Genotyping of high-risk anal human papillomavirus (HPV): ion torrent-next generation sequencing vs. linear array

BACKGROUND: Our next generation sequencing (NGS)-based human papillomavirus (HPV) genotyping assay showed a high degree of concordance with the Roche Linear Array (LA) with as little as 1.25 ng formalin-fixed paraffin-embedded-derived genomic DNA in head and neck and cervical cancer samples. This se...

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Publicado no:Virol J
Main Authors: Nowak, Rebecca G., Ambulos, Nicholas P., Schumaker, Lisa M., Mathias, Trevor J., White, Ruth A., Troyer, Jennifer, Wells, David, Charurat, Manhattan E., Bentzen, Søren M., Cullen, Kevin J.
Formato: Artigo
Idioma:Inglês
Publicado em: BioMed Central 2017
Assuntos:
Short Report
Acesso em linha:https://ncbi.nlm.nih.gov/pmc/articles/PMC5470268/
https://ncbi.nlm.nih.gov/pubmed/28610586
https://ncbi.nlm.nih.govhttp://dx.doi.org/10.1186/s12985-017-0771-z
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spelling pubmed-54702682017-06-19 Genotyping of high-risk anal human papillomavirus (HPV): ion torrent-next generation sequencing vs. linear array Nowak, Rebecca G. Ambulos, Nicholas P. Schumaker, Lisa M. Mathias, Trevor J. White, Ruth A. Troyer, Jennifer Wells, David Charurat, Manhattan E. Bentzen, Søren M. Cullen, Kevin J. Virol J Short Report BACKGROUND: Our next generation sequencing (NGS)-based human papillomavirus (HPV) genotyping assay showed a high degree of concordance with the Roche Linear Array (LA) with as little as 1.25 ng formalin-fixed paraffin-embedded-derived genomic DNA in head and neck and cervical cancer samples. This sensitive genotyping assay uses barcoded HPV PCR broad-spectrum general primers 5+/6+ (BSGP)5+/6+ applicable to population studies, but it’s diagnostic performance has not been tested in cases with multiple concurrent HPV infections. METHODS: We conducted a cross-sectional study to compare the positive and negative predictive value (PPV and NPV), sensitivity and specificity of the NGS assay to detect HPV genotype infections as compared to the LA. DNA was previously extracted from ten anal swab samples from men who have sex with men in Nigeria enrolled on the TRUST/RV368 cohort study. Two-sample tests of proportions were used to examine differences in the diagnostic performance of the NGS assay to detect high vs. low-risk HPV type-specific infections. RESULTS: In total there were 94 type-specific infections detected in 10 samples with a median of 9.5, range (9 to 10) per sample. Using the LA as the gold standard, 84.4% (95% CI: 75.2–91.2) of the same anal type-specific infections detected on the NGS assay had been detected by LA. The PPV and sensitivity differed significantly for high risk (PPV: 90%, 95% CI: 79.5–96.2; sensitivity: 93.1%, 95% CI: 83.3–98.1) as compared to low risk HPV (PPV: 73%, 95% CI: 54.1–87.7; sensitivity: 61.1, 95% CI: 43.5–76.9) (all p < 0.05). The NPV for all types was 92.5% (95% CI: 88.4–95.4). The NPV and specificity were similar for high and low risk HPVs (all p > 0.05). The NGS assay detected 10 HPV genotypes that were not among the 37 genotypes found on LA (30, 32, 43, 44, 74, 86, 87, 90, 91, 114). CONCLUSIONS: The NGS assay accurately detects multiple HPV infections in individual clinical specimens with limited sample volume and has extended coverage compared to LA. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12985-017-0771-z) contains supplementary material, which is available to authorized users. BioMed Central 2017-06-13 /pmc/articles/PMC5470268/ /pubmed/28610586 http://dx.doi.org/10.1186/s12985-017-0771-z Text en © The Author(s). 2017 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
institution US NLM
collection PubMed Central
language Inglês
format Artigo
topic Short Report
spellingShingle Short Report
Nowak, Rebecca G.
Ambulos, Nicholas P.
Schumaker, Lisa M.
Mathias, Trevor J.
White, Ruth A.
Troyer, Jennifer
Wells, David
Charurat, Manhattan E.
Bentzen, Søren M.
Cullen, Kevin J.
Genotyping of high-risk anal human papillomavirus (HPV): ion torrent-next generation sequencing vs. linear array
description BACKGROUND: Our next generation sequencing (NGS)-based human papillomavirus (HPV) genotyping assay showed a high degree of concordance with the Roche Linear Array (LA) with as little as 1.25 ng formalin-fixed paraffin-embedded-derived genomic DNA in head and neck and cervical cancer samples. This sensitive genotyping assay uses barcoded HPV PCR broad-spectrum general primers 5+/6+ (BSGP)5+/6+ applicable to population studies, but it’s diagnostic performance has not been tested in cases with multiple concurrent HPV infections. METHODS: We conducted a cross-sectional study to compare the positive and negative predictive value (PPV and NPV), sensitivity and specificity of the NGS assay to detect HPV genotype infections as compared to the LA. DNA was previously extracted from ten anal swab samples from men who have sex with men in Nigeria enrolled on the TRUST/RV368 cohort study. Two-sample tests of proportions were used to examine differences in the diagnostic performance of the NGS assay to detect high vs. low-risk HPV type-specific infections. RESULTS: In total there were 94 type-specific infections detected in 10 samples with a median of 9.5, range (9 to 10) per sample. Using the LA as the gold standard, 84.4% (95% CI: 75.2–91.2) of the same anal type-specific infections detected on the NGS assay had been detected by LA. The PPV and sensitivity differed significantly for high risk (PPV: 90%, 95% CI: 79.5–96.2; sensitivity: 93.1%, 95% CI: 83.3–98.1) as compared to low risk HPV (PPV: 73%, 95% CI: 54.1–87.7; sensitivity: 61.1, 95% CI: 43.5–76.9) (all p < 0.05). The NPV for all types was 92.5% (95% CI: 88.4–95.4). The NPV and specificity were similar for high and low risk HPVs (all p > 0.05). The NGS assay detected 10 HPV genotypes that were not among the 37 genotypes found on LA (30, 32, 43, 44, 74, 86, 87, 90, 91, 114). CONCLUSIONS: The NGS assay accurately detects multiple HPV infections in individual clinical specimens with limited sample volume and has extended coverage compared to LA. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12985-017-0771-z) contains supplementary material, which is available to authorized users.
author Nowak, Rebecca G.
Ambulos, Nicholas P.
Schumaker, Lisa M.
Mathias, Trevor J.
White, Ruth A.
Troyer, Jennifer
Wells, David
Charurat, Manhattan E.
Bentzen, Søren M.
Cullen, Kevin J.
author_facet Nowak, Rebecca G.
Ambulos, Nicholas P.
Schumaker, Lisa M.
Mathias, Trevor J.
White, Ruth A.
Troyer, Jennifer
Wells, David
Charurat, Manhattan E.
Bentzen, Søren M.
Cullen, Kevin J.
author_sort Nowak, Rebecca G.
title Genotyping of high-risk anal human papillomavirus (HPV): ion torrent-next generation sequencing vs. linear array
title_short Genotyping of high-risk anal human papillomavirus (HPV): ion torrent-next generation sequencing vs. linear array
title_full Genotyping of high-risk anal human papillomavirus (HPV): ion torrent-next generation sequencing vs. linear array
title_fullStr Genotyping of high-risk anal human papillomavirus (HPV): ion torrent-next generation sequencing vs. linear array
title_full_unstemmed Genotyping of high-risk anal human papillomavirus (HPV): ion torrent-next generation sequencing vs. linear array
title_sort genotyping of high-risk anal human papillomavirus (hpv): ion torrent-next generation sequencing vs. linear array
publisher BioMed Central
container_title Virol J
publishDate 2017
url https://ncbi.nlm.nih.gov/pmc/articles/PMC5470268/
https://ncbi.nlm.nih.gov/pubmed/28610586
https://ncbi.nlm.nih.govhttp://dx.doi.org/10.1186/s12985-017-0771-z
_version_ 1819490652798320640

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