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ICGC Oesophageal adenocarcinoma - pilot 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.

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
EGAD00001000704 Illumina HiSeq 2000 -
EGAD00001001048 Illumina HiSeq 2000 -
EGAD00001001071 Illumina HiSeq 2000 10
EGAD00001001457 Illumina HiSeq 2000 24
EGAD00001001960 Illumina HiSeq 2000 -
EGAD00001002218 Illumina HiSeq 2000 10
EGAD00001002241 Illumina HiSeq 2000 6
EGAD00001003292 Illumina HiSeq 2000 34
EGAD00001003580 Illumina HiSeq 2000 38
EGAD00001004137 Illumina HiSeq 2000 -
EGAD00001004417 Illumina HiSeq 2000 -
EGAD00001004775 Illumina HiSeq 2000 -
EGAD00001007785 HiSeq X Five Illumina HiSeq 2000 Illumina NovaSeq 6000 -
EGAD00001011196 HiSeq X Five Illumina HiSeq 2000 Illumina NovaSeq 6000 unspecified 6
Publications Citations
Ordering of mutations in preinvasive disease stages of esophageal carcinogenesis.
Nat Genet 46: 2014 837-843
Mobile element insertions are frequent in oesophageal adenocarcinomas and can mislead paired-end sequencing analysis.
BMC Genomics 16: 2015 473
Mutational signatures in esophageal adenocarcinoma define etiologically distinct subgroups with therapeutic relevance.
Nat Genet 48: 2016 1131-1141
A comparative analysis of whole genome sequencing of esophageal adenocarcinoma pre- and post-chemotherapy.
Genome Res 27: 2017 902-912
Impact of mutations in Toll-like receptor pathway genes on esophageal carcinogenesis.
PLoS Genet 13: 2017 e1006808
The landscape of selection in 551 esophageal adenocarcinomas defines genomic biomarkers for the clinic.
Nat Genet 51: 2019 506-516
Patient-specific cancer genes contribute to recurrently perturbed pathways and establish therapeutic vulnerabilities in esophageal adenocarcinoma.
Nat Commun 10: 2019 3101
The impact of rare germline variants on human somatic mutation processes.
Nat Commun 13: 2022 3724