Comparison of four methods of genotyping IL28B polymorphisms in chronic hepatitis C patients

Detalhes bibliográficos
Autor(a) principal: Delvaux, Nathália
Data de Publicação: 2015
Outros Autores: Costa, Vanessa Duarte da, Costa, Maristella Matos da, Lampe, Elisabeth
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da FIOCRUZ (ARCA)
Texto Completo: https://www.arca.fiocruz.br/handle/icict/12054
Resumo: 2016-07-31
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spelling Delvaux, NatháliaCosta, Vanessa Duarte daCosta, Maristella Matos daLampe, Elisabeth2015-10-22T16:13:35Z2015DELVAUX, Nathália; et al. Comparison of four methods of genotyping IL28B polymorphisms in chronic hepatitis C patients. Journal of Virological Methods, v.220, p.1-4, Aug. 2015.0166-0934https://www.arca.fiocruz.br/handle/icict/1205410.1016/j.jviromet.2015.04.001engElsevierComparison of four methods of genotyping IL28B polymorphisms in chronic hepatitis C patientsinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article2016-07-31Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Hepatites Virais. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Hepatites Virais. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Hepatites Virais. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Hepatites Virais. Rio de Janeiro, RJ, Brasil.Background: Single nucleotide polymorphisms (SNPs) of the interleukin 28B (IL28B) gene are associated with viral clearance and treatment response in hepatitis C virus (HCV) infection; however, most of the available SNP genotyping methods are expensive. Aims: This study sought to evaluate the cost effectiveness of four methods used to genotype the rs12979860 and rs8099917 SNPs of the IL28B gene. Methods: Tetra-primer amplification-refractory mutation system-polymerase chain reaction (ARMSPCR), restriction fragment length polymorphism (RFLP), quantitative (q) PCR and direct sequencing methods were evaluated in terms of specificity, cost and run time in 281 blood samples obtained from chronic HCV patients. Results: In ARMS-PCR method, the primers designed to target both SNPs produced PCR fragments of specific sizes that distinguished the alleles of rs12979860 and rs8099917. In RFLP, the band profile allowed the distinction between genotypes. The qPCR was the faster and easier to perform. Validation by nucleotide sequencing showed 100% agreement among the three methods. The cost for a single reaction was lowest for ARMS-PCR, followed in turn by RFLP, qPCR and sequencing. Conclusions: The methodology described for the ARMS-PCR showed the most favorable cost–benefit ratio. Moreover, this approach is fast and simple, requiring only equipment that is commonly used in molecular diagnosis, which is an essential parameter for use in developing countries where laboratories have scarce financial resources.IL28BSNPHCVBrazilARMS-PCRHepacivirusHepatite CrônicaReação em Cadeia da PolimeraseMétodosinfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZLICENSElicense.txtlicense.txttext/plain; charset=utf-82354https://www.arca.fiocruz.br/bitstream/icict/12054/1/license.txt8b4c200b4e10021c5683c6ccaba07169MD51ORIGINALnathalia_delvaux_etal_IOC_2015.pdfnathalia_delvaux_etal_IOC_2015.pdfapplication/pdf459867https://www.arca.fiocruz.br/bitstream/icict/12054/2/nathalia_delvaux_etal_IOC_2015.pdf609af8cc32ee479be6b0b4b23ede0f20MD52TEXTnathalia_delvaux_etal_IOC_2015.pdf.txtnathalia_delvaux_etal_IOC_2015.pdf.txtExtracted texttext/plain23696https://www.arca.fiocruz.br/bitstream/icict/12054/3/nathalia_delvaux_etal_IOC_2015.pdf.txtab9d0fea4a9ed4f5b8ed71a5a190a814MD53icict/120542023-09-05 10:31:08.437oai:www.arca.fiocruz.br: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Repositório InstitucionalPUBhttps://www.arca.fiocruz.br/oai/requestrepositorio.arca@fiocruz.bropendoar:21352023-09-05T13:31:08Repositório Institucional da FIOCRUZ (ARCA) - Fundação Oswaldo Cruz (FIOCRUZ)false
dc.title.pt_BR.fl_str_mv Comparison of four methods of genotyping IL28B polymorphisms in chronic hepatitis C patients
title Comparison of four methods of genotyping IL28B polymorphisms in chronic hepatitis C patients
spellingShingle Comparison of four methods of genotyping IL28B polymorphisms in chronic hepatitis C patients
Delvaux, Nathália
IL28B
SNP
HCV
Brazil
ARMS-PCR
Hepacivirus
Hepatite Crônica
Reação em Cadeia da Polimerase
Métodos
title_short Comparison of four methods of genotyping IL28B polymorphisms in chronic hepatitis C patients
title_full Comparison of four methods of genotyping IL28B polymorphisms in chronic hepatitis C patients
title_fullStr Comparison of four methods of genotyping IL28B polymorphisms in chronic hepatitis C patients
title_full_unstemmed Comparison of four methods of genotyping IL28B polymorphisms in chronic hepatitis C patients
title_sort Comparison of four methods of genotyping IL28B polymorphisms in chronic hepatitis C patients
author Delvaux, Nathália
author_facet Delvaux, Nathália
Costa, Vanessa Duarte da
Costa, Maristella Matos da
Lampe, Elisabeth
author_role author
author2 Costa, Vanessa Duarte da
Costa, Maristella Matos da
Lampe, Elisabeth
author2_role author
author
author
dc.contributor.author.fl_str_mv Delvaux, Nathália
Costa, Vanessa Duarte da
Costa, Maristella Matos da
Lampe, Elisabeth
dc.subject.en.pt_BR.fl_str_mv IL28B
SNP
HCV
Brazil
ARMS-PCR
topic IL28B
SNP
HCV
Brazil
ARMS-PCR
Hepacivirus
Hepatite Crônica
Reação em Cadeia da Polimerase
Métodos
dc.subject.decs.pt_BR.fl_str_mv Hepacivirus
Hepatite Crônica
Reação em Cadeia da Polimerase
Métodos
description 2016-07-31
publishDate 2015
dc.date.accessioned.fl_str_mv 2015-10-22T16:13:35Z
dc.date.issued.fl_str_mv 2015
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 DELVAUX, Nathália; et al. Comparison of four methods of genotyping IL28B polymorphisms in chronic hepatitis C patients. Journal of Virological Methods, v.220, p.1-4, Aug. 2015.
dc.identifier.uri.fl_str_mv https://www.arca.fiocruz.br/handle/icict/12054
dc.identifier.issn.none.fl_str_mv 0166-0934
dc.identifier.doi.none.fl_str_mv 10.1016/j.jviromet.2015.04.001
identifier_str_mv DELVAUX, Nathália; et al. Comparison of four methods of genotyping IL28B polymorphisms in chronic hepatitis C patients. Journal of Virological Methods, v.220, p.1-4, Aug. 2015.
0166-0934
10.1016/j.jviromet.2015.04.001
url https://www.arca.fiocruz.br/handle/icict/12054
dc.language.iso.fl_str_mv eng
language eng
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
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dc.publisher.none.fl_str_mv Elsevier
publisher.none.fl_str_mv Elsevier
dc.source.none.fl_str_mv reponame:Repositório Institucional da FIOCRUZ (ARCA)
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