The Landscape of Alterations from 1407 Ultra-Rare Sarcomas from the AACR GENIE Database: Clinical Implications

Authors

Ryan A Denu
Justin T Moyers
Mohamed A Gouda
Anthony P Conley
Alexander J Lazar
Vivek Subbiah

Publication Date

11-14-2023

Journal

Clinical Cancer Research

Abstract

Purpose: Ultra-rare sarcomas (URS) comprise a group of orphan diseases with an incidence of ≤1/1,000,000 people per year. We aimed to assess clinically actionable genomic alterations in URS.

Experimental design: Data were extracted from the GENIE database using cBioPortal. OncoKB was used to assess for clinical actionability of mutations. Tumor mutational burden (TMB) was inferred from clinical sequencing data.

Results: Soft tissue (ST) URS made up 23.5% of ST sarcoma cases, and bone URS made up 16.5% of bone sarcoma cases. The most commonly mutated gene in all four groups was TP53. The most common fusions involved EWSR1. The most common copy-number variations included deletions of CDKN2A and CDKN2B and amplifications of MDM2 and CDK4. TMB was generally low across all four categories of sarcoma, though there was considerable heterogeneity, with 3.8% of ST URS and 0.55% of bone URS having high TMB. We find Level 1 alterations (FDA-recognized biomarker predictive of response to an FDA-approved drug) in 10.0% of ST URS compared with 7.1% of ST non-URS, 1.1% of bone URS, and 4.5% of bone non-URS. Level 1-3 alterations (also include alterations for which there are standard-of-care drugs or clinical evidence supporting a drug) were seen in 27.8% of ST URS, 25.2% of ST non-URS, 20.9% of bone URS, and 17.4% of bone non-URS.

Conclusions: Clinically actionable genomic alterations are seen in a substantial fraction of URS. Clinical sequencing in advanced URS has the potential to guide the treatment of a significant portion of patients with URS.

Keywords

Humans, Sarcoma, Mutation, Biomarkers, Tumor, DNA Copy Number Variations, Osteosarcoma, Bone Neoplasms, ultra-rare sarcoma, sequencing, precision medicine, fusion, TMB

DOI

10.1158/1078-0432.CCR-23-0876

PMID

37643131

PMCID

PMC11874058

PubMedCentral® Posted Date

3-3-2025

PubMedCentral® Full Text Version

Author MSS

Published Open-Access

yes