Viral sequences in human cancer

被引：81

作者：

Cantalupo, Paul G. ^{[1
]}

Katz, Joshua P. ^{[1
]}

Pipas, James M. ^{[1
]}

机构：

[1] Univ Pittsburgh, Dept Biol Sci, Pittsburgh, PA 15260 USA

来源：

VIROLOGY | 2018年 / 513卷

关键词：

TCGA; Metagenomics; Cancer; Papillomavirus; Herpesvirus; Virome; COMPREHENSIVE MOLECULAR CHARACTERIZATION; GENOME ATLAS; VIRUS; DNA;

D O I：

10.1016/j.virol.2017.10.017

中图分类号：

Q93 [微生物学];

学科分类号：

071005 ; 100705 ;

摘要：

We have developed a virus detection and discovery computational pipeline, Pickaxe, and applied it to NGS databases provided by The Cancer Genome Atlas (TCGA). We analyzed a collection of whole genome (WGS), exome (WXS), and RNA (RNA-Seq) sequencing libraries from 3052 participants across 22 different cancers. NGS data from nearly all tumor and normal tissues examined contained contaminating viral sequences. Intensive computational and manual efforts are required to remove these artifacts. We found that several different types of cancers harbored Herpesviruses including EBV, CMV, HHV1, HHV2, HHV6 and HHV7. In addition to the reported associations of Hepatitis B and C virus (HBV & HCV) with liver cancer, and Human papillomaviruses (HPV) with cervical cancer and a subset of head and neck cancers, we found additional cases of HPV integrated in a small number of bladder cancers. Gene expression and mutational profiles suggest that HPV drives tumorigenesis in these cases.

引用

页码：208 / 216

页数：9

共 19 条

[1] Presence of Viral DNA in Whole-Genome Sequencing of Brain Tumor Tissues from The Cancer Genome Atlas [J].

Amirian, E. Susan ;

Bondy, Melissa L. ;

Mo, Qianxing ;

Bainbridge, Matthew N. ;

Scheurer, Michael E. .

JOURNAL OF VIROLOGY, 2014, 88 (01) :774-774

[2] Comprehensive molecular characterization of gastric adenocarcinoma [J].

Bass, Adam J. ;

Thorsson, Vesteinn ;

Shmulevich, Ilya ;

Reynolds, Sheila M. ;

Miller, Michael ;

Bernard, Brady ;

Hinoue, Toshinori ;

Laird, Peter W. ;

Curtis, Christina ;

Shen, Hui ;

Weisenberger, Daniel J. ;

Schultz, Nikolaus ;

Shen, Ronglai ;

Weinhold, Nils ;

Keiser, David P. ;

Bowlby, Reanne ;

Sipahimalani, Payal ;

Cherniack, Andrew D. ;

Getz, Gad ;

Liu, Yingchun ;

Noble, Michael S. ;

Pedamallu, Chandra ;

Sougnez, Carrie ;

Taylor-Weiner, Amaro ;

Akbani, Rehan ;

Lee, Ju-Seog ;

Liu, Wenbin ;

Mills, Gordon B. ;

Yang, Da ;

Zhang, Wei ;

Pantazi, Angeliki ;

Parfenov, Michael ;

Gulley, Margaret ;

Piazuelo, M. Blanca ;

Schneider, Barbara G. ;

Kim, Jihun ;

Boussioutas, Alex ;

Sheth, Margi ;

Demchok, John A. ;

Rabkin, Charles S. ;

Willis, Joseph E. ;

Ng, Sam ;

Garman, Katherine ;

Beer, David G. ;

Pennathur, Arjun ;

Raphael, Benjamin J. ;

Wu, Hsin-Ta ;

Odze, Robert ;

Kim, Hark K. ;

Bowen, Jay .

NATURE, 2014, 513 (7517) :202-209

[3] CaPSID: A bioinformatics platform for computational pathogen sequence identification in human genomes and transcriptomes [J].

Borozan, Ivan ;

Wilson, Shane ;

Blanchette, Paola ;

Laflamme, Philippe ;

Watt, Stuart N. ;

Krzyzanowski, Paul M. ;

Sircoulomb, Fabrice ;

Rottapel, Robert ;

Branton, Philip E. ;

Ferretti, Vincent .

BMC BIOINFORMATICS, 2012, 13

[4]

Cantalupo P.G., 2015, J VIROL

[5] HeLa Nucleic Acid Contamination in The Cancer Genome Atlas Leads to the Misidentification of Human Papillomavirus 18 [J].

Cantalupo, Paul G. ;

Katz, Joshua P. ;

Pipas, James M. .

JOURNAL OF VIROLOGY, 2015, 89 (08) :4051-4057

[6] High-resolution human cytomegalovirus transcriptome [J].

Gatherer, Derek ;

Seirafian, Sepehr ;

Cunningham, Charles ;

Holton, Mary ;

Dargan, Derrick J. ;

Baluchova, Katarina ;

Hector, Ralph D. ;

Galbraith, Julie ;

Herzyk, Pawel ;

Wilkinson, Gavin W. G. ;

Davison, Andrew J. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2011, 108 (49) :19755-19760

[7] SummonChimera infers integrated viral genomes with nucleotide precision from NGS data [J].

Katz, Joshua P. ;

Pipas, James M. .

BMC BIOINFORMATICS, 2014, 15

[8]

Kazemian M., 2015, J VIROL

[9] Landscape of DNA Virus Associations across Human Malignant Cancers: Analysis of 3,775 Cases Using RNA-Seq [J].

Khoury, Joseph D. ;

Tannir, Nizar M. ;

Williams, Michelle D. ;

Chen, Yunxin ;

Yao, Hui ;

Zhang, Jianping ;

Thompson, Erika J. ;

Meric-Bernstam, Funda ;

Medeiros, L. Jeffrey ;

Weinstein, John N. ;

Su, Xiaoping .

JOURNAL OF VIROLOGY, 2013, 87 (16) :8916-8926

[10]

Langmead B, 2012, NAT METHODS, V9, P357, DOI [10.1038/NMETH.1923, 10.1038/nmeth.1923]

← 1 2 →