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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.

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 Illumina HiSeq 2000 -
EGAD00001001071 Illumina HiSeq 2000 10
EGAD00001001394 Illumina HiSeq 2000 -
EGAD00001001457 Illumina HiSeq 2000 24
EGAD00001002218 Illumina HiSeq 2000 10
EGAD00001002241 Illumina HiSeq 2000 6
EGAD00001002258 Illumina HiSeq 2000 2
EGAD00001002689 Illumina HiSeq 2000 -
EGAD00001003292 Illumina HiSeq 2000 34
EGAD00001003580 Illumina HiSeq 2000 38
EGAD00001003838 Illumina HiSeq 2000 19
EGAD00001003902 Illumina HiSeq 2000 10
EGAD00001004007 Illumina HiSeq 2000 53
EGAD00001004022 Illumina HiSeq 2000 10
EGAD00001004028 Illumina HiSeq 2000 -
EGAD00001004029 Illumina HiSeq 2000 86
EGAD00001004137 Illumina HiSeq 2000 -
EGAD00001004289 Illumina HiSeq 2000 Illumina MiSeq 60
EGAD00001004417 Illumina HiSeq 2000 -
EGAD00001004775 Illumina HiSeq 2000 -
EGAD00001005384 Illumina HiSeq 2000 9
EGAD00001005434 Illumina HiSeq 2000 -
EGAD00001005438 unspecified -
EGAD00001005455 -
EGAD00001006170 Illumina HiSeq 4000 48
EGAD00001006349 Illumina HiSeq 2000 -
EGAD00001006738 Illumina HiSeq 2000 7
EGAD00001006874 Illumina HiSeq 2000 Illumina NovaSeq 6000 10
EGAD00001006882 Illumina HiSeq 2000 -
EGAD00001007493 HiSeq X Five Illumina HiSeq 2000 Illumina NovaSeq 6000 8
EGAD00001007496 HiSeq X Five Illumina HiSeq 2000 -
EGAD00001007785 HiSeq X Five Illumina HiSeq 2000 Illumina NovaSeq 6000 -
EGAD00001007808 Illumina HiSeq 2000 -
EGAD00001010074 unspecified 16
EGAD00001011095 HiSeq X Five Illumina HiSeq 2000 -
EGAD00001011187 HiSeq X Five Illumina HiSeq 2000 Illumina NovaSeq 6000 unspecified 63
EGAD00001011188 unspecified 170
EGAD00001011191 HiSeq X Five Illumina HiSeq 2000 Illumina NovaSeq 6000 unspecified 42
EGAD00001011196 HiSeq X Five Illumina HiSeq 2000 Illumina NovaSeq 6000 unspecified 6
EGAD00001011255 unspecified 28
EGAD00010001834 Illumina 100
Publications Citations
Whole-genome sequencing provides new insights into the clonal architecture of Barrett's esophagus and esophageal adenocarcinoma.
Nat Genet 47: 2015 1038-1046
172
Between-region genetic divergence reflects the mode and tempo of tumor evolution.
Nat Genet 49: 2017 1015-1024
77
Organoid cultures recapitulate esophageal adenocarcinoma heterogeneity providing a model for clonality studies and precision therapeutics.
Nat Commun 9: 2018 2983
159
Clonal replacement and heterogeneity in breast tumors treated with neoadjuvant HER2-targeted therapy.
Nat Commun 10: 2019 657
29
Genomic evidence supports a clonal diaspora model for metastases of esophageal adenocarcinoma.
Nat Genet 52: 2020 74-83
40
Identification of Subtypes of Barrett's Esophagus and Esophageal Adenocarcinoma Based on DNA Methylation Profiles and Integration of Transcriptome and Genome Data.
Gastroenterology 158: 2020 1682-1697.e1
43
The mutREAD method detects mutational signatures from low quantities of cancer DNA.
Nat Commun 11: 2020 3166
6
Evidence that polyploidy in esophageal adenocarcinoma originates from mitotic slippage caused by defective chromosome attachments.
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.
Gastroenterology 161: 2021 1705-1708.e2
6
Genomic Analysis of Response to Neoadjuvant Chemotherapy in Esophageal Adenocarcinoma.
Cancers (Basel) 13: 2021 3394
4
Multi-omic cross-sectional cohort study of pre-malignant Barrett's esophagus reveals early structural variation and retrotransposon activity.
Nat Commun 13: 2022 1407
11
Rearrangement processes and structural variations show evidence of selection in oesophageal adenocarcinomas.
Commun Biol 5: 2022 335
8
Low-cost and clinically applicable copy number profiling using repeat DNA.
BMC Genomics 23: 2022 599
1
Regulatory chromatin rewiring promotes metabolic switching during adaptation to oncogenic receptor tyrosine kinase inhibition.
Oncogene 41: 2022 4808-4822
2
Oncogenic ERRB2 signals through the AP-1 transcription factor to control mesenchymal-like properties of oesophageal adenocarcinoma.
NAR Cancer 5: 2023 zcad001
1
eRNA profiling uncovers the enhancer landscape of oesophageal adenocarcinoma and reveals new deregulated pathways.
Elife 12: 2023 e80840
4
Single-Cell RNA Sequencing Unifies Developmental Programs of Esophageal and Gastric Intestinal Metaplasia.
Cancer Discov 13: 2023 1346-1363
7
Primary human organoids models: Current progress and key milestones.
Front Bioeng Biotechnol 11: 2023 1058970
5
Extrachromosomal DNA in the cancerous transformation of Barrett's oesophagus.
Nature 616: 2023 798-805
18
The transcriptional landscape of endogenous retroelements delineates esophageal adenocarcinoma subtypes.
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.
Gut 73: 2024 729-740
1
Evolving copy number gains promote tumor expansion and bolster mutational diversification.
Nat Commun 15: 2024 2025
1
Disentangling oncogenic amplicons in esophageal adenocarcinoma.
Nat Commun 15: 2024 4074
0