{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"dataset_type":["N/A"],"full_dataset_link":["https://ega-archive.org/datasets/EGAD00001000704"],"sample_count":["0"],"description":["EGA dataset EGAD00001000704"],"repository":["EGA"],"title":["Sequencing data for ICGC Oesophageal Adenocarcinoma tissue samples - pilot normal and pre/post-chemo"],"pubmed_abstract":["Cancer genome sequencing studies have identified numerous driver genes, but the relative timing of mutations in carcinogenesis remains unclear. The gradual progression from premalignant Barrett's esophagus to esophageal adenocarcinoma (EAC) provides an ideal model to study the ordering of somatic mutations. We identified recurrently mutated genes and assessed clonal structure using whole-genome sequencing and amplicon resequencing of 112 EACs. We next screened a cohort of 109 biopsies from 2 key transition points in the development of malignancy: benign metaplastic never-dysplastic Barrett's esophagus (NDBE; n=66) and high-grade dysplasia (HGD; n=43). Unexpectedly, the majority of recurrently mutated genes in EAC were also mutated in NDBE. Only TP53 and SMAD4 mutations occurred in a stage-specific manner, confined to HGD and EAC, respectively. Finally, we applied this knowledge to identify high-risk Barrett's esophagus in a new non-endoscopic test. In conclusion, mutations in EAC driver genes generally occur exceptionally early in disease development with profound implications for diagnostic and therapeutic strategies."],"pubmed_title":["Ordering of mutations in preinvasive disease stages of esophageal carcinogenesis."],"pubmed_authors":["Weaver Jamie M J JMJ, Ross-Innes Caryn S CS, Shannon Nicholas N, Lynch Andy G AG, Forshew Tim T, Barbera Mariagnese M, Murtaza Muhammed M, Ong Chin-Ann J CJ, Lao-Sirieix Pierre P, Dunning Mark J MJ, Smith Laura L, Smith Mike L ML, Anderson Charlotte L CL, Carvalho Benilton B, O'Donovan Maria M, Underwood Timothy J TJ, May Andrew P AP, Grehan Nicola N, Hardwick Richard R, Davies Jim J, Oloumi Arusha A, Aparicio Sam S, Caldas Carlos C, Eldridge Matthew D MD, Edwards Paul A W PAW, Rosenfeld Nitzan N, Tavaré Simon S, Fitzgerald Rebecca C RC"],"additional_accession":[]},"is_claimable":false,"name":"ICGC Oesophageal Adenocarcinoma sequence data - pilot normal and pre-chemo - samples","description":"Description not provided","dates":{"updated":"2023-08-02 12:38:22"},"accession":"EGAD00001000704","cross_references":{"TAXONOMY":["9606"],"pubmed":["24952744"],"EGA":["EGAC00001000010","EGAS00001000559"]}}