HNSCC Broad (Stransky 2011)

Overview

Whole-exome sequencing study of 74 head and neck squamous cell carcinoma (HNSCC) tumors generated by the Broad Institute and Dana-Farber Cancer Institute. Initially 92 patients were sequenced; 18 were excluded for stromal admixture. Two tumors also underwent whole-genome sequencing. The dataset characterized the mutational landscape of HNSCC including HPV-associated tumors across oral cavity, oropharynx, hypopharynx, larynx, and sinonasal cavity subsites.

Composition

  • Cancer type: HNSC, n = 74 tumors with matched normals.
  • Subsites: oral cavity, oropharynx, hypopharynx, larynx, sinonasal cavity.
  • 89% reported tobacco use; 79% alcohol use; 14% HPV-16 positive by PCR/ISH.
  • Assay: whole-exome-seq at 150x mean coverage (87% of loci >20x); two tumors also underwent whole-genome-seq at 31x mean coverage.
  • Copy number profiled by SNP arrays.

Assays / panels (linked)

Papers using this cohort

  • PMID:21798893 — Stransky et al. 2011, Science; discovery sequencing study.

Notable findings derived from this cohort

  • Mean non-synonymous mutation rate of 3.3 mutations/Mb; HPV-positive tumors had lower rates (2.28 vs 4.83 mutations/Mb; p = 0.004) PMID:21798893.
  • MutSig identified 39 significantly mutated genes (FDR q < 0.1), with NOTCH1 mutated in 11% (predominantly loss-of-function) and TP53 nearly universally inactivated PMID:21798893.
  • A squamous differentiation gene set (NOTCH1, IRF6, TP63) was the top enriched functional category among significantly mutated genes PMID:21798893.
  • G-to-T transversion frequency (mean 12%) characteristic of tobacco exposure; HPV-negative laryngeal cancers had highest rates PMID:21798893.

Sources

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