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Bead-Based Multiplex Genotyping of 58 Cutaneous Human Papillomavirus Types

Michael, K. M.; Forslund, Ola LU ; Bacevskij, O.; Waterboer, T.; Bravo, I. G.; Pawlita, M. and Schmitt, M. (2011) In Journal of Clinical Microbiology 49(10). p.3560-3567
Abstract
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... (More)
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. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Journal of Clinical Microbiology
volume
49
issue
10
pages
3560 - 3567
publisher
American Society for Microbiology
external identifiers
  • wos:000295360700019
  • scopus:80053502784
ISSN
1098-660X
DOI
10.1128/JCM.01173-11
language
English
LU publication?
yes
id
6a853dee-63ae-4f3c-a2d8-37c892424a7c (old id 2212724)
date added to LUP
2011-12-01 08:34:00
date last changed
2017-08-27 04:36:52
@article{6a853dee-63ae-4f3c-a2d8-37c892424a7c,
  abstract     = {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 &lt;= 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.},
  author       = {Michael, K. M. and Forslund, Ola and Bacevskij, O. and Waterboer, T. and Bravo, I. G. and Pawlita, M. and Schmitt, M.},
  issn         = {1098-660X},
  language     = {eng},
  number       = {10},
  pages        = {3560--3567},
  publisher    = {American Society for Microbiology},
  series       = {Journal of Clinical Microbiology},
  title        = {Bead-Based Multiplex Genotyping of 58 Cutaneous Human Papillomavirus Types},
  url          = {http://dx.doi.org/10.1128/JCM.01173-11},
  volume       = {49},
  year         = {2011},
}