Ann Lab Med 2018; 38(2): 139-146  
Comparison of Four Human Papillomavirus Genotyping Methods: Next-generation Sequencing, INNO-LiPA, Electrochemical DNA Chip, and Nested-PCR
Pornjarim Nilyanimit, M.S.1, Jira Chansaenroj, M.S.1, Witthaya Poomipak, M.S.2, Kesmanee Praianantathavorn, M.S.3, Sunchai Payungporn, Ph.D.3, and Yong Poovorawan, M.D.1
Center of Excellence in Clinical Virology1, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok; Research Affairs2, Faculty of Medicine, Chulalongkorn University, Bangkok; Department of Biochemistry3, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
Correspondence to: Yong Poovorawan
Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
Tel: +66-2256-4909
Fax: +66-2256-4929
E-mail: yong.p@chula.ac.th
Received: March 22, 2017; Revised: June 9, 2017; Accepted: November 2, 2017; Published online: March 1, 2018.
© The Korean Society for Laboratory Medicine. All rights reserved.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Abstract
Background: Human papillomavirus (HPV) infection causes cervical cancer, thus necessitating early detection by screening. Rapid and accurate HPV genotyping is crucial both for the assessment of patients with HPV infection and for surveillance studies.
Methods: Fifty-eight cervicovaginal samples were tested for HPV genotypes using four methods in parallel: nested-PCR followed by conventional sequencing, INNO-LiPA, electrochemical DNA chip, and next-generation sequencing (NGS).
Results: Seven HPV genotypes (16, 18, 31, 33, 45, 56, and 58) were identified by all four methods. Nineteen HPV genotypes were detected by NGS, but not by nested-PCR, INNO-LiPA, or electrochemical DNA chip.
Conclusions: Although NGS is relatively expensive and complex, it may serve as a sensitive HPV genotyping method. Because of its highly sensitive detection of multiple HPV genotypes, NGS may serve as an alternative for diagnostic HPV genotyping in certain situations.
Keywords: Human papillomavirus, Genotyping, Next-generation sequencing, Nested-PCR, INNO-LiPA, Electrochemical DNA chip



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