Back to Search
Start Over
A comparative analysis of whole genome sequencing of esophageal adenocarcinoma pre- and post-chemotherapy
- Publication Year :
- 2017
-
Abstract
- The whole-genome sequencing data from this study have been submitted to the European Genome-phenome Archive (EGA; https://www.ebi.ac.uk/ega/home) under accession number EGAD00001002241. Mutation calls can be found within the ICGC data portal (https://dcc.icgc.org/) under project ID ESADUK and library IDs listed in Supplemental Table S2. 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. Publisher PDF
- Subjects :
- Male
Time Factors
DNA Copy Number Variations
Esophageal Neoplasms
Antineoplastic Agents
Adenocarcinoma
Polymorphism, Single Nucleotide
RC0254
Esophagus
Mutation Rate
SDG 3 - Good Health and Well-being
Humans
Point Mutation
Prospective Studies
Aged
Genome, Human
RC0254 Neoplasms. Tumors. Oncology (including Cancer)
Research
Gene Expression Profiling
Computational Biology
High-Throughput Nucleotide Sequencing
DAS
Middle Aged
Neoadjuvant Therapy
Neoplasm Proteins
Gene Expression Regulation, Neoplastic
Cell Transformation, Neoplastic
Female
Corrigendum
Subjects
Details
- Language :
- English
- Database :
- OpenAIRE
- Accession number :
- edsair.doi.dedup.....dd729aad8374af38defe20808b1dd39e