Lung Adenocarcinoma (TCGA, PanCancer Atlas 2018)

Overview

The TCGA Lung Adenocarcinoma PanCancer Atlas 2018 cohort is the LUAD arm of the TCGA PanCancer Atlas, available in cBioPortal as luad_tcga_pan_can_atlas_2018. It encompasses approximately 566 lung adenocarcinoma samples with uniformly reprocessed mutation calls (MC3 pipeline), copy-number, and RNA-seq expression. LUAD is characterized by high mutation burden (tobacco-associated), a clinically important never-smoker subset with enrichment for druggable fusions, and arm-level aneuploidy patterns distinct from squamous lung carcinoma.

Composition

  • Cancer type: Lung Adenocarcinoma (LUAD), OncoTree code LUAD.
  • Approximately 566 tumor samples.
  • Data modalities: WES, RNA-seq, SNP array.
  • Somatic mutations from MC3 ensemble pipeline; LUAD has one of the highest median SNVs per sample (tobacco-associated).
  • Copy-number from Affymetrix SNP 6.0 / ABSOLUTE.

Assays / panels (linked)

Papers using this cohort

Notable findings derived from this cohort

  • EML4-ALK and other ALK fusions were identified in 5 LUAD samples (total 20 ALK fusions across 8 cancer types); EML4 is the most frequent 5′ partner (7/17 of all ALK-fusion cases), with ALK overexpression copy-number neutral — supporting the rationale for crizotinib and approved ALK inhibitors PMID:29617662.
  • Never-smoker LUAD cohort within this dataset is dramatically enriched for druggable fusions: 20% (15/75) of never-smokers vs. 2.1% (9/425) of smokers harbor a druggable fusion (chi-square p < 1e-6); data supports prioritizing fusion screening in non-smoking NSCLC patients PMID:29617662.
  • RET fusions (e.g., CCDC6-RET) also seen in LUAD in addition to THCA PMID:29617662.
  • Pan-cancer aneuploidy analysis placed LUAD in the epithelial cluster (alongside BRCA and HCC) defined by 1q gain; fewer than 50% of LUAD tumors had 3p loss and only 13% had 3q gain — a pattern strikingly different from the squamous LUSC subtype where 3p loss is present in ~80% of tumors PMID:29617662.
  • LUAD has one of the highest median SNVs per sample in the MC3 pan-cancer analysis, consistent with tobacco-associated mutagenesis (C>A transversions), alongside SKCM and LUSC PMID:29617662.

Sources

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