Biliary Tract and Hepatocellular Carcinoma Hidden-Genome Classifier, MSK, Clin Cancer Res 2024

Overview

MSK cohort of 1,370 patients with histologically confirmed biliary tract cancer, hepatocellular carcinoma, or biphenotypic IHC/HCC tumors sequenced 2003–2022 by MSK-IMPACT. Used to train and apply a supervised “hidden-genome” machine-learning classifier that scores each intrahepatic cholangiocarcinoma’s genetic similarity to EHC/GBC versus HCC reference classes PMID:38864854.

Composition

  • 1,370 patients total; 527 IHCH classified against reference classes EHCH, GBC, and HCC PMID:38864854.
  • Sequenced on MSK-IMPACT panels 341/410/468/505; 341 genes common across versions were used PMID:38864854.

Assays / panels (linked)

Papers using this cohort

  • PMID:38864854 — Song et al., A Novel Approach to Quantify Heterogeneity of Intrahepatic Cholangiocarcinoma: the Hidden-Genome Classifier, Clin Cancer Res 2024.

Notable findings derived from this cohort

  • 410 IHC (78%) had >50% genetic homology with EHC/GBC; 122 (23%) exceeded >90% homology (“biliary-class”), characterized by KRAS, SMAD4, and CDKN2A loss PMID:38864854.
  • 117 IHC (22%) had >50% homology with HCC; 30 (5.7%) exceeded >90% (“HCC-class”), characterized by TERT alterations PMID:38864854.
  • Median OS (unresectable): biliary-class 1.0 y vs non-biliary-class 1.8 y; (resectable): 2.4 y vs 5.1 y PMID:38864854.
  • Classifier predicted OS independently of FGFR2 and IDH1 alterations and outperformed histologic subtyping PMID:38864854.

Sources

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