WCM Soft Tissue Myoepithelial Carcinoma WGS Study (2022)

Overview

Institutional case series from Weill Cornell Medicine providing the first whole-genome sequencing (WGS) characterization of soft tissue myoepithelial carcinomas (MECs). Two male patients (ages 27 and 37) contributed 12 total tumor samples (primary plus metastatic/recurrent) profiled by WES (mean coverage 98.5x) and WGS (22–29x tumor coverage). RNA-seq was performed on one sample per patient for fusion validation. The dataset is deposited to cBioPortal as stmyec_wcm_2022.

Composition

  • 2 patients with soft tissue MYEC; 12 total tumor samples.
  • WES (mean 98.5x coverage) on all 12 samples; WGS on primary tumor from each patient (Patient 1: 29x tumor/25x normal; Patient 2: 22x tumor/15x normal).
  • RNA-seq on one sample per patient for fusion gene validation.
  • Key clinical fields: age at diagnosis, sex, primary vs metastatic/recurrent sample designation, SMARCB1 and SMARCA2 IHC status.

Assays / panels (linked)

  • whole-exome-seq — all 12 samples, mean 98.5x coverage
  • whole-genome-seq — primary tumor from each patient, 22–29x
  • rna-seq — one sample per patient for fusion validation
  • FISH — confirmatory EWSR1 rearrangement testing

Papers using this cohort

  • PMID:36577525 — Cyrta et al., Cold Spring Harbor Molecular Case Studies 2022. Whole-genome characterization of myoepithelial carcinomas of the soft tissue.

Notable findings derived from this cohort

  • Both MECs displayed very low tumor mutation burden (mean 1.35 mutations/Mb, range 0.43–2.98), consistent with fusion-driven oncogenesis and absence of targetable point mutations by WES PMID:36577525.
  • Patient 1 harbored a novel ASCC2::GGNBP2 in-frame fusion, homozygous SMARCB1 deletion, and biallelic NF1 loss, all arising from a single >30-way biallelic chromoplexy event involving chromosomes 17, 19, and 22 — detectable only by WGS PMID:36577525.
  • Patient 2 harbored an EWSR1::KLF15 rearrangement and high-level (>10 copy) ELK4 amplification via double minute, also identified by WGS PMID:36577525.
  • COSMIC Signature 3 (HR-deficiency-associated) contributed 36.8% and 17.4% of SNVs in MEC1 and MEC2 respectively, despite no detectable somatic HR pathway alterations PMID:36577525.

Sources

  • cBioPortal study: stmyec_wcm_2022
  • Associated publication: PMID:36577525

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