Pancreatic Cystic Tumors (JHU, 2011)

Overview

This cohort was assembled at Johns Hopkins University and comprises 32 surgically resected neoplastic pancreatic cysts (8 serous cystadenomas, 8 intraductal papillary mucinous neoplasms, 8 mucinous cystic neoplasms, and 8 solid pseudopapillary neoplasms) with matched normal tissue from the same patients. The study was designed to define the genomic landscapes of all four major pancreatic cystic neoplasm subtypes simultaneously by whole-exome sequencing.

Composition

  • 32 microdissected cyst samples (>33% neoplastic cellularity required) with matched germline DNA.
  • Cancer types: IPMN, MCN, SPN, and serous cystadenoma (SCA; no OncoTree code); progression target PAAD.
  • An additional 18 SCA cyst fluids and 28 IPMN + 3 MCN cyst fluids were screened for selected mutations.

Assays / panels (linked)

  • Whole-exome sequencing: Agilent 50-Mb SureSelect capture on Illumina GAIIx/HiSeq; mean unique coverage ~120-fold (+/- 40) across 64 libraries.
  • Customized VHL capture chip for validation of SCA cyst fluids.
  • Ligation-based mutation confirmation assays for selected variants.

Papers using this cohort

  • PMID:22158988 — Primary WES study defining the somatic mutation landscape of all four cyst types.

Notable findings derived from this cohort

  • A five-gene panel (VHL, RNF43, CTNNB1, GNAS, KRAS) distinguishes all four cyst types in cyst fluid with complete molecular specificity, enabling non-surgical diagnostic classification PMID:22158988.
  • RNF43 established as a novel tumor suppressor recurrently inactivated in IPMN (6/8) and MCN (3/8); probability of being a passenger < 10^-12 PMID:22158988.
  • SPNs had only 2.9 +/- 2.1 nonsynonymous mutations per tumor with universal CTNNB1 mutations, the fewest somatic alterations of any tumor type profiled by WES at the time PMID:22158988.

Sources

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