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Brian Rood

Children’s National Hospital
Washington, DC USA

CBTN Samples Used

40

CBTN Participants

45

CBTN Samples

CBTN Data Used

Backer

Philanthropic Foundation Support

About this

Project

Cancers commonly arise as the result of changes affecting the DNA sequence of cells including single nucleotide variations, small insertions and deletions, and structural variations including deletions, duplications, inversions, and translocations. In addition to these, cancer specific splicing alterations can also give rise to proteins not commonly found in normal tissues. Structural variations (SV) result in a “knitting together” of non-contiguous DNA sequences that can result in fusion proteins, losses of stop codons, alteration of splice sites, alternative promoter recruitment and the creation of “super-enhancers”. SVs that may concatenate two different genes to form a new gene and new protein product are named gene fusions.

We will use the identification of novel peptides mapping to aberrant tumor specific RNA transcripts to identify true genomic alterations. By virtue of their presence in the proteome, they will also represent aberrant proteins with the potential to influence cellular function.

Ask The

Scientists

Ask the scientists

What are the goals of this project?

The goals of this project are to construct a custom RNA-seq based database of genomic fusion events against which peptide sequences can be searched. Through this project, we aim to detect and do a proteomic validation of tumor specific genomic structural variations such as splice variants, SNVs, deletions, insertions, inversions, translocations, and duplications. Finally, we will establish that our proteogenomic approach to SV identification can be personalized to yield a biomarker of an individual’s tumor.

What is the impact of this project?

The integration of proteomic and genomic data provides a more comprehensive view of the biological features that drive cancer than genomic analysis alone. Using this approach, identified oncoproteins can be studied for their functional contribution to tumorigenesis or tumor maintenance. In addition, DNA SVs represent potential biomarkers detectable by liquid biopsy/ddPCR. Lastly, tumor specific fusion proteins could be potential neoantigens for immunotherapeutic targeting.

Why the CBTN request is important to this project?

We will begin this project with medulloblastoma utilizing CBTN sequence data and tissues. Simulataneously, we will be performing an identical discovery pipeline for DIPG using CBTN sequence data.

Specimen Data

The Children's Brain Tumor Network provided flash frozen tissue samples for proteomic peptide sequencing, CSF for ddPCR and RNA samples for targeted long read nanopore sequencing. CBTN also provided access to the Pediatric Brain Tumor Atlas.

Explore the data in these informatics portals

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