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High-resolution characterization of a hepatocellular carcinoma genome


Hepatocellular carcinoma, one of the most common virus-associated cancers, is the third most frequent cause of cancer-related death worldwide1. By massively parallel sequencing2 of a primary hepatitis C virus–positive hepatocellular carcinoma (36× coverage) and matched lymphocytes (>28× coverage) from the same individual, we identified more than 11,000 somatic substitutions of the tumor genome that showed predominance of T>C/A>G transition and a decrease of the T>C substitution on the transcribed strand, suggesting preferential DNA repair. Gene annotation enrichment analysis3 of 63 validated non-synonymous substitutions revealed enrichment of phosphoproteins. We further validated 22 chromosomal rearrangements, generating four fusion transcripts that had altered transcriptional regulation (BCORL1-ELF4) or promoter activity. Whole-exome sequencing4,5 at a higher sequence depth (>76× coverage) revealed a TSC1 nonsense substitution in a subpopulation of the tumor cells. This first high-resolution characterization of a virus-associated cancer genome identified previously uncharacterized mutation patterns, intra-chromosomal rearrangements and fusion genes, as well as genetic heterogeneity within the tumor.

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Figure 1: Somatic substitution pattern of the liver cancer genome.
Figure 2: Characterization of rearrangements in liver cancer.
Figure 3: Intra-tumoral genetic heterogeneity detected by exon-capture sequencing.


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We thank K.K. Khanna (The Queensland Institute of Medical Research) for providing a human BCORL1 cDNA clone; T.D. Taylor (RIKEN) for comments on the manuscript; T. Urushidate, S. Ohashi, S. Ohnami, A. Kokubu, N. Okada, K. Shiina, H. Meguro and K. Nakano for their excellent technical assistance. This work was supported by the Program for Promotion of Fundamental Studies in Health Sciences of the National Institute of Biomedical Innovation (NIBIO), Japan, and the Industrial Technology Research Grant Program from the New Energy and Industrial Technology Development Organization (NEDO), Japan. This study is associated with the International Cancer Genome Consortium (ICGC), and the mutation data were deposited at and released from the ICGC web site.

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The study was designed by T. Shibata, H.A., T.Y. and J.K. Sequencing and data analyses were conducted by Y.T., K.T., S.Y., S.T., K. Sonoda and H.T. Allele typing and copy number analyses were performed by H.S. and S.I. Other molecular studies were done by Y.A., F.H., T. Shirakihara, and L.W.; H.O., K. Shimada, T.K., T.O. and K.K. coordinated collection of clinical sample and information. The manuscript was written by Y.T., T. Shibata, K.T., S.Y., H.A. and T.Y.

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Correspondence to Tatsuhiro Shibata.

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The authors declare no competing financial interests.

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Supplementary Note, Supplementary Figures 1–13 and Supplementary Tables 1–9. (PDF 4987 kb)

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Totoki, Y., Tatsuno, K., Yamamoto, S. et al. High-resolution characterization of a hepatocellular carcinoma genome. Nat Genet 43, 464–469 (2011).

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