ICGC Oesophageal adenocarcinoma - normal 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. - This study contains the Normal tissue samples.

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

41 Datasets 26 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	-
EGAD00001001071	Samples from the "100" project that are in the ICGC PanCancer project.	Illumina HiSeq 2000	10
EGAD00001001394	Samples from Ross Innes et. al 2015 - doi:10.1038/ng.3357	Illumina HiSeq 2000	-
EGAD00001001457	All samples from the "100" project	Illumina HiSeq 2000	24
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
EGAD00001002258	None	Illumina HiSeq 2000	2
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
EGAD00001003838	None	Illumina HiSeq 2000	19
EGAD00001003902	None	Illumina HiSeq 2000	10
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
EGAD00001004022	None	Illumina HiSeq 2000	10
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	-
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	-
EGAD00001005384	None	Illumina HiSeq 2000	9
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		-
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
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	-
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
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	-
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	-
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
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
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
EGAD00010001834	Array data for oesophageal and related samples â€“ sj_paper_methyl_normal_release	Illumina	100

Publications	Citations
Whole-genome sequencing provides new insights into the clonal architecture of Barrett's esophagus and esophageal adenocarcinoma. Ross-Innes CS, Becq J, Warren A, Cheetham RK, Northen H, O'Donovan M, Malhotra S, di Pietro M, Ivakhno S, He M, Weaver JMJ, Lynch AG, Kingsbury Z, Ross M, Humphray S, Bentley D, Fitzgerald RC. Nat Genet 47: 2015 1038-1046	178
Between-region genetic divergence reflects the mode and tempo of tumor evolution. Sun R, Hu Z, Sottoriva A, Graham TA, Harpak A, Ma Z, Fischer JM, Shibata D, Curtis C. Nat Genet 49: 2017 1015-1024	79
Organoid cultures recapitulate esophageal adenocarcinoma heterogeneity providing a model for clonality studies and precision therapeutics. Li X, Francies HE, Secrier M, Perner J, Miremadi A, Galeano-Dalmau N, Barendt WJ, Letchford L, Leyden GM, Goffin EK, Barthorpe A, Lightfoot H, Chen E, Gilbert J, Noorani A, Devonshire G, Bower L, Grantham A, MacRae S, Grehan N, Wedge DC, Fitzgerald RC, Garnett MJ. Nat Commun 9: 2018 2983	172
Clonal replacement and heterogeneity in breast tumors treated with neoadjuvant HER2-targeted therapy. Caswell-Jin JL, McNamara K, Reiter JG, Sun R, Hu Z, Ma Z, Ding J, Suarez CJ, Tilk S, Raghavendra A, Forte V, Chin SF, Bardwell H, Provenzano E, Caldas C, Lang J, West R, Tripathy D, Press MF, Curtis C. Nat Commun 10: 2019 657	31
Genomic evidence supports a clonal diaspora model for metastases of esophageal adenocarcinoma. Noorani A, Li X, Goddard M, Crawte J, Alexandrov LB, Secrier M, Eldridge MD, Bower L, Weaver J, Lao-Sirieix P, Martincorena I, Debiram-Beecham I, Grehan N, MacRae S, Malhotra S, Miremadi A, Thomas T, Galbraith S, Petersen L, Preston SD, Gilligan D, Hindmarsh A, Hardwick RH, Stratton MR, Wedge DC, Fitzgerald RC. Nat Genet 52: 2020 74-83	41
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	45
The mutREAD method detects mutational signatures from low quantities of cancer DNA. Perner J, Abbas S, Nowicki-Osuch K, Devonshire G, Eldridge MD, Tavaré S, Fitzgerald RC. Nat Commun 11: 2020 3166	6
Evidence that polyploidy in esophageal adenocarcinoma originates from mitotic slippage caused by defective chromosome attachments. Scott SJ, Li X, Jammula S, Devonshire G, Lindon C, Fitzgerald RC, D'Avino PP. Cell Death Differ 28: 2021 2179-2193	4
Serial Circulating Tumor DNA Detection Using a Personalized, Tumor-Informed Assay in Esophageal Adenocarcinoma Patients Following Resection. Ococks E, Sharma S, Ng AWT, Aleshin A, Fitzgerald RC, Smyth E. Gastroenterology 161: 2021 1705-1708.e2	6
Genomic Analysis of Response to Neoadjuvant Chemotherapy in Esophageal Adenocarcinoma. Izadi F, Sharpe BP, Breininger SP, Secrier M, Gibson J, Walker RC, Rahman S, Devonshire G, Lloyd MA, Walters ZS, Fitzgerald RC, Rose-Zerilli MJJ, Underwood TJ, On Behalf Of Occams. Cancers (Basel) 13: 2021 3394	5
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	13
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
Low-cost and clinically applicable copy number profiling using repeat DNA. Abujudeh S, Zeki SS, van Lanschot MCJ, Pusung M, Weaver JMJ, Li X, Noorani A, Metz AJ, Bornschein J, Bower L, Miremadi A, Fitzgerald RC, Morrissey ER, Lynch AG. BMC Genomics 23: 2022 599	1
Regulatory chromatin rewiring promotes metabolic switching during adaptation to oncogenic receptor tyrosine kinase inhibition. Ogden S, Carys K, Ahmed I, Bruce J, Sharrocks AD. Oncogene 41: 2022 4808-4822	3
Oncogenic ERRB2 signals through the AP-1 transcription factor to control mesenchymal-like properties of oesophageal adenocarcinoma. Ogden S, Ahmed I, Yang SH, Fullwood P, OCCAMS consortium, Francavilla C, Sharrocks AD. NAR Cancer 5: 2023 zcad001	2
eRNA profiling uncovers the enhancer landscape of oesophageal adenocarcinoma and reveals new deregulated pathways. Ahmed I, Yang SH, Ogden S, Zhang W, Li Y, OCCAMs consortium, Sharrocks AD. Elife 12: 2023 e80840	5
Single-Cell RNA Sequencing Unifies Developmental Programs of Esophageal and Gastric Intestinal Metaplasia. Nowicki-Osuch K, Zhuang L, Cheung TS, Black EL, Masqué-Soler N, Devonshire G, Redmond AM, Freeman A, di Pietro M, Pilonis N, Januszewicz W, O'Donovan M, Tavaré S, Shields JD, Fitzgerald RC. Cancer Discov 13: 2023 1346-1363	14
Primary human organoids models: Current progress and key milestones. Calà G, Sina B, De Coppi P, Giobbe GG, Gerli MFM. Front Bioeng Biotechnol 11: 2023 1058970	9
Extrachromosomal DNA in the cancerous transformation of Barrett's oesophagus. Luebeck J, Ng AWT, Galipeau PC, Li X, Sanchez CA, Katz-Summercorn AC, Kim H, Jammula S, He Y, Lippman SM, Verhaak RGW, Maley CC, Alexandrov LB, Reid BJ, Fitzgerald RC, Paulson TG, Chang HY, Wu S, Bafna V, Mischel PS. Nature 616: 2023 798-805	40
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
Understanding the malignant potential of gastric metaplasia of the oesophagus and its relevance to Barrett's oesophagus surveillance: individual-level data analysis. Black EL, Ococks E, Devonshire G, Ng AWT, O'Donovan M, Malhotra S, Tripathi M, Miremadi A, Freeman A, Coles H, Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) Consortium, Fitzgerald RC. Gut 73: 2024 729-740	2
Evolving copy number gains promote tumor expansion and bolster mutational diversification. Wang Z, Xia Y, Mills L, Nikolakopoulos AN, Maeser N, Dehm SM, Sheltzer JM, Sun R. Nat Commun 15: 2024 2025	7
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
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
Massively parallel reporter assays identify enhancer elements in oesophageal Adenocarcinoma. Yang SH, Ahmed I, Li Y, Bleaney CW, Sharrocks AD. NAR Cancer 6: 2024 zcae041	0
Non-genetic differences underlie variability in proliferation among esophageal epithelial clones. Reyes Hueros RA, Gier RA, Shaffer SM. PLoS Comput Biol 20: 2024 e1012360	1