Study

ICGC Oesophageal adenocarcinoma - tumour samples

Study ID Alternative Stable ID Type
EGAS00001000725 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.

Study Datasets 22 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 86
EGAD00001001394
Samples from Ross Innes et. al 2015 - doi:10.1038/ng.3357
Illumina HiSeq 2000 101
EGAD00001001960
upcoming publication
Illumina HiSeq 2000 171
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 258
EGAD00001002241
Sequencing data for ICGC Oesophageal Adenocarcinoma tissue samples - chemo_cohort
Illumina HiSeq 2000 270
EGAD00001002260
Sequencing data for ICGC Oesophageal Adenocarcinoma tissue samples - 129_rnaseq EAC expression data - Publication Secrier & Li et al., 2016, Nature Genetics
Illumina HiSeq 2000 15
EGAD00001002689
ICGC Oesophageal Adenocarcinoma tissue samples
Illumina HiSeq 2000 10
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 520
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 620
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 69
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 127
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 832
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 86
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 758
EGAD00001004423
Data supporting: "The landscape of selection in 551 Esophageal Adenocarcinomas defines genomic biomarkers for the clinic." Frankell et al. RNAseq (BAM files) 116 tumours
Illumina HiSeq 2000 116
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 521
EGAD00001004776
Data supporting: "Patient-specific detection of cancer genes reveals recurrently perturbed processes in esophageal adenocarcinoma." Mourikis et al. RNAseq (BAM files) 137 samples
Illumina HiSeq 2000 137
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 134
EGAD00001005915
Data supporting: "Repurposing of KLF5 activates a cell cycle signature during the progression from Barrett’s Oesophagus to Oesophageal Adenocarcinoma." Rogerson et al. RNA-seq data 2 samples
Illumina HiSeq 2000 2
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
EGAD00010001822
Array data for oesophageal and related samples – sj_paper_methyl_tumour_release
Illumina 285

Who archives the data?

Publications

Citations

Retrieving...
Retrieving...
Retrieving...
Retrieving...
Retrieving...
Retrieving...
Retrieving...
Retrieving...
Retrieving...
Retrieving...
Retrieving...
Retrieving...
Retrieving...
Retrieving...
Retrieving...
Retrieving...
Retrieving...
Retrieving...