DOI: 10.5061/dryad.hf93m
title: Data from: Reporting tumor molecular heterogeneity in histopathological diagnosis

description: Background: Detection of molecular tumor heterogeneity has become of
 paramount importance with the advent of targeted therapies. Analysis for
 detection should be comprehensive, timely and based on routinely available
 tumor samples. Aim: To evaluate the diagnostic potential of targeted
 multigene next-generation sequencing (TM-NGS) in characterizing
 gastrointestinal cancer molecular heterogeneity. Methods: 35
 gastrointestinal tract tumors, five of each intestinal type gastric
 carcinomas, pancreatic ductal adenocarcinomas, pancreatic intraductal
 papillary mucinous neoplasms, ampulla of Vater carcinomas, hepatocellular
 carcinomas, cholangiocarcinomas, pancreatic solid pseudopapillary tumors
 were assessed for mutations in 46 cancer-associated genes, using Ion
 Torrent semiconductor-based TM-NGS. One ampulla of Vater carcinoma cell
 line and one hepatic carcinosarcoma served to assess assay sensitivity.
 TP53, PIK3CA, KRAS, and BRAF mutations were validated by conventional
 Sanger sequencing. Results: TM-NGS yielded overlapping results on matched
 fresh-frozen and formalin-fixed paraffin-embedded (FFPE) tissues, with a
 mutation detection limit of 1% for fresh-frozen high molecular weight DNA
 and 2% for FFPE partially degraded DNA. At least one somatic mutation was
 observed in all tumors tested; multiple alterations were detected in 20/35
 (57%) tumors. Seven cancers displayed significant differences in allelic
 frequencies for distinct mutations, indicating the presence of intratumor
 molecular heterogeneity; this was confirmed on selected samples by
 immunohistochemistry of p53 and Smad4, showing concordance with mutational
 analysis. Conclusions: TM-NGS is able to detect and quantitate multiple
 gene alterations from limited amounts of DNA, moving one step closer to a
 next-generation histopathologic diagnosis that integrates morphologic,
 immunophenotypic, and multigene mutational analysis on routinely processed
 tissues, essential for personalized cancer therapy.
description: AVC1 Sequences
 fileThese files contain
 next-generation sequencing data (sequencer: Ion Torrent PGM) aligned to
 hg19 genome used to produce the data presented in tables and figures of
 the manuscript.AVC1.bamAVC2 Sequences fileThese files contain next-generation sequencing data (sequencer: Ion Torrent PGM) aligned to hg19 genome used to produce the data presented in tables and figures of the manuscript.AVC2.bamAVC3 Sequences fileThese files contain next-generation sequencing data (sequencer: Ion Torrent PGM) aligned to hg19 genome used to produce the data presented in tables and figures of the manuscript.AVC3.bamAVC4 Sequences fileThese files contain next-generation sequencing data (sequencer: Ion Torrent PGM) aligned to hg19 genome used to produce the data presented in tables and figures of the manuscript.AVC4.bamAVC5 Sequences fileThese files contain next-generation sequencing data (sequencer: Ion Torrent PGM) aligned to hg19 genome used to produce the data presented in tables and figures of the manuscript.AVC5.bamGC1 Sequences fileThese files contain next-generation sequencing data (sequencer: Ion Torrent PGM) aligned to hg19 genome used to produce the data presented in tables and figures of the manuscript.GC1.bamGC2 Sequences fileThese files contain next-generation sequencing data (sequencer: Ion Torrent PGM) aligned to hg19 genome used to produce the data presented in tables and figures of the manuscript.GC2.bamGC3 Sequences fileThese files contain next-generation sequencing data (sequencer: Ion Torrent PGM) aligned to hg19 genome used to produce the data presented in tables and figures of the manuscript.GC3.bamGC4 Sequences fileThese files contain next-generation sequencing data (sequencer: Ion Torrent PGM) aligned to hg19 genome used to produce the data presented in tables and figures of the manuscript.GC4.bamGC5 Sequences fileThese files contain next-generation sequencing data (sequencer: Ion Torrent PGM) aligned to hg19 genome used to produce the data presented in tables and figures of the manuscript.GC5.bamHCC1 Sequences fileThese files contain next-generation sequencing data (sequencer: Ion Torrent PGM) aligned to hg19 genome used 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hg19 genome used to produce the data presented in figure 2A of the manuscript.frozen_dilutioncurve_50_percent_tumorThese files contain next-generation sequencing data (sequencer: Ion Torrent PGM) aligned to hg19 genome used to produce the data presented in figure 2A of the manuscript.ffpe_dilutioncurve_0_percent_hepatocarcinomaThese files contain next-generation sequencing data (sequencer: Ion Torrent PGM) aligned to hg19 genome used to produce the data presented in figure 2B of the manuscript.ffpe_dilutioncurve_10_percent_hepatocarcinomaThese files contain next-generation sequencing data (sequencer: Ion Torrent PGM) aligned to hg19 genome used to produce the data presented in figure 2B of the manuscript.ffpe_dilutioncurve_25_percent_hepatocarcinomaThese files contain next-generation sequencing data (sequencer: Ion Torrent PGM) aligned to hg19 genome used to produce the data presented in figure 2B of the manuscript.ffpe_dilutioncurve_50_percent_hepatocarcinomaThese files contain next-generation sequencing data (sequencer: Ion Torrent PGM) aligned to hg19 genome used to produce the data presented in figure 2B of the manuscript.ffpe_dilutioncurve_75_percent_hepatocarcinomaThese files contain next-generation sequencing data (sequencer: Ion Torrent PGM) aligned to hg19 genome used to produce the data presented in figure 2B of the manuscript.ffpe_dilutioncurve_90_percent_hepatocarcinomaThese files contain next-generation sequencing data (sequencer: Ion Torrent PGM) aligned to hg19 genome used to produce the data presented in figure 2B of the manuscript.ffpe_dilutioncurve_95_percent_hepatocarcinomaThese files contain next-generation sequencing data (sequencer: Ion Torrent PGM) aligned to hg19 genome used to produce the data presented in figure 2B of the manuscript.ffpe_dilutioncurve_100_percent_hepatocarcinomaThese files contain next-generation sequencing data (sequencer: Ion Torrent PGM) aligned to hg19 genome used to produce the data presented in figure 2B of the manuscript.