Lung Adenocarcinoma Tumour Sequencing Project (TSP)

Overview

The Tumour Sequencing Project (TSP) LUAD cohort is a multi-institutional effort that performed targeted sequencing of 623 candidate cancer genes across 188 primary lung adenocarcinoma tumours with matched normals. Samples were contributed by Dana-Farber, MD Anderson, Memorial Sloan-Kettering, University of Michigan, and Washington University. The dataset is publicly available via dbGaP (phs000144.v1.p1) and GEO (GSE12667 for expression data).

Composition

  • 188 primary LUAD tumours (minimum 70% tumour content), with matched normal tissue.
  • Targeted DNA sequencing of 623 candidate cancer genes (all coding exons and splice sites); 247 Mb of tumour DNA analysed per sample.
  • SNP array (Affymetrix 250K StyI) copy number data on 383 tumours.
  • Gene expression (Affymetrix U133Plus2) on 75 tumours.
  • Clinical fields include smoking status, tumour grade, and histological subtype.

Assays / panels (linked)

  • targeted-dna-seq — 623-gene cancer gene panel covering all coding exons and splice sites.
  • SNP array (Affymetrix 250K StyI) for copy number analysis.
  • Gene expression array (Affymetrix U133Plus2).

Papers using this cohort

  • PMID:18948947 — Ding et al. 2008, Nature: Somatic mutations affect key pathways in lung adenocarcinoma.

Notable findings derived from this cohort

  • Targeted sequencing of 623 candidate cancer genes across 188 primary LUAD tumours (dbGaP phs000144.v1.p1), identifying 1,013 somatic mutations and 26 significantly mutated genes including NF1, ATM, RB1, APC, ERBB4, and EPHA3 as novel recurrently mutated genes in lung adenocarcinoma PMID:18948947.

Sources

  • dbGaP: phs000144.v1.p1
  • GEO: GSE12667 (expression data)

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