The DOI matches its Crossref record; 9 of the 9 references it cites were found in a registry or an index.
Genome-wide analysis of HPV integration in human cancers reveals recurrent, focal genomic instability
Open accessAbstract
Genomic instability is a hallmark of human cancers, including the 5% caused by human papillomavirus (HPV). Here we report a striking association between HPV integration and adjacent host genomic structural variation in human cancer cell lines and primary tumors. Whole-genome sequencing revealed HPV integrants flanking and bridging extensive host genomic amplifications and rearrangements, including deletions, inversions, and chromosomal translocations. We present a model of “looping” by which HPV integrant-mediated DNA replication and recombination may result in viral–host DNA concatemers, frequently disrupting genes involved in oncogenesis and amplifying HPV oncogenes E6 and E7. Our high-resolution results shed new light on a catastrophic process, distinct from chromothripsis and other mutational processes, by which HPV directly promotes genomic instability.
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
The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041
Fast and accurate short read alignment with Burrows-Wheeler transform
Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607
BEDTools: a flexible suite of utilities for comparing genomic features
Quinlan, A. R., & Hall, I. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq033 · Cited by 27,437
<tt>BLAT</tt> —The <tt>BLAST</tt> -Like Alignment Tool
Kent, W. J. (2002) · Genome Research · doi:10.1101/gr.229202 · Cited by 8,480
A map of human genome variation from population-scale sequencing.
The 1000 Genomes Project Consortium (2010) · Nature · doi:10.1038/nature09534 · Cited by 7,877
Detection of large-scale variation in the human genome
Iafrate, A. J., Feuk, L., Rivera, M. N., Listewnik, M. L., Donahoe, P. K., Qi, Y., Scherer, S. W., & Lee, C. (2004) · Nature Genetics · doi:10.1038/ng1416 · Cited by 2,892
Fast and SNP-tolerant detection of complex variants and splicing in short reads
Wu, T. D., & Nacu, S. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq057 · Cited by 1,894
DNA breaks and chromosome pulverization from errors in mitosis
Crasta, K., Ganem, N. J., Dagher, R., Lantermann, A. B., Ivanova, E. V., Pan, Y., Nezi, L., Protopopov, A., Chowdhury, D., & Pellman, D. (2012) · Nature · doi:10.1038/nature10802 · Cited by 1,227
The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line
Adey, A., Burton, J. N., Kitzman, J. O., Hiatt, J. B., Lewis, A. P., Martin, B. K., Qiu, R., Lee, C., & Shendure, J. (2013) · Nature · doi:10.1038/nature12064 · Cited by 362
Cited by
The role of integration in oncogenic progression of HPV-associated cancers
McBride, A. A., & Warburton, A. (2017) · PLOS Pathogens · doi:10.1371/journal.ppat.1006211 · Cited by 376
Genome Analysis of Latin American Cervical Cancer: Frequent Activation of the PIK3CA Pathway
Lou, H., Villagran, G., Boland, J. F., Im, K. M., Polo, S., Zhou, W., Odey, U., Juárez-Torres, E., Medina-Martínez, I., Roman-Basaure, E., et al. (2015) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-14-1837 · Cited by 88
HPV E2, E4, E5 drive alternative carcinogenic pathways in HPV positive cancers
Ren, S., Gaykalova, D. A., Guo, T., Favorov, A. V., Fertig, E. J., Tamayo, P., Callejas-Valera, J. L., Allevato, M., Gilardi, M., Santos, J., et al. (2020) · Oncogene · doi:10.1038/s41388-020-01431-8 · Cited by 93
Engineering virus resistance via CRISPR–Cas systems
Mahas, A., & Mahfouz, M. (2018) · Current Opinion in Virology · doi:10.1016/j.coviro.2018.06.002 · Cited by 74
Morgan, I., DiNardo, L., & Windle, B. (2017) · Viruses · doi:10.3390/v9080208 · Cited by 65
Metadata
- Authors
- Akagi, K., Li, J., Broutian, T. R., Padilla-Nash, H., Xiao, W., Jiang, B., Rocco, J. W., Teknos, T. N., Kumar, B., Wangsa, D., He, D., Ried, T., Symer, D. E., & Gillison, M. L.
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2013-11-07
- Volume
- 24
- Issue
- 2
- Pages
- 185-199
- ISSN
- 1088-9051 (ISSN-L)
- OpenAlex
- W2081116295
- Cited by
- 468
- References
- 9
- Type
- posted content
- Language
- en
- Open access
- bronze
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
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Genome-wide analysis of HPV integration in human cancers reveals recurrent, focal genomic instability. https://app.cochat.ai/papers/10.1101/gr.164806.113
- The paper
- Akagi, K., Li, J., Broutian, T. R., Padilla-Nash, H., Xiao, W., Jiang, B., Rocco, J. W., Teknos, T. N., Kumar, B., Wangsa, D., He, D., Ried, T., Symer, D. E., & Gillison, M. L. (2014). Genome-wide analysis of HPV integration in human cancers reveals recurrent, focal genomic instability. Genome Research. https://doi.org/10.1101/gr.164806.113
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.
