ICGC Oesophageal adenocarcinoma - pilot samples

The oesophageal project will focus on adenocarcinoma which is increasing in incidence in the UK and other developed countries and has a very poor outcome. The primary aims of this project are to deeply sequence tumour and normal genomic DNA (including the precursor condition Barrett's oesophagus when material is available) to provide a comprehensive catalogue of somatic mutations. This will be achieved through a UK-wide network of hospitals involved in a research collaboration called the OCCAMS consortium. The goal of this project is to use high quality clinical material with accurately annotated clinic-pathological, treatment and outcome data.

Type: Other
Archiver: European Genome-Phenome Archive (EGA)

15 Datasets 13 Publications

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD00001000704	None	Illumina HiSeq 2000	-
EGAD00001001048	Samples from Edwards et al 2015 - doi:10.1186/s12864-015-1685-z	Illumina HiSeq 2000	-
EGAD00001001071	Samples from the "100" project that are in the ICGC PanCancer project.	Illumina HiSeq 2000	10
EGAD00001001457	All samples from the "100" project	Illumina HiSeq 2000	24
EGAD00001001960	upcoming publication	Illumina HiSeq 2000	-
EGAD00001002218	Sequencing data for ICGC Oesophageal Adenocarcinoma tissue samples - 129_cohort EAC whole genomic sequencing data - Publication Secrier & Li et al., 2016, Nature Genetics	Illumina HiSeq 2000	10
EGAD00001002241	Sequencing data for ICGC Oesophageal Adenocarcinoma tissue samples - chemo_cohort	Illumina HiSeq 2000	6
EGAD00001003292	WGS sequencing for cases from the ICGC ESAD-UK project Tumours 50x Normals 30x HiSeq X BAM files These samples are all available in ICGC release 24	Illumina HiSeq 2000	34
EGAD00001003580	WGS sequencing for 303 cases (620 samples) from the ICGC ESAD-UK project Tumours 50x Normals 30x HiSeq X BAM files These samples are all available in ICGC release 26	Illumina HiSeq 2000	38
EGAD00001004137	WGS sequencing for 409 cases (832 samples) from the ICGC ESAD-UK project Tumours 50x Normals 30x HiSeq X BAM files These samples are all available in ICGC release 28	Illumina HiSeq 2000	-
EGAD00001004417	Data supporting: "The landscape of selection in 551 Esophageal Adenocarcinomas defines genomic biomarkers for the clinic." Frankell et al. WGS (BAM files) 379 matched tumour-normal pairs	Illumina HiSeq 2000	-
EGAD00001004775	Data supporting: "Patient-specific detection of cancer genes reveals recurrently perturbed processes in esophageal adenocarcinoma." Mourikis et al. WGS (BAM files) 521 samples	Illumina HiSeq 2000	-
EGAD00001007785	Data from 496 OCCAMS (Oesophageal Cancer Clinical And Molecular Stratification) cases. WGS BAM files 496x oesophageal adenocarcinoma samples 496x normal samples	HiSeq X Five Illumina HiSeq 2000 Illumina NovaSeq 6000	-
EGAD00001011191	Data supporting: "TBC" Ganguli et al (WGS for 1298 samples)	HiSeq X Five Illumina HiSeq 2000 Illumina NovaSeq 6000 unspecified	42
EGAD00001011196	Data supporting: "Mutational signature dynamics shaping the evolution of oesophageal adenocarcinoma" Abbas et al (WGS for 1397 samples)	HiSeq X Five Illumina HiSeq 2000 Illumina NovaSeq 6000 unspecified	6

Publications	Citations
Ordering of mutations in preinvasive disease stages of esophageal carcinogenesis. Weaver JMJ, Ross-Innes CS, Shannon N, Lynch AG, Forshew T, Barbera M, Murtaza M, Ong CJ, Lao-Sirieix P, Dunning MJ, Smith L, Smith ML, Anderson CL, Carvalho B, O'Donovan M, Underwood TJ, May AP, Grehan N, Hardwick R, Davies J, Oloumi A, Aparicio S, Caldas C, Eldridge MD, Edwards PAW, Rosenfeld N, Tavaré S, Fitzgerald RC, OCCAMS consortium. Nat Genet 46: 2014 837-843	215
Mobile element insertions are frequent in oesophageal adenocarcinomas and can mislead paired-end sequencing analysis. Paterson AL, Weaver JM, Eldridge MD, Tavaré S, Fitzgerald RC, Edwards PA, OCCAMs Consortium. BMC Genomics 16: 2015 473	14
Mutational signatures in esophageal adenocarcinoma define etiologically distinct subgroups with therapeutic relevance. Secrier M, Li X, de Silva N, Eldridge MD, Contino G, Bornschein J, MacRae S, Grehan N, O'Donovan M, Miremadi A, Yang TP, Bower L, Chettouh H, Crawte J, Galeano-Dalmau N, Grabowska A, Saunders J, Underwood T, Waddell N, Barbour AP, Nutzinger B, Achilleos A, Edwards PA, Lynch AG, Tavaré S, Fitzgerald RC, Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) Consortium. Nat Genet 48: 2016 1131-1141	221
A comparative analysis of whole genome sequencing of esophageal adenocarcinoma pre- and post-chemotherapy. Noorani A, Bornschein J, Lynch AG, Secrier M, Achilleos A, Eldridge M, Bower L, Weaver JMJ, Crawte J, Ong CA, Shannon N, MacRae S, Grehan N, Nutzinger B, O'Donovan M, Hardwick R, Tavaré S, Fitzgerald RC, Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) Consortium. Genome Res 27: 2017 902-912	15
Impact of mutations in Toll-like receptor pathway genes on esophageal carcinogenesis. Fels Elliott DR, Perner J, Li X, Symmons MF, Verstak B, Eldridge M, Bower L, O'Donovan M, Gay NJ, OCCAMS Consortium, Fitzgerald RC. PLoS Genet 13: 2017 e1006808	11
The landscape of selection in 551 esophageal adenocarcinomas defines genomic biomarkers for the clinic. Frankell AM, Jammula S, Li X, Contino G, Killcoyne S, Abbas S, Perner J, Bower L, Devonshire G, Ococks E, Grehan N, Mok J, O'Donovan M, MacRae S, Eldridge MD, Tavaré S, Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) Consortium, Fitzgerald RC. Nat Genet 51: 2019 506-516	115
Patient-specific cancer genes contribute to recurrently perturbed pathways and establish therapeutic vulnerabilities in esophageal adenocarcinoma. Mourikis TP, Benedetti L, Foxall E, Temelkovski D, Nulsen J, Perner J, Cereda M, Lagergren J, Howell M, Yau C, Fitzgerald RC, Scaffidi P, Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) Consortium, Ciccarelli FD. Nat Commun 10: 2019 3101	23
The impact of rare germline variants on human somatic mutation processes. Vali-Pour M, Park S, Espinosa-Carrasco J, Ortiz-Martínez D, Lehner B, Supek F. Nat Commun 13: 2022 3724	12
Identification of neoantigens in oesophageal adenocarcinoma. Nicholas B, Bailey A, McCann KJ, Wood O, Walker RC, Parker R, Ternette N, Elliott T, Underwood TJ, Johnson P, Skipp P. Immunology 168: 2023 420-431	6
Long-molecule scars of backup DNA repair in BRCA1- and BRCA2-deficient cancers. Setton J, Hadi K, Choo ZN, Kuchin KS, Tian H, Da Cruz Paula A, Rosiene J, Selenica P, Behr J, Yao X, Deshpande A, Sigouros M, Manohar J, Nauseef JT, Mosquera JM, Elemento O, Weigelt B, Riaz N, Reis-Filho JS, Powell SN, Imieliński M. Nature 621: 2023 129-137	3
Most large structural variants in cancer genomes can be detected without long reads. Choo ZN, Behr JM, Deshpande A, Hadi K, Yao X, Tian H, Takai K, Zakusilo G, Rosiene J, Da Cruz Paula A, Weigelt B, Setton J, Riaz N, Powell SN, Busam K, Shoushtari AN, Ariyan C, Reis-Filho J, de Lange T, Imieliński M. Nat Genet 55: 2023 2139-2148	8
Multi-Omic Analysis of Esophageal Adenocarcinoma Uncovers Candidate Therapeutic Targets and Cancer-Selective Posttranscriptional Regulation. O'Neill JR, Yébenes Mayordomo M, Mitulović G, Al Shboul S, Bedran G, Faktor J, Hernychova L, Uhrik L, Gómez-Herranz M, Kocikowski M, Save V, Vojtěšek B, Arends MJ, OCCAMS Consortium, Hupp T, Alfaro JA. Mol Cell Proteomics 23: 2024 100764	0
Disentangling oncogenic amplicons in esophageal adenocarcinoma. Ng AWT, McClurg DP, Wesley B, Zamani SA, Black E, Miremadi A, Giger O, Hoopen RT, Devonshire G, Redmond AM, Grehan N, Jammula S, Blasko A, Li X, Aparicio S, Tavaré S, Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) Consortium, Nowicki-Osuch K, Fitzgerald RC. Nat Commun 15: 2024 4074	1