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Data released on May 31, 2012

Hepatocellular carcinoma genomic data from the Asia Cancer Research Group.

Ariyaratne, P, N; Barber, T, D; Buser, C; Chan, K, L; Chen, R; Chou, W; Fernandez, J; Gao, H; Gong, Z; Hao, K; Hauptschein, R; Hu, Y; Kan, Z; Lee, N, P; Lee, W, H; Li, S; Liu, A, M; Liu, X; Mulawadi, F, H; Rejto, P, A; Tennakoon, C; Wang, B; Wang, G; Wang, J; Willard, M, D; Wong, K, F; Xu, J; Zhang, Q; Zheng, H; Lin, Z; Peng, Z; Zhou, W; Yi, K; Chen, S; Fan, X; Li, L; Yang, J; Ye, R; Ju, J; Wang, K; Estrella, H; Deng, S; Wulur, I, H; Liu, J; Ehsani, M, E; Zhang, C; Loboda, A; Sung, W; Aggarwal, A; Poon, R, T; Fan, S, T; Wang, J; Hardwick, J; Reinhard, C; Dai, H; Li, Y; Luk, J, M; Mao, M; the Asian Cancer Research Group, (2012): Hepatocellular carcinoma genomic data from the Asia Cancer Research Group. GigaScience. http://dx.doi.org/10.5524/100034 RIS BibTeX Text

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.

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Related manuscripts:

doi:10.1038/ng.2295 (PubMed: 22634754)

Accessions (data included in GigaDB):

ERA: ERP001196

Accessions (data not in GigaDB):

GEO: GSE25097

Genomic

http://gigadb.org/images/data/cropped/100034_Hepatocellular_carcinoma.jpg

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

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).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
File Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDFile 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).

History:

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