HNSCC JHU (Agrawal 2011)

Overview

Whole-exome sequencing study of 32 primary HNSCC tumors with matched normals from Johns Hopkins University. A prevalence set of up to 88 additional HNSCC tumors was included for targeted validation of 6 recurrently mutated genes, for 120 total tumors analyzed. Platforms included Illumina GAIIx/HiSeq (17 tumors) and SOLiD V3/V4 (15 tumors) for sequencing, with Affymetrix SNP6.0 copy number analysis on 42 tumor/normal pairs and Sanger sequencing for validation.

Composition

  • Cancer type: HNSC, n = 32 discovery tumors + 88 prevalence set = 120 total.
  • Platforms: Illumina GAIIx/HiSeq and SOLiD V3/V4 at 77-fold (Illumina) and 44-fold (SOLiD) average coverage.
  • Assays: whole-exome-seq; affymetrix-snp6 on 42 tumor/normal pairs; sanger-sequencing for validation.

Assays / panels (linked)

Papers using this cohort

  • PMID:21798897 — Agrawal et al. 2011, Science; discovery sequencing study.

Notable findings derived from this cohort

  • 911 candidate somatic mutations identified in 725 genes across 32 tumors; 609 (67%) confirmed by orthogonal sequencing PMID:21798897.
  • NOTCH1 was the second most frequently mutated gene (15%), with 39% truncating mutations and 7 patients harboring biallelic mutations; first report establishing tumor suppressor role in HNSCC PMID:21798897.
  • HPV-negative tumors had significantly more mutations than HPV-positive tumors (20.6 vs 4.8 per tumor; p < 0.05) PMID:21798897.
  • Recurrent copy number gains at 11q (CCND1), 3q (PIK3CA), and 7p (EGFR); recurrent deletions at 9p21.3 (CDKN2A) PMID:21798897.

Sources

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