Bladder Urothelial Carcinoma (TCGA, PanCancer Atlas 2018)

Overview

The TCGA Bladder Urothelial Carcinoma PanCancer Atlas 2018 cohort is the BLCA arm of the TCGA PanCancer Atlas, available in cBioPortal as blca_tcga_pan_can_atlas_2018. It covers approximately 411 bladder urothelial carcinoma samples with uniformly reprocessed mutation calls (MC3 pipeline), copy-number, and RNA-seq expression. BLCA had greater than 90% concordance with the legacy PanCan12 MAF for mutation calls.

Composition

  • Cancer type: Bladder Urothelial Carcinoma (BLCA), OncoTree code BLCA.
  • Approximately 411 tumor samples.
  • Data modalities: WES, RNA-seq, SNP array.
  • Somatic mutations from MC3 ensemble pipeline; >90% concordance with PanCan12 legacy calls.
  • Copy-number from Affymetrix SNP 6.0 / ABSOLUTE.

Assays / panels (linked)

Papers using this cohort

Notable findings derived from this cohort

  • FGFR3-TACC3 is the most recurrent kinase fusion in BLCA (2.0% of samples), one of the highest rates across all cancer types for this specific activating inframe kinase fusion; FGFR3 is a druggable target nominated across 15 cancer types by DEPO annotation PMID:29617662.
  • Pan-cancer fusion analysis (9,624 TCGA tumors) placed BLCA among cancer types with median 1 fusion per sample; FGFR3 and TACC3 emerge as the defining recurrent fusion partners for this tumor type PMID:29617662.
  • BLCA had greater than 90% concordance between MC3 mutation calls and the legacy PanCan12 MAF, indicating stable and reproducible mutation calling for this tumor type across pipeline iterations PMID:29617662.

Sources

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