WGS of liver cancer in the Japanese population - EGA European Genome-Phenome Archive

Study ID	Alternative Stable ID	Type
EGAS00001000678		Other

Study ID

Alternative Stable ID

Type

EGAS00001000678

Other

Study Description

Hepatocellular carcinoma (HCC) is the third leading cancer-related cause of death and the seventh most common form of cancer worldwide, with an estimate of more than 700,000 new cases each year. The most established risk factors of HCC are chronic HBV and HCV infection. HBV infection is responsible for over 50% of the worldwide attributable risk of HCC, especially in East Asia and Africa, while in Japan and several Western countries HCV infection is the most common risk factor for HCC. To gain insights into the molecular alterations of virus-associated HCC, we performed whole genome sequencing (WGS) of 321 HCC tumors from 159 patients. This work was performed as a part of the ICGC (International Cancer Genome Consortium) project.

Dataset ID	Description	Technology	Samples
EGAD00001000808	RIKEN collection WGS reads for 321 HCC and blood matched samples from 158 donors submitted to ICGC for release 15 RIKEN collection WGS reads for 321 HCC and blood matched samples from 158 donors submitted to ICGC for release 15	Illumina Genome Analyzer IIx,Illumina HiSeq 2000	321
EGAD00001000809	RIKEN collection WGS reads for 61 liver cancer and matched blood samples from 30 donors displaying biliary phenotype RIKEN collection WGS reads for 61 liver cancer and matched blood samples from 30 donors displaying biliary phenotype	Illumina HiSeq 2000	61
EGAD00001000842	RIKEN collection WGS reads for 100 HCC and matched blood samples from 50 donors submitted to ICGC for release 16 RIKEN collection WGS reads for 100 HCC and matched blood samples from 50 donors submitted to ICGC for release 16	Illumina HiSeq 2000	100
EGAD00001001035	RIKEN collection WGS and RNA-seq reads for 66 HBV-associated HCC and matched blood or liver samples from 22 donors. RIKEN collection WGS and RNA-seq reads for 66 HBV-associated HCC and matched blood or liver samples from 22 donors.	Illumina Genome Analyzer IIx,Illumina HiSeq 2000	66
EGAD00001001642	RIKEN collection of WGS reads of 530 liver cancer and matched blood samples from 260 donors. RIKEN collection of WGS reads of 530 liver cancer and matched blood samples from 260 donors.	Illumina Genome Analyzer IIx,Illumina HiSeq 2000	530
EGAD00001001643	RIKEN collection of WGS read of 59 multi-centric liver cancers or intra-haptatic metastasis and matched blood samples from 19 donors. RIKEN collection of WGS read of 59 multi-centric liver cancers or intra-haptatic metastasis and matched blood samples from 19 donors.	Illumina Genome Analyzer IIx,Illumina HiSeq 2000	59
EGAD00001001880	RIKEN collection of RNA-seq reads for 458 liver cancer samples and matched normal liver from 247 donors. RIKEN collection of RNA-seq reads for 458 liver cancer samples and matched normal liver from 247 donors.	Illumina Genome Analyzer IIx,Illumina HiSeq 2000	458
EGAD00001001881	RIKEN collection of WGS reads for 269 liver cancer tumors and matched normal blood or liver tissue from 258 donors. In total there are 1864 paired fastq sets sequenced on Illumina HiSeq 2000 or Genome Analyzer II instruments with paired reads of 75–101 bp. Quality control and duplication removal has not been performed. RIKEN collection of WGS reads for 269 liver cancer tumors and matched normal blood or liver tissue from 258 donors. In total there are 1864 paired fastq sets sequenced on Illumina HiSeq 2000 or Genome Analyzer II instruments with paired reads of 75–101 bp. Quality control and duplication removal has not been performed.	Illumina Genome Analyzer IIx,Illumina HiSeq 2000	528
EGAD00001001996	RIKEN collection of WGS reads for 13 multicentric liver cancers or intrahepatic metastasis and matched blood samples for 12 donors. RIKEN collection of WGS reads for 13 multicentric liver cancers or intrahepatic metastasis and matched blood samples for 12 donors.	Illumina HiSeq 2000	13

Dataset ID

Description

Technology

Samples

EGAD00001000808

RIKEN collection WGS reads for 321 HCC and blood matched samples from 158 donors submitted to ICGC for release 15

Illumina Genome Analyzer IIx,Illumina HiSeq 2000

321

EGAD00001000809

RIKEN collection WGS reads for 61 liver cancer and matched blood samples from 30 donors displaying biliary phenotype

Illumina HiSeq 2000

EGAD00001000842

RIKEN collection WGS reads for 100 HCC and matched blood samples from 50 donors submitted to ICGC for release 16

Illumina HiSeq 2000

100

EGAD00001001035

RIKEN collection WGS and RNA-seq reads for 66 HBV-associated HCC and matched blood or liver samples from 22 donors.

Illumina Genome Analyzer IIx,Illumina HiSeq 2000

EGAD00001001642

RIKEN collection of WGS reads of 530 liver cancer and matched blood samples from 260 donors.

Illumina Genome Analyzer IIx,Illumina HiSeq 2000

530

EGAD00001001643

RIKEN collection of WGS read of 59 multi-centric liver cancers or intra-haptatic metastasis and matched blood samples from 19 donors.

Illumina Genome Analyzer IIx,Illumina HiSeq 2000

EGAD00001001880

RIKEN collection of RNA-seq reads for 458 liver cancer samples and matched normal liver from 247 donors.

Illumina Genome Analyzer IIx,Illumina HiSeq 2000

458

EGAD00001001881

RIKEN collection of WGS reads for 269 liver cancer tumors and matched normal blood or liver tissue from 258 donors. In total there are 1864 paired fastq sets sequenced on Illumina HiSeq 2000 or Genome Analyzer II instruments with paired reads of 75–101 bp. Quality control and duplication removal has not been performed.

Illumina Genome Analyzer IIx,Illumina HiSeq 2000

528

EGAD00001001996

RIKEN collection of WGS reads for 13 multicentric liver cancers or intrahepatic metastasis and matched blood samples for 12 donors.

Illumina HiSeq 2000

Study

Study Description

Study Datasets 9 datasets.

Who archives the data?

Publications

Citations

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