ICGC Oesophageal adenocarcinoma - Barrett's 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)

32 Datasets 4 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
EGAD00001001379	None	Illumina HiSeq 2000	29
EGAD00001001394	Samples from Ross Innes et. al 2015 - doi:10.1038/ng.3357	Illumina HiSeq 2000	-
EGAD00001003840	None	Illumina HiSeq 2000	3
EGAD00001003900	None	Illumina HiSeq 2000	83
EGAD00001003901	None	Illumina HiSeq 2000	3
EGAD00001004023	None	Illumina HiSeq 2000	52
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
EGAD00001005375	None	Illumina HiSeq 2000	73
EGAD00001005385	None	Illumina HiSeq 2000	64
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	-
EGAD00001005438	Data supporting: “Deep molecular phenotyping reveals the identity of Barrett’s esophagus and its malignant transition.” Nowicki-Osuch, Zhuang et al. scRNAseq (BAM files) 38 Barrett's and normal samples	unspecified	-
EGAD00001005455	Data supporting: “Deep molecular phenotyping reveals the identity of Barrett’s esophagus and its malignant transition.” Nowicki-Osuch, Zhuang et al. Single cell metadata and analysis 38 Barrett's and normals		-
EGAD00001006033	Data supporting: "Genomic copy number predicts esophageal cancer years before transformation." Killcoyne, Gregson et al. sWGS data 1000 samples BAM files	Illumina HiSeq 2500 Illumina HiSeq 4000	1000
EGAD00001006349	Data supporting: “Multi-omic cross-sectional cohort study of pre-malignant Barrett’s esophagus reveals structural variation and retrotransposon activity occur early in cancer evolution.” Katz-Summercorn, Jammula et al. WGS (BAM files)	Illumina HiSeq 2000	-
EGAD00001006353	Data supporting: “Multi-omic cross-sectional cohort study of pre-malignant Barrett’s esophagus reveals structural variation and retrotransposon activity occur early in cancer evolution.” Katz-Summercorn, Jammula et al. RNAseq (BAM files)	Illumina HiSeq 2000	-
EGAD00001006874	Data supporting: “Deep molecular phenotyping reveals the identity of Barrett’s esophagus and its malignant transition.” Nowicki-Osuch, Zhuang et al. WGS (BAM files) 5 Barrett's samples 5 normal oesophageal samples 5 normal gastric cardia samples 5 normal duodenal samples	Illumina HiSeq 2000 Illumina NovaSeq 6000	10
EGAD00001006882	Data supporting: “Deep molecular phenotyping reveals the identity of Barrett’s esophagus and its malignant transition.” Nowicki-Osuch, Zhuang et al. RNAseq (BAM files) 12 Barrett's samples 12 normal oesophageal samples 11 normal gastric cardia samples	Illumina HiSeq 2000	-
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	-
EGAD00001010074	Data supporting: “Single-cell RNA sequencing unifies developmental programs of Esophageal and Gastric Intestinal Metaplasia.” Nowicki-Osuch, Zhuang et al. scRNAseq (FASTQ files) 59 samples	unspecified	16
EGAD00001011076	Data supporting: "The transcriptional landscape of endogenous retroelements delineates esophageal adenocarcinoma subtypes" RNAseq for 279 samples	Illumina HiSeq 2000 unspecified	-
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
EGAD00001011189	Data supporting: "TBC" Ganguli et al (sWGS for 75 samples)	Illumina HiSeq 2500 Illumina HiSeq 4000	1
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
EGAD00001011255	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 BOs/normals)	unspecified	28
EGAD00001011269	Data supporting: "Mutational signature dynamics shaping the evolution of oesophageal adenocarcinoma" Abbas et al (RNA for 197 samples)	Illumina HiSeq 2000	-
EGAD00010001795	Array data for oesophageal and related samples â€“ kno_paper_methyl_release	Illumina	78
EGAD00010001838	Array data for oesophageal and related samples â€“ sj_paper_methyl_barretts_release	Illumina	150
EGAD00010001972	Array data for oesophageal and related samples - aks_paper_methyl_barretts_release	Illumina	107

Publications	Citations
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	41
Genomic copy number predicts esophageal cancer years before transformation. Killcoyne S, Gregson E, Wedge DC, Woodcock DJ, Eldridge MD, de la Rue R, Miremadi A, Abbas S, Blasko A, Kosmidou C, Januszewicz W, Jenkins AV, Gerstung M, Fitzgerald RC. Nat Med 26: 2020 1726-1732	47
Multi-omic cross-sectional cohort study of pre-malignant Barrett's esophagus reveals early structural variation and retrotransposon activity. Katz-Summercorn AC, Jammula S, Frangou A, Peneva I, O'Donovan M, Tripathi M, Malhotra S, di Pietro M, Abbas S, Devonshire G, Januszewicz W, Blasko A, Nowicki-Osuch K, MacRae S, Northrop A, Redmond AM, Wedge DC, Fitzgerald RC. Nat Commun 13: 2022 1407	9
Genomic signatures of past and present chromosomal instability in Barrett's esophagus and early esophageal adenocarcinoma. Bao C, Tourdot RW, Brunette GJ, Stewart C, Sun L, Baba H, Watanabe M, Agoston AT, Jajoo K, Davison JM, Nason KS, Getz G, Wang KK, Imamura Y, Odze R, Bass AJ, Stachler MD, Zhang CZ. Nat Commun 14: 2023 6203	2