ICGC Oesophageal adenocarcinoma - tumour 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)

47 Datasets 10 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
EGAD00001001048	Samples from Edwards et al 2015 - doi:10.1186/s12864-015-1685-z	Illumina HiSeq 2000	-
EGAD00001001394	Samples from Ross Innes et. al 2015 - doi:10.1038/ng.3357	Illumina HiSeq 2000	-
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
EGAD00001002259	None	Illumina HiSeq 2000	37
EGAD00001002260	Sequencing data for ICGC Oesophageal Adenocarcinoma tissue samples - 129_rnaseq EAC expression data - Publication Secrier & Li et al., 2016, Nature Genetics	Illumina HiSeq 2000	15
EGAD00001002689	ICGC Oesophageal Adenocarcinoma tissue samples	Illumina HiSeq 2000	-
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
EGAD00001003839	None	Illumina HiSeq 2000	26
EGAD00001003900	None	Illumina HiSeq 2000	83
EGAD00001004007	Data supporting: "Esophageal adenocarcinoma organoid cultures recapitulate human disease heterogeneity and provide a model for clonality studies and precision therapeutics." Li et al. WGS (BAM files) RNAseq (BAM files) Tumours, organoids, normals	Illumina HiSeq 2000	53
EGAD00001004021	None	Illumina HiSeq 2000	32
EGAD00001004028	WGS sequencing for 63 cases (126 samples) from the ICGC ESAD-UK project Tumours 50x Normals 30x HiSeq X BAM files These samples are earmarked for inclusion in ICGC release 27 (deferred to release 28)	Illumina HiSeq 2000	-
EGAD00001004029	WGS sequencing for 43 cases (86 samples) from the ICGC ESAD-UK project Tumours 50x Normals 30x HiSeq X BAM files These samples are earmarked for inclusion in ICGC release 28	Illumina HiSeq 2000	86
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	-
EGAD00001004289	Data supporting: "Low-cost and clinically applicable copy number profiling using repeat DNA." Abujudeh et al. DNA WGS (BAM files) DNA fastSeq (fastq files) Tumours, Barrett's, normals.	Illumina HiSeq 2000 Illumina MiSeq	60
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	-
EGAD00001004423	Data supporting: "The landscape of selection in 551 Esophageal Adenocarcinomas defines genomic biomarkers for the clinic." Frankell et al. RNAseq (BAM files) 116 tumours	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	-
EGAD00001004776	Data supporting: "Patient-specific detection of cancer genes reveals recurrently perturbed processes in esophageal adenocarcinoma." Mourikis et al. RNAseq (BAM files) 137 samples	Illumina HiSeq 2000	-
EGAD00001005375	None	Illumina HiSeq 2000	73
EGAD00001005376	None	Illumina HiSeq 2000	11
EGAD00001005377	None	Illumina HiSeq 2000	10
EGAD00001005383	None	Illumina HiSeq 2000	20
EGAD00001005388	Data supporting: “Deep molecular phenotyping reveals the identity of Barrett’s esophagus and its malignant transition.” Nowicki-Osuch, Zhuang et al. RNAseq (BAM files) 241 tumour samples	Illumina HiSeq 2000	-
EGAD00001005434	Data supporting: "Genomic evidence supports a clonal diaspora model for metastases of esophageal adenocarcinoma." Noorani et al. WGS (BAM files) 134 samples for 18 cases Includes primary, lymph-node, distant metastatic, Barrett's and normal samples.	Illumina HiSeq 2000	-
EGAD00001005915	Data supporting: "Repurposing of KLF5 activates a cell cycle signature during the progression from Barrett’s Oesophagus to Oesophageal Adenocarcinoma." Rogerson et al. RNA-seq data 2 samples	Illumina HiSeq 2000	-
EGAD00001006170	Data supporting: "The mutREAD method detects mutational signatures from low quantities of cancer DNA." Perner et al. WGS, sWGS, WES, and reduced representation sequencing data tumour and normal samples BAM files	Illumina HiSeq 4000	48
EGAD00001006373	Data supporting: “Longitudinal tracking of 97 esophageal adenocarcinomas (EAC) using liquid biopsy sampling.” Ococks, Frankell, Masque Soler et al. ctDNA (BAM files) 333 samples	NextSeq 500	48
EGAD00001006738	Data supporting: "Evidence that polyploidy in esophageal adenocarcinoma originates from mitotic slippage caused by defective chromosome attachments" Scott et al. WGS and RNAseq sequencing data Organoid, tumour and normal samples BAM files	Illumina HiSeq 2000	7
EGAD00001007493	Data supporting: "Genomic analysis of response to neoadjuvant chemotherapy in esophageal adenocarcinoma" Izadi et al. WGS for tumour and normal samples. RNAseq for tumour samples.	HiSeq X Five Illumina HiSeq 2000 Illumina NovaSeq 6000	8
EGAD00001007496	Data supporting: "Widespread reorganisation of the regulatory chromatin landscape facilitates resistance to inhibition of oncogenic ERBB2 signalling" Ogden et al. WGS for tumour and normal samples. RNAseq for tumour samples.	HiSeq X Five 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	-
EGAD00001007808	Data supporting "Interplay of processes shapes structural variations undergoing selection in oesophageal adenocarcinoma" Ng, Contino et al. WGS (BAM files) 383 oesophageal adenocarcinoma samples 383 normal samples	Illumina HiSeq 2000	-
EGAD00001007809	Data supporting: "Interplay of processes shapes structural variations undergoing selection in oesophageal adenocarcinoma" Ng, Contino et al. RNAseq (BAM files) 214 oesophageal adenocarcinoma samples	Illumina HiSeq 2000	-
EGAD00001011065	Data supporting: "SMAD4 and KCNQ3 Alterations are Associated with Lymph Node Metastases in Oesophageal Adenocarcinoma" RNAseq (FASTQ files) 6 samples	unspecified	6
EGAD00001011076	Data supporting: "The transcriptional landscape of endogenous retroelements delineates esophageal adenocarcinoma subtypes" RNAseq for 279 samples	Illumina HiSeq 2000 unspecified	-
EGAD00001011095	Data supporting: "The transcriptional landscape of endogenous retroelements delineates esophageal adenocarcinoma subtypes" WGS for 452 samples	HiSeq X Five Illumina HiSeq 2000	-
EGAD00001011187	Data supporting: "Understanding the malignant potential of gastric metaplasia of the oesophagus and its relevance to Barrett’s Oesophagus surveillance: individual-level data analysis" Black et al (WGS OACs/BOs/normals)	HiSeq X Five Illumina HiSeq 2000 Illumina NovaSeq 6000 unspecified	63
EGAD00001011188	Data supporting: "Understanding the malignant potential of gastric metaplasia of the oesophagus and its relevance to Barrett’s Oesophagus surveillance: individual-level data analysis" Black et al (WES OACs/BOs/normals)	unspecified	170
EGAD00001011190	Data supporting: "TBC" Ganguli et al (RNA for 394 samples)	Illumina HiSeq 2000 unspecified	49
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
EGAD00001011269	Data supporting: "Mutational signature dynamics shaping the evolution of oesophageal adenocarcinoma" Abbas et al (RNA for 197 samples)	Illumina HiSeq 2000	-
EGAD00010001822	Array data for oesophageal and related samples â€“ sj_paper_methyl_tumour_release	Illumina	285

Publications	Citations
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	224
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
Identification of Subtypes of Barrett's Esophagus and Esophageal Adenocarcinoma Based on DNA Methylation Profiles and Integration of Transcriptome and Genome Data. Jammula S, Katz-Summercorn AC, Li X, Linossi C, Smyth E, Killcoyne S, Biasci D, Subash VV, Abbas S, Blasko A, Devonshire G, Grantham A, Wronowski F, O'Donovan M, Grehan N, Eldridge MD, Tavaré S, Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) consortium, Fitzgerald RC. Gastroenterology 158: 2020 1682-1697.e1	46
Repurposing of KLF5 activates a cell cycle signature during the progression from a precursor state to oesophageal adenocarcinoma. Rogerson C, Ogden S, Britton E, OCCAMS Consortium, Ang Y, Sharrocks AD. Elife 9: 2020 e57189	13
Endogenous aldehyde accumulation generates genotoxicity and exhaled biomarkers in esophageal adenocarcinoma. Antonowicz S, Bodai Z, Wiggins T, Markar SR, Boshier PR, Goh YM, Adam ME, Lu H, Kudo H, Rosini F, Goldin R, Moralli D, Green CM, Peters CJ, Habib N, Gabra H, Fitzgerald RC, Takats Z, Hanna GB. Nat Commun 12: 2021 1454	11
Rearrangement processes and structural variations show evidence of selection in oesophageal adenocarcinomas. Ng AWT, Contino G, Killcoyne S, Devonshire G, Hsu R, Abbas S, Su J, Redmond AM, Weaver JMJ, Eldridge MD, Tavaré S, Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) Consortium, Edwards PAW, Fitzgerald RC. Commun Biol 5: 2022 335	9
The transcriptional landscape of endogenous retroelements delineates esophageal adenocarcinoma subtypes. Kazachenka A, Loong JH, Attig J, Young GR, Ganguli P, Devonshire G, Grehan N, The OCCAMS Consortium , Ciccarelli FD, Fitzgerald RC, Kassiotis G. NAR Cancer 5: 2023 zcad040	0
Comprehensive analyses of partially methylated domains and differentially methylated regions in esophageal cancer reveal both cell-type- and cancer-specific epigenetic regulation. Zheng Y, Ziman B, Ho AS, Sinha UK, Xu LY, Li EM, Koeffler HP, Berman BP, Lin DC. Genome Biol 24: 2023 193	4
Early detection and diagnosis of cancer with interpretable machine learning to uncover cancer-specific DNA methylation patterns. Newsham I, Sendera M, Jammula SG, Samarajiwa SA. Biol Methods Protoc 9: 2024 bpae028	1