Exome sequencing of hepatitis B virus–associated hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is one of the most common cancers worldwide and shows a propensity to metastasize and infiltrate adjacent and more distant tissues 1 . 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. Hepatocellular carcinoma is associated with infection with HBV or hepatitis C virus (HCV), alcohol consumption and aflatoxin B1 (AFB1) contamination of food. Individuals with HCC with PVTTs, which are caused by tumor invasion and metastasis via the intra­ hepatic portal vein, have extremely poor prognoses 2,3 . To identify the genetic lesions in advanced HBV ­ associated HCC with intrahepatic metastasis, we employed two types of exome sequenc­ ing strategies, the Illumina/Solexa Genome Analyzer II and the ABI SOLiD platforms, to identify the somatic mutations in ten individuals with HCC with PVTTs (Supplementary Table 1). The average cov­ erage of each base in the target regions was 28 ­ fold and 88 ­ fold per tumor sample (primary tumor and matched PVTT) for the Illumina and ABI platforms, respectively (Online Methods, Supplementary Fig. 1 and Supplementary Table 2). Here, we propose 475 candidate