Ewing sarcoma (EwS) is an aggressive pediatric cancer driven primarily by aberrant transcriptional activity of the EWS::FLI1 fusion oncoprotein. Despite this uniform genetic driver, EwS tumors display substantial epigenetic and transcriptional heterogeneity, suggesting additional elements influence tumor identity and behavior.
In collaboration with Seattle Children’s Hospital and Fred Hutchinson Cancer Center, we performed multi-omic analysis of ATAC-seq, single-cell RNA-seq (scRNA-seq), and Fiber-seq data from nine EwS tumor cell lines. Sequencing data was analyzed on Talapas, the University of Oregon’s high-performance computing cluster.
Our goal was to characterize how chromatin architecture, structural variation, and transcriptional programs individually or collectively interact to produce heterogeneity in EwS. An understanding of these mechanisms may enable the discovery of more robust diagnostic markers and inform the development of more effective, targeted therapeutic strategies for patients with Ewing Sarcoma.
The results of our project were presented at the 2026 Genomics in Action conference:
Annotation of structural variants (SVs) identified from Fiber-seq data.
Single-cell RNA-seq cell line and cell-type annotations, along with analysis of ATAC-seq data to evaluate differential expression and differential chromatin accessibility across cellular states.
Examination of Fiber-seq–derived chromatin peaks to assess differences in chromatin accessibility across genomic regions and between cell lines.
Inspection of halpotagged Fiber-seq reads to investigate methylation patterns in:
- Fusion genes vs. wild-type loci
- Cell lines that are SV-positive vs. cell lines that are SV-negative
Development and validation of filtering strategies to ensure accurate Variant Call Format (VCF) outputs derived from Fiber-seq data.
Initial analyses focused on a curated set of known EwS-associated genes, later expanded to include all genes.
Our research notebooks.
Figures and design of our Genomics in Action poster.