Study
ICGC Oesophageal adenocarcinoma - normal samples
Study ID | Alternative Stable ID | Type |
---|---|---|
EGAS00001000723 | Other |
Study Description
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.
Study Datasets 28 datasets.
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 | N/A |
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 | N/A |
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 |
EGAD00001002689 |
ICGC Oesophageal Adenocarcinoma tissue samples
|
Illumina HiSeq 2000 | N/A |
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 |
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 |
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 | N/A |
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 | N/A |
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 | N/A |
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 | N/A |
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 | N/A |
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 | N/A |
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
|
N/A | |
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,Illumina NovaSeq 6000 | N/A |
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 | N/A |
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 | N/A |
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 | N/A |
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 |
EGAD00010001834 |
Array data for oesophageal and related samples – sj_paper_methyl_normal_release
|
Illumina | 100 |
Who archives the data?

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