Human papillomavirus genotyping by Linear Array and Next-Generation Sequencing in cervical samples from Western Mexico
Identifieur interne : 000046 ( Main/Exploration ); précédent : 000045; suivant : 000047Human papillomavirus genotyping by Linear Array and Next-Generation Sequencing in cervical samples from Western Mexico
Auteurs : María Guadalupe Flores-Miramontes [Mexique] ; Luis Alberto Torres-Reyes [Mexique] ; Liliana Alvarado-Ruíz [Mexique] ; Salvador Angel Romero-Martínez [Mexique] ; Verenice Ramírez-Rodríguez [Mexique] ; Luz María Adriana Balderas-Pe A ; Ver Nica Vallejo-Ruíz ; Patricia Pi A-Sánchez [Mexique] ; Elva Irene Cortés-Gutiérrez ; Luis Felipe Jave-Suárez ; Adriana Aguilar-LemarroySource :
- Virology Journal [ 1743-422X ] ; 2015.
Abstract
The Linear Array® (LA) genotyping test is one of the most used methodologies for Human papillomavirus (HPV) genotyping, in that it is able to detect 37 HPV genotypes and co-infections in the same sample. However, the assay is limited to a restricted number of HPV, and sequence variations in the detection region of the HPV probes could give false negatives results. Recently, 454 Next-Generation sequencing (NGS) technology has been efficiently used also for HPV genotyping; this methodology is based on massive sequencing of HPV fragments and is expected to be highly specific and sensitive. In this work, we studied HPV prevalence in cervixes of women in Western Mexico by LA and confirmed the genotypes found by NGS.
Two hundred thirty three cervical samples from women Without cervical lesions (WCL,
We identified 35 HPV genotypes, among which 30 were identified by both technologies; in addition, the HPV genotypes 32, 44, 74, 102 and 114 were detected by NGS. These latter genotypes, to our knowledge, have not been previously reported in Mexican population. Furthermore, we found that LA did not detect, in some diagnosis groups, certain HPV genotypes included in the test, such as 6, 11, 16, 26, 35, 51, 58, 68, 73, and 89, which indicates possible variations at the species level.
There are HPV genotypes in Mexican population that cannot be detected by LA, which is, at present, the most complete commercial genotyping test. More studies are necessary to determine the impact of HPV-44, 74, 102 and 114 on the risk of developing CC. A greater number of samples must be analyzed by NGS for the most accurate determination of Mexican HPV variants.
The online version of this article (doi:10.1186/s12985-015-0391-4) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s12985-015-0391-4
PubMed: 26444975
PubMed Central: 4596464
Affiliations:
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Independencia, 44340 Guadalajara, Jalisco Mexico</nlm:aff><wicri:noCountry code="subfield">Jalisco Mexico</wicri:noCountry></affiliation></author><author><name sortKey="Aguilar Lemarroy, Adriana" sort="Aguilar Lemarroy, Adriana" uniqKey="Aguilar Lemarroy A" first="Adriana" last="Aguilar-Lemarroy">Adriana Aguilar-Lemarroy</name><affiliation><nlm:aff id="Aff1">División de Inmunología, Centro de Investigación Biomédica de Occidente (CIBO)-Instituto Mexicano del Seguro Social (IMSS), Sierra Mojada No. 800, Col. Independencia, 44340 Guadalajara, Jalisco Mexico</nlm:aff><wicri:noCountry code="subfield">Jalisco Mexico</wicri:noCountry></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">26444975</idno><idno type="pmc">4596464</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4596464</idno><idno type="RBID">PMC:4596464</idno><idno type="doi">10.1186/s12985-015-0391-4</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">000047</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000047</idno><idno type="wicri:Area/Pmc/Curation">000047</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000047</idno><idno type="wicri:Area/Pmc/Checkpoint">000032</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000032</idno><idno type="wicri:Area/Ncbi/Merge">000238</idno><idno type="wicri:Area/Ncbi/Curation">000238</idno><idno type="wicri:Area/Ncbi/Checkpoint">000238</idno><idno type="wicri:Area/Main/Merge">000045</idno><idno type="wicri:Area/Main/Curation">000046</idno><idno type="wicri:Area/Main/Exploration">000046</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Human papillomavirus genotyping by Linear Array and Next-Generation Sequencing in cervical samples from Western Mexico</title><author><name sortKey="Flores Miramontes, Maria Guadalupe" sort="Flores Miramontes, Maria Guadalupe" uniqKey="Flores Miramontes M" first="María Guadalupe" last="Flores-Miramontes">María Guadalupe Flores-Miramontes</name><affiliation><nlm:aff id="Aff1">División de Inmunología, Centro de Investigación Biomédica de Occidente (CIBO)-Instituto Mexicano del Seguro Social (IMSS), Sierra Mojada No. 800, Col. Independencia, 44340 Guadalajara, Jalisco Mexico</nlm:aff><wicri:noCountry code="subfield">Jalisco Mexico</wicri:noCountry></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff2">Programa de Doctorado en Ciencias Biomédica, Centro Universitario de Ciencias de la Salud (CUCS), Universidad de Guadalajara, Jalisco, Mexico</nlm:aff><country xml:lang="fr">Mexique</country><wicri:regionArea>Programa de Doctorado en Ciencias Biomédica, Centro Universitario de Ciencias de la Salud (CUCS), Universidad de Guadalajara, Jalisco</wicri:regionArea><wicri:noRegion>Jalisco</wicri:noRegion></affiliation></author><author><name sortKey="Torres Reyes, Luis Alberto" sort="Torres Reyes, Luis Alberto" uniqKey="Torres Reyes L" first="Luis Alberto" last="Torres-Reyes">Luis Alberto Torres-Reyes</name><affiliation><nlm:aff id="Aff1">División de Inmunología, Centro de Investigación Biomédica de Occidente (CIBO)-Instituto Mexicano del Seguro Social (IMSS), Sierra Mojada No. 800, Col. Independencia, 44340 Guadalajara, Jalisco Mexico</nlm:aff><wicri:noCountry code="subfield">Jalisco Mexico</wicri:noCountry></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff2">Programa de Doctorado en Ciencias Biomédica, Centro Universitario de Ciencias de la Salud (CUCS), Universidad de Guadalajara, Jalisco, Mexico</nlm:aff><country xml:lang="fr">Mexique</country><wicri:regionArea>Programa de Doctorado en Ciencias Biomédica, Centro Universitario de Ciencias de la Salud (CUCS), Universidad de Guadalajara, Jalisco</wicri:regionArea><wicri:noRegion>Jalisco</wicri:noRegion></affiliation></author><author><name sortKey="Alvarado Ruiz, Liliana" sort="Alvarado Ruiz, Liliana" uniqKey="Alvarado Ruiz L" first="Liliana" last="Alvarado-Ruíz">Liliana Alvarado-Ruíz</name><affiliation><nlm:aff id="Aff1">División de Inmunología, Centro de Investigación Biomédica de Occidente (CIBO)-Instituto Mexicano del Seguro Social (IMSS), Sierra Mojada No. 800, Col. Independencia, 44340 Guadalajara, Jalisco Mexico</nlm:aff><wicri:noCountry code="subfield">Jalisco Mexico</wicri:noCountry></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff2">Programa de Doctorado en Ciencias Biomédica, Centro Universitario de Ciencias de la Salud (CUCS), Universidad de Guadalajara, Jalisco, Mexico</nlm:aff><country xml:lang="fr">Mexique</country><wicri:regionArea>Programa de Doctorado en Ciencias Biomédica, Centro Universitario de Ciencias de la Salud (CUCS), Universidad de Guadalajara, Jalisco</wicri:regionArea><wicri:noRegion>Jalisco</wicri:noRegion></affiliation></author><author><name sortKey="Romero Martinez, Salvador Angel" sort="Romero Martinez, Salvador Angel" uniqKey="Romero Martinez S" first="Salvador Angel" last="Romero-Martínez">Salvador Angel Romero-Martínez</name><affiliation wicri:level="1"><nlm:aff id="Aff3">Diagnostics Division, Roche México, Mexico City, Mexico</nlm:aff><country xml:lang="fr">Mexique</country><wicri:regionArea>Diagnostics Division, Roche México, Mexico City</wicri:regionArea><wicri:noRegion>Mexico City</wicri:noRegion></affiliation></author><author><name sortKey="Ramirez Rodriguez, Verenice" sort="Ramirez Rodriguez, Verenice" uniqKey="Ramirez Rodriguez V" first="Verenice" last="Ramírez-Rodríguez">Verenice Ramírez-Rodríguez</name><affiliation wicri:level="1"><nlm:aff id="Aff3">Diagnostics Division, Roche México, Mexico City, Mexico</nlm:aff><country xml:lang="fr">Mexique</country><wicri:regionArea>Diagnostics Division, Roche México, Mexico City</wicri:regionArea><wicri:noRegion>Mexico City</wicri:noRegion></affiliation></author><author><name sortKey="Balderas Pe A, Luz Maria Adriana" sort="Balderas Pe A, Luz Maria Adriana" uniqKey="Balderas Pe A L" first="Luz María Adriana" last="Balderas-Pe A">Luz María Adriana Balderas-Pe A</name><affiliation><nlm:aff id="Aff4">Unidad de Investigación Médica en Epidemiología Clínica, UMAE Hospital de Especialidades, Centro Médico Nacional de Occidente (CMNO)-IMSS, Guadalajara, Jalisco Mexico</nlm:aff><wicri:noCountry code="subfield">Jalisco Mexico</wicri:noCountry></affiliation></author><author><name sortKey="Vallejo Ruiz, Ver Nica" sort="Vallejo Ruiz, Ver Nica" uniqKey="Vallejo Ruiz V" first="Ver Nica" last="Vallejo-Ruíz">Ver Nica Vallejo-Ruíz</name><affiliation><nlm:aff id="Aff5">Centro de Investigación Biomédica de Oriente (CIBIOR)—IMSS, Metepec, Puebla Mexico</nlm:aff><wicri:noCountry code="subfield">Puebla Mexico</wicri:noCountry></affiliation></author><author><name sortKey="Pi A Sanchez, Patricia" sort="Pi A Sanchez, Patricia" uniqKey="Pi A Sanchez P" first="Patricia" last="Pi A-Sánchez">Patricia Pi A-Sánchez</name><affiliation wicri:level="1"><nlm:aff id="Aff6">Laboratorio de Oncología Molecular, Unidad de Investigación Médica en Enfermedades Oncológicas (UIMEO)—IMSS, Mexico City, Mexico</nlm:aff><country xml:lang="fr">Mexique</country><wicri:regionArea>Laboratorio de Oncología Molecular, Unidad de Investigación Médica en Enfermedades Oncológicas (UIMEO)—IMSS, Mexico City</wicri:regionArea><wicri:noRegion>Mexico City</wicri:noRegion></affiliation></author><author><name sortKey="Cortes Gutierrez, Elva Irene" sort="Cortes Gutierrez, Elva Irene" uniqKey="Cortes Gutierrez E" first="Elva Irene" last="Cortés-Gutiérrez">Elva Irene Cortés-Gutiérrez</name><affiliation><nlm:aff id="Aff7">Centro de Investigación Biomédica del Noreste (CIBIN)—IMSS, Monterrey, Nuevo León Mexico</nlm:aff><wicri:noCountry code="subfield">Nuevo León Mexico</wicri:noCountry></affiliation></author><author><name sortKey="Jave Suarez, Luis Felipe" sort="Jave Suarez, Luis Felipe" uniqKey="Jave Suarez L" first="Luis Felipe" last="Jave-Suárez">Luis Felipe Jave-Suárez</name><affiliation><nlm:aff id="Aff1">División de Inmunología, Centro de Investigación Biomédica de Occidente (CIBO)-Instituto Mexicano del Seguro Social (IMSS), Sierra Mojada No. 800, Col. Independencia, 44340 Guadalajara, Jalisco Mexico</nlm:aff><wicri:noCountry code="subfield">Jalisco Mexico</wicri:noCountry></affiliation></author><author><name sortKey="Aguilar Lemarroy, Adriana" sort="Aguilar Lemarroy, Adriana" uniqKey="Aguilar Lemarroy A" first="Adriana" last="Aguilar-Lemarroy">Adriana Aguilar-Lemarroy</name><affiliation><nlm:aff id="Aff1">División de Inmunología, Centro de Investigación Biomédica de Occidente (CIBO)-Instituto Mexicano del Seguro Social (IMSS), Sierra Mojada No. 800, Col. Independencia, 44340 Guadalajara, Jalisco Mexico</nlm:aff><wicri:noCountry code="subfield">Jalisco Mexico</wicri:noCountry></affiliation></author></analytic><series><title level="j">Virology Journal</title><idno type="eISSN">1743-422X</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>The Linear Array® (LA) genotyping test is one of the most used methodologies for Human papillomavirus (HPV) genotyping, in that it is able to detect 37 HPV genotypes and co-infections in the same sample. However, the assay is limited to a restricted number of HPV, and sequence variations in the detection region of the HPV probes could give false negatives results. Recently, 454 Next-Generation sequencing (NGS) technology has been efficiently used also for HPV genotyping; this methodology is based on massive sequencing of HPV fragments and is expected to be highly specific and sensitive. In this work, we studied HPV prevalence in cervixes of women in Western Mexico by LA and confirmed the genotypes found by NGS.</p></sec><sec><title>Methods</title><p>Two hundred thirty three cervical samples from women Without cervical lesions (WCL, <italic>n</italic> = 48), with Cervical intraepithelial neoplasia grade 1 (CIN I, <italic>n</italic> = 98), or with Cervical cancer (CC, <italic>n</italic> = 87) were recruited, DNA was extracted, and HPV positivity was determined by PCR amplification using PGMY09/11 primers. All HPV- positive samples were genotyped individually by LA. Additionally, pools of amplicons from the PGMY-PCR products were sequenced using 454 NGS technology. Results obtained by NGS were compared with those of LA for each group of samples.</p></sec><sec><title>Results</title><p>We identified 35 HPV genotypes, among which 30 were identified by both technologies; in addition, the HPV genotypes 32, 44, 74, 102 and 114 were detected by NGS. These latter genotypes, to our knowledge, have not been previously reported in Mexican population. Furthermore, we found that LA did not detect, in some diagnosis groups, certain HPV genotypes included in the test, such as 6, 11, 16, 26, 35, 51, 58, 68, 73, and 89, which indicates possible variations at the species level.</p></sec><sec><title>Conclusions</title><p>There are HPV genotypes in Mexican population that cannot be detected by LA, which is, at present, the most complete commercial genotyping test. More studies are necessary to determine the impact of HPV-44, 74, 102 and 114 on the risk of developing CC. A greater number of samples must be analyzed by NGS for the most accurate determination of Mexican HPV variants.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s12985-015-0391-4) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Zur Hausen, H" uniqKey="Zur Hausen H">H Zur Hausen</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Bosch, Fx" uniqKey="Bosch F">FX Bosch</name></author><author><name sortKey="Manos, Mm" uniqKey="Manos M">MM Manos</name></author><author><name sortKey="Mu Oz, N" uniqKey="Mu Oz N">N Muñoz</name></author><author><name sortKey="Sherman, M" uniqKey="Sherman M">M Sherman</name></author><author><name sortKey="Jansen, Am" uniqKey="Jansen A">AM Jansen</name></author><author><name 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Adriana" uniqKey="Aguilar Lemarroy A" first="Adriana" last="Aguilar-Lemarroy">Adriana Aguilar-Lemarroy</name><name sortKey="Balderas Pe A, Luz Maria Adriana" sort="Balderas Pe A, Luz Maria Adriana" uniqKey="Balderas Pe A L" first="Luz María Adriana" last="Balderas-Pe A">Luz María Adriana Balderas-Pe A</name><name sortKey="Cortes Gutierrez, Elva Irene" sort="Cortes Gutierrez, Elva Irene" uniqKey="Cortes Gutierrez E" first="Elva Irene" last="Cortés-Gutiérrez">Elva Irene Cortés-Gutiérrez</name><name sortKey="Jave Suarez, Luis Felipe" sort="Jave Suarez, Luis Felipe" uniqKey="Jave Suarez L" first="Luis Felipe" last="Jave-Suárez">Luis Felipe Jave-Suárez</name><name sortKey="Vallejo Ruiz, Ver Nica" sort="Vallejo Ruiz, Ver Nica" uniqKey="Vallejo Ruiz V" first="Ver Nica" last="Vallejo-Ruíz">Ver Nica Vallejo-Ruíz</name></noCountry><country name="Mexique"><noRegion><name sortKey="Flores Miramontes, Maria Guadalupe" sort="Flores Miramontes, Maria Guadalupe" uniqKey="Flores Miramontes M" first="María Guadalupe" last="Flores-Miramontes">María Guadalupe Flores-Miramontes</name></noRegion><name sortKey="Alvarado Ruiz, Liliana" sort="Alvarado Ruiz, Liliana" uniqKey="Alvarado Ruiz L" first="Liliana" last="Alvarado-Ruíz">Liliana Alvarado-Ruíz</name><name sortKey="Pi A Sanchez, Patricia" sort="Pi A Sanchez, Patricia" uniqKey="Pi A Sanchez P" first="Patricia" last="Pi A-Sánchez">Patricia Pi A-Sánchez</name><name sortKey="Ramirez Rodriguez, Verenice" sort="Ramirez Rodriguez, Verenice" uniqKey="Ramirez Rodriguez V" first="Verenice" last="Ramírez-Rodríguez">Verenice Ramírez-Rodríguez</name><name sortKey="Romero Martinez, Salvador Angel" sort="Romero Martinez, Salvador Angel" uniqKey="Romero Martinez S" first="Salvador Angel" last="Romero-Martínez">Salvador Angel Romero-Martínez</name><name sortKey="Torres Reyes, Luis Alberto" sort="Torres Reyes, Luis Alberto" uniqKey="Torres Reyes L" first="Luis Alberto" last="Torres-Reyes">Luis Alberto Torres-Reyes</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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