumor tissue bank of the Tumor Tissue and Pathology Shared Resource at Wake Forest Baptist Comprehensive Cancer Center has two RTK-fused iHGG (both babies are clinically in remission after gross-total resection alone, no adjuvant therapy administered), along with a very large cadre
- [Use of ependymoma cell lines to test for new therapeutic vulnerabilities](https://cbtn.org/projects/use-of-ependymoma-cell-lines-to-test-for-new-therapeutic-vulnerabilities/) - The availability of ependymoma cell lines and PDX models representing the disease is limited and therefore the source of these 7 requested ependymoma cell lines and the PDX model is of high value for our project to test new therapeutic vulnerabilities.
- [Characterizing the blood brain pediatric brain tumors](https://cbtn.org/projects/characterizing-the-blood-brain-pediatric-brain-tumors/) - Because these tumors are very rare, the CBTN is an invaluable resource for studying these diseases. Furthermore, the genomic resources for pediatric brain tumors are incomparable. We will include all patients with MRI available within the CBTN (n=243) for preliminary analysis, though only those with T1 pre-contrast, T1 post-contrast, and T2-FLAIR sequences will be included
- [CBTN and Count Me In, Pediatric Brain Tumor Molecular Characterization Initiative for retrospective subjects enrolled in CBTN](https://cbtn.org/projects/cbtn-and-count-me-in-pediatric-brain-tumor-molecular-characterization-initiative-for-retrospective-subjects-enrolled-in-cbtn/) - The goal of the project Count Me In is to generate WGS & RNAseg data for ATRT & DMG subjects from CBTN and deposit it back to Cavatica.
- [Precision Imaging of Pediatric High-grade Gliomas with Quantitative Diffusion Weighted Imaging and Texture Analysis to Identify Imaging Biomarkers That Predict Tumor Genetics and Patient Outcomes](https://cbtn.org/projects/precision-imaging-of-pediatric-high-grade-gliomas-with-quantitative-diffusion-weighted-imaging-and-texture-analysis-to-identify-imaging-biomarkers-that-predict-tumor-genetics-and-patient-outcomes/) - Our group focuses on characterizing the imaging features within pediatric brain tumors that predict tumor molecular subgroups and patient outcomes. The goal of our project is to develop imaging based classification of pediatric high grade gliomas that will stimulate discovery of novel imaging biomarkers that predict driver mutations in these tumors.
- [Targeting Master Regulator Dependencies in Diffuse Intrinsic Pontine Glioma (DIPG)](https://cbtn.org/projects/targeting-master-regulator-dependencies-in-diffuse-intrinsic-pontine-glioma-dipg/) - A novel cancer systems biology approach identifies master regulator (MR) proteins that are necessary for tumor growth and predicts and prioritizes drugs that reverse their effects. This study will apply such an approach to identify much-needed new treatment strategies in DIPG, a universally fatal disease. We will analyze the PBTA-CBTTC and other DIPG gene expression
- [Structural Variants in Human and Canine Cancer datasets](https://cbtn.org/projects/structural-variants-in-human-and-canine-cancer-datasets/) - By leveraging our expertise in analyzing structural variants (SV), we will investigate SVs in human and canine cancer datasets, including sequencing data. Furthermore, we will combine our dataset, including Pacbio long-read sequencing and Illumina short-read sequencing data of canine glioma and osteosarcoma, to discover the critical gene variants in both species.
- [Searching for Differences in Molecular Profile of Pediatric Gliomas](https://cbtn.org/projects/searching-for-differences-in-molecular-profile-of-pediatric-gliomas/) - Childhood brain cancer is a devastating disease that is still poorly understood. Glioma is a type of brain cancer in which a specific type of cells in the brain (called glial cells), become cancerous. In our study, we will examine how the DNA in glioma cells varies between different groups of patients. We will also
- [Aberrant splicing candidates as potential neoantigen expression in HGG](https://cbtn.org/projects/aberrant-splicing-candidates-as-potential-neoantigen-expression-in-hgg/) - The objective of this project is to investigate whether aberrant splicing candidates resulting from transcriptome-wide dysregulation of alternative splicing in high grade gliomas (HGGs) could be a source for novel neoantigen expression in tumors, that are distinct from missense mutations. We will leverage large-scale multi-omics datasets with state-of-the-art technologies to inform novel targets for CAR
- [Detecting driver mutations of central nervous system germ cell tumors](https://cbtn.org/projects/detecting-driver-mutations-of-central-nervous-system-germ-cell-tumors/) - Intracranial germ cell tumor is a very dangerous disease but lacking sufficient study. In this project, we aim to collect enough intracranial germ cell tumor cases to study the genome variation of this cancer. With proper DNA data analysis, we hope to find novel pathogenic mechanism of this disease on genome level and provide potential
- [Investigating the immune response in pediatric glioma subsets](https://cbtn.org/projects/investigating-the-immune-response-in-pediatric-glioma-subsets/) - Different tumors have different types of immune responses. We would like to better understand the drivers of this differential response so that we can best treat these tumors.
- [High dimensional protein characterization of tumor tissues and relevance to outcomes in immunotherapy clinical trials](https://cbtn.org/projects/high-dimensional-protein-characterization-of-tumor-tissues-and-relevance-to-outcomes-in-immunotherapy-clinical-trials/) - This collaborative project by CBTTC and Parker Institute (PICI) investigators aims to examine the immune and tumor microenvironment in situ in pediatric brain tumor tissues, particularly in response to immunotherapy. Integration of single cell multiplex imaging of tissue microarray targets (TMAs) with existing orthogonal genomic, proteomic, and clinical datasets offer the hope of advancing immunotherapy
- [Artificial Intelligence for Pediatric Brain Tumor Detection and Prediction of Disease Progression](https://cbtn.org/projects/artificial-intelligence-for-pediatric-brain-tumor-detection-and-prediction-of-disease-progression/) - We intend to develop a set of tools which will use artificial intelligence (AI) to aid with the clinical management of pediatric brain tumors. These tools will automatically detect brain tumors in MRI scans, and provide predictions as to what subtype of tumor the patient has. We will also use AI to help detect early
- [Genetic architecture of molecular phenotypes in pediatric brain cancers](https://cbtn.org/projects/genetic-architecture-of-molecular-phenotypes-in-pediatric-brain-cancers/) - We will assess to what extent protein expression levels are under genetic control in pediatric brain cancers.
- [Sex-specific gene expression signatures in pediatric brain tumors](https://cbtn.org/projects/sex-specific-gene-expression-signatures-in-pediatric-brain-tumors/) - Normal human development, disease risk, and response to treatments are often different in males and females. Cancer is no exception, and we are working to determine whether cancer treatments should be optimized independently for males and females. The analysis of the CBTTC's Pediatric Brain Tumor Atlas data will be a critical component of moving this
- [Determining Prognostic Factors and Genetic Markers that Impact Survival in Recurrent Pediatric Medulloblastoma](https://cbtn.org/projects/determining-prognostic-factors-and-genetic-markers-that-impact-survival-in-recurrent-pediatric-medulloblastoma/) - Recurrent pediatric medulloblastoma is almost universally fatal, and guidelines for treatment have not been established. This project will analyze patient and tumor factors to determine what impacts survival in this patient population.
- [A study of outcomes in patients with CNS tumors with BCOR mutations](https://cbtn.org/projects/a-study-of-outcomes-in-patients-with-cns-tumors-with-bcor-mutations/) - We plan to assess all patients with CNS tumors containing BCOR mutations. We owuld liek to study the differences amongst these patients including variety of tumor types, age at diagnosis, PFS/OS, and treatment regimens.
- [Genetic Variability Across Major Histocompatibility Complex](https://cbtn.org/projects/genetic-variability-across-major-histocompatibility-complex/) - The major histocompatibility complex (MHC) has been documented to be involved in a variety of immunological processes; however, it often eludes understanding because of the complexity of the region due to factors like strong linkage disequilibrium (LD) and highly polymorphic loci. To better understand this region of the genome and how it ties to diseases,
- [Pediatric Pan-Cancer Analysis of Structural Variants](https://cbtn.org/projects/pediatric-pan-cancer-analysis-of-structural-variants/) - We have developed new and improved computational tools for the analysis of structural variants based on tumor sequencing data. We now aim to perform a pediatric pan-cancer analysis focused on the discovery of new structural variants and other genomic rearrangements using our new tools.
- [BRAIN MATCH](https://cbtn.org/projects/brain-match/) - We aim to identify cell and time of origin of pediatric brain tumors by comparing gene expression profile of tumor sample with that of a developing brain.
- [Cross-species omics integration to identify oncogenic events in pediatric brain tumors](https://cbtn.org/projects/cross-species-omics-integration-to-identify-oncogenic-events-in-pediatric-brain-tumors/) - Our goal is to integrate mouse and human multi-omics data to identify oncogenic events in pediatric brain tumors. In our recent study, we profiled transcriptome, whole proteome and phosphoproteome in two glioma mouse models. We plan to use whole genome sequence and RNAseq data of pediatric brain cancer tissues and perform a cross-species comparisons with
- [Mechanistic Modeling of high-grade glioma](https://cbtn.org/projects/mechanistic-modeling-of-high-grade-glioma/) - We will use a computer model to find potential drug treatments for high grade glioma patients. We will use the expression and mutation data of glioma patients as a basis for personalized in silico modeling of drug responses.
- [Exploring the somatic landscape of adult and paediatric chordoma](https://cbtn.org/projects/exploring-the-somatic-landscape-of-adult-and-paediatric-chordoma/) - Our research seeks to uncover more about why adult and paediatric chordoma by studying the genetic patterns. By understanding these patterns we hope to identify new treatments.
- [The Role of Mutational Signatures in the Development of Childhood Cancer](https://cbtn.org/projects/the-role-of-mutational-signatures-in-the-development-of-childhood-cancer/) - In this study we aim to identify genetic aberrations across different histological types of childhood cancer. And to evaluate the importance of these aberrations in development of childhood cancers.
- [Splicing analysis in ependymoma](https://cbtn.org/projects/splicing-analysis-in-ependymoma/) - RNA-Seq data of ependymoma (and other brain tumors) will be analyzed to identify differential splicing between tumor types. Ideally, we would like to link results to clinical data, such as age, gender, tumor location, and outcome. If necessary, we would also like to link potential isoforms to mutations in the DNA.
- [Mitochondrial mutations in pediatric brain cancer](https://cbtn.org/projects/mitochondrial-mutations-in-pediatric-brain-cancer/) - I will be looking for mutations in the mitochondrial DNA and compare the presence of these to mutations in nuclear DNA to try to understand the biology of mutations in these cancer types.
- [Novel neoantigen detection from complex transcriptomic structures in pediatric Brain Tumors](https://cbtn.org/projects/novel-neoantigen-detection-from-complex-transcriptomic-structures-in-pediatric-brain-tumors/) - We are proposing a new pipeline that can predict novel and more accurate neoantigens for pediatric brain tumors using an approach independent from the assembled genomes. This project helps support current efforts being made to implement immunotherapy for this type of childhood tumors.
- [Developing Summative Measures of Paediatric Cancer Risk](https://cbtn.org/projects/developing-summative-measures-of-paediatric-cancer-risk/) - Understanding the genetic reasons why some families develop cancer at a young age is critical for effective screening and identifying at-risk individuals. Currently, we mostly look at the effect of individual mutations in well-known cancer genes to determine a patient's likely cancer risk. Here, we propose to develop new methods which look at far more
- [Comparison of fusion calling platforms in pediatric DIPG and high‐grade glioma](https://cbtn.org/projects/comparison-of-fusion-calling-platforms-in-pediatric-dipg-and-high‐grade-glioma/) - In this proposal, we will collaborate with theChildren's Brain Tumor Tissue Consortium (CBTTC) to compare the CODAC tool against other established computational tools on the RNA-sequencing data of over 100 DIPG tumors. To confirm that fusions called by the CODAC pipeline are tumor driving (not false positives), we will model them in various in vitro
- [Stand Up 2 Cancer](https://cbtn.org/projects/stand-up-2-cancer/) - Investigating biomarker for treatment respondors and non-respondors in PDX model experiment.
- [Defining Molecular Neighborhoods for Pediatric HGG](https://cbtn.org/projects/defining-molecular-neighborhoods-for-pediatric-hgg/) - We want to see if we can take NGS and associated data for children with HGG and define a finite series of groupings that reflect the range of variability of genetic data for this diagnosis. If this is possible, we should then be able to determine the recommended treatment for each group identified and use
- [Proteomic Analysis of CBTTC Cell Lines (Procan)](https://cbtn.org/projects/proteomic-analysis-of-cbttc-cell-lines-procan/) - CBTTC investigators are able to grow cancer cells from children's brain cancers in the laboratory and to test their response to cancer drugs. In this project, thousands of types of protein molecules will be measured in each of the cancer cell lines, and in the corresponding cancers, to understand more about the cancers. Advanced computational
- [Defining the role of the histone 3 (H3.3G34R) mutation in the pathogenesis of pediatric high grade astrocytoma](https://cbtn.org/projects/defining-the-role-of-the-histone-3-h3-3g34r-mutation-in-the-pathogenesis-of-pediatric-high-grade-astrocytoma/) - High grade astrocytoma is the main cause of pediatric brain tumor death. Decades of clinical trials, largely informed by work on adult brain tumors, have been ineffective at improving their treatment. The discovery of frequent G34R mutations in histone H3 occurring in pediatric tumors suggests that histone biology plays a critical role in their development,
- [Decoding the Dark Matter of the High-Risk Paediatric Cancer Genome](https://cbtn.org/projects/decoding-the-dark-matter-of-the-high-risk-paediatric-cancer-genome/) - High-risk paediatric cancers have dismal survival rates, and despite best efforts using advanced DNA sequencing, we find very few mutations to explain this aggressiveness. We reasoned that whole classes of under-explored mutations in the "noncoding genome" may explain their poor outcomes, and we propose innovative ways to study these in the largest study of patients
- [The Australian Bioinformatics Commons Paediatric Cancer Pathfinder Project](https://cbtn.org/projects/the-australian-bioinformatics-commons-paediatric-cancer-pathfinder-project/) - In partnership with investigators from CAVATICA, we are developing The Australian Bioinformatics Commons, which is the largest genomic data sharing initiative undertaken in Australia. This platform will be able to link data in Australia, with data in CAVATICA in the United States, allowing seamless data analysis and integration across geographical borders. We thus request access
- [Multi-scale model of children with brain tumors](https://cbtn.org/projects/multi-scale-model-of-children-with-brain-tumors/) - We will test a multi-scale model that was developed in adult brain tumor patients and test this model on pediatric brain tumor data. We will evaluate whether existing models can be used, or if the model needs to be fine tuned to pediatric brain tumor data.
- [Genomics of radiation-induced cavernomas in pediatric tumor patients](https://cbtn.org/projects/genomics-of-radiation-induced-cavernomas-in-pediatric-tumor-patients/) - Many pediatric patients with tumors receive subsequent radiation therapy. A select cohort of these patients develop cavernomas. We want to analyze and compare the genetic data of these patients to genetic data of patients with familial and sporadic cavernomas.
- [Detecting Gene Fusions and Subtype Discovery in Pediatric Solid Tumors RNA-Seq using CICERO](https://cbtn.org/projects/detecting-gene-fusions-and-subtype-discovery-in-pediatric-solid-tumors-rna-seq-using-cicero/) - Find new childhood brain tumor gene fusions and sub-groups by analyzing the CBTTC data in tandem with St. Jude Cloud data.
- [Targeting Immunosuppressive Macrophage in Pediatric Brain Tumors](https://cbtn.org/projects/targeting-immunosuppressive-macrophage-in-pediatric-brain-tumors/) - We hypothesize that macrophages within pediatric brain tumors (PBT) may enable local tumor regrowth and spinal metastasis. To determine the burden of infiltrating macrophage in human PBT tissue samples, we plan to correlate gene expression of macrophage signature genes with patterns of clinical progression and outcome.
- [Cancer Stemness of Pediatric Tumors](https://cbtn.org/projects/cancer-stemness-of-pediatric-tumors/) - Self-renewal and pluripotency have been initially attributed to normal stem cells that posses the ability to give rise to all cell types in the adult organism. Seminal findings in acute myeloid leukemia in the late 1990s led to the identification of cancer stem cells (CSCs). Since then, they have been an intense focus of cancer
- [PNOC and SJCRH Collaborative DIPG Radiogenomic Investigation](https://cbtn.org/projects/pnoc-and-sjcrh-collaborative-dipg-radiogenomic-investigation/) - Semiquantitative imaging parameters extracted from magnetic resonance imaging (radiomics) have been suggested as a means to both identify and better characterize tumor biology and molecular features. We aim to define the relationship between quantitative and qualitative imaging features and molecularly defined subtypes of pediatric brainstem glioma and to evaluate the relationship between longitudinal changes in
- [Body Mass Index Trajectories in Craniopharyngioma](https://cbtn.org/projects/body-mass-index-trajectories-in-craniopharyngioma/) - The objective of this project is to examine the trajectories of height, weight, and body mass index (BMI) in individuals in the CBTTC with pathological diagnoses of craniopharyngioma. Our overarching research goal is to develop a risk prediction model for the development of hypothalamic obesity related to craniopharyngioma that will inform the design and testing
- [CENTRAL NERVOUS SYSTEM CANCERS IN PATIENTS WITH NON-NEUROFIBROMATOSIS TYPE 1 RASopathies](https://cbtn.org/projects/central-nervous-system-cancers-in-patients-with-non-neurofibromatosis-type-1-rasopathies/) - The association of non-neurofibromatosis type 1 (NF-1)-RASopathies (e.g., Noonan syndrome [NS]) with central nervous system (CNS) cancers is uncommon (less than 40 described cases). NS, which is reported to be as common as NF-1, causes a variable phenotype with age and in severity, with a large proportion of mildly affected subjects who may be misdiagnosed
- [CLINICAL, RADIOLOGIC, AND MOLECULAR CHARACTERISTICS OF ANAPLASTIC PLEOMORPHIC XANTHOASTROCYTOMAS](https://cbtn.org/projects/clinical-radiologic-and-molecular-characteristics-of-anaplastic-pleomorphic-xanthoastrocytomas/) - Anaplastic pleomorphic xanthoastrocytomas (PXAs) are rare and poorly understood brain and spinal cord cancers which were not recognized as potentially deadly throughout the world until 2016. Except for small studies that found a few important genetic abnormalities (e.g., BRAF gene mutations), there is limited understanding of the molecular characteristics and potential markers of disease aggressiveness
- [Descriptive "pharmacogenomics analysis" of the CBTTC PBTA cohort](https://cbtn.org/projects/descriptive-pharmacogenomics-analysis-of-the-cbttc-pbta-cohort/) - Pharmacogenomics is an emerging field, using an individual's genotype to predict toxicities and/or response to specific drugs. To date, there has been limited information published in pediatric brain tumor patients. This proposal will directly address this gap in knowledge and help to inform clinical care for future patients.
- [Landscape of tumor-infiltrating T cell repertoire of pediatric brain tumors](https://cbtn.org/projects/landscape-of-tumor-infiltrating-t-cell-repertoire-of-pediatric-brain-tumors-2/) - T-cells are immune cells within the body which can fight disease including cancer. Our project will examine similarities and differences in T-cells between patients and tumor types. This will be important information for the development of new immune therapies for these patients.
- [Gene expression correlates of High grade versus low grade Glioma](https://cbtn.org/projects/gene-expression-correlates-of-high-grade-versus-low-grade-glioma/) - We will examine RNA-seq dataset to define gene expression correlates distinguishing high grade from low grade pediatric glioma, and see how mRNA correlates relate to protein correlates as obtained using CPTAC data. We will compare the glioma-associated molecular correlates with correlates of high grade versus low grade cancer for other cancer types (e.g. lung, renal).
- [Cross disease variant lookup in CBTTC](https://cbtn.org/projects/cross-disease-variant-lookup-in-cbttc/) - This project aims at identifying variants in the CBTTC germline DNA whole genome sequencing data that are reported and/or found in other diseases, esp. birth defects and rare Mendelian disorders, hoping to explain/reveal shared genetics between pediatric cancer and rare diseases.
- [NF HACKATHON](https://cbtn.org/projects/nf-hackathon/) - Announcing the NF HACKATHON! Over 120 researchers, data scientists, and engineers will come together on September 13-15 at the Google Launchpad in San Francisco to explore and analyze data from the NF Data Portal, the leading open source collection of genomic and clinical data dedicated to the genetic disorder neurofibromatosis. This intensive 3-day event will
- [A highly usable and fully comprehensive proteogenomic method leveraging the breadth of genetic variation for oncogenic and//or therapeutic novel protein discovery](https://cbtn.org/projects/a-highly-usable-and-fully-comprehensive-proteogenomic-method-leveraging-the-breadth-of-genetic-variation-for-oncogenic-and-or-therapeutic-novel-protein-discovery-2/) - Proteogenomics, as a concept, utilizes patient or sample-specific genetic data to streamline the chemical identification of proteins occurring in a real cell or tumor sample. Our software handles certain genetic peculiarities of tumors more accurately than its predecessors. We anticipate that analysis of the CBTTC (+CPTAC) dataset using our method will enable discovery of tumor-associated
- [Evaluating the landscape of compound heterozygous variants in pediatric diseases](https://cbtn.org/projects/evaluating-the-landscape-of-compound-heterozygous-variants-in-pediatric-diseases/) - In most children who are diagnosed with brain tumors, the underlying cause is unknown. It is likely that in many cases, inherited DNA mutations cause pediatric brain tumors, but researchers have been able to find such evidence for relatively few pediatric brain tumors; thus there is an urgent need to identify such mutations. Using datasets
- [Germline and Somatic Microsatellite Genotypes in Pediatric Brain Tumors](https://cbtn.org/projects/germline-and-somatic-microsatellite-genotypes-in-pediatric-brain-tumors/) - We hypothesize that a permissive genetic environment is created by the cooperation of DNA microsatellite repeat elements affecting the transcriptional and translational landscape of an individual, making them susceptible to tumor formation through modulation of foundational cellular processes. We have used germline sequencing and our innovative microsatellite genotyping software to construct and validate a microsatellite
- [Molecular characterization of choroid plexus tumors](https://cbtn.org/projects/molecular-characterization-of-choroid-plexus-tumors/) - Choroid plexus tumors (CPT) are brain tumors predominantly arising in children and adolescents. CPT comprise different histologic and epigenetic subgroups with variable clinical outcome, but despite frequent copy-number alterations and some CPT harboring TP53 mutations, recurrent driver mutations are unknown. The aim of our project is to evaluate the occurrence of fusion transcripts in CPT.
- [Relationships Between Genomic, Imaging, and Histopathologic Characteristics in Pediatric Brain Tumors](https://cbtn.org/projects/relationships-between-genomic-imaging-and-histopathologic-characteristics-in-pediatric-brain-tumors/) - We wish to correlate genomic sequences of pediatric brain tumor samples with radiology and histopathologic text-based reports in the same samples using novel machine learning algorithms.
- [Epigenetic drivers in diffuse intrinsic pontine gliomas (DIPG)](https://cbtn.org/projects/epigenetic-drivers-in-diffuse-intrinsic-pontine-gliomas-dipg/) - We will employ WGS data to identify alterations in the non-coding genome of Diffuse intrinsic pontine gliomas (DIPG) that may drive oncogenesis.
- [Epigenetic drivers in Medulloblastoma](https://cbtn.org/projects/epigenetic-drivers-in-medulloblastoma/) - We will employ next generation sequencing data to identify alterations in the non-coding genome that may drive remodeling of enhancer chromatin in Medulloblastoma.
- [Comprehensive analysis of structural variants in pediatric brain tumors](https://cbtn.org/projects/comprehensive-analysis-of-structural-variants-in-pediatric-brain-tumors/) - Structural variations (SVs) are large scale changes of DNA typically affecting more nucleotides than other forms of genetic variants. We aim to study how somatic SVs are formed, how they drive disease progression and how they impact treatment in pediatric brain tumors.
- [Pediatric Brain Tumor Classification and Segmentation using Transfer Learning from Adult Datasets](https://cbtn.org/projects/pediatric-brain-tumor-classification-and-segmentation-using-transfer-learning-from-adult-datasets/) - Apply ML transfer learning techniques in order to get better classification and segmentation performance on the pediatric brain tumor dataset using data from the adult brain tumor dataset.
- [Germline mtDNA variants and somatic mtDNA mutations in Pediatric Brain Tumors](https://cbtn.org/projects/germline-mtdna-variants-and-somatic-mtdna-mutations-in-pediatric-brain-tumors/) - The goals of this study is to interrogate the whole-genome sequencing data of the pediatric brain tumor patients for germline mitochondrial DNA (mtDNA) variants and somatic mtDNA mutations, in order to understand their contributory roles, if any, to both the genetic risk for and the cancer development of pediatric brain tumors.
- [Hudson Monash Paediatric Precision Medicine Program](https://cbtn.org/projects/hudson-monash-paediatric-precision-medicine-program/) - The program focuses on developing and utilising individual patients' tumour cells to identify new therapeutic targets and repurpose existing targets using functional genomics technologies.
- [Predictive models for transcriptome variations](https://cbtn.org/projects/predictive-models-for-transcriptome-variations/) - We plan to map the RNASeq and run quantify expression and mRNA splicing variations across the samples using software we developed (MAJIQ) and other available tools. The genetic variations derived from the WGS will be evaluated for pathogenicity and their possible effect on splicing using in house algorithms such as our splicing codes, and publicly
- [Genomic correlates with radiation injury](https://cbtn.org/projects/genomic-correlates-with-radiation-injury/) - We would like to identify genetic alterations that correlate with radiation injury.
- [Deciphering the molecular characteristics of
pediatric meningiomas](https://cbtn.org/projects/deciphering-the-molecular-characteristics-ofpediatric-meningiomas/) - The biology of pediatric meningioma is poorly understood. Our project aims at a better characterization of the molecular underpinnings of these extremely rare tumors and compare them to those underlying adult meningiomas development. This project will lead to a better design of therapies for meningiomas that will be more specific to the pediatric population.
- [Germline variants in pediatric glioblastoma](https://cbtn.org/projects/germline-variants-in-pediatric-glioblastoma/) - Pediatric glioblastoma is characterized by extensive genetic heterogeneity and undergoes rapid evolution at recurrence.
- [Long non-coding RNA signature of medulloblastoma and AT/RT subtypes](https://cbtn.org/projects/long-non-coding-rna-signature-of-medulloblastoma-and-at-rt-subtypes/) - We are investigating non-coding RNA signature of pediatric CNS tumors, namely medulloblastoma and AT/RT, that could help derive better diagnostic and or prognostic markers. Identifying group specific and highly expressed non-coding RNAs will help us better understand the role of non-coding RNAs in medulloblastoma subtypes and AT/RT. Future research will focus on understanding mechanistic role
- [Heath Disparities of Pediatric Brain Tumors](https://cbtn.org/projects/heath-disparities-of-pediatric-brain-tumors/) - We aim to look at survival disparity in pediatric research use statement brain tumors among children of different racial/ethnic groups.
- [Alternative splicing in CBTTC data](https://cbtn.org/projects/alternative-splicing-in-cbttc-data/) - Aberrant pre-mRNA alternative splicing frequently occurs in cancer cells and is a major contributor to tumorigenesis and metastasis. In this project we will analyze the CBTTC RNA sequencing data to identify cancer-associated changes in pre-mRNA alternative splicing patterns. This will lead to a better understanding of the cancer genomes and transcriptomes, and could reveal novel cancer
- [Germline determinants of pediatric brain tumors](https://cbtn.org/projects/germline-determinants-of-pediatric-brain-tumors/) - We will study the inherited DNA of children with brain tumors to systematically identify differences that may have caused their disease. By comparing their DNA sequence with that of hundreds of thousands of normal adults without cancer, we aim to find new combinations of inherited DNA sequences that may predispose to early onset of cancer.
- [Discover new therapeutics for DIPG using a systems-based approach:](https://cbtn.org/projects/discover-new-therapeutics-for-dipg-using-a-systems-based-approach-2/) - Novel approaches are urgently needed to treat Diffuse intrinsic pontine glioma (DIPG) . We hypothesize that reversing signature gene expression derived from DIPG RNA-Seq samples will facilitate novel therapeutic discovery for DIPG. We therefore request the raw RNA-Seq FASTQ files to build DIPG gene expression signature which will be fed into our computational pipeline to
- [Comparison of CBTTC patient data with molecularly defined stem cell models of pediatric brain tumors](https://cbtn.org/projects/comparison-of-cbttc-patient-data-with-molecularly-defined-stem-cell-models-of-pediatric-brain-tumors/) - Our goal is to understand brain tumor development and progression by identifying genes that are differentially regulated in pediatric brain tumors as compared to normal brain samples. We are currently generating animal models for specific malignant childhood brain tumors. By comparing data from our models to global patient datasets, we hope to identify gene expression
- [Detection of cooperative and mutually exclusive genetic alterations in pediatric cancer](https://cbtn.org/projects/detection-of-cooperative-and-mutually-exclusive-genetic-alterations-in-pediatric-cancer/) - Cancers arise and progress by acquiring combinations of mutations in the genome, genetic interactions are specific combinations of mutations in gene pairs that have an unexpected effects. In this project, we will study genetic interactions in childhood cancer and their relationship with different cancer types. Our goal is to gain more insight in the underlying
- [Characterizing the Prevalence of ETMR by Molecular Signature](https://cbtn.org/projects/characterizing-the-prevalence-of-etmr-by-molecular-signature/) - ETMR is a rare and aggressive tumor that occurs in young children. ETMR has only recently been identified as a distinct clinical entity with a unique molecular signature and the prevalence of this tumor is unknown. Through a query of the CBTTC data set, we aim to identify ETMR specimens and characterize the prevalence of
- [identify novel therapeutic targets and biomarkers in non-coding genome of pediatric cancers](https://cbtn.org/projects/identify-novel-therapeutic-targets-and-biomarkers-in-non-coding-genome-of-pediatric-cancers/) - We identified a novel pathway hyperactive in pediatric cancer. We plan to integrate CBTTC data to validate and extend our preliminary result.
- [Immunogenomic landscape of pediatric cancers](https://cbtn.org/projects/immunogenomic-landscape-of-pediatric-cancers/) - We seek to understand immune composition of childhood cancers. CBTTC datasets plus data from our collaborator will allow us to outline the role of immune cells in children with wide range of cancers.
- [Identifying New Cell Surface Targets for Immunotherapy treatment of Poor Prognosis Pediatric Brain Tumors](https://cbtn.org/projects/identifying-new-cell-surface-targets-for-immunotherapy-treatment-of-poor-prognosis-pediatric-brain-tumors/) - We aim to screen the established CBTTC database of pediatric brain tumor tissue to identify a list of proteins. We then aim to use an established protocol to compare this list to normal tissue expression lists, to potentially compile a list of proteins expressed in pediatric brain tumors
- [Genomic Landscape of Mixed Glial Neuronal Tumors](https://cbtn.org/projects/genomic-landscape-of-mixed-glial-neuronal-tumors/) - This study aims to examine the genomic landscape research use statement (3 sentences MAX) of mixed neuronal-glial tumors in pediatric patients. We are examining molecular/genomic signatures and correlating them with patient features (seizures, survival, etc).
- [Cancer Predisposition in Pediatric Brain Tumors](https://cbtn.org/projects/cancer-predisposition-in-pediatric-brain-tumors/) - Some children with brain tumors have changes in genes leading to an increased likelihood of tumor development. These are changes that are either inherited, or new to the child. We would like to query the CBTTC germline (blood) and somatic (tumor) DNA data to identify cancer predisposing variants, and compare these findings to clinical data,
- [Comparison of Clinical Targeted Next Generation Sequencing (NGS) in FFPE with whole genome sequencing (WGS) of snap frozen pediatric brain tumors](https://cbtn.org/projects/comparison-of-clinical-targeted-next-generation-sequencing-ngs-in-ffpe-with-whole-genome-sequencing-wgs-of-snap-frozen-pediatric-brain-tumors/) - Many brain tumor patients at our institution have clinical sequencing of their tumors in addition to having tissue sent to CBTTC and included in the whole bank sequencing project. We want to compare the genetic results of our clinical NGS performed on the Oncoplex platform with the results of WGS performed through the CBTTC. To
- [Cooperating mutations in brain tumors of patients with NF1](https://cbtn.org/projects/cooperating-mutations-in-brain-tumors-of-patients-with-nf1/) - I am looking to identify cooperating mutations with NF1 in Neurofibromatosis type I patients with brain tumors. This information will help model the tumors these patients develop more accurately.
- [Defining the mutational landscape of pediatric brain tumors](https://cbtn.org/projects/defining-the-mutational-landscape-of-pediatric-brain-tumors/) - The objective of this study is to perform a primary analysis of recently-generated whole genome sequencing (WGS) of tumor-normal pairs and matched RNA-sequencing within the CBTTC. Our goal is to define the mutational landscape across the diverse cancers sequenced and to identify pleotropic and/or histotypes-specific alterations driving the development and progression of central nervous system
- [Spatial evolution and somatic mutations spectrum of Gliomatosis Cerebri](https://cbtn.org/projects/spatial-evolution-and-somatic-mutations-spectrum-of-gliomatosis-cerebri/) - An analysis of the spatial evolution and genetic-epigenetic landscape in Gliomatosis Cerebri and other HGG. Using innovative tools in computational biology to map the spatial differences in glioma progression.
- [Derek Wainright on IDO1 expression with all the CBTTC RNA-Seq data](https://cbtn.org/projects/derek-wainright-on-ido1-expression-with-all-the-cbttc-rna-seq-data/) - We previously showed that increased IDO1 expression is associated with decreased adult glioblastoma patient survival. We are interested in determining its relevance in malignant pediatric brain tumors.
- [In silico neo-antigen detection in high grade pediatric brain tumors utilizing RNA-seq and WGS](https://cbtn.org/projects/in-silico-neo-antigen-detection-in-high-grade-pediatric-brain-tumors-utilizing-rna-seq-and-wgs-2/) - Our goal is to identify novel antigens in pediatric high grade brain tumors that can be used for immunotherapy. We will use whole genome sequencing data and RNA-seq data to identify novel antigens with two bioinformatic techniques (one validated and one in production). The results will help to develop new immunotherapy targets and pipelines for
- [Fusion Analysis in CBTTC RNAseq data](https://cbtn.org/projects/fusion-analysis-in-cbttc-rnaseq-data/) - We plan to do analyse the pediatric brain tumor RNAseq data for fusions.We have a small cohort of the same tumors at Weill Cornell and we want to compare both the cohorts.This will really strengthen our findings if we find something we already found in our small cohort.
- [Identification of non-coding drivers from brain tumour genomes](https://cbtn.org/projects/identification-of-non-coding-drivers-from-brain-tumour-genomes/) - Cancer somatic mutations and associated RNA-seq and clinical data will be used to identify and validate potential novel coding and non-coding elements that are important for pediatric brain cancer development.
- [Genetic Polymorphisms and Neurocognitive Outcomes in Pediatric Brain Tumor Survivors](https://cbtn.org/projects/genetic-polymorphisms-and-neurocognitive-outcomes-in-pediatric-brain-tumor-survivors/) - This research will evaluate associations between the presence or absence of various polymorphisms from BT biospecimens and neuropsychological functioning. The study will include measures of cognitive, emotional, social and behavioral functioning through the use of direct assessment, self-, and parent- report measures. Overall, we hypothesize that PBTS will have different neurocognitive and behavioral outcomes depending
- [Treehouse Childhood Cancer Initiative: Identification of therapeutic leads for individual pediatric cancer patients via pan-cancer analysis](https://cbtn.org/projects/treehouse-childhood-cancer-initiative-identification-of-therapeutic-leads-for-individual-pediatric-cancer-patients-via-pan-cancer-analysis/) - The focal point of this project is comparing genomic data of an individual pediatric patient's tumor to the genomic data of thousands of pediatric and adult tumors. Although pediatric cancer is rare, by comparing to all the pediatric cancer and adult data possible, similarities can be spotted. These similarities offer information about possible therapeutic directions
- [Children's Brain Tumor Tissue Consortium Pediatric Brain Tumor Proteomics Pilot](https://cbtn.org/projects/childrens-brain-tumor-tissue-consortium-pediatric-brain-tumor-proteomics-pilot/) - The analysis of proteomics data with whole genome and transcriptomic data will provide new insights into the classification of tumors, prognosis, as well as provide for novel therapeutic strategies targeting actionable activity protein targets.
- [Analysis of chromatin pathways as regulators of high grade glioma gene expression patterns](https://cbtn.org/projects/analysis-of-chromatin-pathways-as-regulators-of-high-grade-glioma-gene-expression-patterns/) - To goal of our research is identify genes that are up- and down-regulated in brain tumors compared to normal tissue samples and genes that are up- and down-regulated in brain tumors with different mutations. We will compare these patient-derived gene expression profiles to data we have generated using human brain cancer cells grown in the
- [Radiogenomics and survival correlation of MRI based biomarker using deep learning](https://cbtn.org/projects/radiogenomics-and-survival-correlation-of-mri-based-biomarker-using-deep-learning/) - We are looking for correlating radiological imaging based phenotypes with genotypes and survival anallysis. We have done this with adult gliomas, after having discussion with patient support groups (e.g. Brain Tumour Charity), we thing pediatric gliomas would also benefit from similar studies.
- [Using AI for Diagnostic and Prognostic Prediction in Paediatric Brain Cancer](https://cbtn.org/projects/using-ai-for-diagnostic-and-prognostic-prediction-in-paediatric-brain-cancer/) - Childhood brain cancer is the second most common form of childhood cancer, though it holds the highest mortality rate. The need for invasive surgeries, radiation therapy, and/or chemotherapy is both traumatic for the child and can result in lifelong disabilities. These disabilities can be intellectual, physical, and/or developmental. While radiologist and oncologists can differentiate between
- [Brain tumor prediction using lstm and rnn](https://cbtn.org/projects/brain-tumor-prediction-using-lstm-and-rnn/) - Brain tumor prediction
- [Multiparametric Magnetic Resonance Imaging and Machine Learning-Based Predicts Prognosis and Treatment Response in Pediatric Medulloblastoma](https://cbtn.org/projects/multiparametric-magnetic-resonance-imaging-and-machine-learning-based-predicts-prognosis-and-treatment-response-in-pediatric-medulloblastoma/) - Pediatric medulloblastomas exhibit heterogeneous symptoms and varying responses to therapy, leading to poor outcomes in cases of tumor progression and incomplete resection. Early prediction of treatment responsiveness and applicability of immunotherapy has the potential to improve clinical management and outcomes.
- [Quantitative analysis of radiographic images and its application to automated diagnosis to improve healthcare efficiency](https://cbtn.org/projects/quantitative-analysis-of-radiographic-images-and-its-application-to-automated-diagnosis-to-improve-healthcare-efficiency/) - Brain tumors, particularly malignant types, pose significant challenges in diagnosis and treatment due to their rapid progression and variability among patients. Magnetic Resonance Imaging (MRI) is widely used for diagnosis, but traditional visual assessments have limitations in accurately identifying subtle features and predicting disease progression. This study aims to leverage artificial intelligence (AI) and machine
- [Artificial Intelligence Meets Medulloblastoma: Breaking Barriers in Subgroup Prediction](https://cbtn.org/projects/artificial-intelligence-meets-medulloblastoma-breaking-barriers-in-subgroup-prediction/) - Medulloblastoma is the most common malignant brain tumour in children, and early, accurate diagnosis is crucial for effective treatment. Current methods for identifying molecular subgroups of medulloblastoma rely on invasive biopsies and genetic testing, which are costly and not always accessible. This project aims to develop an artificial intelligence (AI) model that can predict medulloblastoma
- [Characterizing the landscape of cancer-specific splicing aberrations across pediatric tumors](https://cbtn.org/projects/characterizing-the-landscape-of-cancer-specific-splicing-aberrations-across-pediatric-tumors/) - Our team is investigating how changes in RNA splicing—the process by which cells edit genetic messages—may contribute to the development and progression of pediatric brain tumors. In a recent study published in Nature, we discovered that many cancers produce unique, tumor-specific signals called "neoantigens" through abnormal splicing events. These neoantigens can potentially be targeted by
- [FOXR2 driver events and clinical outcomes in CNS neuroblastoma with FOXR2 activation](https://cbtn.org/projects/foxr2-driver-events-and-clinical-outcomes-in-cns-neuroblastoma-with-foxr2-activation/) - The goal of this study is to identify cases of CNS neuroblastoma with FOXR2 activation and utilize tumor data, including changes in copy number, changes in RNA, changes in DNA, and methylation to identify the FOXR2-altering events that drive these tumors. Importantly, given this is a recent and newly identified type of brain tumor, there
- [Understanding the role of glioma-associated oligodendroglia in glioma progression](https://cbtn.org/projects/understanding-the-role-of-glioma-associated-oligodendroglia-in-glioma-progression/) - Pediatric low-grade gliomas (pLGGs) are the most common solid brain tumors in children and can lead to serious long-term health issues and even death. These tumors are often driven by genetic changes, particularly mutations in the BRAF gene, which can cause tumor cells to grow uncontrollably. Additionally, when other genetic changes co-occur with the BRAF
- [Identification of medulloblastoma metastases](https://cbtn.org/projects/identification-of-medulloblastoma-metastases/) - Medulloblastoma is the most common malignant pediatric central nervous system tumor in children. Leptomeningeal metastasis is present at initial diagnosis 5-45% of patients depending on molecular subgroup and is an independent predictor of survival. It is currently unknown if medulloblastoma cells bind to the arachnoid, pia, or both. Determining this has putative therapeutic implications in
- [Automated Segmentation and Radiomics Integration for Non-Invasive Genetic and Prognostic Prediction in Pediatric High-Grade Gliomas](https://cbtn.org/projects/automated-segmentation-and-radiomics-integration-for-non-invasive-genetic-and-prognostic-prediction-in-pediatric-high-grade-gliomas/) - We want to train an AI tool to make clinically useful predictions about pediatric brain tumors. This would assist treating physicians by providing information that can guide therapy. We need the CBTN data to have enough data to power the prediction models we aim to create.
- [Molecular Predictors of e-Radiation Resistance in H3K27M alerted diffuse midline gliomas](https://cbtn.org/projects/molecular-predictors-of-e-radiation-resistance-in-h3k27m-alerted-diffuse-midline-gliomas/) - For our study, we will create both a clinical model, including genomic data and radiographic model to predict and risk stratify patients with H3K27M altered diffuse midline glioma (DMG) for re-radiation therapy. This study is significant because it will allow neuro oncologist to predict which patients may respond to re-radiation at progression and avoid further
- [Clinical Outcomes Following Volumetric Analysis of Extent of Resection in Medulloblastoma](https://cbtn.org/projects/clinical-outcomes-following-volumetric-analysis-of-extent-of-resection-in-medulloblastoma/) - We are interested in performing a volumetric analysis regarding extent of resection in patients with medulloblastoma that have undergone surgery. We want to determine if this volumetric analysis demonstrates any relationship with survival.
- [Image-Based Classification of Pediatric Posterior Fossa Tumors: An End-to-End Solution](https://cbtn.org/projects/image-based-classification-of-pediatric-posterior-fossa-tumors-an-end-to-end-solution/) - This computational solution presents an innovative approach to classifying brain tumors located in the posterior fossa of children, utilizing anonymized magnetic resonance imaging (MRI) scans obtained prior to surgery. The process involves a comprehensive end-to-end pipeline that begins with advanced image processing techniques to enhance and prepare the scans, followed by precise tumor segmentation to
- [HD-GLIO 2.0](https://cbtn.org/projects/hd-glio-2-0/) - Delineation of the different tumor compartments is an essential procedure for image data analysis as well as quantitative follow-up of tumor volume for response assessment. Artificial neural networks allow us to automate this process by providing automated tumor segmentations with low effort and improved precision compared to manual segmentation by human raters. In this project,
- [Long read sequencing for rapid diagnosis of pediatric brain tumors](https://cbtn.org/projects/long-read-sequencing-for-rapid-diagnosis-of-pediatric-brain-tumors/) - The study is to assess and validate the feasibility of a Nanopore based long read sequencing assay to aid in rapid molecular profiling of pediatric brain tumors. The end goal is to perform this assay intraoperatively to provide the neurosurgeon with a molecular diagnosis which may aid in decision making.
- [Characterizing Tumor Diffusion in Gliomatosis Cerebri Using Radiology and MRI Data](https://cbtn.org/projects/characterizing-tumor-diffusion-in-gliomatosis-cerebri-using-radiology-and-mri-data/) - Gliomatosis cerebri is a rare and aggressive brain tumor that spreads across multiple areas of the brain, making it difficult to diagnose and treat. This project will identify and study cases within the Children’s Brain Tumor Network using clinical records and MRI scans, creating a cohort that researchers can use to better understand the disease.
- [Classification of Pediatric Brain Tumor](https://cbtn.org/projects/classification-of-pediatric-brain-tumor/) - This project aims to develop an improved system for classifying pediatric brain tumors using computational and data-driven approaches. Accurate classification of brain tumors in children is essential for guiding treatment decisions and improving survival outcomes. By analyzing medical data and imaging information, this study seeks to identify distinguishing patterns among tumor types. Access to CBTN’s
- [Advancing Pediatric Cancer Diagnosis: Unveiling ecDNA Patterns in FFPE Tissue Images Using Machine Learning](https://cbtn.org/projects/advancing-pediatric-cancer-diagnosis-unveiling-ecdna-patterns-in-ffpe-tissue-images-using-machine-learning/) - Our study is driven by the critical need for biomarkers that can enhance the detection of residual disease, evaluate therapy response, and predict cancer recurrence. We're focusing on extrachromosomal DNA (ecDNA), a unique genetic feature characterized by its circularization and amplification of multiple oncogenes. Understanding ecDNA's role has become crucial in deciphering cancer aggressiveness and
- [Prediction of radiotherapy benefit using genomic-adjusted radiation dose in pediatric low grade gliomas and ependymomas](https://cbtn.org/projects/prediction-of-radiotherapy-benefit-using-genomic-adjusted-radiation-dose-in-pediatric-low-grade-gliomas-and-ependymomas/) - Radiotherapy (RT) in pediatric cancer: Radiotherapy is a critical component of cure for many pediatric malignancies. However, there is often hesitation to prescribe RT for children out of concern for late effects of treatment, particularly for central nervous system tumors. For some malignancies, such as low grade gliomas, the most common brain tumor in children,
- [Evolutionary trajectories of pediatric cancers](https://cbtn.org/projects/evolutionary-trajectories-of-pediatric-cancers/) - Whole-Genome Sequencing can be used to trace tumour evolutionary trajectories on an individual base. The role of such information is key to interpret the process of malignant transformation, how and when it starts, and we can counteract it from an evolutionary standpoint. The possibility of studying that in the pediatric context, with treatment-associated followup, is
- [AI/ML derivation and experimental validation of ATRT biomarkers of survival and response to treatment](https://cbtn.org/projects/ai-ml-derivation-and-experimental-validation-of-atrt-biomarkers-of-survival-and-response-to-treatment/) - Atypical teratoid rhabdoid tumors (ATRT) are challenging pediatric brain tumors that most often affect children age 3 and younger. While there have been improvements in clinical outcomes with multimodal therapy, there remains significant morbidity and toxicities associated with intensive therapy. The goal of this study is to utilize computer and mathematical algorithms to make predictions
- [lncRNA Regulation of Chromatin Remodeling in Pediatric Brain Tumors](https://cbtn.org/projects/lncrna-regulation-of-chromatin-remodeling-in-pediatric-brain-tumors/) - Systems biology integration of RNA-seq & DNA-seq data will reveal lncRNA regulation of chromatin modifications in pediatric brain tumors, potentially leading to novel biomarkers and treatment strategies. We will leverage whole-genome and RNA sequencing data to identify novel transcripts arising from alternative splicing, differential exon usage, and transcript length variation. These novel transcripts will then
- [Automated Multimodal Data Integration and Analysis for Pediatric Brain Tumor Imaging and Pathology](https://cbtn.org/projects/automated-multimodal-data-integration-and-analysis-for-pediatric-brain-tumor-imaging-and-pathology/) - This project aims to develop an advanced, automated system to improve the diagnosis and treatment of pediatric brain tumors. By integrating various types of medical data, including MRI scans, digital pathology slides, and clinical reports, we hope to create a comprehensive tool that can assist clinicians and researchers in more effectively identifying and understanding these
- [HG34-mutant gliomas](https://cbtn.org/projects/hg34-mutant-gliomas/) - H3G34-mutant gliomas are rare but aggressive pediatric diffuse high-grade gliomas with a median survival time of just 18-22 months (37509641). These gliomas typically feature missense mutations within the histone gene H3F3A, resulting in very poor prognosis in pediatric populations. While H3G34-mutant gliomas have been studied histologically in the past, very few papers have explored how
- [Role of CRK and CRKL in high grade glioma cell migration](https://cbtn.org/projects/role-of-crk-and-crkl-in-high-grade-glioma-cell-migration/) - Our research goal is to block the diffuse invasion of brain tumors into neighboring healthy brain tissues, increasing the efficacy of standard care and reducing recurrence. The two proteins that we have studied for the last two decades play critical roles in tumor cell migration in adult brain tumor cells. We will remove the two
- [Advancing radiomic tools for brain tumours: Enriching data sets and developing novel AI approaches](https://cbtn.org/projects/advancing-radiomic-tools-for-brain-tumours-enriching-data-sets-and-developing-novel-ai-approaches/) - Brain tumours are the most common cause of cancer death in children. Despite impressive advances in our understanding of these tumours, it can often take several weeks to reach a diagnosis, and the ability to predict those who will survive is still limited. Biological studies have increasingly defined a larger number of tumour types and
- [Deep Learning Based Interpretable Pediatric Brain Tumors Segmentation and Classification](https://cbtn.org/projects/deep-learning-based-interpretable-pediatric-brain-tumors-segmentation-and-classification/) - The project project seeks to address key challenges in pediatric brain tumor imaging by creating a novel, interpretable deep learning framework that integrates tumor segmentation and classification. By leveraging interdisciplinary collaboration between AI scientists and healthcare professionals, this project aims to improve diagnosis, treatment planning, and patient outcomes for Pediatric Brain Tumors. The project will
- [Digitizing Pathology: Enhancing Tumor Diagnosis with AI and Whole Slide Imaging](https://cbtn.org/projects/digitizing-pathology-enhancing-tumor-diagnosis-with-ai-and-whole-slide-imaging/) - Until recently, pathology has relied heavily on manual methods, such as creating glass slides and examining tissue samples with a microscope, without much help from digital technology. The conversion of physical glass slides to digital whole slide images makes storage easier, enables remote access, and allows the use of advanced computational tools like Augmented Intelligence
- [Integrative Multi-omics Approaches to identify novel biomarker-informed therapeutic targets for childhood cancer.](https://cbtn.org/projects/integrative-multi-omics-approaches-to-identify-novel-biomarker-informed-therapeutic-targets-for-childhood-cancer/) - Childhood cancer is often most deadly when it involves tumors in the central nervous system. One major challenge is the lack of pediatric cancer models compared to adult ones. To address this, our team at the Next Generation Precision Medicine Program, led by Prof. Ron Firestein, has spent more than five years building the Childhood
- [Automated Classification of Pediatric Posterior Fossa Tumors Using Machine Learning and Deep Learning on MRI Data](https://cbtn.org/projects/automated-classification-of-pediatric-posterior-fossa-tumors-using-machine-learning-and-deep-learning-on-mri-data/) - This project aims to develop advanced machine learning and deep learning models to help radiologists and clinicians accurately identify and differentiate types of posterior fossa tumors in children using MRI scans. These tumors are relatively rare but represent a significant portion of pediatric brain tumors and have various subtypes with differing treatment protocols and prognoses.
- [Assessing the importance of reoperation in overall survival in pediatric malignant brain tumors](https://cbtn.org/projects/assessing-the-importance-of-reoperation-in-overall-survival-in-pediatric-malignant-brain-tumors/) - Numerous studies have shown a survival benefit association with increased extent of resection, and particularly in children that have had a gross total resection for malignant brain tumors at the time of initial diagnosis. However, it is unknown if reoperation with the goal of a GTR/NTR for pediatric malignant brain tumors at recurrence/progression increases OS
- [Design, implementation, and validation of novel multimodal deep learning algorithms for clinical translation of diagnostic and prognostic tools for pediatric brain tumors](https://cbtn.org/projects/design-implementation-and-validation-of-novel-multimodal-deep-learning-algorithms-for-clinical-translation-of-diagnostic-and-prognostic-tools-for-pediatric-brain-tumors/) - Pediatric brain tumors are the second most common cancer in children in Canada and the United States. While death from most of these cancers is rare, affected children commonly experience multiple recurrences requiring different types of therapeutic approaches leading to considerable illness. As standard of care, magnetic resonance imaging (MRI) scans of pediatric brain tumors
- [The role of "adult onset" cancer predisposition genes in pediatric cancer](https://cbtn.org/projects/the-role-of-adult-onset-cancer-predisposition-genes-in-pediatric-cancer/) - While survival rates for pediatric cancer have improved in recent decades, cancer remains the leading cause of death by disease in children. Recent advances in genetic testing capabilities, including next generation sequencing (NGS), have led to a better understanding of the genetic causes of pediatric cancer. There is increasing evidence that a significant proportion of
- [circRNA atlas of pediatric brain tumors](https://cbtn.org/projects/circrna-atlas-of-pediatric-brain-tumors/) - Circular RNAs (circRNAs) are a type of RNA which is in a circular form and resistant to degradation. circRNAs have been shown to be involved in many different functions of cancer such as tumor initiation, progression or metastasis. In the past, we have used circRNAs to correctly identify subgroups of medulloblastoma which were previously assigned
- [Radiologic-Molecular Correlation in DMG Recurrence](https://cbtn.org/projects/radiologic-molecular-correlation-in-dmg-recurrence/) - Diffuse midline gliomas (DMGs) are highly aggressive brain tumors most often seen in children between the ages of 6.5-10 years old and have a survival time of less than one year after diagnosis. Magnetic resonance imaging (MRI) is the standard practice for diagnosing DMGs and monitoring their response to therapy. Because of this, nearly every
- [Brain Age as a Biomarker for Survivorship Outcomes in Pediatric Brain Tumor Patients: A Neuroimaging-Based Investigation](https://cbtn.org/projects/brain-age-as-a-biomarker-for-survivorship-outcomes-in-pediatric-brain-tumor-patients-a-neuroimaging-based-investigation/) - This project investigates the effects of brain tumor and its treatments on brain aging and behavioral health outcomes, focusing on identifying predictors of atypical brain aging and adverse behavioral health outcomes. By combining retrospective data from healthy controls (PI has access to that) and brain tumor patients (from CBTN), the study seeks to enhance understanding
- [Personalized Survival Prediction of Glioma via Multi-modal Data](https://cbtn.org/projects/personalized-survival-prediction-of-glioma-via-multi-modal-data/) - The study goal is to predict personalized survival probability of glioma along time by developing AI models. Significance and impact: This will benefit the personalized treatment Why the CBTN request benefits your work: My research locates at the intersection of AI and medical imaging, with the application in cancer area. CBTN provides large-scale multi-modal data,
- [Precision Diagnosis of Pediatric Tumors Based on Artificial Intelligence Pathology Analysis](https://cbtn.org/projects/precision-diagnosis-of-pediatric-tumors-based-on-artificial-intelligence-pathology-analysis/) - This project will develop a new artificial intelligence (AI) system for the automated diagnosis of pediatric tumors through pathological images. We envision that this new technology can improve the accuracy of clinical diagnosis, facilitate disease prediction and timely treatment of pediatric tumors, and save time and costs for the family. Also, we hope this technology
- [Genetic analysis of recurrent medulloblastoma](https://cbtn.org/projects/genetic-analysis-of-recurrent-medulloblastoma/) - We will use sequencing data and supercomputer analyses to the important genetic changes related to cancer formation and therapy resistance in recurrent medulloblastoma.
- [Federated Cancer Data - Paediatric High Grade Glioma Pathfinder Project](https://cbtn.org/projects/federated-cancer-data-paediatric-high-grade-glioma-pathfinder-project/) - Minderoo Foundation is supporting a Federated Cancer Data Solution for pediatric high-grade gliomas bringing together a common data model across the United Kingdom, Australia, and the United States. CBTN data will undergo an ETL process to harmonize with OMOP data model for this federated project. For this first pass of data request, I just need
- [Developing an imaging clinical decision support tool](https://cbtn.org/projects/developing-an-imaging-clinical-decision-support-tool/) - Analyzing pediatric tumors may be more challenging than for adults for multiple reasons, including the rarity of these conditions, their unique characteristics compared to adults, and the developing brain of children. These challenges have negatively impacted technological and methodological progress in pediatric neuro-oncology. As a result, there is currently no accessible and standardized computational infrastructure
- [Identification of pediatric DIPG targets and Drug Discovery](https://cbtn.org/projects/identification-of-pediatric-dipg-targets-and-drug-discovery/) - Diffuse intrinsic pontine glioma (DIPG) is the most common type of brain stem tumor in children, comprising 80% of cases. Aggressive treatment approaches, DIPG remains the leading cause of cancer-related death in children, with a prognosis of less than 2 years after diagnosis. Meta-analysis of gene expression profile of DIPG can help identify druggable target
- [CAR Target discovery](https://cbtn.org/projects/car-target-discovery/) - CBTN data will be used to identify new treatment targets for a form of immunotherapy called chimeric antigen receptor (CAR) T cell therapy. Our analysis seeks to identify novel targets and subtypes in high grade brain tumors. We plan on using imaging data to identify imaging differences at time of diagnosis that might inform further
- [Human-centered design of clinical AI to support the diagnosis of pediatric suprasellar tumors](https://cbtn.org/projects/human-centered-design-of-clinical-ai-to-support-the-diagnosis-of-pediatric-suprasellar-tumors/) - We test an AI system that helps diagnose pediatric brain tumors using preoperative clinical imaging. The study has two phases, retraining AI models and conducting a study with clinical experts. The research aims to use AI to save costs and time and enable earlier treatment.
- [Record ID 1296
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Characterization of splicing-derived neoantigens in pediatric brain tumors](https://cbtn.org/projects/record-id-1296page-8characterization-of-splicing-derived-neoantigens-in-pediatric-brain-tumors/) - The purpose of our research is to identify potential neoantigen targets that are derived from cancer-specific splicing aberrations in pediatric brain tumors. Characterization of this novel source of neoantigens will open new opportunities for cell-based immunotherapies for pediatric brain tumor patients. RNA-sequencing data derived from pediatric brain tumor patients in FASTQ format will be analyzed
- [Exploring Shared and Unique Mechanisms of Focal Amplification in Pediatric and Adult Brain Tumors](https://cbtn.org/projects/exploring-shared-and-unique-mechanisms-of-focal-amplification-in-pediatric-and-adult-brain-tumors/) - In our study, we aim to investigate and compare various ways in which specific genetic material is excessively replicated in brain tumors, both in pediatric and adult patients. The goal is to gain insights into the commonalities and differences in the mechanisms that contribute to these serious diseases. This research holds the potential to enhance
- [Genetic mutations and Epigenetic data](https://cbtn.org/projects/genetic-mutations-and-epigenetic-data/) - Dr. Dalia Haydar, our collaborator, will use bioinformatics and AI analyses to correlate miR profiles with TME signatures and identify correlations with disease progression, response to therapy, and survival. She needs genetic and epigenetic data for her research funding.
- [Novel ADC targets in Pediatric Glioma](https://cbtn.org/projects/novel-adc-targets-in-pediatric-glioma/) - We propose to access the mRNA expression data in the CBTN to identify novel targets for a promising type of therapeutic called an antibody drug conjugate. Such therapeutics have performed exceptionally well in adult cancers provided that a strong cell-surface receptor can be identified. We will seek to identify such a receptor for the brain
- [Genomic and transcriptomic profiling](https://cbtn.org/projects/genomic-and-transcriptomic-profiling/) - To obtain genomic and RNA data for SDGIDs: CBTN 7316-8575, 7316-7667, 7316-5766, 7316-8579, 7316-7700, 7316-9625, 7316-10414, 7316-9072, 7316-11299. We will conduct data analysis using our bioinformatician to identify pathogenic mutations and gene upregulation and downregulation leading to tumor progression. We will employ our bioinformaticians to analyze these data and correlate the results of these data
- [Enhancing Clinical Data for CBTN through Automated EHR extraction](https://cbtn.org/projects/enhancing-clinical-data-for-cbtn-through-automated-ehr-extraction/) - Clinical data, especially high-quality longitudinal data, has challenging to obtain and utilize as it currently requires primarily manual extraction and different tools to enable ongoing flows of clinical data to the community. Additionally, raw EHR data are often not of immediate use for researchers as related EHR data elements may be stored disparately, and data
- [An integrated deep learning model to accurately predicts DNA methylation signatures and tumor types from histopathology in central nervous system tumors](https://cbtn.org/projects/an-integrated-deep-learning-model-to-accurately-predicts-dna-methylation-signatures-and-tumor-types-from-histopathology-in-central-nervous-system-tumors/) - We are going to use special computer programs (i.e., deep learning method) to look at brain tumor pictures (Histopathological slides) from the Children's Brain Tumor Network. These programs can find patterns in the pictures that might not be obvious to humans. By spotting these patterns, we hope to better understand the differences between various types
- [Germline mutations in pediatric brain tumors](https://cbtn.org/projects/germline-mutations-in-pediatric-brain-tumors/) - We will look at germline and somatic mutations in a new way, to identify processes of tumorigenesis that have not been fully elucidates yet.
- [No Change](https://cbtn.org/projects/no-change/) - NA
- [None Provided](https://cbtn.org/projects/none-provided/) - We are looking at non-coding mutations in the tumors and in the germline. We have a program that aims to understand how non-coding genetic variants contribute to brain tumor pathobiology.
- [Understanding a rare familial cancer syndrome associated with multifocal malignant peripheral nerve sheath tumors](https://cbtn.org/projects/understanding-a-rare-familial-cancer-syndrome-associated-with-multifocal-malignant-peripheral-nerve-sheath-tumors/) - We have undertaken hole genome sequencing of the germline and tumors in a family with aggressive multifocal nerve sheath tumors. We have identified a number of potentially causal germline and recurrent somatic mutations, We wish to compare these with those observed in the CBTN databases.
- [DMG genomic signatures as predictors of radiation response](https://cbtn.org/projects/dmg-genomic-signatures-as-predictors-of-radiation-response/) - We will explore molecular profiles of individual DMG tumors as predictors of radiation response and survival.
- [Hypoxia and Immune Infiltration in Medulloblastoma](https://cbtn.org/projects/hypoxia-and-immune-infiltration-in-medulloblastoma/) - Solid tumors like medulloblastoma often lack adequate blood supply, leading to low oxygen levels known as hypoxia. Hypoxia fuels cancer growth in part by changing the immune environment around them tumor, making it more supportive of cancer cells. Despite understanding hypoxia’s role in many cancers, its impact on medulloblastoma is not well-studied. Our project aims
- [Alternative Splicing Analysis of pHGG](https://cbtn.org/projects/alternative-splicing-analysis-of-phgg/) - Pediatric glioblastoma is a recalcitrant cancer with few treatment options. Aberrant alternative splicing is a classic hallmark of many cancer types. We will use RNA-sequencing data from the CBTN pHGG atlas and integrate it with normal samples to identity differential splicing events to enhance our understanding of the cancer and lead to potential molecular target
- [Which Pediatric High-Grade Glioma Patients Respond to Double Alkylator Chemotherapy?](https://cbtn.org/projects/which-pediatric-high-grade-glioma-patients-respond-to-double-alkylator-chemotherapy/) - Successful completion of this work would define which pHGG subtypes should be receiving this treatment as standard of care, since this is the only chemotherapy approach that has made a survival difference in this disease, but the trial was conducted before molecular subtypes were understood.
- [Predicting Overall Survival for DMG Tumors Based on pre and post-RT MRI](https://cbtn.org/projects/predicting-overall-survival-for-dmg-tumors-based-on-pre-and-post-rt-mri/) - This study aims to use machine learning for prediction of overall survival in diffuse midline gliomas.
- [Predictive Analytics in Pediatric High-Grades Gliomas](https://cbtn.org/projects/predictive-analytics-in-pediatric-high-grades-gliomas/) - This project focus is on developing a predictive analytics approach to identify favorable (and unfavorable) clinical and molecular features in pHGGs.
- [Deep learning enabled medulloblastoma prognosis and biomarker discovery](https://cbtn.org/projects/deep-learning-enabled-medulloblastoma-prognosis-and-biomarker-discovery/) - We requested CBTN specimens to complete our research program, mostly for test the generalization ability of trained deep learning model. Currently we do not have enough medulloblastoma pathology slides for external test, which makes it difficult to obtain credible conclusions. we need to use CBTN pathology whole slide images for deep learning to find out
- [Integrated Imaging and Genomic Characterization of the Immunogenicity of Pediatric Low Grade Gliomas](https://cbtn.org/projects/integrated-imaging-and-genomic-characterization-of-the-immunogenicity-of-pediatric-low-grade-gliomas/) - This research aims to understand the immune properties of low grade gliomas. Given the identification of immune clusters from genomics data and the use of imaging data to predict those clusters, we aim to leverage pathology reports to determine whether tumor stains confirm our genomics-based observations.
- [Deciphering RNA modifications and functional characterization of RNA modification enzymes in Medulloblastoma](https://cbtn.org/projects/deciphering-rna-modifications-and-functional-characterization-of-rna-modification-enzymes-in-medulloblastoma/) - Brain cancer in young people is an aggressive form of cancer. Young people with brain cancer have very poor chance of survival. WHO estimate that almost 45-60% of people with brain cancer do not survive. Brain cancer in young people is divided into subgroups and it has impact on success of cancer treatment. Subgroups also
- [Correlating molecular profiles of pediatric glioma specimens to multiparametric analysis of MR voxels at biopsy sites](https://cbtn.org/projects/correlating-molecular-profiles-of-pediatric-glioma-specimens-to-multiparametric-analysis-of-mr-voxels-at-biopsy-sites/) - This study will evaluate the diagnosis, staging, and treatment monitoring of pediatric brain tumors. We will focus on quantifying cellular and molecular heterogeneity using non-invasive medical imaging techniques. The outputs of this project are expected to improve the treatment of pediatric brain tumors by optimization of treatment strategy by genomic mutation status.
- [The evolution of alternative splicing in pediatric brain tumor under therapy](https://cbtn.org/projects/the-evolution-of-alternative-splicing-in-pediatric-brain-tumor-under-therapy/) - Alternative-splicing (AS) events have recently been identified as a source of neoantigens that are suitable for immunotherapy. We want to identify novel targets for therapeutic development of pediatric brain tumor based on research of AS.
- [Molecular Basis of Pediatric Brain Tumor Morphology](https://cbtn.org/projects/molecular-basis-of-pediatric-brain-tumor-morphology/) - Our research aims to use machine learning to understand how the shape and location of brain tumors relate to their genetic and molecular characteristics in pediatric patients. By studying the characteristics of brain tumor images, we can make MRI scans better and more accurate. This will help doctors diagnose brain tumors more precisely and improve
- [Integrative multi-omics analysis reveals dynamic interaction between brain tumors and the immune system](https://cbtn.org/projects/integrative-multi-omics-analysis-reveals-dynamic-interaction-between-brain-tumors-and-the-immune-system/) - Our study aims to understand the complex interactions between brain tumors and the immune system through the analysis of multi-omics data. By creating a comprehensive map of tumor-immune interactions, we seek to develop new immunotherapy approaches for brain tumors and provide a user-friendly web portal for collaboration among researchers. To achieve our goals, we require
- [Finding genetic and imaging biomarkers of tumour subtype and clinical outcome in childhood brain cancer](https://cbtn.org/projects/finding-genetic-and-imaging-biomarkers-of-tumour-subtype-and-clinical-outcome-in-childhood-brain-cancer/) - This project's goal is to discover new predictors of brain cancer aggression and response to treatment, that can hopefully be eventually used for clinical diagnosis. It will combine statistics and biologically-aware machine learning models to find predictors from pathology slides as well as genetic data
- [Classification of central nervous system tumors based on predicting DNA methylation from digital pathology.](https://cbtn.org/projects/classification-of-central-nervous-system-tumors-based-on-predicting-dna-methylation-from-digital-pathology/) - This project seeks to classify central nervous system tumors using a novel deep-learning approach that predicts DNA methylation from H&E slide images. By bridging these two data types, we aim to develop faster diagnostic tools that bypass the need for molecular data. Ultimately, our work could expedite the creation of personalized treatment strategies for patients
- [Explainable AI prediction model with radiogebomics analysis](https://cbtn.org/projects/explainable-ai-prediction-model-with-radiogebomics-analysis/) - We will construct the "explainable AI model". It could provide us to the process of prediction and prognostic factor from the medical image. Now, we proceed it using the medical image and gene expression data. We will propose the translation system of the cancer micro-environment information from the medical image.
- [Neoadjuvant LAG-3 Inhibitor + PD-1 Inhibitor in Children with Recurrent or Progressive High-Grade Glioma and Ependymoma](https://cbtn.org/projects/neoadjuvant-lag-3-inhibitor-pd-1-inhibitor-in-children-with-recurrent-or-progressive-high-grade-glioma-and-ependymoma/) - In this proposed study, we will expand on recent data demonstrating that neoadjuvant PD-1 blockade improved survival among adult recurrent GBM patients by answering the following questions: 1) Does pre-surgical (neo-adjuvant) checkpoint inhibition serve as a primer to enhance the anti-tumor immune response in pediatric patients with recurrent malignant brain tumors 2) Can effective anti-tumor
- [Analysis of allele specific copy-number profiles in the CBTN HGG HOPE cohort](https://cbtn.org/projects/analysis-of-allele-specific-copy-number-profiles-in-the-cbtn-hgg-hope-cohort/) - We will interrogate copy-number variation from whole-genome sequencing data in the HGG cohort. These analyses will facilitate downstream proteogenomics analyses.
- [Pediatric and Young Adult Meningioma](https://cbtn.org/projects/pediatric-and-young-adult-meningioma/) - We are analyzing DNA methylation data for young adult and pediatric menigiomas. We would like to correlate these findings with clinical information. Ideally, we will help to better risk stratify meningiomas in these age groups
- [GDF15 in Pediatric Neuro-Oncology Patients](https://cbtn.org/projects/gdf15-in-pediatric-neuro-oncology-patients/) - We intend to better understand the role of inflammation in pediatric brain tumors, specifically GDF15 which has been associated with cachexia and higher rates of complications in adults with cancer. We will evaluate if GDF15 is expressed in higher magnitudes in different pediatric brain tumors. Finally, we hope to determine if there is an association
- [Defining the global impact of germline structural variation on the transcriptome of human pediatric brain cancers](https://cbtn.org/projects/defining-the-global-impact-of-germline-structural-variation-on-the-transcriptome-of-human-pediatric-brain-cancers/) - By integrative analysis of germline SVs and gene expression data from pediatric brain cancers, we will identify genes for which the nearby presence of a germline SV breakpoint is associated with altered expression. Most of the significant genes by integrated germline SV-expression analysis would not necessarily have specific roles in cancer but would instead simply
- [Clinical Characteristics and Factors Influencing Outcomes of Diffuse Hemispheric Glioma, H3 G34-mutant: A Multi-Institutional Retrospective Cohort Study](https://cbtn.org/projects/clinical-characteristics-and-factors-influencing-outcomes-of-diffuse-hemispheric-glioma-h3-g34-mutant-a-multi-institutional-retrospective-cohort-study/) - We have developed this multicenter study as a subsequent study to previous research in order to describe the PFS and OS for patients with G34-DHG in a non-biased sample, to identify the clinical, radiologic, treatment, and molecular factors associated with G34-DHG, determine which variables can influence patient OS, and determine if any biomarkers can be
- [Spatiotemporal multi-omics analysis of childhood ependymoma](https://cbtn.org/projects/spatiotemporal-multi-omics-analysis-of-childhood-ependymoma/) - The characteristics of samples from distant recurrence in ependymoma could be identified compared to primary tissue through analysis of spatiotemporal samples, and potential treatment targets could be proposed.
- [The role and regulation of tumor suppressor SETD2 in pediatric high grade glioma](https://cbtn.org/projects/the-role-and-regulation-of-tumor-suppressor-setd2-in-pediatric-high-grade-glioma/) - SETD2 is a H3K36 tri-methyltransferase and tumor suppressor that is frequently mutated in pediatric high grade glioma. SETD2 loss may be linked to transcription defects that promote gliomagenesis.
- [Pediatric Brain Tumor Classification](https://cbtn.org/projects/pediatric-brain-tumor-classification/) - In the world of digital data, data science and machine learning is emerging as a new trend to solve various problems in healthcare which are normally not possible manually. This project will also contribute towards the enhancement of the life of children by predicting brain tumor in advance. This will in turn help in early
- [Self-attention feature pyramid network for multimodal medical image segmentation](https://cbtn.org/projects/self-attention-feature-pyramid-network-for-multimodal-medical-image-segmentation/) - My research project aims to utilise the data of the CBTN dataset to demonstrate the proof of concept of a novel model for automated medical anomaly detection in magnetic resonance images and to incorporate it into a bigger dataset designed to investigate the generalisability of the proposed model for multi-institutional data. This project constitutes a
- [OpenPBTA: An Open Pediatric Brain Tumor Atlas](https://cbtn.org/projects/openpbta-an-open-pediatric-brain-tumor-atlas/) - The goal of this submission was to add the project to the CBTN website.
- [Optimal validation of DNA-methylation based tumor purity estimation](https://cbtn.org/projects/optimal-validation-of-dna-methylation-based-tumor-purity-estimation/) - We wish to test computerized methods of identifying how much tumor exists in a cancer specimen. This will be attempted by using multiple different computerized measures.
- [Universal Pediatric CNS Tumor Genomic Profiling](https://cbtn.org/projects/universal-pediatric-cns-tumor-genomic-profiling/) - The overall objective of this study is to estimate the potential impacts of genetic characterization of childhood central nervous system (CNS) tumors on diagnosis and treatment. We will describe the frequency of potentially actionable findings by summarizing the findings of data-sets previously collected for clinical and/or research purposes. These summarized findings will be used to
- [Evaluating immune biomarkers overlapping in tumor and CSF in diffuse midline glioma (DMG)](https://cbtn.org/projects/evaluating-immune-biomarkers-overlapping-in-tumor-and-csf-in-diffuse-midline-glioma-dmg/) - The potential of this project is to identify a therapeutic biomarker - a biological signal that is released as a response to treatment such as radiation, chemotherapy, or immunotherapy - in the cerebrospinal fluid (CSF) of patients with Diffuse Midline Glioma. In assessing unique biological signals that appear after treatment administration in BOTH the CSF
- [Characterize the immune microenvironment of DMG using single-cell based deconvolution approaches](https://cbtn.org/projects/characterize-the-immune-microenvironment-of-dmg-using-single-cell-based-deconvolution-approaches/) - Diffuse midline gliomas (DMGs) are brain malignancies that are highly aggressive, challenging to treat, and remain one of the leading causes of morbidity and mortality in pediatric patients. Understanding the underlying cellular and molecular components is critical for developing novel therapeutic strategies. Our approach is expected to validate the use of deconvolution analysis of CBTN
- [A CBTN case study utilizing network analysis](https://cbtn.org/projects/a-cbtn-case-study-utilizing-network-analysis/) - The research aim for the CBTN case study is to use network analysis to connect the imaging and omics network/s and identify the individual clinical factors which impact on these networks.
- [An investigation into the role of novel and understudied genes in the initiation and progression of medulloblastoma](https://cbtn.org/projects/an-investigation-into-the-role-of-novel-and-understudied-genes-in-the-initiation-and-progression-of-medulloblastoma/) - This project serves as the first investigation into a specific class of understudied and novel genes within medulloblastoma. Through innovative bioinformatics analysis comparing gene expression and gene activity between medulloblastoma patients and normal brain samples, we aim to identify critical genetic variants for medulloblastoma tumorigenesis. Successful completion of this work will provide new avenues for
- [Creating Methylation Classifier for CNS Tumors](https://cbtn.org/projects/creating-methylation-classifier-for-cns-tumors/) - The CBTN methylation data will be used to build a CNS tumor methylation classifier.
- [Methotrexate Outcomes in Infant Medulloblastoma and ETMR Outcomes](https://cbtn.org/projects/methotrexate-outcomes-in-infant-medulloblastoma-and-etmr-outcomes/) - Describe outcomes for young children children within the CBTN data with 1. Infant medulloblastoma 2. ETMR
- [Clinicopathologic analysis of novel IDH-wildtype cerebral and posterior fossa diffuse high-grade gliomas](https://cbtn.org/projects/clinicopathologic-analysis-of-novel-idh-wildtype-cerebral-and-posterior-fossa-diffuse-high-grade-gliomas/) - Novel brain tumor methylation classes will be studied to understand biology, prognoses and appropriate treatment.
- [Deciphering the 3D genome of pediatric brain tumors](https://cbtn.org/projects/deciphering-the-3d-genome-of-pediatric-brain-tumors/) - There is increasing evidence that three-dimensional (3D) genome folding can affect gene expression and regulatory processes, with consequences on development and cancer. In this project, we explore the 3D genome of pediatric brain tumors using a deep-learning model (Akita) that is capable of predicting 3D genome structure from sequencing data to uncover novel regulators and
- [Medulloblastoma Multi-Omics](https://cbtn.org/projects/medulloblastoma-multi-omics/) - Applying multiomics approaches to study tumor heterogeneity and molecular mechanisms underlying medulloblastoma in molecular groups
- [Biology of choroid plexus carcinoma](https://cbtn.org/projects/biology-of-choroid-plexus-carcinoma/) - We will use data provided by the CBTN generated from patients with choroid plexus carcinoma (a rare tumor of childhood) to try and better understand the reasons why this tumor develops and grows. We will use this biologic data to help design a clinical trial for patients with this tumor.
- [MHC-1 and Histon mutation](https://cbtn.org/projects/mhc-1-and-histon-mutation/) - We aim to analyze gene expression level in patients with a certain type of mutation.
- [Semi-automated variant curation algorithm](https://cbtn.org/projects/semi-automated-variant-curation-algorithm/) - Development of an AI-enabled somatic variant ranking algorithm to automate genomic curation for the expansion of our personalised medicine program.
- [MRI-based tracking of cell population dynamics to design personalised adaptive treatment protocols for glioma patients](https://cbtn.org/projects/mri-based-tracking-of-cell-population-dynamics-to-design-personalised-adaptive-treatment-protocols-for-glioma-patients/) - The aim of the project is to work towards a machine-learning predictive model that can predict the proportions of brain tumour cell types of a patient given an input MRI image.
- [Discovering new mutations in pediatric neurocancer](https://cbtn.org/projects/discovering-new-mutations-in-pediatric-neurocancer/) - Our lab will use a modernized approach to identify the additional histone mutations in pediatric CNS tumours. Having CBTN access allows us to perform analysis on the whole genome sequencing data to validate our claims. Our project fills up the knowledge gap about the effect of histone mutation in tumour progression in pediatric brain cancer.
- [Optimizing radiation for ATRT: Understanding the implications of dose and volume on outcomes](https://cbtn.org/projects/optimizing-radiation-for-atrt-understanding-the-implications-of-dose-and-volume-on-outcomes/) - This is a clinical retrospective study of children with ATRT assessing the impact of radiation on survival outcomes in all patients and across different methylation subgroups.
- [Genome-wide Sequencing to Identify the Genes Responsible for Enchondromatoses and Related Malignant Tumors](https://cbtn.org/projects/genome-wide-sequencing-to-identify-the-genes-responsible-for-enchondromatoses-and-related-malignant-tumors/) - We will access tumor (and corresponding non-tumor tissue) WGS data from 829 patients from the Pediatric Brain Tumor Atlas and investigate these data for variants in HIF-1 related genes including our preliminary HIF-1 related candidate genes. Data will be accessed through the Gabriella Miller Kids First Pediatric Research Program Data Resource Center and CAVATICA.
- [Paediatric Brain Tumour Classification and Segmentation](https://cbtn.org/projects/paediatric-brain-tumour-classification-and-segmentation/) - It's just for our final year project to complete our bachelor's in computer science. We just need MRI images of children with or without brain tumors so we can apply machine-learning algorithms to those images. We don't need any kind of information at all apart from MRI images
- [Developing Novel Precision Medicine for Glioblastoma](https://cbtn.org/projects/developing-novel-precision-medicine-for-glioblastoma/) - Glioblastoma (GBM) demonstrates some of the worst survival outcomes, likely due to poor clinical predictive information and limited treatment options. We have developed a clinical test for adult GBM that can predict the risk of tumor advancement based on the activity of the patient's own genes. Our goal is to investigate if this clinical test
- [Is KIF20A overexpressed in pediatric high-grade glioma?](https://cbtn.org/projects/is-kif20a-overexpressed-in-pediatric-high-grade-glioma/) - I would like to analyze data from patients with pediatric high-grade glioma to determine whether a novel drug, a small molecule inhibitor of the protein MKLP2, is likely to be effective.
- [Comparing gene expression patterns in high v low grade gliomas to understand drivers of tumor cell invasion.](https://cbtn.org/projects/comparing-gene-expression-patterns-in-high-v-low-grade-gliomas-to-understand-drivers-of-tumor-cell-invasion/) - We aim to identify genes that are differentially expressed in high v low grade gliomas and tumor numbers for this analysis at one institution are too low to make meaningful conclusions.
- [Characterizing the molecular landscape of pediatric and adult meningiomas](https://cbtn.org/projects/characterizing-the-molecular-landscape-of-pediatric-and-adult-meningiomas/) - I would include these data after dimension reduction analysis in our oncoscape platform (oncoscape.org) to identify molecular determinants of cancer severity and progression that could aid in the diagnosis and treatment of brain tumors.
- [Characterization of pediatric CNS tumors using nanopore sequencing](https://cbtn.org/projects/characterization-of-pediatric-cns-tumors-using-nanopore-sequencing/) - CBTN tissue is crucial for this project, as all pediatric brain tumor specimens are quite rare. While the Lineberger CCC at UNC-Chapel Hill has a tissue repository, it has only recently been amended to include pediatric CNS tumors. Therefore, we simply do not have enough samples internally to investigate this novel diagnostic platform. In addition
- [Developing Deep-Learning Approaches for the Automated Segmentation of Pediatric Tumors on Multi-Modal MRI Sequences](https://cbtn.org/projects/developing-deep-learning-approaches-for-the-automated-segmentation-of-pediatric-tumors-on-multi-modal-mri-sequences/) - My project will aim to develop machine-learning methods for the automated segmentation of pediatric brain tumors. The CBTN would be of invaluable assistance if they could share some pediatric brain tumor MRI scans to widen my dataset, and if the CBTN is in posession Ground Truth masks for those pediatric scans then I would be
- [Validation of a transcriptomic biomarker of pediatric meningioma outcomes and radiotherapy response](https://cbtn.org/projects/validation-of-a-transcriptomic-biomarker-of-pediatric-meningioma-outcomes-and-radiotherapy-response/) - We have developed a test using RNA from meningioma patients' tumors which can help physicians predict how likely a tumor is to come back after surgery, and whether a patient is likely to benefit from radiation therapy or not. We propose to use data from the CBTN's unique collection of pediatric meningioma cases to investigate
- [BRATS validation study/no public access](https://cbtn.org/projects/brats-validation-study-no-public-access/) - I am collaborating with MICCAI brain tumor segmentation challenge (BraTS) as a co-organizer for pediatric population analysis. The aim of the challenge is to evaluate the performance of algorithms developed for segmentation of adult brain tumors on pediatric data. The validation data (pediatric images) will not be publicly or privately shared outside of BraTS organizing
- [Factors Associated with High Incidence of Pediatric Bran and Central Nervous System Tumors in Kentucky](https://cbtn.org/projects/factors-associated-with-high-incidence-of-pediatric-bran-and-central-nervous-system-tumors-in-kentucky/) - Germline data will be used to compare cohorts of Kentucky subjects, which are only having germline sequencing done recently, with subjects from CBTN in order to understand the sequencing further. To help compare the data found through the sequencing of Kentucky subjects, the group would like to utilize the germline sequencing from the CBTN in
- [Posterior Fossa Deep Learning Model Validation](https://cbtn.org/projects/posterior-fossa-deep-learning-model-validation/) - We have developed a model for automatic segmentation and classification of posterior fossa ependymomas and their respective subtypes. We are aiming to use the CHOP cohort as an external validation subset to ensure our model performs well on non-Hopkins datasets/patients.
- [Regulation and Function of Circular RNAs in Atypical Teratoid Rhabdoid Tumor](https://cbtn.org/projects/regulation-and-function-of-circular-rnas-in-atypical-teratoid-rhabdoid-tumor/) - CBTN request is vital to our study as it will grant us the opportunity of harnessing the enormous ATRT genomic dataset available in CBTN archive. In addition, in future studies we hope to access these highly valuable and rare clinical samples. All of these will support our study’s progress immensely.
- [Mathematical modelling of drug delivery in brain tumour using thermosensitive hydrogel](https://cbtn.org/projects/mathematical-modelling-of-drug-delivery-in-brain-tumour-using-thermosensitive-hydrogel/) - This project is to use mathematical model to simulate the drug distribution in brain tumour using thermosensitive hydrogel.
- [Exploring microbial signatures in childhood tumors](https://cbtn.org/projects/exploring-microbial-signatures-in-childhood-tumors/) - The microbiome has been steadily gaining attention for its relation to human disease and could be one of the hidden factors that leads to childhood brain tumors. This study will leverage the unique and valuable dataset in CBTN to identify microorganism composition and integrate it with clinical and genomics data. Our findings can help identify
- [PDGFRA expression in K27M gliomas](https://cbtn.org/projects/pdgfra-expression-in-k27m-gliomas/) - The CBTN dataset is thorough and comprehensive, as well as rich in clinical metadata. This will allow us to integrate genomic and expression information in order to help justify the use of PDGFRA targeted therapy in H3K27M high grade gliomas.
- [Multi-institutional analysis of recurrent central nervous system germinomas](https://cbtn.org/projects/multi-institutional-analysis-of-recurrent-central-nervous-system-germinomas/) - Recurrence of central nervous system germinomas is rare; reports have been limited to within larger clinical trials and cohorts. To our knowledge, there has not been a multi-institutional study that includes only patients with central nervous system germinomas. Analysis of a retrospective cohort that includes patients from across multiple institutions and different treatment protocols may
- [Using histopathology to discover genetic alterations in pediatric brain tumors](https://cbtn.org/projects/using-histopathology-to-discover-genetic-alterations-in-pediatric-brain-tumors/) - In depth understanding of the molecular make up of brain tumors is critical to inform therapy decision making. Often tumor tissue is limited for this type of analysis and it will be very beneficial to derive detail molecular information from basic pathology slides. Herein we aim to use machine learning to develop such program that
- [Investigating the etiology of genomic rearrangements in human cancers](https://cbtn.org/projects/investigating-the-etiology-of-genomic-rearrangements-in-human-cancers/) - Pediatric cancers are highly enriched with leukemias. We have enrolled >3000 leukemia samples. On the other hand, brain tumors and solid tumors are underrepresented due to lower incidence rate (we currently have ~1500 pediatric brain tumor/solid tumor samples). The addition of 867 brain tumors from CBTN will enhance our power of discovery and also allow
- [Germline determinants of the pediatric tumor immune microenvironment](https://cbtn.org/projects/germline-determinants-of-the-pediatric-tumor-immune-microenvironment/) - While immunotherapy shows promise for treating tumors, progress in the pediatric setting has been slow. Our porposal will investigate the role of heritable genetic variation in promoting an immune suppressed microenvironment in pediatric tumors. These studies will provide insight into barriers to immunotherapy unique to the pediatric setting, and inform future strategies to adapt these
- [Synthetic trial of everolimus in recurrent pediatric LGG patients](https://cbtn.org/projects/synthetic-trial-of-everolimus-in-recurrent-pediatric-lgg-patients/) - Within this project we aim to assess how the CBTN dataset compares to a prospectively performed trial via PNOC. We are looking to assess the images and determine the PFS of pediatric LGG patients via central imaging review and compare results to the clinical trial PNOC001.
- [Molecular signatures underlying radiation resistance in diffuse midline gliomas](https://cbtn.org/projects/molecular-signatures-underlying-radiation-resistance-in-diffuse-midline-gliomas/) - The CBTN clinical data will enhance existing understanding of the role of radiotherapy in treating diffuse midline gliomas
- [Automatic segmentation of radiosentitive brain structure in pediatric patients with CNS tumor](https://cbtn.org/projects/automatic-segmentation-of-radiosentitive-brain-structure-in-pediatric-patients-with-cns-tumor/) - We realise that most CBTN projects are related to genomics while our research is more focused on technical properties/ image analysis. However, it has proven extremely challenging to find a large and varied dataset of images of pediatric patients with CNS tumours, As such, the imaging data in CBTN would be extremely helpful for our
- [Pediatric brain tumor image analytics using AI](https://cbtn.org/projects/pediatric-brain-tumor-image-analytics-using-ai/) - The overall objective of the research is to analyze the pediatric brain tumor radiology and histology images using artificial intelligence (AI) to predict the diagnosis and perform detailed segmentation in the images.
- [Mechanistic-based DIPG precision therapy](https://cbtn.org/projects/mechanistic-based-dipg-precision-therapy/) - The data request is placed to identify the detected somatic mutation in the patient from whom the cell line was derived. At the current moment, we only know a short report of the genetic alterations reported in this patient’s tumor. However, getting to know all the somatic mutations that were detected in this tumor will
- [TRK fusion primary CNS tumors](https://cbtn.org/projects/trk-fusion-primary-cns-tumors/) - We believe that CBTN contains the world’s largest dataset of patients with primary CNS tumors known to harbor NTRK1/2/3 fusions.
- [3D U-Net Segmentation Network for Measurement and Characterization of Pediatric Low-Grade Gliomas](https://cbtn.org/projects/3d-u-net-segmentation-network-for-measurement-and-characterization-of-pediatric-low-grade-gliomas/) - While our group has ongoing work with pediatric low-grade gliomas at our institution, the CBTN dataset of low-grade gliomas is unique in that it combined imaging, genetic, and clinical information into one organized dataset, with a large group of patients. Given the requirements of artificial intelligence algorithms for large datasets, the CBTN forms an optimal
- [Predicting distant metastasis and chemotherapy benefit in pediatric brain cancer](https://cbtn.org/projects/predicting-distant-metastasis-and-chemotherapy-benefit-in-pediatric-brain-cancer/) - Not all pediatric patients can benefit from adjuvant chemotherapy, and particularly, some pediatric patients may even get worse outcomes after the treatment. The aim of our research is to develop and validate an MRI-based artificial intelligence model for the prediction of chemotherapy benefits within a multi-center dataset. The artificial intelligence model is to discriminate pediatric
- [Morphological Molecular Correlation of Pediatric Brain Tumors](https://cbtn.org/projects/morphological-molecular-correlation-of-pediatric-brain-tumors/) - Brain tumors are traditionally diagnosed and classified according to their characteristics under the microscopic examination. Recent advances in science allowed for the classification of these tumors according to their genetic alteration but no such comparable advances happened to the traditional microscopic features. This study aimed to fill the gap between these 2 modalities for better
- [Investigating the Role of ERV Expression in Ependymoma](https://cbtn.org/projects/investigating-the-role-of-erv-expression-in-ependymoma/) - To understand the processes that regulate gene expression in a pediatric brain tumor called ependymoma.
- [DEI Ancestry Project](https://cbtn.org/projects/dei-ancestry-project/) - We will use genomic data to identify ancestry of individual patients and compare to clinical characteristics/outcomes and self reported race and ethnicity.
- [The Radiogenomics of Molecularly-defined Pediatric Brain Tumors](https://cbtn.org/projects/the-radiogenomics-of-molecularly-defined-pediatric-brain-tumors/) - I am working on characterizing the qualitative and quantitative imaging features of molecularly-defined pediatric brain tumor types as described in the WHO CNS5, specifically ependymomas, pediatric-type low grade diffuse gliomas, and pediatric-type high grade diffuse gliomas.
- [Comparison of RNA-binding protein expressions in pediatric and adult glioblatstoma](https://cbtn.org/projects/comparison-of-rna-binding-protein-expressions-in-pediatric-and-adult-glioblatstoma/) - We will select RNA-binding protein genes of interest and check their expression levels in RNA-seq data.
- [Growth hormone signaling in craniopharyngioma](https://cbtn.org/projects/growth-hormone-signaling-in-craniopharyngioma/) - To our knowledge, there is no other existing craniopharyngioma dataset with available RNA specimens and/or existing RNA expression profiles. This work is important to improving clinical care for our patient population, but is solely unique to the large dataset of genomic and phenotypic characteristics that CBTN provides.
- [Methylation profiling of pediatric CNS tumors to define molecular subtype-specific signatures](https://cbtn.org/projects/methylation-profiling-of-pediatric-cns-tumors-to-define-molecular-subtype-specific-signatures/) - Despite the emerging utility of tumor methylation profiling for diagnosis, and for identification of clinically relevant molecular changes, much of the biology of the DNA methylation landscape across pediatric tumors of the central nervous system remain unexplored. Especially contributons of the immune system which can be monitored via DNA methylation is of increasing importance given
- [Targeting histone H3K4me3 for the treatment of pediatric gliomas](https://cbtn.org/projects/targeting-histone-h3k4me3-for-the-treatment-of-pediatric-gliomas/) - Pediatric high-grade gliomas (pHGGs) are a fatal childhood cancer of the brain. Deregulation of specific histone modifications, both with and without a direct link to specific mutations, have been identified in these tumors. This project will investigate histone H3 post-translational modifications (PTMs) in pHGGs to advance our understanding of tumor development and understanding of biologic
- [Genetic risk factors for pediatric brain tumors](https://cbtn.org/projects/genetic-risk-factors-for-pediatric-brain-tumors/) - We are studying if and how germline genetic factors increase the risk of developing a tumor in childhood.
- [Radiogenomic Analysis of Pediatric Brain Tumors](https://cbtn.org/projects/radiogenomic-analysis-of-pediatric-brain-tumors/) - Our goal is to identify approaches using machine learning that can reliably integrate imaging, histopathological, and molecular data for improved disease subtype stratification and to identify alternative treatment options for pediatric tumors with poor prognosis
- [The landscape of pediatric RTK-driven gliomas](https://cbtn.org/projects/the-landscape-of-pediatric-rtk-driven-gliomas/) - Oncogenic fusions involving receptor tyrosine kinases (RTK) provide an excellent opportunity for therapeutic targeting but the clinical and molecular landscape of pediatric RTK-driven gliomas remains largely uncharted. To define clinically-relevant tumor subgroups and assess their prognostic significance, we will evaluate the correlation between molecular and clinical characteristics. This project will provide mechanistic insights into RTK-fused
- [DIPG International Prevalence of Germline Mutations (DIPG-M)](https://cbtn.org/projects/dipg-international-prevalence-of-germline-mutations-dipg-m/) - DIPG and DMG are devastating brain cancers of childhood, but little is known about why these cancers form. This study will investigate whether genetic factors contribute to the formation of these cancers. The results of this study will inform genetic testing in the clinic, and may point to new therapies for these very difficult cancers.
- [Correlating genomic features with the immune microenvironment in pediatric glioma](https://cbtn.org/projects/correlating-genomic-features-with-the-immune-microenvironment-in-pediatric-glioma/) - It is critical that we understand what immune phenotypes may be present based on immunogenomic profiling and it does not make sense to recollect and process new cases especially when limited to only one center. This will also help to decide the final panel to stain for qmIF. In review of cases from CUIMC we
- [Molecular Mechanisms and Functional Impact of Aberrant Splicing in Diffuse Midline Gliomas](https://cbtn.org/projects/molecular-mechanisms-and-functional-impact-of-aberrant-splicing-in-diffuse-midline-gliomas/) - We propose integrating large-scale multi-omics datasets with RNA splicing algorithms to elucidate mechanisms of alternative splicing dysregulation underlying DMG tumorigenesis with the goal of identifying novel therapeutic targets for this disease.
- [Characterizing the blood-brain-barrier in pediatric brain tumors](https://cbtn.org/projects/characterizing-the-blood-brain-barrier-in-pediatric-brain-tumors/) - Because these tumors are very rare, the CBTN is an invaluable resource for studying these diseases. Furthermore, the genomic resources for pediatric brain tumors are incomparable. We will include all patients with MRI available within the CBTN (n=243) for preliminary analysis, though only those with T1 pre-contrast, T1 post-contrast, and T2-FLAIR sequences will be included
- [Landscape of germline histone mutations in pediatric brain tumor patients](https://cbtn.org/projects/landscape-of-germline-histone-mutations-in-pediatric-brain-tumor-patients/) - Recent studies have identified a link between germline histone mutations and an increased risk for developmental and neurological disorders, however few studies have investigated the landscape of germline histone mutations in diffuse midline glioma (DMG) and other pediatric CNS tumors. We propose to address this gap by investigating germline mutations affecting histone-encoding genes in pediatric
- [A Comparison of Hallmark Mutations in Pediatric and Adult Brain Tumors](https://cbtn.org/projects/a-comparison-of-hallmark-mutations-in-pediatric-and-adult-brain-tumors/) - The WHO classification of brain tumors puts heavy emphasis on the molecular genetics that drive the pathogenesis of these tumors. It is still unclear if there are other genetic targets that could be targeted with novel therapies. We are interested in different genomic factors that drive the pathogenesis of these tumors in hopes of finding
- [Development of a new therapy against Diffuse Intrinsic Pontine Glioma](https://cbtn.org/projects/development-of-a-new-therapy-against-diffuse-intrinsic-pontine-glioma/) - Diffuse intrinsic pontine glioma (DIPG) is a rare childhood brain cancer that is fatal in over 99% of all cases. We believe that ion channels, pore-forming proteins that move chemicals like calcium and potassium in and out of cells, have a role in drug resistance. WE will use this data to determine what ion channels
- [Identification of novel therapeutic approaches for paediatric high-grade gliomas](https://cbtn.org/projects/identification-of-novel-therapeutic-approaches-for-paediatric-high-grade-gliomas/) - We are planning to use a combination of mouse and patient-derived models to identify novel therapeutic approaches for pHGGs.
- [Leveraging existing pediatric low-grade tumor specimens, clinical and imaging outcome data and artificial intelligence innovations to develop integrated biomarkers of response for children with low-grade glioma](https://cbtn.org/projects/leveraging-existing-pediatric-low-grade-tumor-specimens-clinical-and-imaging-outcome-data-and-artificial-intelligence-innovations-to-develop-integrated-biomarkers-of-response-for-children-with-low-g-2/) - This study will utilize artificial intelligence algorithms to predict underlying mutational status and outcomes for pediatric low grade glioma based on complex brain tumor MRI imaging features.
- [Analyze the relationship between the expression of specific genes and the prognosis in pediatric gliomas.](https://cbtn.org/projects/analyze-the-relationship-between-the-expression-of-specific-genes-and-the-prognosis-in-pediatric-gliomas-2/) - The protein encoded by SETD1A (SET Domain Containing 1A, Histone Lysine Methyltransferase) is a component of a histone methyltransferase (HMT) complex that produces mono-, di-, and trimethylated histone H3 at Lys4. Literatures have found that SETD1A is required for survival of acute myeloid leukemia (AML) cells. H3K4me3 levels positively correlate with WHO grade malignancy in
- [Integrative analyses of data as part of the CFDE](https://cbtn.org/projects/integrative-analyses-of-data-as-part-of-the-cfde/) - As part of the Common Fund Data Ecosystem (CFDE) we will be performing comparisons of datasets across Common Fund projects with a goal of enhancing integrative and cloud-based analyses of these data. We will assess whether and to what extent harmonization of metadata fields might help searching across datasets, and whether harmonization of raw data
- [Immune receptor recombinations in childhood brain cancer](https://cbtn.org/projects/immune-receptor-recombinations-in-childhood-brain-cancer/) - Project is designed to further understand the impact of the immune system on childhood brain cancers.
- [Survival outcome of iMB treated without adjuvant craniospinal irradiation: a pooled data analysis in the molecular era](https://cbtn.org/projects/survival-outcome-of-imb-treated-without-adjuvant-craniospinal-irradiation-a-pooled-data-analysis-in-the-molecular-era/) - We wish to describe the progression-free survival and overall survival of infants and young children with molecularly characterized medulloblastoma treated without upfront CSI. In addition, we wishe to describe the potential prognostics factors including clinical, treatment intensity, molecular subgroup, molecular subtype, and pathologic variables associated with progression-free survival. Finally, we wish to describe the pattern

## Publications

- [EZHIP Boosts Neuronal-Like Synaptic Gene Programs And Depresses Polyamine Metabolism](https://cbtn.org/publications/ezhip-boosts-neuronal-like-synaptic-gene-programs-and-depresses-polyamine-metabolism/) - It is currently understood that the characteristic loss of the repressive histone mark H3K27me3 in PFA ependymoma and diffuse midline glioma (DMG) are caused by complementary mechanisms mediated by EZHIP and the oncohistone H3K27M, respectively. To support the complementarity of these mechanisms, rare H3K27M-negative DMGs express EZHIP. Interestingly, EZHIP is one of the few genes
- [The Social Deprivation Index And Deep Brain Stimulation: A Cohort Study](https://cbtn.org/publications/the-social-deprivation-index-and-deep-brain-stimulation-a-cohort-study/) - Deep brain stimulation (DBS) is an important treatment option for patients with movement disorders; however, prior studies have demonstrated inequitable access to this important treatment. We used the Social Deprivation Index (SDI), an index of neighborhood affluence, to examine the distribution of DBS cases and to determine the association between the SDI and outcomes.
- [Utility Of Ultrasound In The Diagnosis And Management Of A Radial Nerve Perineurioma In A Pediatric Patient](https://cbtn.org/publications/utility-of-ultrasound-in-the-diagnosis-and-management-of-a-radial-nerve-perineurioma-in-a-pediatric-patient/) - Intraneural perineuriomas are tumors originating from the perineurial cells surrounding nerve sheath fascicles. Intraneural perineuriomas represent about 1% of peripheral nerve tumors and are often misdiagnosed due to their rarity. In this case, we report a pediatric patient with a radial nerve perineurioma, in which ultrasound played a key role in diagnosis.
- [Detailed Analysis Of Hydrocephalus Patterns And Associated Variables In Patients After Open Fetal Repair And Postnatal Myelomeningocele/Myeloschisis Closure](https://cbtn.org/publications/detailed-analysis-of-hydrocephalus-patterns-and-associated-variables-in-patients-after-open-fetal-repair-and-postnatal-myelomeningocele-myeloschisis-closure/) - Myelomeningocele (MMC) and myeloschisis (MS) are severe neural tube defects that result in neurodevelopmental impairments and hydrocephalus due to prenatal spinal cord exposure to amniotic fluid. Fetal MMC/MS (fMMC/MS) repair has become the standard of care in appropriately selected patients, demonstrating improved outcomes, including a reduction in the need for cerebrospinal fluid (CSF) diversion compared
- [Interictal Spikes And Evoked Cortical Potentials Share Common Spatiotemporal Constraints In Human Epilepsy](https://cbtn.org/publications/interictal-spikes-and-evoked-cortical-potentials-share-common-spatiotemporal-constraints-in-human-epilepsy/) - Interictal epileptiform discharges (IEDs) are pathologic hallmarks of epilepsy which frequently arise and spread through networks of functionally-connected brain regions. Recent studies demonstrate that the sequential recruitment of brain regions by propagating IEDs is highly conserved across repeated discharges, suggesting that IED propagation is spatiotemporally constrained by features of the underlying epileptic network.
- [Germline Pathogenic Variation Impacts Somatic Alterations And Patient Outcomes In Pediatric Central Nervous System Tumors](https://cbtn.org/publications/germline-pathogenic-variation-impacts-somatic-alterations-and-patient-outcomes-in-pediatric-central-nervous-system-tumors/) - The contribution of rare pathogenic/likely pathogenic (P/LP) germline variants to pediatric central nervous system (CNS) tumor development remains understudied. Here, we characterized the prevalence and clinical significance of germline P/LP variants in cancer predisposition genes across 830 CNS tumor patients from the Pediatric Brain Tumor Atlas (PBTA).
- [Germline Structural Variations Involving The Pediatric Brain Tumor Transcriptome Include Disease-Relevant And Ancestry-Related Genes](https://cbtn.org/publications/germline-structural-variations-involving-the-pediatric-brain-tumor-transcriptome-include-disease-relevant-and-ancestry-related-genes/) - Germline Structural Variants (SVs) represent an important source of genetic diversity, in large part due to their influence on gene transcription. It is necessary to systematically catalog germline SVs and their associated impacted genes across different cohorts and tissue and cellular contexts, including pediatric brain or Central Nervous System (CNS) tumors.
- [The Open Pediatric Cancer Project](https://cbtn.org/publications/the-open-pediatric-cancer-project/) - In 2019, the Open Pediatric Brain Tumor Atlas (OpenPBTA) was created as a global, collaborative open-science initiative to genomically characterize 1,074 pediatric brain tumors and 22 patient-derived cell lines. Here, we present an extension of the OpenPBTA called the Open Pediatric Cancer (OpenPedCan) Project, a harmonized open-source multiomic dataset from 6,112 pediatric cancer patients with
- [NRCAM Variant Defined By Microexon Skipping Is A Targetable Cell Surface Proteoform In High-Grade Gliomas](https://cbtn.org/publications/nrcam-variant-defined-by-microexon-skipping-is-a-targetable-cell-surface-proteoform-in-high-grade-gliomas-2/) - To overcome the paucity of known tumor-specific surface antigens in pediatric high-grade glioma (pHGG), we contrasted splicing patterns in pHGGs and normal brain samples. Among alternative splicing events affecting extracellular protein domains, the most pervasive alteration was the skipping of ≤30-nt-long exons.
- [Claudin 6 Is A Suitable Target For Car T-Cell Therapy In Atypical Teratoid/Rhabdoid Brain Tumors And Other Pediatric Solid Tumors](https://cbtn.org/publications/claudin-6-is-a-suitable-target-for-car-t-cell-therapy-in-atypical-teratoid-rhabdoid-brain-tumors-and-other-pediatric-solid-tumors/) - Solid tumors comprise approximately 60% of all pediatric cancers. Relapsed or refractory tumors of the central nervous system (CNS), such as atypical teratoid/rhabdoid tumors (AT/RTs), are the leading cause of death in children with cancer. Claudin 6 (CLDN6)-specific chimeric antigen receptor (CAR) T cells have demonstrated activity in preclinical and clinical studies in various solid
- [Artificial Intelligence For Response Assessment In Pediatric Neuro-Oncology (Ai-Rapno), Part 1: Review Of The Current State Of The Art](https://cbtn.org/publications/artificial-intelligence-for-response-assessment-in-pediatric-neuro-oncology-ai-rapno-part-1-review-of-the-current-state-of-the-art/) - Artificial intelligence (AI) has the potential to enable more precise, efficient, and reproducible interpretation of medical imaging data to improve patient care in paediatric neuro-oncology. Paediatric brain tumours present distinct histopathological, molecular, and clinical challenges that require tailored AI solutions.
- [Artificial Intelligence For Response Assessment In Pediatric Neuro-Oncology (Ai-Rapno), Part 2: Challenges, Opportunities, And Recommendations For Clinical Translation](https://cbtn.org/publications/artificial-intelligence-for-response-assessment-in-pediatric-neuro-oncology-ai-rapno-part-2-challenges-opportunities-and-recommendations-for-clinical-translation/) - The Response Assessment in Pediatric Neuro-Oncology (RAPNO) criteria provide an important framework for evaluating treatment efficacy and tumour progression in clinical studies of paediatric brain tumours. As artificial intelligence (AI) rapidly transforms clinical practice, integrating AI into the RAPNO framework presents a unique opportunity to enhance quantitative, data-driven approaches for response assessment.
- [Role Of Repulsive Guidance Signaling And Gpr180 In Pediatric Low-Grade Glioma Infiltration](https://cbtn.org/publications/role-of-repulsive-guidance-signaling-and-gpr180-in-pediatric-low-grade-glioma-infiltration/) - Pediatric low-grade gliomas (pLGGs) are the most common brain tumors in children with varying degrees of infiltration. Despite having a positive prognosis, if the standard treatment, gross total resection, is impossible due to tumor location or diffuseness, outcomes worsen. Development of targeted therapeutics for diverse subtypes of pLGGs is limited by a lack of genetic
- [Germline Pathogenic Variation Impacts Somatic Alterations And Patient Outcomes In Pediatric Central Nervous System Tumors](https://cbtn.org/publications/germline-pathogenic-variation-impacts-somatic-alterations-and-patient-outcomes-in-pediatric-central-nervous-system-tumors-2/) - The contribution of rare pathogenic/likely pathogenic (P/LP) germline variants to pediatric central nervous system (CNS) tumor development remains understudied. Here, we characterize the prevalence and biological significance of germline P/LP variants in cancer predisposition genes across 830 CNS tumor patients from the Pediatric Brain Tumor Atlas (PBTA)
- [Clinical Utility of [F18]-Fluciclovine PET/MRI for Differentiating True Progression from Treatment-Related Changes in Patients with Glioblastoma](https://cbtn.org/publications/clinical-utility-of-f18-fluciclovine-pet-mri-for-differentiating-true-progression-from-treatment-related-changes-in-patients-with-glioblastoma/) - Differentiating true progression from treatment-related changes in patients with glioblastoma (GBM) remains a major diagnostic challenge. Amino acid PET tracers such as [F18]-Fluciclovine provide biologically specific information, but clinical real-world validation across institutions is limited. We aimed to evaluate the clinical diagnostic performance of [F18]-Fluciclovine PET/MRI for distinguishing true progression from treatment-related change in patients
- [Transient mRNA CAR T Cells Targeting Gd2 Provide Dose-Adjusted Efficacy Against Diffuse Midline Glioma And High Grade Glioma Models](https://cbtn.org/publications/transient-mrna-car-t-cells-targeting-gd2-provide-dose-adjusted-efficacy-against-diffuse-midline-glioma-and-high-grade-glioma-models/) - Transient mRNA CAR T cells targeting GD2 provide dose-adjusted efficacy against diffuse midline glioma and high grade glioma models.
- [Genetic Ancestry Superpopulations Show Distinct Prevalence And Outcomes Across Pediatric Central Nervous System Tumors From The Pediatric Brain Tumor Atlas And Pediatric Neuro-Oncology Consortium](https://cbtn.org/publications/genetic-ancestry-superpopulations-show-distinct-prevalence-and-outcomes-across-pediatric-central-nervous-system-tumors-from-the-pediatric-brain-tumor-atlas-and-pediatric-neuro-oncology-consortium/) - Genetic ancestry superpopulations show distinct prevalence and outcomes across pediatric central nervous system tumors from the Pediatric Brain Tumor Atlas and Pediatric Neuro-Oncology Consortium.
- [Empowering Data Sharing in Neuroscience: A Deep Learning Deidentification Method for Pediatric Brain MRIs](https://cbtn.org/publications/empowering-data-sharing-in-neuroscience-a-deep-learning-deidentification-method-for-pediatric-brain-mris/) - Empowering Data Sharing in Neuroscience: A Deep Learning Deidentification Method for Pediatric Brain MRIs.
- [Evaluating the Potential of PSMA Targeting in CNS Tumors: Insights from Large-Scale Transcriptome Profiling](https://cbtn.org/publications/evaluating-the-potential-of-psma-targeting-in-cns-tumors-insights-from-large-scale-transcriptome-profiling/) - Prostate-specific membrane antigen (PSMA) is a well-established target in prostate cancer therapy that has shown potential as a theranostic target across non-central nervous system (CNS) and CNS tumor types. We aimed to investigate the pan-tissue expression pattern of the PSMA-encoding gene FOLH1 to assess whether transcriptome profiling can inform tumor diagnostic and theranostic probes.
- [Measles Oncolytic Virus as an Immunotherapy for Recurrent/Refractory Pediatric Medulloblastoma and Atypical Teratoid/Rhabdoid Tumor: Results from PNOC005](https://cbtn.org/publications/measles-oncolytic-virus-as-an-immunotherapy-for-recurrent-refractory-pediatric-medulloblastoma-and-atypical-teratoid-rhabdoid-tumor-results-from-pnoc005/) - Pediatric recurrent medulloblastoma and atypical teratoid/rhabdoid tumor (ATRT) are largely incurable and warrant novel therapies. PNOC005 is a phase I clinical trial investigating the safety and tolerability of intratumoral or intrathecal administration of oncolytic measles virus (MV-NIS) in children and young adults with recurrent medulloblastoma or ATRT.
- [Longitudinal Risk Prediction for Pediatric Glioma with Temporal Deep Learning](https://cbtn.org/publications/longitudinal-risk-prediction-for-pediatric-glioma-with-temporal-deep-learning/) - Pediatric glioma recurrence can cause morbidity and mortality; however, recurrence patterns and severity are heterogeneous and challenging to predict with established clinical and genomic markers. As a result, almost all children undergo frequent, long-term, magnetic resonance imaging (MRI) brain surveillance regardless of individual recurrence risk. Longitudinal deep-learning analysis of serial MRI scans may be an
- [The DNA Methylome Of Pediatric Brain Tumors Appears Shaped By Structural Variation And Predicts Survival](https://cbtn.org/publications/the-dna-methylome-of-pediatric-brain-tumors-appears-shaped-by-structural-variation-and-predicts-survival/) - Structural variation heavily influences the molecular landscape of cancer, in part by impacting DNA methylation-mediated transcriptional regulation. Here, using multi-omic datasets involving >2400 pediatric brain and central nervous system tumors of diverse histologies from the Children's Brain Tumor Network, we report hundreds of genes and associated CpG islands (CGIs) for which the nearby presence of
- [Stepwise Transfer Learning for Expert-level Pediatric Brain Tumor MRI Segmentation in a Limited Data Scenario](https://cbtn.org/publications/stepwise-transfer-learning-for-expert-level-pediatric-brain-tumor-mri-segmentation-in-a-limited-data-scenario/) - Purpose To develop, externally test, and evaluate clinical acceptability of a deep learning pediatric brain tumor segmentation model using stepwise transfer learning. Materials and Methods In this retrospective study, the authors leveraged two T2-weighted MRI datasets (May 2001 through December 2015) from a national brain tumor consortium (n = 184; median age, 7 years [range,
- [The Landscape Of Primary Mismatch Repair Deficient Gliomas In Children, Adolescents, And Young Adults: A Multi-Cohort Study](https://cbtn.org/publications/the-landscape-of-primary-mismatch-repair-deficient-gliomas-in-children-adolescents-and-young-adults-a-multi-cohort-study/) - Gliomas are a major cause of cancer-related death among children, adolescents, and young adults (age 0-40 years). Primary mismatch repair deficiency (MMRD) is a pan-cancer mechanism with unique biology and therapeutic opportunities. We aimed to determine the extent and impact of primary MMRD in gliomas among children, adolescents, and young adults.
- [Germline Analysis Of An International Cohort Of Pediatric Diffuse Midline Glioma Patients](https://cbtn.org/publications/germline-analysis-of-an-international-cohort-of-pediatric-diffuse-midline-glioma-patients/) - Factors that drive the development of diffuse midline gliomas (DMG) are unknown. Our study aimed to determine the prevalence of pathogenic/likely pathogenic (P/LP) germline variants in pediatric patients with DMG.
- [Clinical Characteristics and Outcomes of Central Nervous System Tumors Harboring NTRK Gene Fusions](https://cbtn.org/publications/clinical-characteristics-and-outcomes-of-central-nervous-system-tumors-harboring-ntrk-gene-fusions/) - Tropomyosin receptor kinase (TRK) fusions are detected in less than 2% of central nervous system tumors. There are limited data on the clinical course of affected patients.
- [NRCAM Variant Defined By Microexon Skipping Is A Targetable Cell Surface Proteoform In High-Grade Gliomas](https://cbtn.org/publications/nrcam-variant-defined-by-microexon-skipping-is-a-targetable-cell-surface-proteoform-in-high-grade-gliomas/) - To overcome the paucity of known tumor-specific surface antigens in pediatric high-grade glioma (pHGG), we contrasted splicing patterns in pHGGs and normal brain samples. Among alternative splicing events affecting extracellular protein domains, the most pervasive alteration was the skipping of ≤30-nt-long exons.
- [Automated Pediatric Brain Tumor Imaging Assessment Tool From CBTN: Enhancing Suprasellar Region Inclusion And Managing Limited Data With Deep Learning](https://cbtn.org/publications/automated-pediatric-brain-tumor-imaging-assessment-tool-from-cbtn-enhancing-suprasellar-region-inclusion-and-managing-limited-data-with-deep-learning/) - Fully automatic skull-stripping and tumor segmentation are crucial for monitoring pediatric brain tumors (PBT). Current methods, however, often lack generalizability, particularly for rare tumors in the sellar/suprasellar regions and when applied to real-world clinical data in limited data scenarios. To address these challenges, we propose AI-driven techniques for skull-stripping and tumor segmentation.
- [A Longitudinal Single-Cell And Spatial Multiomic Atlas Of Pediatric High-Grade Glioma](https://cbtn.org/publications/a-longitudinal-single-cell-and-spatial-multiomic-atlas-of-pediatric-high-grade-glioma/) - Pediatric high-grade glioma (pHGG) is an incurable central nervous system malignancy that is a leading cause of pediatric cancer death. While pHGG shares many similarities to adult glioma, it is increasingly recognized as a molecularly distinct, yet highly heterogeneous disease.
- [Characterization Of Aberrant Splicing In Pediatric Central Nervous System Tumors Reveals Clk1 As A Candidate Oncogenic Dependency](https://cbtn.org/publications/characterization-of-aberrant-splicing-in-pediatric-central-nervous-system-tumors-reveals-clk1-as-a-candidate-oncogenic-dependency/) - Pediatric brain cancer is the leading cause of disease-related mortality in children, yet many aggressive tumors lack effective therapies. Aberrant RNA splicing is a hallmark of cancer, but its role in pediatric central nervous system (CNS) tumors remains underexplored.
- [Training And Comparison Of Nnu-Net And Deepmedic Methods For Autosegmentation Of Pediatric Brain Tumors](https://cbtn.org/publications/training-and-comparison-of-nnu-net-and-deepmedic-methods-for-autosegmentation-of-pediatric-brain-tumors/) - Tumor segmentation is essential in surgical and treatment planning and response assessment and monitoring in pediatric brain tumors, the leading cause of cancer-related death among children. However, manual segmentation is time-consuming and has high interoperator variability, underscoring the need for more efficient methods. After training, we compared 2 deep-learning-based 3D segmentation models, DeepMedic and nnU-Net,
- [Multiparametric MRI Along With Machine Learning Predicts Prognosis And Treatment Response In Pediatric Low-Grade Glioma](https://cbtn.org/publications/multiparametric-mri-along-with-machine-learning-predicts-prognosis-and-treatment-response-in-pediatric-low-grade-glioma/) - Pediatric low-grade gliomas (pLGGs) exhibit heterogeneous prognoses and variable responses to treatment, leading to tumor progression and adverse outcomes in cases where complete resection is unachievable. Early prediction of treatment responsiveness and suitability for immunotherapy has the potential to improve clinical management and outcomes. Here, we present a radiogenomic analysis of pLGGs, integrating MRI and
- [Imaging Clusters of Pediatric Low-Grade Glioma Are Associated with Distinct Molecular Characteristics](https://cbtn.org/publications/imaging-clusters-of-pediatric-low-grade-glioma-are-associated-with-distinct-molecular-characteristics/) - Cancers show heterogeneity at various levels, from genome to radiologic imaging. This study aimed to explore the interplay between genomic, transcriptomic, and radiophenotypic data in pediatric low-grade glioma (pLGG), the most common group of brain tumors in children.
- [Unilateral Versus Bilateral Endoscopic Resection of Olfactory Neuroblastoma: Pooled Analysis From Prospective and Retrospective Multicenter Data](https://cbtn.org/publications/unilateral-versus-bilateral-endoscopic-resection-of-olfactory-neuroblastoma-pooled-analysis-from-prospective-and-retrospective-multicenter-data/) - Olfactory neuroblastoma (ONB) is a rare sinonasal malignancy primarily treated with surgery. For tumors arising from the olfactory area, traditional treatment involves transcribriform resection of the anterior cranial fossa. Surgery can be performed with unilateral or bilateral resection depending on extent of involvement; however, there are currently no studies comparing outcomes between the two.
- [In Utero Progression Of Cephaloceles: Prenatal To Postnatal Analysis](https://cbtn.org/publications/in-utero-progression-of-cephaloceles-prenatal-to-postnatal-analysis/) - The natural history of cephaloceles is not well understood. The goal of this study was to better understand the natural history of fetal cephaloceles from prenatal diagnosis to the postnatal period.
- [Retrospective Dataset And Survey Analyses Identify Gaps In Data Collection For Craniopharyngioma And Priorities Of Patients And Families Affected By The Disease](https://cbtn.org/publications/retrospective-dataset-and-survey-analyses-identify-gaps-in-data-collection-for-craniopharyngioma-and-priorities-of-patients-and-families-affected-by-the-disease/) - Craniopharyngioma is a rare type of brain tumor located in the suprasellar region of the brain, close to important structures like the pituitary gland. This study aimed to better understand patient outcomes associated with existing therapies and to inform new treatment strategies. Our team collected clinical, genomic, and outcome data from a retrospective cohort of
- [Past, Present And Future Of Focused Ultrasound As An Adjunct Or Complement To Dipg/Dmg Therapy: A Consensus Of The 2021 Fusf Dipg Meeting](https://cbtn.org/publications/past-present-and-future-of-focused-ultrasound-as-an-adjunct-or-complement-to-dipg-dmg-therapy-a-consensus-of-the-2021-fusf-dipg-meeting/) - Diffuse Midline Glioma (DMG) is a type of brain tumor that mainly affects children and has limited treatment options and a poor prognosis. One of the major obstacles to treating DMG is the blood-brain barrier, which prevents most drugs from reaching the tumor. Focused Ultrasound (FUS) is a noninvasive medical technology that has been shown
- [Developing H3K27M Mutant Selective Radiosensitization Strategies In Diffuse Intrinsic Pontine Glioma](https://cbtn.org/publications/developing-h3k27m-mutant-selective-radiosensitization-strategies-in-diffuse-intrinsic-pontine-glioma/) - This study examines a rare and deadly brain tumor called diffuse intrinsic pontine glioma (DIPG), which mainly affects children and teenagers. The current standard of care, which involves radiotherapy, has minimal benefit for DIPG patients, and efforts to combine chemotherapy with radiation therapy have been unsuccessful. However, recent advances in understanding how epigenetics affect the
- [Indigenous Peoples And Inclusion In Clinical And Genomic Research: Understanding The History And Navigating Contemporary Engagement](https://cbtn.org/publications/indigenous-peoples-and-inclusion-in-clinical-and-genomic-research-understanding-the-history-and-navigating-contemporary-engagement/) - The survival rates for pediatric cancer patients have improved significantly, but there are still significant disparities among underrepresented racial and ethnic groups. To address this issue, the Pacific Pediatric Neuro-Oncology Consortium (PNOC) and Children's Brain Tumor Network (CBTN) created a Diversity, Equity, and Inclusion (DEI) working group in 2020. The DEI working group is committed
- [Myxoid Glioneuronal Tumor: Histopathologic, Neuroradiologic, And Molecular Features In A Single Center Series](https://cbtn.org/publications/myxoid-glioneuronal-tumor-histopathologic-neuroradiologic-and-molecular-features-in-a-single-center-series/) - Myxoid glioneuronal tumor (MGT) is a non-cancerous type of brain tumor that was recently added to the World Health Organization (WHO) classification of central nervous system (CNS) tumors. MGTs are usually found in specific areas of the brain, such as the septum pellucidum, foramen of Monro, or periventricular white matter of the lateral ventricle. They
- [Recent Progress And Novel Approaches To Treating Atypical Teratoid Rhabdoid Tumor](https://cbtn.org/publications/recent-progress-and-novel-approaches-to-treating-atypical-teratoid-rhabdoid-tumor/) - Atypical teratoid rhabdoid tumors (AT/RT) are malignant central nervous system (CNS) tumors that occur mostly in young children and have historically carried a very poor prognosis. While recent clinical trial results show that this tumor is curable, outcomes are still poor compared to other central nervous system embryonal tumors. We here review prior AT/RT clinical
- [Current State Of Pediatric Neuro-Oncology Imaging, Challenges And Future Directions](https://cbtn.org/publications/current-state-of-pediatric-neuro-oncology-imaging-challenges-and-future-directions/) - Imaging plays an important role in the diagnosis, treatment, and monitoring of brain tumors. With the development of new imaging technologies and data analysis methods, doctors can create large databases of brain images that can be used to improve patient care. In this review, researchers discusses various types of imaging techniques and their pros and
- [The Promise Of Metabolic Imaging In Diffuse Midline Glioma](https://cbtn.org/publications/the-promise-of-metabolic-imaging-in-diffuse-midline-glioma/) - Gliomas are a type of brain tumor that can be challenging to diagnose and treat, especially in children. Diffuse midline glioma (DMG) is a newly defined subtype that has a very poor prognosis. The diagnosis of DMG is based on clinical presentation and characteristic features on conventional magnetic resonance imaging (MRI). However, advanced MRI and
- [Why Haven’t We Solved Intracranial Pediatric Ependymoma? Current Questions And Barriers To Treatment Advances.](https://cbtn.org/publications/why-havent-we-solved-intracranial-pediatric-ependymoma-current-questions-and-barriers-to-treatment-advances/) - Pediatric intracranial ependymoma, a type of brain tumor, has recently been divided into subgroups based on specific characteristics. This new information can make it more difficult to draw conclusions from past treatments, but it also presents an opportunity to better understand the disease and develop effective therapies. This publication reviews some of the most important
- [Leptomeningeal Dissemination in Pediatric Brain Tumors](https://cbtn.org/publications/leptomeningeal-dissemination-in-pediatric-brain-tumors/) - A condition called leptomeningeal disease (LMD) is not well understood in children with brain tumors. LMD is when the cancer cells spread to the tissues surrounding the brain and spinal cord. It can happen at the same time as the primary tumor, after the tumor comes back, or even without a tumor in the brain.
- [Macrophages in SHH Subgroup Medulloblastoma Display Dynamic Heterogeneity That Varies With Treatment Modality](https://cbtn.org/publications/macrophages-in-shh-subgroup-medulloblastoma-display-dynamic-heterogeneity-that-varies-with-treatment-modality/) - Medulloblastoma (MB) is the most common malignant brain tumor of childhood, accounting for more than 20% of pediatric brain tumors. It is biologically heterogeneous, comprising four major molecular subgroups: WNT, sonic hedgehog (SHH), group 3, and group 4. Given the high-grade nature of this tumor type, treatment is aggressive and involves surgical resection, chemotherapy, and
- [Translational Considerations For Immunotherapy Clinical Trials In Pediatric Neuro-Oncology](https://cbtn.org/publications/translational-considerations-for-immunotherapy-clinical-trials-in-pediatric-neuro-oncology/) - This scientific publication explores the progress and challenges of using immunotherapy to treat pediatric central nervous system (CNS) tumors. Despite recent advancements in immunotherapy for other pediatric cancers, its impact on CNS tumors in children has been limited. The article reviews current and future immunotherapeutic clinical trials for CNS tumors, discussing unique challenges such as
- [Single-Cell Transcriptomic Profile Reveals Macrophage Heterogeneity in Medulloblastoma and Their Treatment-Dependent Recruitment](https://cbtn.org/publications/single-cell-transcriptomic-profile-reveals-macrophage-heterogeneity-in-medulloblastoma-and-their-treatment-dependent-recruitment/) - The role of macrophages in medulloblastoma, the most common malignant pediatric brain tumor, is unclear. Using single-cell RNA sequencing in a mouse model of sonic hedgehog medulloblastoma and analysis of bulk RNA sequencing of human medulloblastoma, we investigated macrophage heterogeneity. Our findings reveal differential recruitment of macrophages with molecular-targeted versus radiation therapy and identify an
- [Cell Ecosystem and Signaling Pathways of Primary and Metastatic Pediatric Posterior Fossa Ependymoma](https://cbtn.org/publications/cell-ecosystem-and-signaling-pathways-of-primary-and-metastatic-pediatric-posterior-fossa-ependymoma/) - Pediatric ependymoma is a devastating brain cancer marked by its relapsing pattern and lack of effective chemotherapies. This shortage of treatments is partially due to limited knowledge about ependymoma tumorigenic mechanisms. Although there is evidence that ependymoma originates in radial glia, the specific pathways underlying the progression and metastasis of these tumors are unknown. By
- [The Children's Brain Tumor Tissue Consortium (CBTTC) Infrastructure Facilitates Collaborative Research in Pediatric Central Nervous System Tumors](https://cbtn.org/publications/the-childrens-brain-tumor-tissue-consortium-cbttc-infrastructure-facilitates-collaborative-research-in-pediatric-central-nervous-system-tumors/) - The Children’s Brain Tumor Tissue Consortium (CBTTC) is a multi-institutional, international research collaboration comprised of 13 institutions utilizing an infrastructure of web based open source tools to accelerate pediatric brain tumor research. The CBTTC mission is to provide the largest accessible, de-identified, longitudinal clinical data set linked to available biospecimens and -omic data in the
- [GERM-01: Genetic and Epigenetic Landscape of Central Nervous System Germ Cell Tumors](https://cbtn.org/publications/germ-01-genetic-and-epigenetic-landscape-of-central-nervous-system-germ-cell-tumors/) - Central nervous system germ cell tumors (CNS GCTs) are the second most common central nervous system tumors in patients under 14 in Japan. To elucidate molecular basis of CNS GCTs, tumor samples and patients’ data were collected from the Intracranial Germ Cell Tumor Genome Analysis Consortium, a nationwide multi-center collaborative body to study CNS GCTs
- [EXTH-58. Effects of TORC1/2 Inhibitor MLN0128 Alone and in Combination with MEK Inhibition in BRAF-mutated Glioma Models in Vitro and In Vivo](https://cbtn.org/publications/exth-58-effects-of-torc1-2-inhibitor-mln0128-alone-and-in-combination-with-mek-inhibition-in-braf-mutated-glioma-models-in-vitro-and-in-vivo/) - INTRODUCTION MLN0128, a second-generation ATP-competitive pan-mTOR kinase inhibitor, acts on both mTORC1 and mTORC2. We investigated the effects of MLN0128 monotherapy and in combination with MEK and BRAFV600E inhibition in models of pediatric low-grade glioma (PLGG). METHODS We used human glioma cell lines expressing BRAFV600E (AM38), wild-type BRAF (LN229, TN98, SF188) and isogenic systems of
- [Interactions Between Immune Microenvironment, Stem Cells, and Cell Proliferation in Pediatric Embryonal Central Nervous System Cancers](https://cbtn.org/publications/interactions-between-immune-microenvironment-stem-cells-and-cell-proliferation-in-pediatric-embryonal-central-nervous-system-cancers/) - Mounting evidence suggests the brain’s own immune cells, microglia, and perivascular macrophages play important roles in immune surveillance/inflammation, but also support proliferation/growth of gliomas, possibly through interactions with tumor stem cells. Immune cells are increasingly regarded as potential targets for cancer therapy, however, the immune microenvironment has not been well-studied in pediatric embryonal CNS tumors.
- [Unregulated T-cell and Interferon-Γ-related Gene Expression is Associated with Increased Survival in Recurrent Pediatric High-Grade Glioma](https://cbtn.org/publications/unregulated-t-cell-and-interferon-γ-related-gene-expression-is-associated-with-increased-survival-in-recurrent-pediatric-high-grade-glioma/) - Recurrent pediatric high-grade glioma (pHGG) is the leading cause of cancer-related mortality in children. Immunotherapy is a successful treatment approach for a growing number of cancers and is being investigated as a treatment strategy for pHGG. Immunotherapy has shown the most benefit in tumors with increased infiltrating T cells at baseline. Our recently published results
- [Telomere Length Analysis of CNS Tumors in the Pediatric Brain Tumor Atlas](https://cbtn.org/publications/telomere-length-analysis-of-cns-tumors-in-the-pediatric-brain-tumor-atlas/) - Subsets of pediatric cancers, including high grade glioma (pHGG), have high rates of uniquely long telomeres, associated with ATRX gene mutations and alternative lengthening of telomeres (ALT). Ultimately, these cancers may benefit from a therapy stratification approach. In order to identify and further characterize pediatric brain tumors with telomere lengthening (TL), we determined the intratelomeric
- [Global Molecular Alterations Involving Recurrence or Progression of Pediatric Brain Tumors](https://cbtn.org/publications/global-molecular-alterations-involving-recurrence-or-progression-of-pediatric-brain-tumors/) - We aimed to identify molecular changes in recurrent or progressive pediatric brain tumors, as compared to the corresponding initial tumors from the same patients, using genomic, transcriptomic, and proteomic data from a unique and large cohort of 55 patients and 63 recurrent or progressive tumors from the Children’s Brain Tumor Tissue Consortium, representing various histologic
- [Puberty Status Modifies the Effects of Genetic Variants, Lifestyle Factors and Their Interactions on Adiponectin: The BCAMS Study](https://cbtn.org/publications/puberty-status-modifies-the-effects-of-genetic-variants-lifestyle-factors-and-their-interactions-on-adiponectin-the-bcams-study/) - Hypoadiponectinemia has been associated with various cardiometabolic disease states. Previous studies in adults have shown that adiponectin levels were regulated by specific genetic and behavioral or lifestyle factors. However, little is known about the influence of these factors on adiponectin levels in children, particularly as mitigated by pubertal development.
- [Splicing Is An Alternate Oncogenic Pathway Activation Mechanism In Glioma](https://cbtn.org/publications/splicing-is-an-alternate-oncogenic-pathway-activation-mechanism-in-glioma/) - High grade diffuse glioma is a deadly brain tumor type. HGG are the leading cause of brain tumor death. Researchers have uncovered the genetics of HGG, but there are many mechanisms that encourage the growth of this tumor. In this project, researchers look at alternative splicing in pediatric and adult HGG compared to patients without
- [Imipridones Affect Tumor Bioenergetics And Promote Cell Lineage Differentiation In Diffuse Midline Gliomas](https://cbtn.org/publications/imipridones-affect-tumor-bioenergetics-and-promote-cell-lineage-differentiation-in-diffuse-midline-gliomas/) - Pediatric diffuse midline gliomas (DMGs) are incurable childhood cancers. Imipridones are chemical compounds used to treat cancers orally. The imipridone ONC201 has shown early positive effects on DMGs. However, the anticancer mechanisms of ONC201 and its derivative ONC206 have not been fully described in this type of tumor. Researchers in this study found that chemicals
- [Medulloblastoma Cerebrospinal Fluid Reveals Metabolites And Lipids Indicative Of Hypoxia And Cancer-Specific Rnas](https://cbtn.org/publications/medulloblastoma-cerebrospinal-fluid-reveals-metabolites-and-lipids-indicative-of-hypoxia-and-cancer-specific-rnas/) - Medulloblastoma (MB) is the most common malignant brain tumor in children, however there is a great need for sensitive diagnostic tools. Diagnostic tools that use cerebrospinal fluid (CSF) present an opportunity for advancement. This study identifies signatures within CSF that are promising pending further validation. Once validated these could be used to help to detect
- [Proteogenomic Characterization of 2002 Human Cancers Reveals Pan-Cancer Molecular Subtypes and Associated Pathways](https://cbtn.org/publications/proteogenomic-characterization-of-2002-human-cancers-reveals-pan-cancer-molecular-subtypes-and-associated-pathways/) - With the inclusion of RNA sequencing data provided by CBTN, researchers assembled a dataset of over 2000 tumors across 14 cancer types. Using this dataset, the research team identified 11 distinct tumor types, including 2 subtypes enriched for brain tumors. This pan-cancer survey reveals interplay between the genome and proteome of cancer types found throughout
- [Pro-inflammatory Cytokines Mediate the Epithelial-to-Mesenchymal-like Transition of Pediatric Posterior Fossa Ependymoma](https://cbtn.org/publications/pro-inflammatory-cytokines-mediate-the-epithelial-to-mesenchymal-like-transition-of-pediatric-posterior-fossa-ependymoma/) - Pediatric ependymoma is a brain tumor known for its pattern of recurrence. Unfortunately, there is a lack of effective chemotherapies targeting ependymoma due to a limited knowledge of how the tumor forms and grows. This shortage of treatments is due to limited knowledge about how ependymoma tumors develop and grow. . In this study, researchers
- [Circular and Fusion RNAs in Medulloblastoma Development](https://cbtn.org/publications/circular-and-fusion-rnas-in-medulloblastoma-development/) - Medulloblastoma is the most common pediatric brain cancer. Using RNA sequencing data from CBTN, researchers on this project detect circular and fusion RNAs within medulloblastoma. Their observations show that the formation of fusion transcripts may be taking place at both the chromosomal and RNA level. They also identified deregulated circular RNA found in the four
- [Upfront Biology-Guided Therapy in Diffuse Intrinsic Pontine Glioma: Therapeutic, Molecular, and Biomarker Outcomes from PNOC003](https://cbtn.org/publications/upfront-biology-guided-therapy-in-diffuse-intrinsic-pontine-glioma-therapeutic-molecular-and-biomarker-outcomes-from-pnoc003/) - Researchers found that biopsies from patients who had not undergone any treatment provided insight into H3K27-altered diffuse intrinsic pontine glioma. Utilizing CBTN data to verify their results, researchers explore molecular alterations and biomarkers for this tumor type.
- [Reversal of Cancer Gene Expression Identifies Repurposed Drugs for Diffuse Intrinsic Pontine Glioma](https://cbtn.org/publications/reversal-of-cancer-gene-expression-identifies-repurposed-drugs-for-diffuse-intrinsic-pontine-glioma/) - Diffuse intrinsic pontine glioma (DIPG) is an aggressive tumor that is very hard to treat with chemotherapy and radiation and impossible to remove with surgery. To increase positive outcomes for patients, researchers worked to identify new potential therapies through drug screening. Once identified, the team tested those drugs against DIPG cell lines. As a result
- [Classification of Pediatric Gangliomas Based on the Histological Infiltration](https://cbtn.org/publications/classification-of-pediatric-gangliomas-based-on-the-histological-infiltration/) - Ganglioglioma is a low-grade glioneuronal tumor with many known morphologies. Morphology refers to the shape and growth pattern of the tumor. This work aimed to bring clarity to the various growth patterns in ganglioglioma. Using imagery and samples provided by CBTN, researchers interrogated growth patterns found in patients with ganglioglioma. This work confirmed the presence
- [The Children'S Brain Tumor Network (CBTN) - Accelerating Research In Pediatric Central Nervous System Tumors Through Collaboration And Open Science](https://cbtn.org/publications/the-childrens-brain-tumor-network-cbtn-accelerating-research-in-pediatric-central-nervous-system-tumors-through-collaboration-and-open-science/) - Pediatric brain tumors are a leading cause of cancer-related deaths in children in the United States, and survivors often suffer long-term side effects. The Children's Brain Tumor Network (CBTN) is a group of 32 institutions working together to collect and distribute biospecimens and data for pediatric brain tumors through open-science research platforms. As of August
- [Children's Brain Tumor Network - Accelerating Research Through Collaboration and Open Science](https://cbtn.org/publications/childrens-brain-tumor-network-accelerating-research-through-collaboration-and-open-science/) - The Children’s Brain Tumor Network (formerly known as Children’s Brain Tumor Consortium- CBTTC) is a global organization pioneering a model of open-science medical research to improve treatment and discover cures. Started in 2011, our objective was to utilize a regulatory, agreement, and governance architecture to remove existing research barriers that slowed down the pace of
- [Interdisciplinary Care Of Children With Diffuse Midline Glioma](https://cbtn.org/publications/interdisciplinary-care-of-children-with-diffuse-midline-glioma/) - Diffuse Midline Glioma (DMG) which includes Diffuse Intrinsic Pontine Glioma (DIPG) is an infiltrative tumor of the midline structures of the central nervous system that demonstrates an aggressive pattern of growth and has no known curative treatment. As these tumors progress, children experience ongoing neurological decline including inability to ambulate, swallow and communicate effectively. We
- [Primary Central Nervous System Germ Cell Tumors in Children and Young Adults: A Review of Controversies in Diagnostic and Treatment Approach](https://cbtn.org/publications/primary-central-nervous-system-germ-cell-tumors-in-children-and-young-adults-a-review-of-controversies-in-diagnostic-and-treatment-approach/)
- [Current Studies and Future Directions for Medulloblastoma: A Review from the Pacific Pediatric Neuro-Oncology Consortium (PNOC) Disease Working Group](https://cbtn.org/publications/current-studies-and-future-directions-for-medulloblastoma-a-review-from-the-pacific-pediatric-neuro-oncology-consortium-pnoc-disease-working-group/) - Medulloblastoma is a type of brain tumor that commonly affects children, and it includes different subtypes that have varying characteristics and outcomes. Even with current treatments, long-term survival rates are low, and survivors often face various health challenges. However, this article discusses new treatment strategies that combine molecular and clinical factors may help to better
- [Unsupervised machine learning using K-means identifies radiomic subgroups of pediatric low-grade gliomas that correlate with key molecular markers](https://cbtn.org/publications/unsupervised-machine-learning-using-k-means-identifies-radiomic-subgroups-of-pediatric-low-grade-gliomas-that-correlate-with-key-molecular-markers/) - This study aimed to investigate if an unsupervised machine learning approach based on radiomic features could reveal distinct imaging subtypes of pediatric low-grade gliomas (pLGGs). The researchers collected multi-parametric MR images from 157 patients with pLGGs and extracted quantitative radiomic features from the tumorous region. They then used K-means clustering to identify three distinct imaging-based
- [Pediatric Low-Grade Glioma: Targeted Therapeutics And Clinical Trials In The Molecular Era](https://cbtn.org/publications/pediatric-low-grade-glioma-targeted-therapeutics-and-clinical-trials-in-the-molecular-era/) - Pediatric Low-Grade Gliomas (pLGGs) are a type of brain tumor found in children. This article outlines some of the recent advances in understanding the genetic changes that cause these tumors have led to new treatments that target specific genes. This has allowed doctors to offer targeted therapies to patients with pLGG, which were not possible
- [Pioneering Models of Pediatric Brain Tumors](https://cbtn.org/publications/pioneering-models-of-pediatric-brain-tumors/) - Brain and central nervous system tumors are the second most common types of cancer in children and adolescents in the United States, after leukemias. Brain cancer remains the leading cause of death in the pediatric population, despite significant progress in diagnosis and treatment. To improve survival, preclinical models play a crucial role. Different models are
- [Locoregional Car T Cells For Children With Cns Tumors: Clinical Procedure And Catheter Safety](https://cbtn.org/publications/locoregional-car-t-cells-for-children-with-cns-tumors-clinical-procedure-and-catheter-safety/) - This study discusses the use of chimeric antigen receptor (CAR) T cell therapy to treat pediatric central nervous system (CNS) tumors. These tumors are the most common solid malignancy in children, and CAR T cell therapy has shown success in treating childhood leukemia and preclinical efficacy against pediatric CNS tumors. However, delivering CAR T cells
- [An Integrative DNA Sequencing and Methylation Panel to Assess Mismatch Repair Deficiency](https://cbtn.org/publications/an-integrative-dna-sequencing-and-methylation-panel-to-assess-mismatch-repair-deficiency/) - Clinical testing for mismatch repair (MMR) deficiency often entails serial testing of tumor and constitutional DNA using multiple assays. To minimize cost and specimen requirements of MMR testing, we developed an integrated targeted sequencing protocol (termed MultiMMR) that tests for promoter methylation, mutations, copy number alterations, copy neutral loss of heterozygosity, and microsatellite instability from
- [Mesenchymal Stem Cells Successfully Deliver Oncolytic Virotherapy to Diffuse Intrinsic Pontine Glioma](https://cbtn.org/publications/mesenchymal-stem-cells-successfully-deliver-oncolytic-virotherapy-to-diffuse-intrinsic-pontine-glioma/) - Diffuse intrinsic pontine glioma (DIPG) is among the deadliest of pediatric brain tumors. Radiation therapy is the standard of care treatment for DIPG, but offers only transient relief of symptoms for DIPG patients without providing significant survival benefit. Oncolytic virotherapy (OV) is an anticancer treatment that has been investigated for treating various types of brain
- [Genomic Characterization of a PPP1CB-ALK Fusion with Fusion Gene Amplification in a Congenital Glioblastoma](https://cbtn.org/publications/genomic-characterization-of-a-ppp1cb-alk-fusion-with-fusion-gene-amplification-in-a-congenital-glioblastoma/) - ALK (Anaplastic lymphoma kinase) fusion proteins are oncogenic and have been seen in various tumors. PPP1CB-ALK fusions are rare but have been reported in a few patients with low- or high-grade gliomas. However, little is known regarding the mechanism of fusion formation and genomic break points of this fusion. We performed genomic characterization of a
- [Systematic Identification of Non-coding Somatic Single Nucleotide Variants Associated with Altered Transcription and DNA Methylation in Adult and Pediatric Cancers](https://cbtn.org/publications/systematic-identification-of-non-coding-somatic-single-nucleotide-variants-associated-with-altered-transcription-and-dna-methylation-in-adult-and-pediatric-cancers/) - Whole-genome sequencing combined with transcriptomics can reveal impactful non-coding single nucleotide variants (SNVs) in cancer. Here, we developed an integrative analytical approach that, as a first step, identifies genes altered in expression or DNA methylation in association with nearby somatic SNVs, in contrast to alternative approaches that first identify mutational hotspots. Using genomic datasets from
- [Braf Fusions In Pediatric Histiocytic Neoplasms Define Distinct Therapeutic Responsiveness To Raf Paradox Breakers](https://cbtn.org/publications/braf-fusions-in-pediatric-histiocytic-neoplasms-define-distinct-therapeutic-responsiveness-to-raf-paradox-breakers/) - Pediatric histiocytic neoplasms are hematopoietic disorders frequently driven by the BRAF‐V600E mutation. Here, we identified two BRAF gene fusions (novel MTAP‐BRAF and MS4A6A‐BRAF) in two aggressive histiocytic neoplasms. In contrast to previously described BRAF fusions, MTAP‐BRAF and MS4A6A‐BRAF do not respond to the paradox breaker RAF inhibitor (RAFi) PLX8394 due to stable fusion dimerization mediated
- [A Pediatric Brain Tumor Atlas of Genes Deregulated by Somatic Genomic Rearrangement](https://cbtn.org/publications/a-pediatric-brain-tumor-atlas-of-genes-deregulated-by-somatic-genomic-rearrangement/) - The global impact of somatic structural variants (SSVs) on gene expression in pediatric brain tumors has not been thoroughly characterised. Here, using whole-genome and RNA sequencing from 854 tumors of more than 30 different types from the Children’s Brain Tumor Tissue Consortium, we report the altered expression of hundreds of genes in association with the
- [Classification of Pediatric Gliomas Based on Immunological Profiling: Implications for Immunotherapy Strategies](https://cbtn.org/publications/classification-of-pediatric-gliomas-based-on-immunological-profiling-implications-for-immunotherapy-strategies/) - Pediatric gliomas (PGs) are the most common brain tumors in children and the leading cause of childhood cancer-related death. The understanding of the immune microenvironment is essential for developing effective antitumor immunotherapies. Transcriptomic data from 495 PGs were analyzed in this study, with 384 as a training cohort and 111 as a validation cohort. Macrophages
- [Proteogenomic and Metabolomic Characterization of Human Glioblastoma](https://cbtn.org/publications/proteogenomic-and-metabolomic-characterization-of-human-glioblastoma/) - Glioblastoma (GBM) is the most aggressive nervous system cancer. Understanding its molecular pathogenesis is crucial to improving diagnosis and treatment. Integrated analysis of genomic, proteomic, post-translational modification and metabolomic data on 99 treatment-naive GBMs provides insights to GBM biology. We identify key phosphorylation events (e.g., phosphorylated PTPN11 and PLCG1) as potential switches mediating oncogenic pathway
- [Mutation-based clustering and classification analysis reveals distinctive age groups and age-related biomarkers for glioma](https://cbtn.org/publications/mutation-based-clustering-and-classification-analysis-reveals-distinctive-age-groups-and-age-related-biomarkers-for-glioma/) - Background Malignant brain tumor diseases exhibit differences within molecular features depending on the patient’s age. Methods In this work, we use gene mutation data from public resources to explore age specifics about glioma. We use both an explainable clustering as well as classification approach to find and interpret age-based differences in brain tumor diseases. We
- [Genomic and Transcriptomic Analyses Reveals ZNF124 as a Critical Regulator in Highly Aggressive Medulloblastomas](https://cbtn.org/publications/genomic-and-transcriptomic-analyses-reveals-znf124-as-a-critical-regulator-in-highly-aggressive-medulloblastomas/) - Medulloblastoma (MB) is the most common malignant pediatric brain tumor, however, the mechanisms underlying tumorigenesis in different MB subgroups remain incompletely understood. Although previous studies of MB predisposition have been conducted in tertiary referral centers primarily in Caucasian cohorts, it is not unclear clear whether there exist population-specific genetic alterations in MBs. In this study,
- [Oculoplastic Considerations in Pediatric Craniofacial Surgery](https://cbtn.org/publications/oculoplastic-considerations-in-pediatric-craniofacial-surgery/) - The orbits are central to the face and of the highest consideration in surgical correction of congenital craniofacial anomalies. In this chapter, we briefly review the general techniques of cranio-orbital surgery and outline the specific use of these techniques in the management of complicated craniofacial disorders. In keeping with the goals of this text, we
- [Meta-Learning Reduces Amount Data Needed to Build AI Models in Oncology](https://cbtn.org/publications/meta-learning-reduces-amount-data-needed-to-build-ai-models-in-oncology/) - Meta-learning is showing promise in recent genomic studies in oncology. Meta-learning can facilitate transfer learning and reduce the amount of data that is needed in a target domain by transferring knowledge from abundant genomic data in different source domains enabling the use of AI in data scarce scenarios.
- [Rp58 Represses Transcriptional Programs Linked To Non-Neuronal Cell Identity And Glioblastoma Subtypes In Developing Neurons](https://cbtn.org/publications/rp58-represses-transcriptional-programs-linked-to-non-neuronal-cell-identity-and-glioblastoma-subtypes-in-developing-neurons/) - How mammalian neuronal identity is progressively acquired and reinforced during development is not understood. We have previously shown that loss of RP58 (ZNF238, ZBTB18), a BTB/POZ and zinc finger containing transcription factor, in the mouse brain leads to microcephaly, corpus callosum agenesis, cerebellum hypoplasia and that it is required for normal neuronal differentiation. The transcriptional
- [Idh-Mutant Brainstem Gliomas In Adolescent And Young Adult Patients: Report Of Three Cases And Review Of The Literature](https://cbtn.org/publications/idh-mutant-brainstem-gliomas-in-adolescent-and-young-adult-patients-report-of-three-cases-and-review-of-the-literature/) - In contrast to adult gliomas, isocitrate dehydrogenase (IDH) mutations are rare in pediatric and adolescent gliomas. In a recent series of over 1000 pediatric low grade gliomas (LGG), the IDH1 R132H mutation was found in only 0.8% of studied cases, with those identified occurring in older children/adolescents (median 15.7 years) and exclusively in the cerebral
- [Prognostic Implications of Immune-related Eight-gene Signature in Pediatric Brain Tumors](https://cbtn.org/publications/prognostic-implications-of-immune-related-eight-gene-signature-in-pediatric-brain-tumors/) - Genomic studies have provided insights into molecular subgroups and oncogenic drivers of pediatric brain tumors (PBT) that may lead to novel therapeutic strategies. Participants of the cohort Pediatric Brain Tumor Atlas: CBTTC (CBTTC cohort), were randomly divided into training and validation cohorts. In the training cohort, Kaplan-Meier analysis and univariate Cox regression model were applied
- [NTRK Fusions Identified in Pediatric Tumors: The Frequency, Fusion Partners, and Clinical Outcome](https://cbtn.org/publications/ntrk-fusions-identified-in-pediatric-tumors-the-frequency-fusion-partners-and-clinical-outcome/) - Neurotrophic tyrosine receptor kinase (NTRK) fusions have been described as oncogenic drivers in a variety of tumors. However, little is known about the overall frequency of NTRK fusion in unselected pediatric tumors. Here, we assessed the frequency, fusion partners, and clinical course in pediatric patients with NTRK fusion–positive tumors. We studied 1,347 consecutive pediatric tumors
- [Deep Learning-Based Studies in Pediatric Brain Tumors Imaging: Narrative Review of Techniques and Challenges](https://cbtn.org/publications/deep-learning-based-studies-in-pediatric-brain-tumors-imaging-narrative-review-of-techniques-and-challenges/) - Brain tumors diagnosis in children is a scientific concern due to rapid anatomical, metabolic, and functional changes arising in the brain and non-specific or conflicting imaging results. Pediatric brain tumors diagnosis is typically centralized in clinical practice on the basis of diagnostic clues such as, child age, tumor location and incidence, clinical history, and imaging
- [Tbio-12. The Spectrum Of Mitochondrial Dna (Mtdna) Mutations In Pediatric Central Nervous System (Cns) Tumors](https://cbtn.org/publications/tbio-12-the-spectrum-of-mitochondrial-dna-mtdna-mutations-in-pediatric-central-nervous-system-cns-tumors/) - To explore the role of mitochondrial DNA mutations in pediatric CNS tumors, we analyzed 749 tumor-normal paired whole genome sequencing data sets from the Children’s Brain Tumor Tissue Consortium (CBTTC). We detected 307 somatic mtDNA mutations in 222 CNS tumors (29.6%). Most frequently observed were missense mutations (38.1%). We also detected 34 loss-of-function mutations. Different
- [Rearrangement-Mediated Cis-Regulatory Alterations In Advanced Patient Tumors Reveal Interactions With Therapy](https://cbtn.org/publications/rearrangement-mediated-cis-regulatory-alterations-in-advanced-patient-tumors-reveal-interactions-with-therapy/) - The global impact of somatic structural variants (SVs) on gene regulation in advanced tumors with complex treatment histories has been mostly uncharacterized. Here, using whole-genome and RNA sequencing from 570 recurrent or metastatic tumors, we report the altered expression of hundreds of genes in association with nearby SV breakpoints, including oncogenes and G-protein-coupled receptor-related genes
- [Proteogenomic Discovery of Neoantigens Facilitates Personalized Multi-antigen Targeted T Cell Immunotherapy for Brain Tumors](https://cbtn.org/publications/proteogenomic-discovery-of-neoantigens-facilitates-personalized-multi-antigen-targeted-t-cell-immunotherapy-for-brain-tumors/) - Neoantigen discovery in pediatric brain tumors is hampered by their low mutational burden and scant tissue availability. Here we develop a proteogenomic approach combining tumor DNA/RNA sequencing and mass spectrometry proteomics to identify tumor-restricted (neoantigen) peptides arising from multiple genomic aberrations to generate a highly target-specific, autologous, personalized T cell immunotherapy. Our data indicate that
- [The Effect And Evolution Of Patient Selection On Outcomes In Endoscopic Third Ventriculostomy For Hydrocephalus: A Large-Scale Review Of The Literature](https://cbtn.org/publications/the-effect-and-evolution-of-patient-selection-on-outcomes-in-endoscopic-third-ventriculostomy-for-hydrocephalus-a-large-scale-review-of-the-literature/) - Endoscopic third ventriculostomy (ETV) has become a popular technique for the treatment of hydrocephalus, but small sample size has limited the generalizability of prior studies. We performed a large-scale review of all available studies to help eliminate bias and determine how outcomes have changed and been influenced by patient selection over time. A systematic literature
- [Novel Findings With Reassessment Of Exome Data: Implications For Validation Testing And Interpretation Of Genomic Data](https://cbtn.org/publications/novel-findings-with-reassessment-of-exome-data-implications-for-validation-testing-and-interpretation-of-genomic-data/) - Purpose The objective of this study was to assess the ability of our laboratory’s exome-sequencing test to detect known and novel sequence variants and identify the critical factors influencing the interpretation of a clinical exome test. Methods We developed a two-tiered validation strategy: (i) a method-based approach that assessed the ability of our exome test
- [The Landscape Of Genomic Alterations Across Childhood Cancers](https://cbtn.org/publications/the-landscape-of-genomic-alterations-across-childhood-cancers/) - Pan-cancer analyses that examine commonalities and differences among various cancer types have emerged as a powerful way to obtain novel insights into cancer biology. Here we present a comprehensive analysis of genetic alterations in a pan-cancer cohort including 961 tumours from children, adolescents, and young adults, comprising 24 distinct molecular types of cancer. Using a
- [Novel Fgfr2-Ina Fusion Identified In Two Low-Grade Mixed Neuronal-Glial Tumors Drives Oncogenesis Via Mapk And Pi3K/Mtor Pathway Activation](https://cbtn.org/publications/novel-fgfr2-ina-fusion-identified-in-two-low-grade-mixed-neuronal-glial-tumors-drives-oncogenesis-via-mapk-and-pi3k-mtor-pathway-activation/) - As a group, mixed neuronal-glial tumors (MNGTs) exhibit genetic variability, including stable genomes, whole chromo- some gains, BRAF-V600E, and FGFR1 mutations. While histologic criteria are described to distinguish MNGT types ganglioglioma (GG) and dysembryoplastic neuroepithelial tumor (DNT), non-specific features preclude confident classification in a high proportion of cases. Herein, we report the characterization of a
- [Purification Of Mrna Encoding Chimeric Antigen Receptor Is Critical For Generation Of Robust T-Cell Response](https://cbtn.org/publications/purification-of-mrna-encoding-chimeric-antigen-receptor-is-critical-for-generation-of-robust-t-cell-response/) - T cells made with messenger RNA (mRNA) encoding chimeric antigen receptor (CAR) offer a safe alternative to those transduced with viral CARs by mitigating the side effects of constitutively active T cells. Previous studies have shown that mRNA CAR T cells are transiently effective but lack persistence and potency across tumor types. It was hypothesized
- [Analysis Of Racial/Ethnic Representation In Select Basic And Applied Cancer Research Studies](https://cbtn.org/publications/analysis-of-racial-ethnic-representation-in-select-basic-and-applied-cancer-research-studies/) - Over the past decades, consistent studies have shown that race/ethnicity have a great impact on cancer incidence, survival, drug response, molecular pathways and epigenetics. Despite the influence of race/ethnicity in cancer outcomes and its impact in health care quality, a comprehensive understanding of racial/ethnic inclusion in oncological research has never been addressed. We therefore explored
- [Use-case Driven Evaluation of Open Databases for Pediatric Cancer Research](https://cbtn.org/publications/use-case-driven-evaluation-of-open-databases-for-pediatric-cancer-research/) - A plethora of Web resources are available offering information on clinical, pre-clinical, genomic and theoretical aspects of cancer, including not only the comprehensive cancer projects as ICGC and TCGA, but also less-known and more specialized projects on pediatric diseases such as PCGP. However, in case of data on childhood cancer there is very little information
- [Increasing Value of Autopsies in Patients with Brain Tumors in the Molecular Era](https://cbtn.org/publications/increasing-value-of-autopsies-in-patients-with-brain-tumors-in-the-molecular-era/) - Pediatric brain tumors are associated with high morbidity and mortality, in part due to insufficient understanding of tumor biology. With limited tissue allocation for research from surgical specimens, a key barrier to improving biological understanding, brain tumor autopsies have become an increasingly valuable resource. This study reviews the brain tumor autopsy practice at our institution
- [Histone Variant and Cell Context Determine H3K27M Reprogramming of the Enhancer Landscape and Oncogenic State](https://cbtn.org/publications/histone-variant-and-cell-context-determine-h3k27m-reprogramming-of-the-enhancer-landscape-and-oncogenic-state/) - Development of effective targeted cancer therapies is fundamentally limited by our molecular understanding of disease pathogenesis. Diffuse intrinsic pontine glioma (DIPG) is a fatal malignancy of the childhood pons characterized by a unique substitution to methionine in histone H3 at lysine 27 (H3K27M) that results in globally altered epigenetic marks and oncogenic transcription. Through primary
- [The Ganglioside GD2 as a Circulating Tumor Biomarker for Neuroblastoma](https://cbtn.org/publications/the-ganglioside-gd2-as-a-circulating-tumor-biomarker-for-neuroblastoma/) - Background: GD2 is a ganglioside that is ubiquitously expressed in the plasma membrane of neuroblastoma and is shed into the circulation. Procedure: GD2 was measured with a high-pressure liquid chromatography/tandem mass spectrometry assay in serum or plasma from 40 children without cancer (controls) and in biobanked samples from 128 (73 high-risk) children with neuroblastic tumors
- [Pediatric High Grade Glioma Resources From the Children’s Brain Tumor Tissue Consortium (CBTTC) and Pediatric Brain Tumor Atlas (PBTA)](https://cbtn.org/publications/pediatric-high-grade-glioma-resources-from-the-childrens-brain-tumor-tissue-consortium-cbttc-and-pediatric-brain-tumor-atlas-pbta/) - Background Pediatric high grade glioma (pHGG) remains a fatal disease. Increased access to richly annotated biospecimens and patient derived tumor models will accelerate pHGG research and support translation of research discoveries. This work describes the pediatric high grade glioma set of the Children’s Brain Tumor Tissue Consortium (CBTTC) from the first release (October 2018) of
- [Gene-22. Re-Programing Chromatin with a Bifunctional LSD1/HDAC Inhibitor Induces Therapeutic Differentiation in DIPG](https://cbtn.org/publications/gene-22-re-programing-chromatin-with-a-bifunctional-lsd1-hdac-inhibitor-induces-therapeutic-differentiation-in-dipg/) - Diffuse intrinsic high grade glioma (DIPG) is an almost universally fatal tumor of childhood characterized by epigenetic dysregulation driven by somatic H3.3/H3.1 K27M mutations observed in >80% of tumors. We conducted a chromatin-focused CRISPR screen and identified a novel strategy to inhibit the growth of patient-derived DIPG cells by co-targeting lysine specific demethylase 1 (LSD1)
- [Data Sharing for Clinical Utility](https://cbtn.org/publications/data-sharing-for-clinical-utility/) - Genomic data offer valuable insights that can be used to help find treatments and cures for disease. Precision medicine, defined by the NIH as “an emerging approach for disease treatment and prevention that takes into account individual variability in genes, environment, and lifestyle for each person,” is gaining acceptance among physicians, who are beginning to
- [Integrative Analysis Identifies Candidate Tumor Microenvironment and Intracellular Signaling Pathways that Define Tumor Heterogeneity in NF1](https://cbtn.org/publications/integrative-analysis-identifies-candidate-tumor-microenvironment-and-intracellular-signaling-pathways-that-define-tumor-heterogeneity-in-nf1/) - Neurofibromatosis type 1 (NF1) is a monogenic syndrome that gives rise to numerous symptoms including cognitive impairment, skeletal abnormalities, and growth of benign nerve sheath tumors. Nearly all NF1 patients develop cutaneous neurofibromas (cNFs), which occur on the skin surface, whereas 40-60% of patients develop plexiform neurofibromas (pNFs), which are deeply embedded in the peripheral
- [CAMKV is a Candidate Immunotherapeutic Target in MYCN Amplified Neuroblastoma](https://cbtn.org/publications/camkv-is-a-candidate-immunotherapeutic-target-in-mycn-amplified-neuroblastoma/) - We developed a computational pipeline designed to use RNA sequencing (n = 136) and gene expression profiling (n = 250) data from neuroblastoma tumors to identify cell surface proteins predicted to be highly expressed in MYCN amplified neuroblastomas and with little or no expression in normal human tissues. We then performed ChIP-seq in the MYCN
- [Ancestry And Frequency Of Genetic Variants In The General Population Are Confounders In The Characterization Of Germline Variants Linked To Cancer](https://cbtn.org/publications/ancestry-and-frequency-of-genetic-variants-in-the-general-population-are-confounders-in-the-characterization-of-germline-variants-linked-to-cancer/) - Pediatric high-grade gliomas (pHGGs) are incurable malignant brain cancers. Clear somatic genetic drivers are difficult to identify in the majority of cases. We hypothesized that this may be due to the existence of germline variants that influence tumor etiology and/or progression and are filtered out using traditional pipelines for somatic mutation calling. In this study,
- [Harmonization of Postmortem Donations for Pediatric Brain Tumors and Molecular Characterization of Diffuse Midline Gliomas](https://cbtn.org/publications/harmonization-of-postmortem-donations-for-pediatric-brain-tumors-and-molecular-characterization-of-diffuse-midline-gliomas/) - Children diagnosed with brain tumors have the lowest overall survival of all pediatric cancers. Recent molecular studies have resulted in the discovery of recurrent driver mutations in many pediatric brain tumors. However, despite these molecular advances, the clinical outcomes of high grade tumors, including H3K27M diffuse midline glioma (H3K27M DMG), remain poor. To address the
- [Yap1-Fam118B Fusion Defines A Rare Subset Of Childhood And Young Adulthood Meningiomas](https://cbtn.org/publications/yap1-fam118b-fusion-defines-a-rare-subset-of-childhood-and-young-adulthood-meningiomas/) - Meningiomas are a central nervous system tumor primarily afflicting adults, with
- [Development of Cancer Prognostic Signature Based on Pan-Cancer Proteomics](https://cbtn.org/publications/development-of-cancer-prognostic-signature-based-on-pan-cancer-proteomics/) - Utilizing genomic data to predict cancer prognosis was insufficient. Proteomics can improve our understanding of the etiology and progression of cancer and improve the assessment of cancer prognosis. And the Clinical Proteomic Tumor Analysis Consortium (CPTAC) has generated extensive proteomics data of the vast majority of tumors. Based on CPTAC, we can perform a proteomic
- [Integrated Proteogenomic Characterization across Major Histological Types of Pediatric Brain Cancer](https://cbtn.org/publications/integrated-proteogenomic-characterization-across-major-histological-types-of-pediatric-brain-cancer/) - We report a comprehensive proteogenomics analysis, including whole-genome sequencing, RNA sequencing, and proteomics and phosphoproteomics profiling, of 218 tumors across 7 histological types of childhood brain cancer: low-grade glioma (n = 93), ependymoma (32), high-grade glioma (25), medulloblastoma (22), ganglioglioma (18), craniopharyngioma (16), and atypical teratoid rhabdoid tumor (12). Proteomics data identify common biological themes
- [Activating Mutations In Braf Characterize A Spectrum Of Pediatric Low-Grade Gliomas](https://cbtn.org/publications/activating-mutations-in-braf-characterize-a-spectrum-of-pediatric-low-grade-gliomas/) - In the present study, DNA from 27 grade I and grade II pediatric gliomas, including ganglioglioma, desmoplastic infantile ganglioglioma, dysembryoplastic neuroepithelial tumor, and pleomorphic xanthoastrocytoma was analyzed using the Illumina 610K Beadchip SNP-based oligonucleotide array. Several consistent abnormalities, including gain of chromosome 7 and loss of 9p21 were observed. Based on our previous studies, in
- [The Genetic Landscape Of The Childhood Cancer Medulloblastoma](https://cbtn.org/publications/the-genetic-landscape-of-the-childhood-cancer-medulloblastoma/) - Medulloblastoma (MB) is the most common malignant brain tumor of children. To identify the genetic alterations in this tumor type, we searched for copy number alterations using high-density microarrays and sequenced all known protein-coding genes and microRNA genes using Sanger sequencing in a set of 22 MBs. We found that, on average, each tumor had
- [Exome Sequencing Identifies Braf Mutations In Papillary Craniopharyngiomas](https://cbtn.org/publications/exome-sequencing-identifies-braf-mutations-in-papillary-craniopharyngiomas/) - Craniopharyngiomas are epithelial tumors that typically arise in the suprasellar region of the brain1. Patients experience substantial clinical sequelae from both extension of the tumors and therapeutic interventions that damage the optic chiasm, the pituitary stalk and the hypothalamic area2,3,4. Using whole-exome sequencing, we identified mutations in CTNNB1 (β-catenin) in nearly all adamantinomatous craniopharyngiomas examined
- [Myb-Qki Rearrangements In Angiocentric Glioma Drive Tumorigenicity Through A Tripartite Mechanism](https://cbtn.org/publications/myb-qki-rearrangements-in-angiocentric-glioma-drive-tumorigenicity-through-a-tripartite-mechanism/) - Angiocentric gliomas are pediatric low-grade gliomas (PLGGs) without known recurrent genetic drivers. We performed genomic analysis of new and published data from 249 PLGGs, including 19 angiocentric gliomas. We identified MYB-QKI fusions as a specific and single candidate driver event in angiocentric gliomas. In vitro and in vivo functional studies show that MYB-QKI rearrangements promote
- [The Biorepository Portal Toolkit: An Honest Brokered, Modular Service Oriented Software Tool Set For Biospecimen-Driven Translational Research](https://cbtn.org/publications/the-biorepository-portal-toolkit-an-honest-brokered-modular-service-oriented-software-tool-set-for-biospecimen-driven-translational-research/) - High throughput molecular sequencing and increased biospecimen variety have introduced significant informatics challenges for research biorepository infrastructures. We applied a modular system integration approach to develop an operational biorepository management system. This method enables aggregation of the clinical, specimen and genomic data collected for biorepository resources. Methods We introduce an electronic Honest Broker (eHB) and
- [Transcriptome Analysis Of Il-10-Stimulated (M2C) Macrophages By Next-Generation Sequencing](https://cbtn.org/publications/transcriptome-analysis-of-il-10-stimulated-m2c-macrophages-by-next-generation-sequencing/) - Alternatively activated "M2" macrophages are believed to function during late stages of wound healing, behaving in an anti-inflammatory manner to mediate the resolution of the pro-inflammatory response caused by "M1" macrophages. However, the differences between two main subtypes of M2 macrophages, namely interleukin-4 (IL-4)-stimulated "M2a" macrophages and IL-10-stimulated "M2c" macrophages, are not well understood. M2a
- [Rb Family Proteins Enforce The Homeostasis Of Quiescent Hematopoietic Stem Cells By Repressing Socs3 Expression](https://cbtn.org/publications/rb-family-proteins-enforce-the-homeostasis-of-quiescent-hematopoietic-stem-cells-by-repressing-socs3-expression/) - Prolonged exit from quiescence by hematopoietic stem cells (HSCs) progressively impairs their homeostasis in the bone marrow through an unidentified mechanism. We show that Rb proteins, which are major enforcers of quiescence, maintain HSC homeostasis by positively regulating thrombopoietin (Tpo)-mediated Jak2 signaling. Rb family protein inactivation triggers the progressive E2f-mediated transactivation of Socs3, a potent
- [Data Commons to Support Pediatric Cancer Research](https://cbtn.org/publications/data-commons-to-support-pediatric-cancer-research/) - The falling costs and increasing fidelity of high-throughput biomedical research data have led to a renaissance in cancer surveillance and treatment. Yet, the amount, velocity, and complexity of these data have overcome the capacity of the increasing number of researchers collecting and analyzing this information. By centralizing the data, processing power, and tools, there is
- [The Functional Variant Rs34330 Of Cdkn1B Is Associated With Risk Of Neuroblastoma](https://cbtn.org/publications/the-functional-variant-rs34330-of-cdkn1b-is-associated-with-risk-of-neuroblastoma/) - The genetic aetiology of sporadic neuroblastoma is still largely unknown. We have identified diverse neuroblastoma susceptibility loci by genomewide association studies (GWASs); however, additional SNPs that likely contribute to neuroblastoma susceptibility prompted this investigation for identification of additional variants that are likely hidden among signals discarded by the multiple testing corrections used in the analysis
- [Shared Acvr1 Mutations In Fop And Dipg: Opportunities And Challenges In Extending Biological And Clinical Implications Across Rare Diseases](https://cbtn.org/publications/shared-acvr1-mutations-in-fop-and-dipg-opportunities-and-challenges-in-extending-biological-and-clinical-implications-across-rare-diseases/) - Gain-of-function mutations in the Type I Bone Morphogenic Protein (BMP) receptor ACVR1 have been identified in two diseases: Fibrodysplasia Ossificans Progressiva (FOP), a rare autosomal dominant disorder characterized by genetically driven heterotopic ossification, and in 20-25% of Diffuse Intrinsic Pontine Gliomas (DIPGs), a pediatric brain tumor with no effective therapies and dismal median survival. While
- [Pdtm-40: Pediatric Low-Grade Gliomas With Craf Gene Fusions Are Therapeutically Distinct From Braf Fusions Based On Dimerization Mediated By N-Terminal Fusion Partner](https://cbtn.org/publications/pdtm-40-pediatric-low-grade-gliomas-with-craf-gene-fusions-are-therapeutically-distinct-from-braf-fusions-based-on-dimerization-mediated-by-n-terminal-fusion-partner/) - Pediatric low-grade gliomas (PLGGs) are the most common brain tumors in children mainly defined by activating gene fusions that dysregulate the mitogen-associated protein kinase (MAPK) pathway. Our lab has characterized PLGG-associated KIAA1549-BRAF gene fusion along with response to targeted MAPK inhibitors. We have since gone on to explore non-BRAF gene fusions, specifically CRAF (or RAF1)
- [Craf Gene Fusions In Pediatric Low-Grade Gliomas Define A Distinct Drug Response Based On Dimerization Profiles](https://cbtn.org/publications/craf-gene-fusions-in-pediatric-low-grade-gliomas-define-a-distinct-drug-response-based-on-dimerization-profiles/) - Pediatric low-grade gliomas (PLGGs) are commonly associated with BRAF gene fusions that aberrantly activate the mitogen-activated protein kinase (MAPK) signaling pathway. This has led to PLGG clinical trials utilizing RAF- and MAPK pathway-targeted therapeutics. Whole-genome profiling of PLGGs has also identified rare gene fusions involving another RAF isoform, CRAF/RAF1, in PLGGs and cancers occuring in
- [Gpc2 May Be An Immunotherapeutic Target In High-Risk Neuroblastoma](https://cbtn.org/publications/gpc2-may-be-an-immunotherapeutic-target-in-high-risk-neuroblastoma/) - Major finding: A GPC2-targeting antibody–drug conjugate promotes tumor regression in a high-risk neuroblastoma PDX. Approach: An RNA-seq pipeline identifies candidate cell-surface targets specifically expressed in neuroblastoma. Impact: Immunotherapeutic GPC2 targeting may be beneficial in high-risk neuroblastoma and other embryonal tumors.
- [Identification of GPC2 as an Oncoprotein and Candidate Immunotherapeutic Target in High-Risk Neuroblastoma](https://cbtn.org/publications/identification-of-gpc2-as-an-oncoprotein-and-candidate-immunotherapeutic-target-in-high-risk-neuroblastoma/) - The team developed an RNA-sequencing-based pipeline to discover differentially expressed cell-surface molecules in neuroblastoma that meet criteria for optimal immunotherapeutic target safety and efficacy and show that GPC2 is a strong candidate immunotherapeutic target in this childhood cancer. They demonstrate high GPC2 expression in neuroblastoma due to MYCN transcriptional activation and/or somatic gain of the
- [Integrated Molecular Meta-Analysis of 1,000 Pediatric High-Grade and Diffuse Intrinsic Pontine Glioma](https://cbtn.org/publications/integrated-molecular-meta-analysis-of-1000-pediatric-high-grade-and-diffuse-intrinsic-pontine-glioma/) - We collated data from 157 unpublished cases of pediatric high-grade glioma and diffuse intrinsic pontine glioma and 20 publicly available datasets in an integrated analysis of >1,000 cases. We identified co-segregating mutations in histone-mutant subgroups including loss of FBXW7 in H3.3G34R/V, TOP3Arearrangements in H3.3K27M, and BCOR mutations in H3.1K27M. Histone wild-type subgroups are refined by
- [Pediatric Low-grade Gliomas: Next Biologically Driven Steps](https://cbtn.org/publications/pediatric-low-grade-gliomas-next-biologically-driven-steps/) - Despite the fact that they are not typically life-threatening, low-grade gliomas (LGGs) remain a significant clinical challenge in pediatric neuro-oncology due to comorbidities associated with these tumors and/or their treatments, and their propensity to multiply recurs. LGGs, in total the most common brain tumors arising in childhood, can often become a chronic problem requiring decades
- [Comprehensive Analysis of Hypermutation in Human Cancer](https://cbtn.org/publications/comprehensive-analysis-of-hypermutation-in-human-cancer/) - We present an extensive assessment of mutation burden through sequencing analysis of >81,000 tumors from pediatric and adult patients, including tumors with hypermutation caused by chemotherapy, carcinogens, or germline alterations. Hypermutation was detected in tumor types not previously associated with high mutation burden. Replication repair deficiency was a major contributing factor. We uncovered new driver
- [Developing Cancer Informatics Applications and Tools Using the NCI Genomic Data Commons API](https://cbtn.org/publications/developing-cancer-informatics-applications-and-tools-using-the-nci-genomic-data-commons-api/) - The NCI Genomic Data Commons (GDC) was launched in 2016 and makes available over 4 petabytes (PB) of cancer genomic and associated clinical data to the research community. This dataset continues to grow and currently includes over 14,500 patients. The GDC is an example of a biomedical data commons, which collocates biomedical data with storage
- [Overcoming Resistance To Single-Agent Therapy For Oncogenic Braf Gene Fusions Via Combinatorial Targeting Of Mapk And Pi3K/Mtor Signaling Pathways](https://cbtn.org/publications/overcoming-resistance-to-single-agent-therapy-for-oncogenic-braf-gene-fusions-via-combinatorial-targeting-of-mapk-and-pi3k-mtor-signaling-pathways/) - Pediatric low-grade gliomas (PLGGs) are frequently associated with activating BRAF gene fusions, such as KIAA1549-BRAF, that aberrantly drive the mitogen activated protein kinase (MAPK) pathway. Although RAF inhibitors (RAFi) have been proven effective in BRAF-V600E mutant tumors, we have previously shown how the KIAA1549-BRAF fusion can be paradoxically activated by RAFi. While newer classes of
- [Aggressive Triple Negative Breast Cancers Have Unique Molecular Signature On The Basis Of Mitochondrial Genetic And Functional Defects](https://cbtn.org/publications/aggressive-triple-negative-breast-cancers-have-unique-molecular-signature-on-the-basis-of-mitochondrial-genetic-and-functional-defects/) - Metastatic breast cancer is a leading cause of cancer-related deaths in women worldwide. Patients with triple negative breast cancer (TNBCs), a highly aggressive tumor subtype, have a particularly poor prognosis. Multiple reports demonstrate that altered content of the multicopy mitochondrial genome (mtDNA) in primary breast tumors correlates with poor prognosis. We earlier reported that mtDNA

## Research Partners

- [Sabine Mueller, MD, PhD, MAS](https://cbtn.org/research-partners/sabine-mueller-md-phd-mas/) - Dr. Sabine Mueller is a globally recognized pediatric neuro-oncologist, researcher, and advocate for children with brain tumors. As Executive Chair of CBTN, she brings a bold, international perspective to the network’s mission, advancing cross-border collaboration, clinical trial readiness, and equitable research practices. Based at UCSF, Dr. Mueller leads translational efforts that combine bedside care with
- [Adam Resnick, PhD](https://cbtn.org/research-partners/adam-resnick-phd/) - A leading voice in research-driven pediatric neuro-oncology and precision medicine, Dr. Adam Resnick champions a future where open science, AI-powered platforms, and global collaboration radically transform outcomes for children with brain tumors through his role as the Scientific Co-Director of CBTN. Dr. Resnick’s vision helped shape CBTN’s data-driven ecosystem, now powering thousands of researchers worldwide.
- [Tatiana Patton](https://cbtn.org/research-partners/tatiana-patton/) - Tatiana Patton, Director of Operations at the Children’s Brain Tumor Network, leads core operational strategy, infrastructure development, and organizational alignment across the network. She brings to the table expertise in managing complex research programs, optimizing processes, and fostering collaboration among scientific, clinical, and administrative teams. Tatiana’s leadership plays an essential role in strengthening CBTN’s capacity
- [John Prensner, MD](https://cbtn.org/research-partners/john-prensner-md/) - Dr. John Prensner is a physician-scientist and pediatric hematologist/oncologist specializing in the treatment of children with brain tumors. He is a Principal Investigator of an independent biomedical research laboratory focused on the study of the cancer genome in childhood brain cancers. His research interests include the molecular mechanisms and driver genes of brain cancers such
- [Javad Nazarian, PhD](https://cbtn.org/research-partners/javad-nazarian-phd/) - Dr. Javad Nazarian is an internationally renowned researcher whose work has reshaped the landscape of pediatric brain tumor science. As a Scientific Chair of CBTN, he helps guide the network’s global research collaborations, with a special focus on rare and hard-to-treat diseases such as diffuse midline gliomas. His leadership spans continents and institutions, combining molecular
- [Jena Lilly](https://cbtn.org/research-partners/jena-lilly/) - Jena Lilly has over a decade of leadership in pediatric research operations, with a singular focus on building collaborative systems that accelerate cures. As Executive Director of CBTN, she oversees the strategic and operational growth of one of the world’s largest open-access pediatric brain tumor research initiatives. Under her guidance, CBTN has expanded our global
- [Phillip “Jay” Storm, MD](https://cbtn.org/research-partners/phillip-jay-storm-md/) - As one of the nation’s foremost pediatric neurosurgeons, Dr. Jay Storm combines clinical leadership with a deep commitment to advancing brain tumor research. In his dual role as Scientific Co-Director of CBTN and Chief of Neurosurgery at CHOP, Dr. Storm is a driving force behind the integration of patient care and scientific discovery. His expertise
- [Brian Rood, MD](https://cbtn.org/research-partners/brian-rood-md/) - Dr. Brian Rood is a leading clinician-scientist dedicated to changing the standard of care for children with brain tumors. As Executive Chair of CBTN, he plays a pivotal role in integrating clinical insight with the network’s research strategy. Dr. Rood has helped build CBTN into a powerful platform for discovery, ensuring that data and biospecimens

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