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Reference

Whole-genome sequencing of liver cancers identifies etiological influences on mutation patterns and recurrent mutations in chromatin regulators.

Paper Id
COSP28909
Authors
Fujimoto A,Totoki Y,Abe T,Boroevich KA,Hosoda F,Nguyen HH,Aoki M,Hosono N,Kubo M,Miya F,Arai Y,Takahashi H,Shirakihara T,Nagasaki M,Shibuya T,Nakano K,Watanabe-Makino K,Tanaka H,Nakamura H,Kusuda J,Ojima H,Shimada K,Okusaka T,Ueno M,Shigekawa Y,Kawakami Y,Arihiro K,Ohdan H,Gotoh K,Ishikawa O,Ariizumi S,Yamamoto M,Yamada T,Chayama K,Kosuge T,Yamaue H,Kamatani N,Miyano S,Nakagama H,Nakamura Y,Tsunoda T,Shibata T and Nakagawa H
Affiliation
1] Center for Genomic Medicine, RIKEN, Yokohama, Japan. [2].
Journal
Nature genetics 2012;44(7):760-4
ISSN:1546-1718
PUBMED:22634756
Abstract
Hepatocellular carcinoma (HCC) is the third leading cause of cancer-related death worldwide. We sequenced and analyzed the whole genomes of 27 HCCs, 25 of which were associated with hepatitis B or C virus infections, including two sets of multicentric tumors. Although no common somatic mutations were identified in the multicentric tumor pairs, their whole-genome substitution patterns were similar, suggesting that these tumors developed from independent mutations, although their shared etiological backgrounds may have strongly influenced their somatic mutation patterns. Statistical and functional analyses yielded a list of recurrently mutated genes. Multiple chromatin regulators, including ARID1A, ARID1B, ARID2, MLL and MLL3, were mutated in ∼50% of the tumors. Hepatitis B virus genome integration in the TERT locus was frequently observed in a high clonal proportion. Our whole-genome sequencing analysis of HCCs identified the influence of etiological background on somatic mutation patterns and subsequent carcinogenesis, as well as recurrent mutations in chromatin regulators in HCCs.
Paper Status
Curated
Genes Analysed
21
Mutated Samples
21
Total No. of Samples
27
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This tab shows genes with mutations in the selected study/paper [more details]
Genes Samples CDS Mutation AA Mutation
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Non-Mutant Genes Gene Id (COSG)
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Non-Mutant Samples Sample Id (COSS)
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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 gene expression and copy number variation data for this study. [more details]

Table Information

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The table currently shows only high value (numeric) copy number data. Copy number segments are excluded if the total copy number and minor allele values are unknown.

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Sample Gene Expression Expr Level (Z-Score)

Over Expressed; Z-Score > 2.0

Under Expressed; Z-Score < -2.0

Normal; Z-Score within the range -2.0 to 2.0

CN Type Minor Allele Copy Number CN Segment Posn. Average Ploidy

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

2. For TCGA samples, the ASCAT algorithm was used to calculate the average ploidy.

3. For CGP samples, the PICNIC algorithm was used to calculate the average ploidy.

CNV
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