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

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