StudyType	PubMedID	Author	Title	Journal	PublishDate	Chromosome	Disease	Technology	Species	CaseID	Platform	CNA	Connection	Gene	Affiliation	Abstract	GenomeAssembly	GEO	dbGaP	ENA	IsCancer	FusionGene
Research	22267523	Jiang Z, Jhunjhunwala S, Liu J, Haverty PM, Kennemer MI, Guan Y, Lee W, Carnevali P, Stinson J, Johnson S, Diao J, Yeung S, Jubb A, Ye W, Wu TD, Kapadia SB, de Sauvage FJ, Gentleman RC, Stern HM, Seshagiri S, Pant KP, Modrusan Z, Ballinger DG, Zhang Z	The effects of hepatitis B virus integration into the genomes of hepatocellular carcinoma patients	Genome Research	2012 Apr	11	Hepatocellular carcinoma	Next Generation Sequencing	Homo sapiens	H384			hs1:237459374-237459731,hs11:69326266-69326793;hs1:237803220-237803554,hs11:69030220-69030519;hs11:68174928-68175207,hs11:111576997-111577265;hs11:68263776-68263934,hs11:111568063-111568201;hs11:68834611-68835103,hs11:69063232-69063535;hs11:69455238-69455748,hs11:99220072-99220607;hs11:69462705-69463095,hs11:99264863-99265121;hs11:69463061-69463415,hs11:69520345-69520543;hs11:69463944-69464292,hs13:111314565-111314959;hs11:69488929-69489325,hs11:99528987-99529335;hs11:99100510-99100897,hsX:1907040-1907618;hs12:7177879-7178352,hs12:7299289-7299792;hs13:107169509-107169692,hs13:108423879-108424078;hs13:107183258-107183591,hs13:107213137-107213501;hs13:108210800-108211323,hs13:109282898-109283336	CCND1;CNTN5;FGF19;LRP5;MYEOV;ORAOV1;PPP6R3;SIK2;TPCN2;	Department of Bioinformatics and Computational Biology, Genentech Inc, South San Francisco, California 94080, USA	Hepatitis B virus (HBV) infection is a leading risk factor for hepatocellular carcinoma (HCC). HBV integration into the host genome has been reported, but its scale, impact and contribution to HCC development is not clear. Here, we sequenced the tumor and nontumor genomes (>80X coverage) and transcriptomes of four HCC patients and identified 255 HBV integration sites. Increased sequencing to 240X coverage revealed a proportionally higher number of integration sites. Clonal expansion of HBV-integrated hepatocytes was found specifically in tumor samples. We observe a diverse collection of genomic perturbations near viral integration sites, including direct gene disruption, viral promoter-driven human transcription, viral-human transcript fusion, and DNA copy number alteration. Thus, we report the most comprehensive characterization of HBV integration in hepatocellular carcinoma patients. Such widespread random viral integration will likely increase carcinogenic opportunities in HBV-infected individuals.	GRCh37/hg19		phs000384		Yes	CCND1,CARS2;CCND1,CNTN5;CCND1,FGF19;LRP5,SIK2;ORAOV1,CNTN5;PPP6R3,SIK2;TPCN2,MYEOV