HIVID: An efficient method to detect HBV integration using low coverage sequencing

Genomics

Volumn 102, Issue 4, 2013, Pages 338-344

  Li, Weiyang ^a,b   Zeng, Xi ^a   Lee, Nikki P ^c   Liu, Xiao ^a   Chen, Shengpei ^a   Guo, Bing ^a   Yi, Shang ^a   Zhuang, Xuehan ^a   Chen, Fang ^a   Wang, Guan ^a   Poon, Ronnie T ^c   Fan, Sheung Tat ^c   Mao, Mao ^d   Li, Yingrui ^a   Li, Songgang ^a   Wang, Jun ^a   JianWang, ^a   Xu, Xun ^a   Jiang, Hui ^a   Zhang, Xiuqing ^a  

^a BGI SHENZHEN   (China)

^b SOUTH CHINA UNIVERSITY OF TECHNOLOGY   (China)

^c UNIVERSITY OF HONG KONG   (Hong Kong)

^d PFIZER INC   (United States)

Author keywords

Capture; Cost effective; Hepatocellular carcinoma; High throughput; Integration

Indexed keywords

ARTICLE; CCNE1 GENE; CONTROLLED STUDY; COST EFFECTIVENESS ANALYSIS; GENE; GENE LOCATION; GENE SEQUENCE; GENOMIC FRAGMENT; HEPATITIS B; HEPATITIS B VIRUS; HIGH THROUGHPUT SEQUENCING; HIGH THROUGHPUT VIRAL INTEGRATION DETECTION; LIVER CELL CARCINOMA; MLL4 GENE; NONHUMAN; PRIORITY JOURNAL; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS; TERT GENE; VIRUS DETECTION; VIRUS DNA CELL DNA INTERACTION; VIRUS GENOME;

HEPATITIS B VIRUS;

CAPTURE; COST-EFFECTIVE; HEPATOCELLULAR CARCINOMA; HIGH-THROUGHPUT; INTEGRATION;

CARCINOMA, HEPATOCELLULAR; CHINA; CYCLIN E; DNA BREAKS; DNA-BINDING PROTEINS; GENOME, HUMAN; GENOME, VIRAL; HEPATITIS B VIRUS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; LIVER NEOPLASMS; ONCOGENE PROTEINS; TELOMERASE; VIRUS INTEGRATION;

EID: 84886258354     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2013.07.002     Document Type: Article

References (22)

1. Shamay M., Barak O., Shaul Y. HBXAP, a novel PHD-finger protein, possesses transcription repression activity. Genomics 2002, 79:523-529.
2. Michielsen P., Ho E. Viral hepatitis B and hepatocellular carcinoma. Acta Gastroenterol. Belg. 2011, 74:4-8.
3. Farazi P.A., DePinho R.A. Hepatocellular carcinoma pathogenesis: from genes to environment. Nat. Rev. Cancer 2006, 6:674-687.
4. Chemin I., Zoulim F. Hepatitis B virus induced hepatocellular carcinoma. Cancer Lett. 2009, 286:52-59.
5. Bouchard M.J., Navas-Martin S. Hepatitis B and C virus hepatocarcinogenesis: lessons learned and future challenges. Cancer Lett. 2011, 305:123-143.
6. Ishikawa T. Clinical features of hepatitis B virus-related hepatocellular carcinoma. World J. Gastroenterol. 2010, 16:2463-2467.
7. Paterlini-Brechot P., et al. Hepatitis B virus-related insertional mutagenesis occurs frequently in human liver cancers and recurrently targets human telomerase gene. Oncogene 2003, 22:3911-3916.
8. Gozuacik D., et al. Identification of human cancer-related genes by naturally occurring hepatitis B virus DNA tagging. Oncogene 2001, 20:6233-6240.
9. Murakami Y., et al. Large scaled analysis of hepatitis B virus (HBV) DNA integration in HBV related hepatocellular carcinomas. Gut 2005, 54:1162-1168.
10. Saigo K., et al. Integration of hepatitis B virus DNA into the myeloid/lymphoid or mixed-lineage leukemia (MLL4) gene and rearrangements of MLL4 in human hepatocellular carcinoma. Hum. Mutat. 2008, 29:703-708.
11. Sung W.K., et al. Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma. Nat. Genet. 2012, 44:765-769.
12. Jiang Z., et al. The effects of hepatitis B virus integration into the genomes of hepatocellular carcinoma patients. Genome Res. 2012, 22:593-601.
13. Tamori A., et al. Alteration of gene expression in human hepatocellular carcinoma with integrated hepatitis B virus DNA. Clin. Cancer Res. 2005, 11:5821-5826.
14. Leamon J.H., Link D.R., Egholm M., Rothberg J.M. Overview: methods and applications for droplet compartmentalization of biology. Nat. Methods 2006, 3:541-543.
15. Li R., et al. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 2009, 25:1966-1967.
16. Li H., Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 2010, 26:589-595.
17. Horikawa I., Barrett J.C. cis-Activation of the human telomerase gene (hTERT) by the hepatitis B virus genome. J. Natl. Cancer Inst. 2001, 93:1171-1173.
18. Nakayama N., et al. Gene amplification CCNE1 is related to poor survival and potential therapeutic target in ovarian cancer. Cancer 2010, 116:2621-2634.
19. Ferber M.J., et al. Integrations of the hepatitis B virus (HBV) and human papillomavirus (HPV) into the human telomerase reverse transcriptase (hTERT) gene in liver and cervical cancers. Oncogene 2003, 22:3813-3820.
20. Wilkens L., et al. Cytogenetic aberrations in primary and recurrent fibrolamellar hepatocellular carcinoma detected by comparative genomic hybridization. Am. J. Clin. Pathol. 2000, 114:867-874.
21. Nakajima T., et al. Centrosome aberration accompanied with p53 mutation can induce genetic instability in hepatocellular carcinoma. Mod. Pathol. 2004, 17:722-727.
22. Fallot G., Neuveut C., Buendia M.A. Diverse roles of hepatitis B virus in liver cancer. Curr. Opin. Virol. 2012, 2:467-473.