PAAD UT Southwestern 2015 (Witkiewicz et al.)

Overview

Microdissected whole-exome sequencing cohort of 109 surgically resected pancreatic ductal adenocarcinoma (PDA) cases from UT Southwestern Medical Center, published in Nature Communications 2015 (PMID:25855536). A key methodological feature was laser or manual needle microdissection of tumor epithelium prior to DNA extraction, which raised the average non-synonymous mutation count to 67/case — substantially higher than the 26/case seen in prior bulk-tissue exome studies. Raw reads deposited at NCBI SRA BioProject PRJNA278883.

Composition

  • N = 109 surgically resected PDA cases with matched germline (normal tissue n=105, peripheral blood n=4).
  • Histological subtypes: ductal carcinoma NOS / PAAD 86% (n=94), adenosquamous / PAASC 10% (n=11), colloid / PAAC 4% (n=4).
  • Stage: mostly stage I (n=5) or II (n=97); stage III (n=6) or IV (n=1).
  • Median overall survival: 21 months. Median age 66 (range 29–86); 50% male.
  • Tumor cellularity: >50% (achieved via microdissection); tumor epithelium manually needle-dissected under dissecting microscope.

Assays / panels (linked)

  • whole-exome-seq — TruSeq Exome Enrichment (FC-121-1048) or Nextera Exome Enrichment (FC-140-1003) on Illumina HiSeq 2500; mean depth 51.28× (95% CI 49.5–53.1); 21 cases re-sequenced to ~123×. Reads aligned with bwa to UCSC hg19.
  • mutect — SNV calling (≥14 tumor reads, ≥8 normal reads).
  • varscan — INDEL calling (≥8 reference reads, ≥3 variant reads); indels manually inspected in IGV.
  • oncotator — variant annotation (Broad Institute).
  • gistic — copy-number calls (join_segment_size=4, conf=0.95; ExomeCNV + DNAcopy segmentation).
  • mutsig — MutSigCV for significantly mutated gene discovery; combined 208-case meta-cohort with Biankin et al. ICGC.
  • sanger-sequencing — validation of 248 non-silent mutations in 84 cases (92% confirmation rate, 95% CI 87.6–94.6%).
  • fish — Vysis LSI MYC dual-colour break-apart probe for 8q24 MYC amplification confirmation.
  • immunohistochemistry — ARID1A, p53, pERK, p63; ARID1A IHC in independent 296-case cohort.
  • random-forest-classifier — unsupervised pathway-alteration subtype clustering.

Papers using this cohort

  • PMID:25855536 — Witkiewicz et al., Nature Communications 2015: whole-exome sequencing of 109 microdissected PDA; primary discovery study for this cohort.

Notable findings derived from this cohort

  • 24 significantly mutated genes (MutSigCV); KRAS mutated in 92%; MYC amplification at 8q24.13 uniquely associated with poor overall survival (P=0.0013) and adenosquamous histology. PMID:25855536
  • KRAS codon-61 mutations (Q61H/K/R) associated with favorable overall survival (P=0.02) and lower pERK staining versus codon-12 mutations, demonstrating allele-specific MAPK output differences. PMID:25855536
  • BRAF V600E in 3% of cases (mutually exclusive with KRAS); patient-derived cell line PDA_014 confirmed sensitive to vemurafenib. PMID:25855536
  • ARID1A protein loss by IHC in independent 296-case cohort associated with poor overall survival (P=0.0202); ARID1A-deficient PDA cell lines vulnerable to ARID1B depletion (synthetic lethal). PMID:25855536
  • RBM10 mutations (4%) associated with prolonged overall survival (P=0.0345) despite aggressive histological features. PMID:25855536
  • High-CNV clusters (5 & 6) enriched for biallelic DNA double-strand-break repair gene loss (ATM, BRCA1, BRCA2, Fanconi-anaemia genes); cluster 6 trended toward worst survival (HR=3.91, P=0.034). PMID:25855536

Sources

  • cBioPortal study: paad_utsw_2015
  • NCBI SRA BioProject: PRJNA278883

This page was processed by crosslinker on 2026-05-14.