Bead-Based Multiplex Genotyping of 58 Cutaneous Human Papillomavirus Types

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Bead-Based Multiplex Genotyping of 58 Cutaneous Human Papillomavirus Types. / Michael, K. M.; Forslund, Ola; Bacevskij, O.; Waterboer, T.; Bravo, I. G.; Pawlita, M.; Schmitt, M.

In: Journal of Clinical Microbiology, Vol. 49, No. 10, 2011, p. 3560-3567.

Research output: Contribution to journalArticle

Harvard

Michael, KM, Forslund, O, Bacevskij, O, Waterboer, T, Bravo, IG, Pawlita, M & Schmitt, M 2011, 'Bead-Based Multiplex Genotyping of 58 Cutaneous Human Papillomavirus Types', Journal of Clinical Microbiology, vol. 49, no. 10, pp. 3560-3567. https://doi.org/10.1128/JCM.01173-11

APA

Michael, K. M., Forslund, O., Bacevskij, O., Waterboer, T., Bravo, I. G., Pawlita, M., & Schmitt, M. (2011). Bead-Based Multiplex Genotyping of 58 Cutaneous Human Papillomavirus Types. Journal of Clinical Microbiology, 49(10), 3560-3567. https://doi.org/10.1128/JCM.01173-11

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MLA

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Author

Michael, K. M. ; Forslund, Ola ; Bacevskij, O. ; Waterboer, T. ; Bravo, I. G. ; Pawlita, M. ; Schmitt, M. / Bead-Based Multiplex Genotyping of 58 Cutaneous Human Papillomavirus Types. In: Journal of Clinical Microbiology. 2011 ; Vol. 49, No. 10. pp. 3560-3567.

RIS

TY - JOUR

T1 - Bead-Based Multiplex Genotyping of 58 Cutaneous Human Papillomavirus Types

AU - Michael, K. M.

AU - Forslund, Ola

AU - Bacevskij, O.

AU - Waterboer, T.

AU - Bravo, I. G.

AU - Pawlita, M.

AU - Schmitt, M.

PY - 2011

Y1 - 2011

N2 - Cutaneous human papillomaviruses (HPVs) are a heterogeneous, nonmonophyletic assembly, comprising about 50 characterized types and at least 133 isolates putatively representing new types. Their natural history of infection and potential association with nonmelanoma skin cancer are not well understood. Several PCR systems have been developed that amplify a broad spectrum of cutaneous HPVs. However, amplicon genotyping by sequencing or reverse line blot assays are complex and not well suited for high-throughput analyses. We developed a novel multiplex cutaneous papillomavirus genotyping (McPG) assay for 38 defined and 20 putative cutaneous HPVs of the beta, gamma, mu, and nu genera. Viral DNA was amplified by the use of a modified single-tube nested "hanging-droplet" FAP PCR. The amplifiable papillomavirus (PV) spectrum was enlarged by the use of 9 outer and 13 inner primers. Biotinylated PCR products were hybridized to type-specific oligonucleotide probes coupled to fluorescence-labeled polystyrene beads and analyzed using Luminex technology. Analytical sensitivity was analyzed for 38 defined HPVs and was <= 100 genome copies for all types. Integrated beta-globin primers allow for simultaneous DNA quality control. McPG is characterized by high reproducibility (kappa = 0.84, 95% confidence interval = 0.79 to 0.88), good concordance with the original nested FAP PCR, followed by sequencing (70.2% complete or partial agreement) when 322 skin biopsy DNA samples were analyzed, and improved ability to detect multiple infections (on average 2.5 HPV types per HPV-positive sample compared to 1.7 HPV types with nested FAP-PCR). In conclusion, McPG is a powerful tool for genotyping multiple cutaneous HPVs in a high-throughput format and is thus suitable for large-scale epidemiological studies.

AB - Cutaneous human papillomaviruses (HPVs) are a heterogeneous, nonmonophyletic assembly, comprising about 50 characterized types and at least 133 isolates putatively representing new types. Their natural history of infection and potential association with nonmelanoma skin cancer are not well understood. Several PCR systems have been developed that amplify a broad spectrum of cutaneous HPVs. However, amplicon genotyping by sequencing or reverse line blot assays are complex and not well suited for high-throughput analyses. We developed a novel multiplex cutaneous papillomavirus genotyping (McPG) assay for 38 defined and 20 putative cutaneous HPVs of the beta, gamma, mu, and nu genera. Viral DNA was amplified by the use of a modified single-tube nested "hanging-droplet" FAP PCR. The amplifiable papillomavirus (PV) spectrum was enlarged by the use of 9 outer and 13 inner primers. Biotinylated PCR products were hybridized to type-specific oligonucleotide probes coupled to fluorescence-labeled polystyrene beads and analyzed using Luminex technology. Analytical sensitivity was analyzed for 38 defined HPVs and was <= 100 genome copies for all types. Integrated beta-globin primers allow for simultaneous DNA quality control. McPG is characterized by high reproducibility (kappa = 0.84, 95% confidence interval = 0.79 to 0.88), good concordance with the original nested FAP PCR, followed by sequencing (70.2% complete or partial agreement) when 322 skin biopsy DNA samples were analyzed, and improved ability to detect multiple infections (on average 2.5 HPV types per HPV-positive sample compared to 1.7 HPV types with nested FAP-PCR). In conclusion, McPG is a powerful tool for genotyping multiple cutaneous HPVs in a high-throughput format and is thus suitable for large-scale epidemiological studies.

U2 - 10.1128/JCM.01173-11

DO - 10.1128/JCM.01173-11

M3 - Article

C2 - 21832015

VL - 49

SP - 3560

EP - 3567

JO - Journal of Clinical Microbiology

JF - Journal of Clinical Microbiology

SN - 1098-660X

IS - 10

ER -