Yates LR, Gerstung M, Knappskog S, Desmedt C, Gundem G, Loo PV, Aas T, Alexandrov LB, Larsimont D, Davies H. Subclonal diversification of primary breast cancer revealed by multiregion sequencing. Nat Med. 2015;21(7):751.
Article
CAS
Google Scholar
Gerlinger M, Rowan AJ, Horswell S, Math M, Larkin J, Endesfelder D, Gronroos E, Martinez P, Matthews N, Stewart A. Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N Engl J Med. 2012;366(10):883–92.
Article
CAS
Google Scholar
Zhang J, Fujimoto J, Zhang J, Wedge DC, Song X, Zhang J, Seth S, Chow CW, Cao Y, Gumbs C. Intratumor heterogeneity in localized lung adenocarcinomas delineated by multiregion sequencing. Science. 2014;346(6206):256.
Article
CAS
Google Scholar
Shi JY, Xing Q, Duan M, Wang ZC, Yang LX, Zhao YJ, Wang XY, Liu Y, Deng M, Ding ZB. Inferring the progression of multifocal liver cancer from spatial and temporal genomic heterogeneity. Oncotarget. 2015;7(3):2867–77.
PubMed Central
Google Scholar
Housman G, Byler S, Heerboth S, Lapinska K, Longacre M, Snyder N, Sarkar S. Drug resistance in Cancer: an overview. Cancers. 2014;6(3):1769–92.
Article
CAS
Google Scholar
Josephidou M, Lynch AG. Tavaré S: multiSNV: a probabilistic approach for improving detection of somatic point mutations from multiple related tumour samples. Nucleic Acids Res. 2015;43(9):e61.
Article
Google Scholar
Morissette G, Flamand L. Herpesviruses and chromosomal integration. J Virol. 2010;84(23):12100–9.
Article
CAS
Google Scholar
Walboomers JM, Jacobs MV, Manos MM, Bosch FX, Kummer JA, Shah KV, Snijders PJ, Peto J, Meijer C. Muñoz N: human papillomavirus is a necessary cause of invasive cervical cancer worldwide. J Pathol. 1999;189(1):12–9.
Article
CAS
Google Scholar
Jiang Z, Jhunjhunwala S, Liu J, Haverty PM, Kennemer MI, Guan Y, Lee W, Carnevali P, Stinson J, Johnson S. The effects of hepatitis B virus integration into the genomes of hepatocellular carcinoma patients. Genome Res. 2012;22(4):593–601.
Article
CAS
Google Scholar
Chen Y, Williams V, Filippova M, Filippov V, Duerksenhughes P. Viral carcinogenesis: factors inducing DNA damage and virus integration. Cancers. 2014;6(4):2155.
Article
CAS
Google Scholar
Hai H, Tamori A, Kawada N. Role of hepatitis B virus DNA integration in human hepatocarcinogenesis. World Journal of Gastroenterology Wjg. 2014;20(20):6236–43.
Article
CAS
Google Scholar
Chen Y, Yao H, Thompson EJ, Tannir NM, Weinstein JN, Su X. VirusSeq: software to identify viruses and their integration sites using next-generation sequencing of human cancer tissue. Bioinformatics. 2013;29(2):266–7.
Article
CAS
Google Scholar
Schelhorn SE, Fischer M, Tolosi L, Altmuller J, Nurnberg P, Pfister H, Lengauer T, Berthold F. Sensitive detection of viral transcripts in human tumor transcriptomes. PLoS Comput Biol. 2013;9(10):e1003228.
Article
Google Scholar
Kostic AD, Ojesina AI, Pedamallu CS, Jung J, Verhaak RG, Getz G, Meyerson M. PathSeq: software to identify or discover microbes by deep sequencing of human tissue. Nat Biotechnol. 2011;29(5):393–6.
Article
CAS
Google Scholar
Bhaduri A, Qu K, Lee CS, Ungewickell A, Khavari PA. Rapid identification of non-human sequences in high-throughput sequencing datasets. Bioinformatics. 2012;28(8):1174–5.
Article
CAS
Google Scholar
Naeem R, Rashid M, Pain A. READSCAN: a fast and scalable pathogen discovery program with accurate genome relative abundance estimation. Bioinformatics. 2013;29(3):391–2.
Article
CAS
Google Scholar
Li JW, Wan R, Yu CS, Co NN, Wong N, Chan TF. ViralFusionSeq: accurately discover viral integration events and reconstruct fusion transcripts at single-base resolution. Bioinformatics. 2013;29(5):649–51.
Article
Google Scholar
Wang Q, Jia P, Zhao Z. VirusFinder: software for efficient and accurate detection of viruses and their integration sites in host genomes through next generation sequencing data. PLoS One. 2013;8(5):e64465.
Article
CAS
Google Scholar
Wang Q, Jia P, Zhao Z. VERSE: a novel approach to detect virus integration in host genomes through reference genome customization. Genome medicine. 2015;7(1):2.
Article
Google Scholar
Li H, Durbin R. Fast and accurate long-read alignment with burrows-wheeler transform. Bioinformatics. 2010;26(5):589–95.
Article
Google Scholar
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. Genome project data processing S: the sequence alignment/map format and SAMtools. Bioinformatics. 2009;25(16):2078–9.
Article
Google Scholar
Durbin BR, Eddy S, Krogh A, Mitchison G. Biological sequence analysis: probabilistic models of proteins and nucleic acids; 1998.
Book
Google Scholar
Wu TD, Watanabe CK. GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics. 2005;21:1859–75.
Article
CAS
Google Scholar
Xia Y, Liu Y, Deng M, Xi R. SVmine improves structural variation detection by integrative mining of predictions from multiple algorithms. Bioinformatics. 2017;33(21):3348–54.
Article
CAS
Google Scholar
Ho DWH, Sze KMF, Ng IOL. Virus-clip: a fast and memory-efficient viral integration site detection tool at single-base resolution with annotation capability. Oncotarget. 2015;6(25):20959–63.
Article
Google Scholar
Kao C. HBV genotypes: epidemiology and implications regarding natural history. Current Hepatitis Reports. 2006;5(1):5–13.
Article
Google Scholar
Huang W, Li L, Myers JR, Marth GT. ART: a next-generation sequencing read simulator. Bioinformatics. 2012;28(4):593–4.
Article
Google Scholar
Gao Q, Wang ZC, Duan M, Lin YH, Zhou XY, Worthley DL, Wang XY, Niu G, Xia Y, Deng M, et al. Cell culture system for analysis of genetic heterogeneity within hepatocellular carcinomas and response to pharmacologic agents. Gastroenterology. 2016;152(1):232–42.
Sung WK, Zheng H, Li S, Chen R, Liu X, Li Y, Lee NP, Lee WH, Ariyaratne PN, Tennakoon C, et al. Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma. Nat Genet. 2012;44(7):765–9.
Article
CAS
Google Scholar
Lucifora J, Arzberger S, Durantel D, Belloni L, Strubin M, Levrero M, Zoulim F, Hantz O, Protzer U. Hepatitis B virus X protein is essential to initiate and maintain virus replication after infection. J Hepatol. 2011;55(5):996–1003.
Article
CAS
Google Scholar