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A comparative analysis of whole genome sequencing of esophageal adenocarcinoma pre- and post-chemotherapy
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dc.contributor.author | Noorani, Ayesha | |
dc.contributor.author | Bornschein, Jan | |
dc.contributor.author | Lynch, Andy G | |
dc.contributor.author | Secrier, Maria | |
dc.contributor.author | Achilleos, Achilleas | |
dc.contributor.author | Eldridge, Matthew | |
dc.contributor.author | Bower, Lawrence | |
dc.contributor.author | Weaver, Jamie M.J. | |
dc.contributor.author | Crawte, Jason | |
dc.contributor.author | Ong, Chin-Ann | |
dc.contributor.author | Shannon, Nicholas | |
dc.contributor.author | MacRae, Shona | |
dc.contributor.author | Grehan, Nicola | |
dc.contributor.author | Nutzinger, Barbara | |
dc.contributor.author | O'Donovan, Maria | |
dc.contributor.author | Hardwick, Richard | |
dc.contributor.author | Tavaré, Simon | |
dc.contributor.author | Fitzgerald, Rebecca C. | |
dc.contributor.author | Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) Consortium | |
dc.date.accessioned | 2017-08-11T14:30:10Z | |
dc.date.available | 2017-08-11T14:30:10Z | |
dc.date.issued | 2017-06-01 | |
dc.identifier | 250731829 | |
dc.identifier | e286a118-d797-4221-957b-4b6157d3554e | |
dc.identifier | 85020292652 | |
dc.identifier.citation | Noorani , A , Bornschein , J , Lynch , A G , Secrier , M , Achilleos , A , Eldridge , M , Bower , L , Weaver , J M J , Crawte , J , Ong , C-A , Shannon , N , MacRae , S , Grehan , N , Nutzinger , B , O'Donovan , M , Hardwick , R , Tavaré , S , Fitzgerald , R C & Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) Consortium 2017 , ' A comparative analysis of whole genome sequencing of esophageal adenocarcinoma pre- and post-chemotherapy ' , Genome Research , vol. 27 , no. 6 , pp. 902-912 . https://doi.org/10.1101/gr.214296.116 | en |
dc.identifier.issn | 1088-9051 | |
dc.identifier.other | RIS: urn:3298CF335ADC48C31EA2EC5125C646BE | |
dc.identifier.other | ORCID: /0000-0002-7876-7338/work/35946867 | |
dc.identifier.uri | https://hdl.handle.net/10023/11433 | |
dc.description | 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. | en |
dc.description.abstract | 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. | |
dc.format.extent | 11 | |
dc.format.extent | 1652528 | |
dc.language.iso | eng | |
dc.relation.ispartof | Genome Research | en |
dc.subject | RC0254 Neoplasms. Tumors. Oncology (including Cancer) | en |
dc.subject | DAS | en |
dc.subject | SDG 3 - Good Health and Well-being | en |
dc.subject.lcc | RC0254 | en |
dc.title | A comparative analysis of whole genome sequencing of esophageal adenocarcinoma pre- and post-chemotherapy | en |
dc.type | Journal article | en |
dc.contributor.institution | University of St Andrews. School of Medicine | en |
dc.contributor.institution | University of St Andrews. Statistics | en |
dc.contributor.institution | University of St Andrews. Cellular Medicine Division | en |
dc.identifier.doi | https://doi.org/10.1101/gr.214296.116 | |
dc.description.status | Peer reviewed | en |
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