HCC INSERM France 2015 (Schulze et al.)

Overview

Multi-institutional European whole-exome sequencing cohort of 243 surgically resected hepatocellular carcinomas (HCC) with matched non-tumor liver, assembled by Schulze, Letouzé, Zucman-Rossi and colleagues at INSERM (Paris-Créteil, Bordeaux), with additional cases from Milan (n=41) and Barcelona (n=9). Published in Nature Genetics 2015 (PMID:25822088). Raw data deposited in EGA (EGAS00001000217, EGAS00001000679, EGAS00001001002) and ICGC data portal (release 18, 10 December 2014).

Composition

  • N = 243 surgically resected liver tumors (193 France, 41 Italy, 9 Spain); matched non-tumor liver for all.
  • Cancer type: HCC.
  • Fibrosis: F4 cirrhosis n=118; F2–F3 n=46; F0–F1 non-fibrotic n=79.
  • Risk factors: alcohol 41%, HCV 26%, NASH/metabolic syndrome 18%, HBV 14%, hemochromatosis 7%, unknown etiology 11%.
  • Tumor progression stages: 7 dysplastic macronodules, 7 early HCC, 17 small-progressed HCC, 58 classic HCC, 29 poor-prognosis HCC.

Assays / panels (linked)

  • whole-exome-seq — Agilent SureSelect v2/v3/v4/v5+UTRs on Illumina HiSeq 2000 (paired-end 75 bp); mean depth 72× (~92.6% targeted bases at ≥10×).
  • sanger-sequencing — validation of 11 genes in 155 tumors; 88% sensitivity (95% CI 82–92%), 99% specificity.
  • mutational-signatures — Wellcome Trust Sanger Institute NMF framework; identified 8 signatures including novel signatures 23 and 24.
  • mutsig — MutSigCV for significantly mutated gene discovery.
  • oncotator — variant annotation (alongside Alamut).

Papers using this cohort

  • PMID:25822088 — Schulze et al., Nature Genetics 2015: whole-exome sequencing of 243 HCC; primary discovery study for this cohort.

Notable findings derived from this cohort

Sources

  • cBioPortal study: hcc_inserm_fr_2015
  • EGA: EGAS00001000217, EGAS00001000679, EGAS00001001002
  • ICGC data portal release 18 (10 December 2014)

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