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Article: Machine learning interpretation of extended human papillomavirus genotyping by Onclarity in an Asian cervical cancer screening population
Title | Machine learning interpretation of extended human papillomavirus genotyping by Onclarity in an Asian cervical cancer screening population |
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Authors | |
Keywords | cervical cancer primary screening HPV test Onclarity cobas |
Issue Date | 2019 |
Publisher | American Society for Microbiology. The Journal's web site is located at http://jcm.asm.org/ |
Citation | Journal of Clinical Microbiology, 2019, v. 57 n. 12, article no. e00997-19 How to Cite? |
Abstract | This study aimed (i) to compare the performance of the BD Onclarity human papillomavirus (HPV) assay with the Cobas HPV test in identifying cervical intraepithelial neoplasia 2/3 or above (CIN2/3+) in an Asian screening population and (ii) to explore improving the cervical cancer detection specificity of Onclarity by machine learning. We tested 605 stratified random archived samples of cervical liquid-based cytology samples with both assays. All samples had biopsy diagnosis or repeated negative cytology follow-up. Association rule mining (ARM) was employed to discover coinfection likely to give rise to CIN2/3+. Outcome classifiers interpreting the extended genotyping results of Onclarity were built with different underlying models. The sensitivities (Onclarity, 96.32%; Cobas, 95.71%) and specificities (Onclarity, 46.38%; Cobas, 45.25%) of the high-risk HPV (hrHPV) components of the two tests were not significantly different. When HPV16 and HPV18 were used to further interpret hrHPV-positive cases, Onclarity displayed significantly higher specificity (Onclarity, 87.10%; Cobas, 80.77%). Both hrHPV tests achieved the same sensitivities (Onclarity, 90.91%; Cobas, 90.91%) and similar specificities (Onclarity, 48.46%; Cobas, 51.98%) when used for triaging atypical squamous cells of undetermined significance. Positivity in both HPV16 and HPV33/58 of the Onclarity channels entails the highest probability of developing CIN2/3+. Incorporating other hrHPVs into the outcome classifiers improved the specificity of identifying CIN2/3 to up to 94.32%. The extended genotyping of Onclarity therefore can help to highlight patients having the highest risk of developing CIN2/3+, with the potential to reduce unnecessary colposcopy and negative psychosocial impact on women receiving the reports. |
Persistent Identifier | http://hdl.handle.net/10722/277761 |
ISSN | 2023 Impact Factor: 6.1 2023 SCImago Journal Rankings: 1.653 |
ISI Accession Number ID |
DC Field | Value | Language |
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dc.contributor.author | Wong, OGW | - |
dc.contributor.author | Ng, IFY | - |
dc.contributor.author | Tsun, OKL | - |
dc.contributor.author | Pang, HH | - |
dc.contributor.author | Ip, PPC | - |
dc.contributor.author | Cheung, ANY | - |
dc.date.accessioned | 2019-10-04T08:00:49Z | - |
dc.date.available | 2019-10-04T08:00:49Z | - |
dc.date.issued | 2019 | - |
dc.identifier.citation | Journal of Clinical Microbiology, 2019, v. 57 n. 12, article no. e00997-19 | - |
dc.identifier.issn | 0095-1137 | - |
dc.identifier.uri | http://hdl.handle.net/10722/277761 | - |
dc.description.abstract | This study aimed (i) to compare the performance of the BD Onclarity human papillomavirus (HPV) assay with the Cobas HPV test in identifying cervical intraepithelial neoplasia 2/3 or above (CIN2/3+) in an Asian screening population and (ii) to explore improving the cervical cancer detection specificity of Onclarity by machine learning. We tested 605 stratified random archived samples of cervical liquid-based cytology samples with both assays. All samples had biopsy diagnosis or repeated negative cytology follow-up. Association rule mining (ARM) was employed to discover coinfection likely to give rise to CIN2/3+. Outcome classifiers interpreting the extended genotyping results of Onclarity were built with different underlying models. The sensitivities (Onclarity, 96.32%; Cobas, 95.71%) and specificities (Onclarity, 46.38%; Cobas, 45.25%) of the high-risk HPV (hrHPV) components of the two tests were not significantly different. When HPV16 and HPV18 were used to further interpret hrHPV-positive cases, Onclarity displayed significantly higher specificity (Onclarity, 87.10%; Cobas, 80.77%). Both hrHPV tests achieved the same sensitivities (Onclarity, 90.91%; Cobas, 90.91%) and similar specificities (Onclarity, 48.46%; Cobas, 51.98%) when used for triaging atypical squamous cells of undetermined significance. Positivity in both HPV16 and HPV33/58 of the Onclarity channels entails the highest probability of developing CIN2/3+. Incorporating other hrHPVs into the outcome classifiers improved the specificity of identifying CIN2/3 to up to 94.32%. The extended genotyping of Onclarity therefore can help to highlight patients having the highest risk of developing CIN2/3+, with the potential to reduce unnecessary colposcopy and negative psychosocial impact on women receiving the reports. | - |
dc.language | eng | - |
dc.publisher | American Society for Microbiology. The Journal's web site is located at http://jcm.asm.org/ | - |
dc.relation.ispartof | Journal of Clinical Microbiology | - |
dc.rights | Journal of Clinical Microbiology. Copyright © American Society for Microbiology. | - |
dc.subject | cervical cancer | - |
dc.subject | primary screening | - |
dc.subject | HPV test | - |
dc.subject | Onclarity | - |
dc.subject | cobas | - |
dc.title | Machine learning interpretation of extended human papillomavirus genotyping by Onclarity in an Asian cervical cancer screening population | - |
dc.type | Article | - |
dc.identifier.email | Wong, OGW: wonggw@hkucc.hku.hk | - |
dc.identifier.email | Ng, IFY: idy999@hku.hk | - |
dc.identifier.email | Tsun, OKL: okltsun@hku.hk | - |
dc.identifier.email | Pang, HH: herbpang@hku.hk | - |
dc.identifier.email | Ip, PPC: philipip@hku.hk | - |
dc.identifier.email | Cheung, ANY: anycheun@hkucc.hku.hk | - |
dc.identifier.authority | Pang, HH=rp01857 | - |
dc.identifier.authority | Ip, PPC=rp01890 | - |
dc.identifier.authority | Cheung, ANY=rp00542 | - |
dc.description.nature | link_to_OA_fulltext | - |
dc.identifier.doi | 10.1128/JCM.00997-19 | - |
dc.identifier.scopus | eid_2-s2.0-85075738120 | - |
dc.identifier.hkuros | 306285 | - |
dc.identifier.volume | 57 | - |
dc.identifier.issue | 12 | - |
dc.identifier.spage | article no. e00997-19 | - |
dc.identifier.epage | article no. e00997-19 | - |
dc.identifier.isi | WOS:000504866600005 | - |
dc.publisher.place | United States | - |
dc.identifier.issnl | 0095-1137 | - |