Proposed Analysis: Identify CNS Ewing Sarcomas

[jharenza]

What are the scientific goals of the analysis?

• Confirm/identify all samples with Ewings Sarcoma hallmark fusions are classified as such in integrated_diagnosis.
• Remove CNS EFT-CIC from short_histology for these samples, as these are distinct tumors with different transcriptional regulation and fusion alterations.

What methods do you plan to use to accomplish the scientific goals?

PR 1:

1. Survey all samples for the following fusions:
2. Create 1,0 matrix fusion summary file for ewings (add here) --> fusion_summary_ewings_foi.tsv

PR2
3. Use 2. above to identify samples which should be categorized as Ewings sarcoma:

• Ewings Sarcoma (integrated_diagnosis) and EWS (short_histology)
  • Fusions are one of: EWSR1‐FLI1, EWSR1‐ERG, EWSR1‐PATZ1, or FUS‐ERG

What input data are required for this analysis?

putative_oncogenic_fusions.tsv

How long do you expect is needed to complete the analysis? Will it be a multi-step analysis?

1-2 days

Who will complete the analysis (please add a GitHub handle here if relevant)?

@kgaonkar6

What relevant scientific literature relates to this analysis?

ijms-21-01818.pdf
Specht, et al, 2014

[jaclyn-taroni]

Closed via #635 and #640.