Breast Invasive Carcinoma (TCGA, PanCancer Atlas 2018)

Overview

The TCGA Breast Invasive Carcinoma PanCancer Atlas 2018 cohort is the breast cancer arm of the TCGA PanCancer Atlas, available in cBioPortal as brca_tcga_pan_can_atlas_2018. It encompasses approximately 1,084 breast invasive carcinoma samples with uniformly reprocessed mutation calls (MC3 pipeline), copy-number profiles, and RNA-seq expression. The cohort spans all major molecular subtypes (luminal A, luminal B, HER2-enriched, basal-like, and claudin-low).

Composition

  • Cancer type: Breast Invasive Carcinoma (BRCA), OncoTree code BRCA.
  • Approximately 1,084 tumor samples.
  • Data modalities: WES, RNA-seq, SNP array.
  • Somatic mutations from MC3 ensemble pipeline; BRCA showed >90% concordance with legacy PanCan12 calls.
  • Copy-number from Affymetrix SNP 6.0 / ABSOLUTE; includes HER2-amplified, copy-number-high basal, and diploid luminal subtypes.

Assays / panels (linked)

Papers using this cohort

Notable findings derived from this cohort

  • Pan-cancer RNA-seq fusion analysis (9,624 TCGA tumors) identified 9 ESR1 fusions in BRCA (8 luminal A/B), with strict mutual exclusivity with ESR1 point mutations; ESR1 expression was elevated in fusion-positive samples, suggesting a promoter-swap mechanism distinct from the resistance-associated ESR1 mutations seen in endocrine-treated metastatic BRCA PMID:29617662.
  • Four ERBB2 fusions were identified across TCGA cancer types; 3 of 4 had HPV integration within 1 Mb of ERBB2, with partner genes PPP1R1B and IKZF3 being genomic neighbors suggesting local instability-driven rearrangement as an alternative mechanism of HER2 dysregulation distinct from amplification PMID:29617662.
  • Breast cancer (BRCA) had among the highest concordance (>90%) between MC3 mutation calls and the legacy PanCan12 MAF, indicating stable mutation calling across pipeline versions for this tumor type PMID:29617662.
  • Pan-cancer aneuploidy analysis placed BRCA in the epithelial cluster (alongside LUAD and HCC) defined by 1q gain; copy-number-high serous-like endometrial cancers cluster with BRCA basal-like as a notable inter-disease grouping PMID:29617662.

Sources

This page was processed by crosslinker on 2026-05-15.