Cholangiocarcinoma (TCGA, PanCancer Atlas 2018)

Overview

The TCGA Cholangiocarcinoma PanCancer Atlas 2018 cohort is the CHOL arm of the TCGA PanCancer Atlas, available in cBioPortal as chol_tcga_pan_can_atlas_2018. It covers cholangiocarcinoma (bile duct cancer) samples with uniformly reprocessed mutation calls (MC3 pipeline), copy-number, and RNA-seq expression. CHOL is a relatively small TCGA disease cohort (~51 samples) but is notable for harboring the highest rate of the recurrent FGFR2-BICC1 fusion, an actionable target with approved FGFR inhibitors.

Composition

  • Cancer type: Cholangiocarcinoma (CHOL), OncoTree code CHOL.
  • Approximately 51 tumor samples.
  • Data modalities: WES, RNA-seq, SNP array.
  • Somatic mutations from MC3 ensemble pipeline.
  • Copy-number from Affymetrix SNP 6.0 / ABSOLUTE.

Assays / panels (linked)

Papers using this cohort

Notable findings derived from this cohort

  • FGFR2-BICC1 is the most recurrent fusion in CHOL (5.6% of samples), the highest rate of this specific fusion in any TCGA disease type; FGFR2 is among the most recurrent 5′-kinase fusion partners in the pan-cancer landscape, actionable with FGFR inhibitors PMID:29617662.
  • Pan-cancer RNA-seq fusion analysis (9,624 TCGA tumors) identified CHOL as having cancer-type-specific enrichment of FGFR2 fusions with intact kinase domains; FGFR2 and FGFR3 together dominate the 5′-kinase recurrent fusion set across all 33 TCGA cancer types PMID:29617662.

Sources

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