MSK Gallbladder Carcinoma 2022

Overview

The largest single-institution genomic characterization of gallbladder carcinoma (GBC) to date, from Memorial Sloan Kettering Cancer Center. The study profiled 244 samples from 233 patients collected between 2014 and 2021 using MSK-IMPACT (341–505 gene panel versions), with median sequencing coverage of 634X. Dataset deposited in cBioPortal as gbc_mskcc_2022.

Composition

  • 233 patients / 244 samples of GBC, collected 2014–2021 at Memorial Sloan Kettering Cancer Center.
  • 57% primary tumors, 43% metastases; 85% adenocarcinomas, 10% carcinomas with squamous differentiation, 5% neuroendocrine carcinomas.
  • Median age at collection: 66 years (range 37–90); 63% Caucasian, 12% African American, 12% Asian.
  • 67% stage IV, 18% stage III at time of collection.
  • Microsatellite instability assessed via MSIsensor, MiMSI, and IDYLLA MSI; variants annotated with OncoKB.

Assays / panels (linked)

  • MSK-IMPACT — 341–505 gene panel versions; median coverage 634X (range 72X–1150X)

Papers using this cohort

  • PMID:36228155 — Primary genomic characterization of GBC; identifies frequent alterations, prognostic biomarkers, and actionable targets.

Notable findings derived from this cohort

  • Most frequent oncogenic mutations: TP53 (63%), CDKN2A (21%), SMAD4 (19%), ARID1A (18%), ERBB2 (15% combined mutation + amplification); most frequent CNAs: CDKN2A/CDKN2B deletions (14%), MDM2 amplification (11%), ERBB2 amplification (10%), CCNE1 amplification (9%) PMID:36228155.
  • SMAD4 LOF mutations independently associated with reduced OS in metastatic disease (multivariate HR 2.11, p = 0.012); STK11 LOF mutations also independently associated with reduced OS (multivariate HR 3.76, p = 0.004) PMID:36228155.
  • Actionable alterations (OncoKB levels 1, 3A, or 3B) identified in 35.2% of patients; 18% of metastatic patients received biomarker-directed therapy or enrolled in clinical trials based on MSK-IMPACT findings; 6 tumors (3%) were MSI-High PMID:36228155.
  • LMNA::NTRK1 fusion identified in 1 patient (OncoKB level 1); KRAS G12C in 2 patients (level 3A); FGFR3::TACC3 in-frame fusion in 1 patient; no recurrent structural variants were identified PMID:36228155.

Sources

  • cBioPortal study: gbc_mskcc_2022

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