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Mateusz Koptyra

Children’s Hospital of Philadelphia
Philadelphia, PA, USA

CBTN Samples Used


CBTN Participants


CBTN Samples


Institutional Funds

About this


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: a) the lack of comprehensive molecular characterization involving integration of the DNA-RNA-protein profiling; b) comprehensive and molecularly-driven preclinical tests for informing precision-targeting disease pathways; and c) lack of sensitive methods of assessing tumor response to treatment. The surgery remains the mainstay of pediatric brain tumor treatment and since many tumors are non-resectable and/or progressive/disseminated tumors, this lead to significant tumor-related morbidity. There is ongoing need to discover new tumor specific biomarkers which can be explored in preclinical research and lead to the development novel therapeutic approaches. Biomarker discovery requires access to molecular data which can be generated based on the access to tumor bio-specimens.

Recent efforts from of Children’s Brain Tumor Network (CBTN), Cavatica, Kids First effort and D3b center led to creation the one of the world's most comprehensive collections of childhood brain tumor data. The data is now available to researchers as the Pediatric Brain Tumor Atlas (PBTA), an initiative seeking to transform the discovery process and accelerate the translation of large-scale molecular and clinical datasets to novel therapeutic approaches for children affected by brain tumors. The dataset release represents data collected from more than 1,000 subjects and 30 unique brain tumor types. The openly-available data stored within the Atlas will continue to increase.

The D3b center leading the Kids First program and PBTA effort was presented with a unique opportunity to generate miRNA panel analysis for over 200 specimens with the collaboration with HTG Diagnostics. HTG Diagnostics is offering 224 panel miRNA analysis (~2100 miRNA in panel) free of charge in order to support pediatric brain tumor data generation and Kids First efforts.

The microRNAs (miRNAs) are small RNA molecules, approximately 22 nucleotides long. While histone modifications control the chromatic accessibility and transcriptional activities, miRNA can control their target gene expression post-transcriptionally. The miRNA may bind to complementary sequences in the 3’ UTR of target genes and modify the expression by repressing translation and/or inducing deadenylation and following mRNA degradation. Single miRNAs can target up to several hundreds of mRNAs, while a single mRNA can be targeted by many miRNAs. This enables miRNA to regulate many signaling pathways and cellular processes. The miRNA altered expression is associated with many types of cancers, including pediatric brain tumors including medulloblastoma, ependymoma, gliomas and more.

Ask The


Ask the scientists

What are the goals of this project?

The primary goal for this project is to perform miRNA panel analysis using the HTG EdgeSeq miRNA panel analysis.

What is the impact of this project?

The project will support the CBTN vision of open access and collaboration by generating a significant amount of free data for further analysis by researchers worldwide, both within and outside of the consortium.

Why the CBTN request is important to this project?

The first cohort of PBTA sample subset (utilized in CBTN Pediatric Brain Tumor Proteomics Pilot) which consist of tumor and germline whole genome sequencing, RNAseq and proteomic (targeted and phosphor –proteomic) profiling provides the unique opportunity expand the data set with introduction of miRNA analysis. These already multi-lawyer data sets obtained from the same biospecimens and combined with the clinical and pathology data provide comprehensive meta-analysis exploration possibilities. Expanding this data set with addition of expression data from over 2000 miRNAs will allow for broader data explorations involving key aspects miRNA–messenger RNA (mRNA) regulatory network which is far from being fully understood for majority of pediatric brain tumors. Our data generation effort together with the immediate “no embargo” access not only build the resource for data mining but also support future preclinical research studies and therapeutic development for the pediatric brain tumors.

Specimen Data

The Children's Brain Tumor Network contributed to this project by providing RNA samples for the generation of miRNAseq.