Nested PCR followed by NGS: Validation and application for HPV genotyping of Tunisian cervical samples

Detalhes bibliográficos
Autor(a) principal: Ardhaoui, Monia
Data de Publicação: 2021
Outros Autores: Ennaifer, Emna, Salim, Anna Christina de Matos, Araújo, Flávio Marcos Gomes de, Laasili, Thalja, Boubaker, Med Samir
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da FIOCRUZ (ARCA)
Texto Completo: https://www.arca.fiocruz.br/handle/icict/51749
Resumo: University of Tunis. Tunis, Tunísia
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spelling Ardhaoui, MoniaEnnaifer, EmnaSalim, Anna Christina de MatosAraújo, Flávio Marcos Gomes deLaasili, ThaljaBoubaker, Med Samir2022-03-18T17:40:30Z2022-03-18T17:40:30Z2021ARDHAOUI, Monia et al. Nested PCR followed by NGS: Validation and application for HPV genotyping of Tunisian cervical samples. PLoS one, v. 16, n. 8, e0255914, 2021. doi.org/10.1371/journal.pone.02559141932-6203https://www.arca.fiocruz.br/handle/icict/5174910.1371/journal.pone.0255914engPublic Library of ScienceNested PCR followed by NGS: Validation and application for HPV genotyping of Tunisian cervical samplesinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleUniversity of Tunis. Tunis, TunísiaUniversity of Tunis. Tunis, TunísiaFundação Oswaldo Cruz. Instituto René Rachou. Belo Horizonte, MG, BrasilFundação Oswaldo Cruz. Instituto René Rachou. Belo Horizonte, MG, BrasilUniversity of Tunis. Tunis, TunísiaUniversity of Tunis. Tunis, TunísiaThe most used methodologies for HPV genotyping in Tunisian studies are based on hybridization that are limited to a restricted number of HPV types and to a lack of specificity and sensitivity for same types. Recently, Next-Generation sequencing (NGS) technology has been efficiently used for HPV genotyping. In this work we designed and validated a sensitive genotyping method based on nested PCR followed by NGS. Eighty-six samples were tested for the validation of an HPV genotyping assay based on Nested-PCR followed by NGS. These include, 43 references plasmids and 43 positive HPV clinical cervical specimens previously evaluated with the conventional genotyping method: Reverse Line Hybridization (RLH). Results of genotyping using NGS were compared to those of RLH. The analytical sensitivity of the NGS assay was 1GE/mu l per sample. The NGS allowed the detection of all HPV types presented in references plasmids. On the clinical samples, a total of 19 HPV types were detected versus 14 types using RLH. Besides the identification of more HPV types in multiple infection (6 types for NGS versus 4 for RLH), NGS allowed the identification of HPV types that were not detected by RLH. In addition, the NGS assay detected newly HPV types that were not described in Tunisia so far: HPV81, HPV43, HPV74, and HPV62. The high sensitivity and specificity of NGS for HPV genotyping in addition to the identification of new HPV types may justify the use of such technique to provide with high accuracy the profile of circulating types in epidemiological studiesinfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZLICENSElicense.txtlicense.txttext/plain; charset=utf-83082https://www.arca.fiocruz.br/bitstream/icict/51749/1/license.txt9193a7c197bc67acd023525e72a03240MD51ORIGINALNested PCR followed by NGS_ Validation and application for HPV genotyping of Tunisian cervical samples.pdfNested PCR followed by NGS_ Validation and application for HPV genotyping of Tunisian cervical samples.pdfapplication/pdf3798264https://www.arca.fiocruz.br/bitstream/icict/51749/2/Nested%20PCR%20followed%20by%20NGS_%20Validation%20and%20application%20for%20HPV%20genotyping%20of%20Tunisian%20cervical%20samples.pdfaf1aa2bc8b454bd230ee5772caa20017MD52icict/517492022-03-18 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dc.title.pt_BR.fl_str_mv Nested PCR followed by NGS: Validation and application for HPV genotyping of Tunisian cervical samples
title Nested PCR followed by NGS: Validation and application for HPV genotyping of Tunisian cervical samples
spellingShingle Nested PCR followed by NGS: Validation and application for HPV genotyping of Tunisian cervical samples
Ardhaoui, Monia
title_short Nested PCR followed by NGS: Validation and application for HPV genotyping of Tunisian cervical samples
title_full Nested PCR followed by NGS: Validation and application for HPV genotyping of Tunisian cervical samples
title_fullStr Nested PCR followed by NGS: Validation and application for HPV genotyping of Tunisian cervical samples
title_full_unstemmed Nested PCR followed by NGS: Validation and application for HPV genotyping of Tunisian cervical samples
title_sort Nested PCR followed by NGS: Validation and application for HPV genotyping of Tunisian cervical samples
author Ardhaoui, Monia
author_facet Ardhaoui, Monia
Ennaifer, Emna
Salim, Anna Christina de Matos
Araújo, Flávio Marcos Gomes de
Laasili, Thalja
Boubaker, Med Samir
author_role author
author2 Ennaifer, Emna
Salim, Anna Christina de Matos
Araújo, Flávio Marcos Gomes de
Laasili, Thalja
Boubaker, Med Samir
author2_role author
author
author
author
author
dc.contributor.author.fl_str_mv Ardhaoui, Monia
Ennaifer, Emna
Salim, Anna Christina de Matos
Araújo, Flávio Marcos Gomes de
Laasili, Thalja
Boubaker, Med Samir
description University of Tunis. Tunis, Tunísia
publishDate 2021
dc.date.issued.fl_str_mv 2021
dc.date.accessioned.fl_str_mv 2022-03-18T17:40:30Z
dc.date.available.fl_str_mv 2022-03-18T17:40:30Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.citation.fl_str_mv ARDHAOUI, Monia et al. Nested PCR followed by NGS: Validation and application for HPV genotyping of Tunisian cervical samples. PLoS one, v. 16, n. 8, e0255914, 2021. doi.org/10.1371/journal.pone.0255914
dc.identifier.uri.fl_str_mv https://www.arca.fiocruz.br/handle/icict/51749
dc.identifier.issn.pt_BR.fl_str_mv 1932-6203
dc.identifier.doi.none.fl_str_mv 10.1371/journal.pone.0255914
identifier_str_mv ARDHAOUI, Monia et al. Nested PCR followed by NGS: Validation and application for HPV genotyping of Tunisian cervical samples. PLoS one, v. 16, n. 8, e0255914, 2021. doi.org/10.1371/journal.pone.0255914
1932-6203
10.1371/journal.pone.0255914
url https://www.arca.fiocruz.br/handle/icict/51749
dc.language.iso.fl_str_mv eng
language eng
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Public Library of Science
publisher.none.fl_str_mv Public Library of Science
dc.source.none.fl_str_mv reponame:Repositório Institucional da FIOCRUZ (ARCA)
instname:Fundação Oswaldo Cruz (FIOCRUZ)
instacron:FIOCRUZ
instname_str Fundação Oswaldo Cruz (FIOCRUZ)
instacron_str FIOCRUZ
institution FIOCRUZ
reponame_str Repositório Institucional da FIOCRUZ (ARCA)
collection Repositório Institucional da FIOCRUZ (ARCA)
bitstream.url.fl_str_mv https://www.arca.fiocruz.br/bitstream/icict/51749/1/license.txt
https://www.arca.fiocruz.br/bitstream/icict/51749/2/Nested%20PCR%20followed%20by%20NGS_%20Validation%20and%20application%20for%20HPV%20genotyping%20of%20Tunisian%20cervical%20samples.pdf
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repository.name.fl_str_mv Repositório Institucional da FIOCRUZ (ARCA) - Fundação Oswaldo Cruz (FIOCRUZ)
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