Lung Squamous Cell Carcinoma (TCGA, Nature 2012)

Overview

178 previously untreated stage I-IV lung squamous cell carcinoma tumours with matched normals comprehensively profiled by the Cancer Genome Atlas consortium using whole-exome sequencing, whole-genome sequencing, RNA-seq, miRNA-seq, copy number arrays, and methylation arrays. Published in Nature 2012. The study defined the genomic landscape of LUSC, identified near-universal TP53 mutation, and proposed a potential therapeutic target in 64% of tumours. PMID:22960745

Composition

• 178 previously untreated stage I-IV LUSC tumour-normal pairs.
• 96% of patients had a history of tobacco use; median follow-up 15.8 months.
• WES: 178 tumours + matched normals (mean 121x coverage).
• WGS: 19 tumour-normal pairs (mean 54x).
• RNA-seq: 178 samples; miRNA-seq: 159 samples.
• Affymetrix SNP 6.0 copy number arrays + DNA methylation arrays. PMID:22960745

Assays / panels (linked)

• whole-exome-seq — 178 tumour-normal pairs (mean 121x)
• whole-genome-seq — 19 tumour-normal pairs (mean 54x)
• rna-seq — 178 samples
• affymetrix-snp6 — genome-wide copy number profiling
• gistic — focal amplification/deletion calling from SNP array data
• mutsig — significantly mutated gene discovery

Papers using this cohort

• PMID:22960745 — primary TCGA characterisation (Cancer Genome Atlas Research Network, Nature 2012)
• PMID:27158780 — Campbell et al. 2016, Nature Genetics: 176 TCGA SqCC cases incorporated into the integrated 1,144-NSCLC exome cohort nsclc_tcga_broad_2016.

Notable findings derived from this cohort

• Mean somatic mutation rate of 8.1 mutations/Mb (median 8.4/Mb), highest of all TCGA tumour types at publication (P < 2.2e-16). PMID:22960745
• 10 significantly mutated genes (FDR q < 0.1): TP53 (81–90%), CDKN2A, PTEN, PIK3CA, KEAP1, KMT2D, HLA-A, NFE2L2, NOTCH1, RB1. PMID:22960745
• NFE2L2/KEAP1/CUL3 oxidative-stress pathway altered in 34% of tumours. PMID:22960745
• Squamous differentiation pathway altered in 44%: SOX2/TP63 amplification/overexpression; NOTCH1/2 loss-of-function. PMID:22960745
• PI3K/AKT pathway altered in 47%; CDKN2A/RB1 pathway altered in 72%. PMID:22960745
• Potential therapeutic targets identified in 64% of tumours. PMID:22960745
• 176 cases from this cohort merged into the integrated nsclc_tcga_broad_2016 Pan-Lung analysis; the expanded SqCC sample identified novel SMGs RASA1, CUL3 and novel focal amplifications YES1 and MIR205. PMID:27158780

Sources

• PMID:22960745

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