ICGC Oesophageal adenocarcinoma - 100 tumour samples - EGA European Genome-Phenome Archive

Study ID	Alternative Stable ID	Type
EGAS00001000724		Other

Study ID

Alternative Stable ID

Type

EGAS00001000724

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.

Dataset ID	Description	Technology	Samples
EGAD00001001048	Samples from Edwards et al 2015 - doi:10.1186/s12864-015-1685-z Samples from Edwards et al 2015 - doi:10.1186/s12864-015-1685-z	Illumina HiSeq 2000	86
EGAD00001001071	Samples from the "100" project that are in the ICGC PanCancer project. Samples from the "100" project that are in the ICGC PanCancer project.	Illumina HiSeq 2000	200
EGAD00001001394	Samples from Ross Innes et. al 2015 - doi:10.1038/ng.3357 Samples from Ross Innes et. al 2015 - doi:10.1038/ng.3357	Illumina HiSeq 2000	N/A
EGAD00001001457	All samples from the "100" project All samples from the "100" project	Illumina HiSeq 2000	238
EGAD00001001960	upcoming publication 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 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 Sequencing data for ICGC Oesophageal Adenocarcinoma tissue samples - chemo_cohort	Illumina HiSeq 2000	270
EGAD00001002689	ICGC Oesophageal Adenocarcinoma tissue samples 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 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 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
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 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
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 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
EGAD00001004775	Data supporting: "Patient-specific detection of cancer genes reveals recurrently perturbed processes in esophageal adenocarcinoma." Mourikis et al. WGS (BAM files) 521 samples 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
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. 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
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. 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	160
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. 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 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	992
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 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	766

Dataset ID

Description

Technology

Samples

EGAD00001001048

Samples from Edwards et al 2015 - doi:10.1186/s12864-015-1685-z

Illumina HiSeq 2000

EGAD00001001071

Samples from the "100" project that are in the ICGC PanCancer project.

Illumina HiSeq 2000

200

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

238

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

EGAD00001002689

ICGC Oesophageal Adenocarcinoma tissue samples

Illumina HiSeq 2000

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

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

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

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

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

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

160

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

992

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

766

Study

Study Description

Study Datasets 18 datasets.

Who archives the data?

Publications

Citations

The European Genome-phenome Archive (EGA) is part of the ELIXIR infrastructure.