This tab shows an overview of the selected study/paper [more details]
Reference

Exome sequencing of hepatitis B virus-associated hepatocellular carcinoma.

Paper Id
COSP29621
Authors
Huang J,Deng Q,Wang Q,Li KY,Dai JH,Li N,Zhu ZD,Zhou B,Liu XY,Liu RF,Fei QL,Chen H,Cai B,Zhou B,Xiao HS,Qin LX and Han ZG
Affiliation
1] Human Genome Center of Rui-Jin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China. [2] Shanghai Ministry of Science and Technology (MOST) Key Laboratory for Disease and Health Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China. [3] National Engineering Center for Biochip at Shanghai, Shanghai, China. [4] Shenzhen Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Shenzhen Third People's Hospital, Guangdong Medical College, Shenzhen, China. [5].
Journal
Nature genetics 2012
ISSN:1546-1718
PUBMED:22922871
Abstract
Hepatocellular carcinoma (HCC) is one of the most common cancers worldwide and shows a propensity to metastasize and infiltrate adjacent and more distant tissues. HCC is associated with multiple risk factors, including hepatitis B virus (HBV) infection, which is especially prevalent in China. Here, we used exome sequencing to identify somatic mutations in ten HBV-positive individuals with HCC with portal vein tumor thromboses (PVTTs), intrahepatic metastases. Both C:G>A:T and T:A>A:T transversions were frequently found among the 331 non-silent mutations. Notably, ARID1A, which encodes a component of the SWI/SNF chromatin remodeling complex, was mutated in 14 of 110 (13%) HBV-associated HCC specimens. We used RNA interference to assess the roles of 91 of the confirmed mutated genes in cellular survival. The results suggest that seven of these genes, including VCAM1 and CDK14, may confer growth and infiltration capacity to HCC cells. This study provides a view of the landscape of somatic mutations that may be implicated in advanced HCC.
Paper Status
Curated
Genes Analysed
398
Mutated Samples
10
Total No. of Samples
10
This tab shows genes with mutations in the selected study/paper [more details]
Genes Samples CDS Mutation AA Mutation
This tab shows genes without mutations in the selected study/paper [more details]
Non-Mutant Genes Gene Id (COSG)
This tab shows samples without mutations in the selected study/paper [more details]
Non-Mutant Samples Sample Id (COSS)
This tab shows mutated samples in the selected study/paper [more details]
Sample Name Mutation Count
This tab shows non coding variant in the selected study/paper [more details]
Sample ID Sample Name ID NCV Annotation Zygosity Chromosome Genome start Genome stop Genome version Strand WT seq Mut seq
This tab shows the copy number variation data for this study. Only variants (classified as gain or loss) are listed. [more details]
CNV Gene Sample Position Minor Allele Copy Number Average Ploidy

1. N/A represents cases where average ploidy value is not available( mostly ICGC samples). For some TCGA samples where minor allele information is not available the average ploidy value could not be calculated.

2. For TCGA samples, Ascat algorithm is used to calculate the average ploidy.

3. For CGP samples, Picnic algorithm is used to calculate the average ploidy.

Type
This tab shows a table of count of samples having gain or loss for all genes [more details]
Gene Gain Samples Loss Samples Samples Tested
This tab shows the fusion mutations observed in this sample [more details]
Gene Sample Name Id Sample(COSS) CDS Mutation Somatic status Zygosity Validated Type