NGS-based approach to determine the presence of HPV and their sites of integration in human cancer genome
Identifieur interne : 000029 ( Pmc/Checkpoint ); précédent : 000028; suivant : 000030NGS-based approach to determine the presence of HPV and their sites of integration in human cancer genome
Auteurs : P. Chandrani [Inde] ; V. Kulkarni [Inde] ; P. Iyer [Inde] ; P. Upadhyay [Inde] ; R. Chaubal [Inde] ; P. Das [Inde] ; R. Mulherkar [Inde] ; R. Singh [Inde] ; A. Dutt [Inde]Source :
- British Journal of Cancer [ 0007-0920 ] ; 2015.
Abstract
Human papilloma virus (HPV) accounts for the most common cause of all virus-associated human cancers. Here, we describe the first graphic user interface (GUI)-based automated tool ‘HPVDetector', for non-computational biologists, exclusively for detection and annotation of the HPV genome based on next-generation sequencing data sets.
We developed a custom-made reference genome that comprises of human chromosomes along with annotated genome of 143 HPV types as pseudochromosomes. The tool runs on a dual mode as defined by the user: a ‘quick mode' to identify presence of HPV types and an ‘integration mode' to determine genomic location for the site of integration. The input data can be a paired-end whole-exome, whole-genome or whole-transcriptome data set. The HPVDetector is available in public domain for download:
On the basis of our evaluation of 116 whole-exome, 23 whole-transcriptome and 2 whole-genome data, we were able to identify presence of HPV in 20 exomes and 4 transcriptomes of cervical and head and neck cancer tumour samples. Using the inbuilt annotation module of HPVDetector, we found predominant integration of viral gene
HPVDetector is a simple yet precise and robust tool for detecting HPV from tumour samples using variety of next-generation sequencing platforms including whole genome, whole exome and transcriptome. Two different modes (quick detection and integration mode) along with a GUI widen the usability of HPVDetector for biologists and clinicians with minimal computational knowledge.
Url:
DOI: 10.1038/bjc.2015.121
PubMed: 25973533
PubMed Central: 4580395
Affiliations:
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Kulkarni</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre</institution>, Kharghar, Navi Mumbai, Maharashtra 410210,<country>India</country></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Iyer, P" sort="Iyer, P" uniqKey="Iyer P" first="P" last="Iyer">P. Iyer</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre</institution>, Kharghar, Navi Mumbai, Maharashtra 410210,<country>India</country></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Upadhyay, P" sort="Upadhyay, P" uniqKey="Upadhyay P" first="P" last="Upadhyay">P. Upadhyay</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre</institution>, Kharghar, Navi Mumbai, Maharashtra 410210,<country>India</country></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Chaubal, R" sort="Chaubal, R" uniqKey="Chaubal R" first="R" last="Chaubal">R. Chaubal</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre</institution>, Kharghar, Navi Mumbai, Maharashtra 410210,<country>India</country></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Das, P" sort="Das, P" uniqKey="Das P" first="P" last="Das">P. Das</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre</institution>, Kharghar, Navi Mumbai, Maharashtra 410210,<country>India</country></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Mulherkar, R" sort="Mulherkar, R" uniqKey="Mulherkar R" first="R" last="Mulherkar">R. Mulherkar</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre</institution>, Kharghar, Navi Mumbai, Maharashtra 410210,<country>India</country></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Singh, R" sort="Singh, R" uniqKey="Singh R" first="R" last="Singh">R. Singh</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre</institution>, Kharghar, Navi Mumbai, Maharashtra 410210,<country>India</country></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Dutt, A" sort="Dutt, A" uniqKey="Dutt A" first="A" last="Dutt">A. Dutt</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre</institution>, Kharghar, Navi Mumbai, Maharashtra 410210,<country>India</country></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25973533</idno><idno type="pmc">4580395</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4580395</idno><idno type="RBID">PMC:4580395</idno><idno type="doi">10.1038/bjc.2015.121</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">000035</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000035</idno><idno type="wicri:Area/Pmc/Curation">000035</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000035</idno><idno type="wicri:Area/Pmc/Checkpoint">000029</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000029</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">NGS-based approach to determine the presence of HPV and their sites of integration in human cancer genome</title><author><name sortKey="Chandrani, P" sort="Chandrani, P" uniqKey="Chandrani P" first="P" last="Chandrani">P. Chandrani</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre</institution>, Kharghar, Navi Mumbai, Maharashtra 410210,<country>India</country></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Kulkarni, V" sort="Kulkarni, V" uniqKey="Kulkarni V" first="V" last="Kulkarni">V. Kulkarni</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre</institution>, Kharghar, Navi Mumbai, Maharashtra 410210,<country>India</country></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Iyer, P" sort="Iyer, P" uniqKey="Iyer P" first="P" last="Iyer">P. Iyer</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre</institution>, Kharghar, Navi Mumbai, Maharashtra 410210,<country>India</country></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Upadhyay, P" sort="Upadhyay, P" uniqKey="Upadhyay P" first="P" last="Upadhyay">P. Upadhyay</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre</institution>, Kharghar, Navi Mumbai, Maharashtra 410210,<country>India</country></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Chaubal, R" sort="Chaubal, R" uniqKey="Chaubal R" first="R" last="Chaubal">R. Chaubal</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre</institution>, Kharghar, Navi Mumbai, Maharashtra 410210,<country>India</country></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Das, P" sort="Das, P" uniqKey="Das P" first="P" last="Das">P. Das</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre</institution>, Kharghar, Navi Mumbai, Maharashtra 410210,<country>India</country></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Mulherkar, R" sort="Mulherkar, R" uniqKey="Mulherkar R" first="R" last="Mulherkar">R. Mulherkar</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre</institution>, Kharghar, Navi Mumbai, Maharashtra 410210,<country>India</country></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Singh, R" sort="Singh, R" uniqKey="Singh R" first="R" last="Singh">R. Singh</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre</institution>, Kharghar, Navi Mumbai, Maharashtra 410210,<country>India</country></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Dutt, A" sort="Dutt, A" uniqKey="Dutt A" first="A" last="Dutt">A. Dutt</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre</institution>, Kharghar, Navi Mumbai, Maharashtra 410210,<country>India</country></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author></analytic><series><title level="j">British Journal of Cancer</title><idno type="ISSN">0007-0920</idno><idno type="eISSN">1532-1827</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background:</title><p>Human papilloma virus (HPV) accounts for the most common cause of all virus-associated human cancers. Here, we describe the first graphic user interface (GUI)-based automated tool ‘HPVDetector', for non-computational biologists, exclusively for detection and annotation of the HPV genome based on next-generation sequencing data sets.</p></sec><sec><title>Methods:</title><p>We developed a custom-made reference genome that comprises of human chromosomes along with annotated genome of 143 HPV types as pseudochromosomes. The tool runs on a dual mode as defined by the user: a ‘quick mode' to identify presence of HPV types and an ‘integration mode' to determine genomic location for the site of integration. The input data can be a paired-end whole-exome, whole-genome or whole-transcriptome data set. The HPVDetector is available in public domain for download: <ext-link ext-link-type="uri" xlink:href="http://www.actrec.gov.in/pi-webpages/AmitDutt/HPVdetector/HPVDetector.html">http://www.actrec.gov.in/pi-webpages/AmitDutt/HPVdetector/HPVDetector.html</ext-link>.</p></sec><sec><title>Results:</title><p>On the basis of our evaluation of 116 whole-exome, 23 whole-transcriptome and 2 whole-genome data, we were able to identify presence of HPV in 20 exomes and 4 transcriptomes of cervical and head and neck cancer tumour samples. Using the inbuilt annotation module of HPVDetector, we found predominant integration of viral gene <italic>E7</italic>, a known oncogene, at known 17q21, 3q27, 7q35, Xq28 and novel sites of integration in the human genome. Furthermore, co-infection with high-risk HPVs such as 16 and 31 were found to be mutually exclusive compared with low-risk HPV71.</p></sec><sec><title>Conclusions:</title><p>HPVDetector is a simple yet precise and robust tool for detecting HPV from tumour samples using variety of next-generation sequencing platforms including whole genome, whole exome and transcriptome. Two different modes (quick detection and integration mode) along with a GUI widen the usability of HPVDetector for biologists and clinicians with minimal computational knowledge.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Abreu, Al" uniqKey="Abreu A">AL Abreu</name></author><author><name sortKey="Souza, Rp" uniqKey="Souza R">RP Souza</name></author><author><name sortKey="Gimenes, F" uniqKey="Gimenes F">F Gimenes</name></author><author><name sortKey="Consolaro, Me" uniqKey="Consolaro M">ME Consolaro</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Adler, K" uniqKey="Adler K">K Adler</name></author><author><name sortKey="Erickson, T" uniqKey="Erickson T">T Erickson</name></author><author><name sortKey="Bobrow, M" uniqKey="Bobrow M">M Bobrow</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ameur, A" uniqKey="Ameur A">A Ameur</name></author><author><name 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Br J Cancer</journal-id><journal-id journal-id-type="iso-abbrev">Br. J. Cancer</journal-id><journal-title-group><journal-title>British Journal of Cancer</journal-title></journal-title-group><issn pub-type="ppub">0007-0920</issn><issn pub-type="epub">1532-1827</issn><publisher><publisher-name>Nature Publishing Group</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">25973533</article-id><article-id pub-id-type="pmc">4580395</article-id><article-id pub-id-type="pii">bjc2015121</article-id><article-id pub-id-type="doi">10.1038/bjc.2015.121</article-id><article-categories><subj-group subj-group-type="heading"><subject>Genetics and Genomics</subject></subj-group></article-categories><title-group><article-title>NGS-based approach to determine the presence of HPV and their sites of integration in human cancer genome</article-title><alt-title alt-title-type="running">Presence of HPV and their sites of integration</alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Chandrani</surname><given-names>P</given-names></name><xref ref-type="aff" rid="aff1">1</xref><xref ref-type="author-notes" rid="note1"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Kulkarni</surname><given-names>V</given-names></name><xref ref-type="aff" rid="aff1">1</xref><xref ref-type="author-notes" rid="note1"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Iyer</surname><given-names>P</given-names></name><xref ref-type="aff" rid="aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>Upadhyay</surname><given-names>P</given-names></name><xref ref-type="aff" rid="aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>Chaubal</surname><given-names>R</given-names></name><xref ref-type="aff" rid="aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>Das</surname><given-names>P</given-names></name><xref ref-type="aff" rid="aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>Mulherkar</surname><given-names>R</given-names></name><xref ref-type="aff" rid="aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>Singh</surname><given-names>R</given-names></name><xref ref-type="aff" rid="aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>Dutt</surname><given-names>A</given-names></name><xref ref-type="aff" rid="aff1">1</xref><xref ref-type="corresp" rid="caf1">*</xref></contrib><aff id="aff1"><label>1</label><institution>Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre</institution>, Kharghar, Navi Mumbai, Maharashtra 410210,<country>India</country></aff></contrib-group><author-notes><corresp id="caf1"><label>*</label>E-mail: <email>adutt@actrec.gov.in</email></corresp><fn fn-type="present-address" id="note1"><label>2</label><p>These authors contributed equally to this work.</p></fn></author-notes><pub-date pub-type="ppub"><day>09</day><month>06</month><year>2015</year></pub-date><pub-date pub-type="epub"><day>14</day><month>05</month><year>2015</year></pub-date><pub-date pub-type="pmc-release"><day>9</day><month>6</month><year>2015</year></pub-date><volume>112</volume><issue>12</issue><fpage>1958</fpage><lpage>1965</lpage><history><date date-type="received"><day>31</day><month>07</month><year>2014</year></date><date date-type="rev-recd"><day>03</day><month>03</month><year>2015</year></date><date date-type="accepted"><day>07</day><month>03</month><year>2015</year></date></history><permissions><copyright-statement>Copyright © 2015 Cancer Research UK</copyright-statement><copyright-year>2015</copyright-year><copyright-holder>Cancer Research UK</copyright-holder><license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/4.0/"><pmc-comment>author-paid</pmc-comment>
<license-p>This work is licensed under the Creative Commons Attribution 4.0 International License. To view a copy of this license, visit <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">http://creativecommons.org/licenses/by/4.0/</ext-link></license-p></license></permissions><abstract><sec><title>Background:</title><p>Human papilloma virus (HPV) accounts for the most common cause of all virus-associated human cancers. Here, we describe the first graphic user interface (GUI)-based automated tool ‘HPVDetector', for non-computational biologists, exclusively for detection and annotation of the HPV genome based on next-generation sequencing data sets.</p></sec><sec><title>Methods:</title><p>We developed a custom-made reference genome that comprises of human chromosomes along with annotated genome of 143 HPV types as pseudochromosomes. The tool runs on a dual mode as defined by the user: a ‘quick mode' to identify presence of HPV types and an ‘integration mode' to determine genomic location for the site of integration. The input data can be a paired-end whole-exome, whole-genome or whole-transcriptome data set. The HPVDetector is available in public domain for download: <ext-link ext-link-type="uri" xlink:href="http://www.actrec.gov.in/pi-webpages/AmitDutt/HPVdetector/HPVDetector.html">http://www.actrec.gov.in/pi-webpages/AmitDutt/HPVdetector/HPVDetector.html</ext-link>.</p></sec><sec><title>Results:</title><p>On the basis of our evaluation of 116 whole-exome, 23 whole-transcriptome and 2 whole-genome data, we were able to identify presence of HPV in 20 exomes and 4 transcriptomes of cervical and head and neck cancer tumour samples. Using the inbuilt annotation module of HPVDetector, we found predominant integration of viral gene <italic>E7</italic>, a known oncogene, at known 17q21, 3q27, 7q35, Xq28 and novel sites of integration in the human genome. Furthermore, co-infection with high-risk HPVs such as 16 and 31 were found to be mutually exclusive compared with low-risk HPV71.</p></sec><sec><title>Conclusions:</title><p>HPVDetector is a simple yet precise and robust tool for detecting HPV from tumour samples using variety of next-generation sequencing platforms including whole genome, whole exome and transcriptome. Two different modes (quick detection and integration mode) along with a GUI widen the usability of HPVDetector for biologists and clinicians with minimal computational knowledge.</p></sec></abstract><kwd-group><kwd>HPV detection</kwd><kwd>human cancer</kwd><kwd>next-generation sequencing (NGS)</kwd></kwd-group></article-meta></front><floats-group><fig id="fig1"><label>Figure 1</label><caption><p><bold>Conceptual workflow of the HPVDetector.</bold> The flowchart represents workflow for HPVDetector. Paired-end reads obtained from next-generation sequencing data are aligned to a combined Human–HPV reference database. All discordant read pairs with one read aligning to human and other to the HPV genome are identified and annotated utilising human and HPV database using an inbuilt annotator module.</p></caption><graphic xlink:href="bjc2015121f1"></graphic></fig><fig id="fig2"><label>Figure 2</label><caption><p><bold>Quantitative representation, by number of reads, of HPV types detected in cervical tumours.</bold> The graph represents distribution of total number of HPV reads per million of total reads for all HPV types detected across 17 cervical samples. HPV16 has the highest number of reads across 17 samples followed by HPV(18, 71, 45, 31, 82, 17, 56, 58, 15, 20) in the decreasing order of their read counts.</p></caption><graphic xlink:href="bjc2015121f2"></graphic></fig><fig id="fig3"><label>Figure 3</label><caption><p><bold>HPV gene integration frequency across different cervical cancer samples.</bold> Heatmap representation of HPV types detected across 17 cervical cancer samples. HPV16 in 13 samples, HPV18 in 2 samples, HPV71 in 6 samples, HPV82 in 5 samples, HPV31 in 2 samples, HPV45 in 5 samples, and HPV17, 56, 58, 15, 20 were detected in 1 sample, each. Total coverage of the exome sequencing is indicated in the last column ‘cov'. On the basis of read count, the abundance of HPV is graded in different samples: read counts 1–10 as light grey; read counts 10–50 as dark grey; and read counts >50 as black.</p></caption><graphic xlink:href="bjc2015121f3"></graphic></fig><fig id="fig4"><label>Figure 4</label><caption><p><bold>Sensitivity of HPVDetector as a function of increasing genome sequence coverage.</bold> SiHa WGS data were downsampled to the coverage of 1 × , 2 × , 3 × , 4 × , 5 × , 10 × , 15 × , 20 × , 25 × , and 30 × . HPV16 reads (black) were counted using HPVDetector at varying coverage and plotted along with total number of reads (grey).</p></caption><graphic xlink:href="bjc2015121f4"></graphic></fig><fig id="fig5"><label>Figure 5</label><caption><p><bold>Relative frequency of integration of HPV genes in cervical carcinoma.</bold> HPV16 reads were annotated using an inbuilt annotation module of the HPVDetector to identify the viral genes. Number of reads per viral gene were normalised to the gene length, and frequency reads for individual genes are plotted, as shown.</p></caption><graphic xlink:href="bjc2015121f5"></graphic></fig><fig id="fig6"><label>Figure 6</label><caption><p><bold>Schematic representation of all HPV16 and 18 integration sites in the human genome detected across cervical cancer samples using HPVDetector.</bold> Site of integration as determined by HPVDetector in cervical cancer samples is shown. HPV16 integration sites are depicted by circles and HPV18 by rectangles. Black, open and grey circles or rectangles represent integrations at known fragile sites, at known integration sites and at novel sites, respectively.</p></caption><graphic xlink:href="bjc2015121f6"></graphic></fig><table-wrap id="tbl1"><label>Table 1</label><caption><title>Summary of HPV detection in all samples</title></caption><table frame="hsides" rules="groups" border="1"><colgroup><col align="left"></col><col align="center"></col><col align="center"></col></colgroup><thead valign="bottom"><tr><th align="left" valign="top" charoff="50"><bold>Study type</bold></th><th align="center" valign="top" charoff="50"><bold>Samples tested</bold></th><th align="center" valign="top" charoff="50"><bold>Presence of virus in samples</bold></th></tr></thead><tbody valign="top"><tr><td align="left" valign="top" charoff="50">Cervical cancer exome</td><td align="center" valign="top" charoff="50">36 (22 tumour, 14 paired normal)</td><td align="center" valign="top" charoff="50">18</td></tr><tr><td align="left" valign="top" charoff="50">SiHa cell line WGS</td><td align="center" valign="top" charoff="50">1</td><td align="center" valign="top" charoff="50">1</td></tr><tr><td align="left" valign="top" charoff="50">HNSCC cell line exome</td><td align="center" valign="top" charoff="50">7</td><td align="center" valign="top" charoff="50">1</td></tr><tr><td align="left" valign="top" charoff="50">TSCC exome</td><td align="center" valign="top" charoff="50">47 (24 tumour, 23 paired normal)</td><td align="center" valign="top" charoff="50">0</td></tr><tr><td align="left" valign="top" charoff="50">Gall bladder exome</td><td align="center" valign="top" charoff="50">26 (13 tumour, 13 paired normal)</td><td align="center" valign="top" charoff="50">1</td></tr><tr><td align="left" valign="top" charoff="50">TSCC transcriptome</td><td align="center" valign="top" charoff="50">17 (11 tumour, 6 paired normal)</td><td align="center" valign="top" charoff="50">3</td></tr><tr><td align="left" valign="top" charoff="50">HNSCC cell line transcriptome</td><td align="center" valign="top" charoff="50">5</td><td align="center" valign="top" charoff="50">1</td></tr><tr><td align="left" valign="top" charoff="50">Gall bladder transcriptome</td><td align="center" valign="top" charoff="50">1</td><td align="center" valign="top" charoff="50">0</td></tr><tr><td align="left" valign="top" charoff="50">Liposarcoma WGS</td><td align="center" valign="top" charoff="50">1</td><td align="center" valign="top" charoff="50">0</td></tr><tr><td align="left" valign="top" charoff="50">Total number of samples</td><td align="center" valign="top" charoff="50">141</td><td align="center" valign="top" charoff="50">25</td></tr></tbody></table><table-wrap-foot><fn id="t1-fn1"><p>Abbreviations: HNSCC=head and neck squamous cell carcinoma; HPV=human papilloma virus; TSCC=tongue squamous cell carcinoma; WGS=whole-genome sequencing.</p></fn></table-wrap-foot></table-wrap></floats-group></pmc><affiliations><list><country><li>Inde</li></country></list><tree><country name="Inde"><noRegion><name sortKey="Chandrani, P" sort="Chandrani, P" uniqKey="Chandrani P" first="P" last="Chandrani">P. Chandrani</name></noRegion><name sortKey="Chaubal, R" sort="Chaubal, R" uniqKey="Chaubal R" first="R" last="Chaubal">R. Chaubal</name><name sortKey="Das, P" sort="Das, P" uniqKey="Das P" first="P" last="Das">P. Das</name><name sortKey="Dutt, A" sort="Dutt, A" uniqKey="Dutt A" first="A" last="Dutt">A. Dutt</name><name sortKey="Iyer, P" sort="Iyer, P" uniqKey="Iyer P" first="P" last="Iyer">P. Iyer</name><name sortKey="Kulkarni, V" sort="Kulkarni, V" uniqKey="Kulkarni V" first="V" last="Kulkarni">V. Kulkarni</name><name sortKey="Mulherkar, R" sort="Mulherkar, R" uniqKey="Mulherkar R" first="R" last="Mulherkar">R. Mulherkar</name><name sortKey="Singh, R" sort="Singh, R" uniqKey="Singh R" first="R" last="Singh">R. Singh</name><name sortKey="Upadhyay, P" sort="Upadhyay, P" uniqKey="Upadhyay P" first="P" last="Upadhyay">P. Upadhyay</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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