The scientific community has avoided using tissue samples from patients that have been exposed to systemic chemotherapy to infer the genomic landscape of a given cancer. Esophageal adenocarcinoma is a heterogeneous, chemoresistant tumor for which the availability and size of pretreatment endoscopic samples are limiting. This study compares whole-genome sequencing data obtained from chemo-naive and chemo-treated samples. The quality of whole-genomic sequencing data is comparable across all samples regardless of chemotherapy status. Inclusion of samples collected post-chemotherapy increased the proportion of late-stage tumors. When comparing matched pre- and post-chemotherapy samples from 10 cases, the mutational signatures, copy number, and SNV mutational profiles reflect the expected heterogeneity in this disease. Analysis of SNVs in relation to allele-specific copy-number changes pinpoints the common ancestor to a point prior to chemotherapy. For cases in which pre- and post-chemotherapy samples do show substantial differences, the timing of the divergence is near-synchronous with endoreduplication. Comparison across a large prospective cohort (62 treatment-naive, 58 chemotherapy-treated samples) reveals no significant differences in the overall mutation rate, mutation signatures, specific recurrent point mutations, or copy-number events in respect to chemotherapy status. In conclusion, whole-genome sequencing of samples obtained following neoadjuvant chemotherapy is representative of the genomic landscape of esophageal adenocarcinoma. Excluding these samples reduces the material available for cataloging and introduces a bias toward the earlier stages of cancer.

Original publication

DOI

10.1101/gr.214296.116

Type

Journal article

Journal

Genome research

Publication Date

06/2017

Volume

27

Pages

902 - 912

Addresses

Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge CB2 0XZ, United Kingdom.

Keywords

Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) Consortium, Esophagus, Humans, Adenocarcinoma, Esophageal Neoplasms, Cell Transformation, Neoplastic, Neoplasm Proteins, Antineoplastic Agents, Neoadjuvant Therapy, Prospective Studies, Gene Expression Profiling, Computational Biology, Gene Expression Regulation, Neoplastic, Point Mutation, Polymorphism, Single Nucleotide, Genome, Human, Time Factors, Aged, Middle Aged, Female, Male, DNA Copy Number Variations, High-Throughput Nucleotide Sequencing, Mutation Rate