Hepatocellular carcinoma genomic data from the Asia Cancer Research Group.

Dataset type: Genomic
Data released on May 31, 2012

Hepatocellular carcinoma (HCC) is one of the most common solid tumors worldwide and represents the third leading cause of cancer deaths. Hepatitis B virus (HBV) is a major etiologic agent, leading to an increased risk of developing HCC, in particular those with acute liver disease and cirrhosis. The Asian Cancer Research Group (ACRG) is an independent, not-for-profit company established to accelerate research and improve treatment for patients affected with the most commonly-diagnosed cancers in Asia. With HBV being endemic in China and Southeast Asia, and high levels of HCC being a result, the ACRG have studied the events and effects of HBV integration in the HCC genome. To do this massively parallel sequencing in a cohort of 88 Chinese patients diagnosed with HCC who underwent curative primary hepatectomy or liver transplantation at Queen Mary Hospital (Pokfulam, Hong Kong) was carried out. All patients gave written informed consent to use both tumor (T) and non-tumor (N) liver tissues for the study. Genomic DNA was purified for at least 30-fold coverage paired-end (PE) sequencing, and PE reads were mapped on human reference genome (UCSC build hg19) and HBV (NC_003977). Two sequencing libraries with different insert size were constructed for each genomic DNA sample (200 bp and 800 bp). Paired end, 90bp read length sequencing was performed in the HiSeq 2000 sequencer according to Manufacturer’s instructions. Raw gene expression profiling data of these human HCC samples has also deposited to GEO with the accession number GSE25097.

Additional details

Read the peer-reviewed publication(s):

Sung, W.-K., Zheng, H., Li, S., Chen, R., Liu, X., Li, Y., … Luk, J. M. (2012). Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma. Nature Genetics, 44(7), 765–769. doi:10.1038/ng.2295 (PubMed: 22634754)

Accessions (data included in GigaDB):

ERA: ERP001196

Accessions (data not in GigaDB):

GEO: GSE25097





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
101N9606HumanhumanHomo sapiens Disease status:normal
101T9606HumanhumanHomo sapiens Disease status:DOID:684
105N9606HumanhumanHomo sapiens Disease status:normal
105T9606HumanhumanHomo sapiens Disease status:DOID:684
106N9606HumanhumanHomo sapiens Disease status:normal
106T9606HumanhumanHomo sapiens Disease status:DOID:684
108N9606HumanhumanHomo sapiens Disease status:normal
108T9606HumanhumanHomo sapiens Disease status:DOID:684
113N9606HumanhumanHomo sapiens Disease status:normal
113T9606HumanhumanHomo sapiens Disease status:DOID:684
Displaying 1-10 of 176 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
22NGenome sequenceFASTQ5.29 GB2012-06-22
22NGenome sequenceFASTQ5.45 GB2012-06-22
82NGenome sequenceFASTQ4.73 GB2012-06-22
82NGenome sequenceFASTQ4.88 GB2012-06-22
180NGenome sequenceFASTQ5.04 GB2012-06-22
180NGenome sequenceFASTQ5.21 GB2012-06-22
180TGenome sequenceFASTQ4.33 GB2012-06-22
180TGenome sequenceFASTQ4.48 GB2012-06-22
22TGenome sequenceFASTQ5.21 GB2012-06-22
22TGenome sequenceFASTQ5.37 GB2012-06-22
Displaying 1-10 of 3134 File(s).
Date Action
October 15, 2015 File 100914_I137_FC80139ABXX_L1_HUMohgRAADMAAPE_1.clean.fq.gz updated
October 15, 2015 File 100914_I137_FC80139ABXX_L1_HUMohgRAADMAAPE_1.clean.fq.gz updated
October 26, 2015 File 100914_I137_FC80139ABXX_L1_HUMohgRAADMAAPE_1.clean.fq.gz updated
November 4, 2015 File 100914_I137_FC80139ABXX_L1_HUMohgRAADMAAPE_1.clean.fq.gz updated
November 4, 2015 File 100914_I137_FC80139ABXX_L1_HUMohgRAADMAAPE_2.clean.fq.gz updated
November 4, 2015 File 100914_I137_FC80139ABXX_L2_HUMohgRAGDMAAPE_1.clean.fq.gz updated
November 4, 2015 File 100914_I137_FC80139ABXX_L2_HUMohgRAGDMAAPE_2.clean.fq.gz updated
November 4, 2015 File 100914_I137_FC80139ABXX_L3_HUMohgRAIDMAAPE_1.clean.fq.gz updated
November 4, 2015 File 100914_I137_FC80139ABXX_L3_HUMohgRAIDMAAPE_2.clean.fq.gz updated
November 4, 2015 File 100914_I137_FC80139ABXX_L4_HUMohgRANDMAAPE_1.clean.fq.gz updated
November 4, 2015 File 100914_I137_FC80139ABXX_L4_HUMohgRANDMAAPE_2.clean.fq.gz updated
November 4, 2015 File 100914_I137_FC80139ABXX_L5_HUMohgRBDDMAAPE_1.clean.fq.gz updated
November 4, 2015 File 100914_I137_FC80139ABXX_L5_HUMohgRBDDMAAPE_2.clean.fq.gz updated
November 4, 2015 File 100914_I137_FC80139ABXX_L5_HUMohgRBDDMAAPE_2.clean.fq.gz updated
November 4, 2015 File 101222_I327_FC810M9ABXX_L8_HUMohgRHLDMAAPEI-8_2.clean.fq.gz updated
March 2, 2016 Link updated : ERA:ERP001196