HPV Population Profiling in Healthy Men by Next-Generation Deep Sequencing Coupled with HPV-QUEST
Identifieur interne : 000033 ( Pmc/Curation ); précédent : 000032; suivant : 000034HPV Population Profiling in Healthy Men by Next-Generation Deep Sequencing Coupled with HPV-QUEST
Auteurs : Li Yin ; Jin Yao ; Kaifen Chang ; Brent P. Gardner ; Fahong Yu ; Anna R. Giuliano ; Maureen M. GoodenowSource :
- Viruses [ 1999-4915 ] ; 2016.
Abstract
Multiple-type human papillomaviruses (HPV) infection presents a greater risk for persistence in asymptomatic individuals and may accelerate cancer development. To extend the scope of HPV types defined by probe-based assays, multiplexing deep sequencing of HPV L1, coupled with an HPV-QUEST genotyping server and a bioinformatic pipeline, was established and applied to survey the diversity of HPV genotypes among a subset of healthy men from the HPV in Men (HIM) Multinational Study. Twenty-one HPV genotypes (12 high-risk and 9 low-risk) were detected in the genital area from 18 asymptomatic individuals. A single HPV type, either HPV16, HPV6b or HPV83, was detected in 7 individuals, while coinfection by 2 to 5 high-risk and/or low-risk genotypes was identified in the other 11 participants. In two individuals studied for over one year, HPV16 persisted, while fluctuations of coinfecting genotypes occurred. HPV L1 regions were generally identical between query and reference sequences, although nonsynonymous and synonymous nucleotide polymorphisms of HPV16, 18, 31, 35h, 59, 70, 73, cand85, 6b, 62, 81, 83, cand89 or JEB2 L1 genotypes, mostly unidentified by linear array, were evident. Deep sequencing coupled with HPV-QUEST provides efficient and unambiguous classification of HPV genotypes in multiple-type HPV infection in host ecosystems.
Url:
DOI: 10.3390/v8020028
PubMed: 26821041
PubMed Central: 4776183
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">HPV Population Profiling in Healthy Men by Next-Generation Deep Sequencing Coupled with HPV-QUEST</title>
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(K.C.);<email>brentga@pcom.edu</email>
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<author><name sortKey="Yao, Jin" sort="Yao, Jin" uniqKey="Yao J" first="Jin" last="Yao">Jin Yao</name>
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(K.C.);<email>brentga@pcom.edu</email>
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(B.P.G.);<email>goodenow@ufl.edu</email>
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<front><div type="abstract" xml:lang="en"><p>Multiple-type human papillomaviruses (HPV) infection presents a greater risk for persistence in asymptomatic individuals and may accelerate cancer development. To extend the scope of HPV types defined by probe-based assays, multiplexing deep sequencing of HPV L1, coupled with an HPV-QUEST genotyping server and a bioinformatic pipeline, was established and applied to survey the diversity of HPV genotypes among a subset of healthy men from the HPV in Men (HIM) Multinational Study. Twenty-one HPV genotypes (12 high-risk and 9 low-risk) were detected in the genital area from 18 asymptomatic individuals. A single HPV type, either HPV16, HPV6b or HPV83, was detected in 7 individuals, while coinfection by 2 to 5 high-risk and/or low-risk genotypes was identified in the other 11 participants. In two individuals studied for over one year, HPV16 persisted, while fluctuations of coinfecting genotypes occurred. HPV L1 regions were generally identical between query and reference sequences, although nonsynonymous and synonymous nucleotide polymorphisms of HPV16, 18, 31, 35h, 59, 70, 73, cand85, 6b, 62, 81, 83, cand89 or JEB2 L1 genotypes, mostly unidentified by linear array, were evident. Deep sequencing coupled with HPV-QUEST provides efficient and unambiguous classification of HPV genotypes in multiple-type HPV infection in host ecosystems.</p>
</div>
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</TEI>
<pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Viruses</journal-id>
<journal-id journal-id-type="iso-abbrev">Viruses</journal-id>
<journal-id journal-id-type="publisher-id">viruses</journal-id>
<journal-title-group><journal-title>Viruses</journal-title>
</journal-title-group>
<issn pub-type="epub">1999-4915</issn>
<publisher><publisher-name>MDPI</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">26821041</article-id>
<article-id pub-id-type="pmc">4776183</article-id>
<article-id pub-id-type="doi">10.3390/v8020028</article-id>
<article-id pub-id-type="publisher-id">viruses-08-00028</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Article</subject>
</subj-group>
</article-categories>
<title-group><article-title>HPV Population Profiling in Healthy Men by Next-Generation Deep Sequencing Coupled with HPV-QUEST</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Yin</surname>
<given-names>Li</given-names>
</name>
<xref ref-type="aff" rid="af1-viruses-08-00028">1</xref>
<xref rid="c1-viruses-08-00028" ref-type="corresp">*</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Yao</surname>
<given-names>Jin</given-names>
</name>
<xref ref-type="aff" rid="af2-viruses-08-00028">2</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Chang</surname>
<given-names>Kaifen</given-names>
</name>
<xref ref-type="aff" rid="af1-viruses-08-00028">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Gardner</surname>
<given-names>Brent P.</given-names>
</name>
<xref ref-type="aff" rid="af1-viruses-08-00028">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Yu</surname>
<given-names>Fahong</given-names>
</name>
<xref ref-type="aff" rid="af2-viruses-08-00028">2</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Giuliano</surname>
<given-names>Anna R.</given-names>
</name>
<xref ref-type="aff" rid="af3-viruses-08-00028">3</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Goodenow</surname>
<given-names>Maureen M.</given-names>
</name>
<xref ref-type="aff" rid="af1-viruses-08-00028">1</xref>
</contrib>
</contrib-group>
<contrib-group><contrib contrib-type="editor"><name><surname>Mak</surname>
<given-names>Johnson</given-names>
</name>
<role>Academic Editor</role>
</contrib>
<contrib contrib-type="editor"><name><surname>Walker</surname>
<given-names>Peter</given-names>
</name>
<role>Academic Editor</role>
</contrib>
<contrib contrib-type="editor"><name><surname>Gilbert</surname>
<given-names>Marcus Thomas</given-names>
</name>
<role>Academic Editor</role>
</contrib>
</contrib-group>
<aff id="af1-viruses-08-00028"><label>1</label>
Department of Pathology, Immunology & Laboratory Medicine and UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA;<email>kaifen@pathology.ufl.edu</email>
(K.C.);<email>brentga@pcom.edu</email>
(B.P.G.);<email>goodenow@ufl.edu</email>
(M.M.G.)</aff>
<aff id="af2-viruses-08-00028"><label>2</label>
Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32610, USA;<email>jin.yao2009@gmail.com</email>
(J.Y.);<email>fyu@ufl.edu</email>
(F.Y.)</aff>
<aff id="af3-viruses-08-00028"><label>3</label>
Center for Infection Research in Cancer at H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA;<email>Anna.Giuliano@moffitt.org</email>
</aff>
<author-notes><corresp id="c1-viruses-08-00028"><label>*</label>
Correspondence: <email>yin@pathology.ufl.edu</email>
; Tel.: +1-352-273-8134; Fax: +1-352-273-8285</corresp>
</author-notes>
<pub-date pub-type="epub"><day>25</day>
<month>1</month>
<year>2016</year>
</pub-date>
<pub-date pub-type="collection"><month>2</month>
<year>2016</year>
</pub-date>
<volume>8</volume>
<issue>2</issue>
<elocation-id>28</elocation-id>
<history><date date-type="received"><day>06</day>
<month>10</month>
<year>2015</year>
</date>
<date date-type="accepted"><day>11</day>
<month>1</month>
<year>2016</year>
</date>
</history>
<permissions><copyright-statement>© 2016 by the authors; licensee MDPI, Basel, Switzerland.</copyright-statement>
<copyright-year>2016</copyright-year>
<license><license-p><pmc-comment>CREATIVE COMMONS</pmc-comment>
This article is an open access article distributed under the terms and conditions of the Creative Commons by Attribution (CC-BY) license (<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><p>Multiple-type human papillomaviruses (HPV) infection presents a greater risk for persistence in asymptomatic individuals and may accelerate cancer development. To extend the scope of HPV types defined by probe-based assays, multiplexing deep sequencing of HPV L1, coupled with an HPV-QUEST genotyping server and a bioinformatic pipeline, was established and applied to survey the diversity of HPV genotypes among a subset of healthy men from the HPV in Men (HIM) Multinational Study. Twenty-one HPV genotypes (12 high-risk and 9 low-risk) were detected in the genital area from 18 asymptomatic individuals. A single HPV type, either HPV16, HPV6b or HPV83, was detected in 7 individuals, while coinfection by 2 to 5 high-risk and/or low-risk genotypes was identified in the other 11 participants. In two individuals studied for over one year, HPV16 persisted, while fluctuations of coinfecting genotypes occurred. HPV L1 regions were generally identical between query and reference sequences, although nonsynonymous and synonymous nucleotide polymorphisms of HPV16, 18, 31, 35h, 59, 70, 73, cand85, 6b, 62, 81, 83, cand89 or JEB2 L1 genotypes, mostly unidentified by linear array, were evident. Deep sequencing coupled with HPV-QUEST provides efficient and unambiguous classification of HPV genotypes in multiple-type HPV infection in host ecosystems.</p>
</abstract>
<kwd-group><kwd>HPV</kwd>
<kwd>multiple-type HPV infection</kwd>
<kwd>asymptomatic men</kwd>
<kwd>deep sequencing</kwd>
<kwd>HPV-QUEST</kwd>
<kwd>Linear Array</kwd>
<kwd>Papillomavirus Episteme</kwd>
</kwd-group>
</article-meta>
</front>
</pmc>
</record>
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