molecular-subtyping-EWS

Molecular Subtyping of Ewing's Sarcoma

Module authors: Krutika Gaonkar (@kgaonkar6), Jo Lynne Rokita (@jharenza) and Jaclyn Taroni (@jaclyn-taroni)

EWSR1 fusions are hallmark alterations of Ewing's Sarcoma but we see these fusions in samples with other broad_histologies in our dataset (Diffuse astrocytic and oligodendroglial tumor (1), Metastatic secondary tumors (2), Tumors of sellar region (1)). This analysis will subtype these samples as "EWS" (Ewing's Sarcoma) tumors.

Usage

This module can be run with the following:

bash run_subtyping.sh

Molecular subtyping EWS workflow

Module contents

01-run-subtyping-ewings.Rmd identifies sample_id for RNA-Seq samples with hallmark EWSR1 fusions and matches sample_id with WGS sample and adds molecular_subtype as "EWS" (Ewing Sarcoma). The tabular output (results/EWS_results.tsv) only contains tumors where molecular_subtype == "EWS".