The DOI matches its Crossref record; 42 of the 42 references it cites were found in a registry or an index.
The landscape of viral expression and host gene fusion and adaptation in human cancer
Open accessAbstract
Viruses cause 10–15% of all human cancers. Massively parallel sequencing has recently proved effective for uncovering novel viruses and virus–tumour associations, but this approach has not yet been applied to comprehensive patient cohorts. Here we screen a diverse landscape of human cancer, encompassing 4,433 tumours and 19 cancer types, for known and novel expressed viruses based on >700 billion transcriptome sequencing reads from The Cancer Genome Atlas Research Network. The resulting map confirms and extends current knowledge. We observe recurrent fusion events, including human papillomavirus insertions in RAD51B and ERBB2. Patterns of coadaptation between host and viral gene expression give clues to papillomavirus oncogene function. Importantly, our analysis argues strongly against viral aetiology in several cancers where this has frequently been proposed. We provide a virus–tumour map of unprecedented scale that constitutes a reference for future studies of tumour-associated viruses using transcriptome sequencing data. Viruses contribute to the pathogenesis of certain cancers. Using massively parallel sequencing data from The Cancer Genome Atlas to analyse viral expression in 19 tumour types, Tang et al. both confirm and reject previously described viral associations and present new information on viral integration and host interaction.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Basic local alignment search tool
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669
Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0506580102 · Cited by 53,625
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849
Statistical significance for genomewide studies
Storey, J. D., & Tibshirani, R. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1530509100 · Cited by 9,692
SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler
Luo, R., Liu, B., Xie, Y., Li, Z., Huang, W., Yuan, J., He, G., Chen, Y., Pan, Q., Liu, Y., et al. (2012) · Gigascience · doi:10.1186/2047-217x-1-18 · Cited by 5,307
Quality control and preprocessing of metagenomic datasets
Schmieder, R., & Edwards, R. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr026 · Cited by 5,072
Derrien, T., Johnson, R., Bussotti, G., Tanzer, A., Djebali, S., Tilgner, H., Guernec, G., Martin, D., Merkel, A., Knowles, D. G., et al. (2012) · Genome Research · doi:10.1101/gr.132159.111 · Cited by 5,061
Papillomaviruses and cancer: from basic studies to clinical application
zur Hausen, H. (2002) · Nature Reviews Cancer · doi:10.1038/nrc798 · Cited by 4,024
Clonal Integration of a Polyomavirus in Human Merkel Cell Carcinoma
Feng, H., Shuda, M., Chang, Y., & Moore, P. S. (2008) · Science · doi:10.1126/science.1152586 · Cited by 3,208
A census of human cancer genes
Futreal, P. A., Coin, L., Marshall, M., Down, T., Hubbard, T., Wooster, R., Rahman, N., & Stratton, M. R. (2004) · Nature Reviews Cancer · doi:10.1038/nrc1299 · Cited by 3,184
The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote
Liao, Y., Smyth, G. K., & Shi, W. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt214 · Cited by 3,064
Genomic analysis identifies association of Fusobacterium with colorectal carcinoma
Kostic, A. D., Gevers, D., Pedamallu, C. S., Michaud, M., Duke, F., Earl, A. M., Ojesina, A. I., Jung, J., Bass, A. J., Tabernero, J., et al. (2012) · Genome Research · doi:10.1101/gr.126573.111 · Cited by 1,960
HBx gene of hepatitis B virus induces liver cancer in transgenic mice
Kim, C.-M., Koike, K., Saito, I., Miyamura, T., & Jay, G. (1991) · Nature · doi:10.1038/351317a0 · Cited by 1,158
Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma
Sung, W.-K., Zheng, H., Li, S., Chen, R., Liu, X., Li, Y., Lee, N. P., Lee, W. H., Ariyaratne, P. N., Tennakoon, C., et al. (2012) · Nature Genetics · doi:10.1038/ng.2295 · Cited by 991
Human Papillomavirus Infection as a Risk Factor for Squamous-Cell Carcinoma of the Head and Neck
Mork, J., Lie, A. K., Glattre, E., Clark, S., Hallmans, G., Jellum, E., Koskela, P., Møller, B., Pukkala, E., Schiller, J. T., et al. (2001) · New England Journal of Medicine · doi:10.1056/nejm200104123441503 · Cited by 939
Global challenges in liver disease
Williams, R. (2006) · Hepatology · doi:10.1002/hep.21347 · Cited by 788
Why do viruses cause cancer? Highlights of the first century of human tumour virology
Moore, P. S., & Chang, Y. (2010) · Nature Reviews Cancer · doi:10.1038/nrc2961 · Cited by 745
Biological activities and molecular targets of the human papillomavirus E7 oncoprotein
Münger, K., Basile, J. R., Duensing, S., Eichten, A., Gonzalez, S. L., Grace, M., & Zacny, V. L. (2001) · Oncogene · doi:10.1038/sj.onc.1204860 · Cited by 588
Chapter 3: HPV type-distribution in women with and without cervical neoplastic diseases
Clifford, G., Franceschi, S., Diaz, M., Muñoz, N., & Villa, L. L. (2006) · Vaccine · doi:10.1016/j.vaccine.2006.05.026 · Cited by 568
Pyeon, D., Newton, M. A., Lambert, P. F., den Boon, J. A., Sengupta, S., Marsit, C. J., Woodworth, C. D., Connor, J. P., Haugen, T. H., Smith, E. M., et al. (2007) · Cancer Research · doi:10.1158/0008-5472.can-06-3619 · Cited by 460
The human papillomavirus E7 oncoprotein
McLaughlin-Drubin, M. E., & Münger, K. (2009) · Virology · doi:10.1016/j.virol.2008.10.006 · Cited by 391
Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins
Rozenblatt-Rosen, O., Deo, R. C., Padi, M., Adelmant, G., Calderwood, M. A., Rolland, T., Grace, M., Dricot, A., Askenazi, M., Tavares, M., et al. (2012) · Nature · doi:10.1038/nature11288 · Cited by 378
Wentzensen, N., Vinokurova, S., & Doeberitz, M. V. K. (2004) · Cancer Research · doi:10.1158/0008-5472.can-04-0009 · Cited by 368
The effects of hepatitis B virus integration into the genomes of hepatocellular carcinoma patients
Jiang, Z., Jhunjhunwala, S., Liu, J., Haverty, P. M., Kennemer, M. I., Guan, Y., Lee, W., Carnevali, P., Stinson, J., Johnson, S., et al. (2012) · Genome Research · doi:10.1101/gr.133926.111 · Cited by 324
Slebos, R. J. C., Yi, Y., Ely, K., Carter, J., Evjen, A., Zhang, X., Shyr, Y., Murphy, B. M., Cmelak, A. J., Burkey, B. B., et al. (2006) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-05-2017 · Cited by 311
Consensus on the role of human cytomegalovirus in glioblastoma
Dziurzynski, K., Chang, S. M., Heimberger, A. B., Kalejta, R. F., McGregor Dallas, S. R., Smit, M., Soroceanu, L., Cobbs, C. S., & Symposium, T. H. A. G. (2012) · Neuro-Oncology · doi:10.1093/neuonc/nor227 · Cited by 304
p53 is balancing development, differentiation and de-differentiation to assure cancer prevention
Molchadsky, A., Rivlin, N., Brosh, R., Rotter, V., & Sarig, R. (2010) · Carcinogenesis · doi:10.1093/carcin/bgq101 · Cited by 162
Chen, Y., Yao, H., Thompson, E. J., Tannir, N. M., Weinstein, J. N., & Su, X. (2013) · Bioinformatics · doi:10.1093/bioinformatics/bts665 · Cited by 158
Rickman, D. S., Millon, R., de Reyniès, A., Thomas, E., Wasylyk, C., Müller, D., Abecassis, J., & Wasylyk, B. (2008) · Oncogene · doi:10.1038/onc.2008.251 · Cited by 153
Disease-associated XMRV sequences are consistent with laboratory contamination
Hué, S., Gray, E. R., Gall, A., Katzourakis, A., Tan, C. P., Houldcroft, C. J., McLaren, S., Pillay, D., Futreal, P. A., Garson, J. A., et al. (2010) · Retrovirology · doi:10.1186/1742-4690-7-111 · Cited by 150
Rosty, C., Sheffer, M., Tsafrir, D., Stransky, N., Tsafrir, I., Peter, M., de Crémoux, P., de la Rochefordière, A., Salmon, R. J., Dorval, T., et al. (2005) · Oncogene · doi:10.1038/sj.onc.1208854 · Cited by 146
Xu, H., Jenkinson, H. F., & Dongari‐Bagtzoglou, A. I. (2014) · Molecular Oral Microbiology · doi:10.1111/omi.12049 · Cited by 133
Non-Random Integration of the HPV Genome in Cervical Cancer
Schmitz, M., Driesch, C., Jansen, L., Runnebaum, I. B., & Dürst, M. (2012) · PLoS ONE · doi:10.1371/journal.pone.0039632 · Cited by 129
MCV and Merkel cell carcinoma: a molecular success story
Arora, R., Chang, Y., & Moore, P. S. (2012) · Current Opinion in Virology · doi:10.1016/j.coviro.2012.05.007 · Cited by 115
MYC activation associated with the integration of HPV DNA at the MYC locus in genital tumors
Peter, M., Rosty, C., Couturier, J., Radvanyi, F., Teshima, H., & Sastre-Garau, X. (2006) · Oncogene · doi:10.1038/sj.onc.1209625 · Cited by 114
Frequent genomic structural alterations at HPV insertion sites in cervical carcinoma
Peter, M., Stransky, N., Couturier, J., Hupé, P., Barillot, E., de Crémoux, P., Cottu, P. H., Radvanyi, F., & Sastre‐Garau, X. (2010) · The Journal of Pathology · doi:10.1002/path.2713 · Cited by 97
Bradrick, S. S. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl019 · Cited by 96
Clifford, G. M., & Franceschi, S. (2007) · International Journal of Cancer · doi:10.1002/ijc.23282 · Cited by 91
Detection of human papillomavirus DNA in colorectal carcinomas by polymerase chain reaction.
Cheng, J., Sheu, L. F., Meng, C., Lee, W. H., & Lin, J. (1995) · Gut · doi:10.1136/gut.37.1.87 · Cited by 73
Narisawa‐Saito, M., Handa, K., Yugawa, T., Ohno, S.-I., Fujita, M., & Kiyono, T. (2006) · Oncogene · doi:10.1038/sj.onc.1210118 · Cited by 58
Strong, K., Mathers, C. D., Epping‐Jordan, J. E., Resnikoff, S., & Ullrich, A. (2008) · European Journal of Cancer Prevention · doi:10.1097/cej.0b013e3282b6fda8 · Cited by 24
A Novel Link Between REC2, a DNA Recombinase, the Retinoblastoma Protein, and Apoptosis
Fan, G., Ma, X., Kren, B. T., Rice, M. C., Kmiec, E. B., & Steer, C. J. (1997) · Journal of Biological Chemistry · doi:10.1074/jbc.272.31.19413 · Cited by 6
Cited by
Molecular and genetic properties of tumors associated with local immune cytolytic activity
Rooney, M. S., Shukla, S. A., Wu, C. J., Getz, G., & Hacohen, N. (2015) · Cell · doi:10.1016/j.cell.2014.12.033 · Cited by 3,825
A facile surface chemistry route to a stabilized lithium metal anode
Liang, X., Pang, Q., Kochetkov, I. R., Sempere, M. S., Huang, H., Sun, X., & Nazar, L. F. (2017) · Nature Energy · doi:10.1038/nenergy.2017.119 · Cited by 1,083
RETRACTED ARTICLE: Microbiome analyses of blood and tissues suggest cancer diagnostic approach
Poore, G. D., Kopylova, E., Zhu, Q., Carpenter, C., Fraraccio, S., Wandro, S., Kosciolek, T., Janssen, S., Metcalf, J., Song, S. J., et al. (2020) · Nature · doi:10.1038/s41586-020-2095-1 · Cited by 989
RetractedThe landscape of viral associations in human cancers
Zapatka, M., Borozan, I., Brewer, D. S., Iskar, M., Grundhoff, A., Alawi, M., Desai, N., Sültmann, H., Moch, H., Pathogens, P., et al. (2020) · Nature Genetics · doi:10.1038/s41588-019-0558-9 · Cited by 382
Self-citationA Pan-cancer Landscape of Interactions between Solid Tumors and Infiltrating Immune Cell Populations
Tamborero, D., Rubio-Perez, C., Muiños, F., Sabarinathan, R., Piulats, J. M., Muntasell, A., Dienstmann, R., Lopez-Bigas, N., & Gonzalez-Perez, A. (2018) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-17-3509 · Cited by 359
Metadata
- Authors
- Tang, K.-W., Alaei-Mahabadi, B., Samuelsson, T., Lindh, M., & Larsson, E.
- Venue
- Nature Communications
- Published
- 2013-10-01
- Volume
- 4
- Issue
- 1
- Pages
- 2513-2513
- ISSN
- 2041-1723 (ISSN-L)
- OpenAlex
- W1995462034
- Cited by
- 301
- References
- 42
- FWCI
- 15.81
- Type
- journal article
- Language
- en
- Open access
- hybrid
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
