Development and validation of a new HPV genotyping assay based on next-generation sequencing

American Journal of Clinical Pathology

Volumn 141, Issue 6, 2014, Pages 796-804

  Yi, Xin ^a,b   Zou, Jing ^a   Xu, Jiajia ^b   Liu, Tao ^b   Liu, Tengfei ^a   Hua, Sang ^a   Xi, Feng ^a   Nie, Xifang ^b   Ye, Lili ^a   Luo, Yufen ^a   Xu, Lin ^a   Du, Hui ^c   Wu, Ruifang ^c   Yang, Ling ^b   Liu, Ren ^d   Yang, Bin ^e   Wang, Jian ^a   Belinson, Jerome L ^e  

^a BGI SHENZHEN   (China)

^b BGI Tianjin   (China)

^c PEKING UNIVERSITY SHENZHEN HOSPITAL   (China)

^d THE FIRST AFFILIATED HOSPITAL OF SHENZHEN UNIVERSITY   (China)

^e LERNER RESEARCH INSTITUTE   (United States)

Author keywords

Cervical cancer screening; HPV genotyping test; Ion torrent PGM; MiSeq; Next generation sequencing (NGS); Self sampling

Indexed keywords

ARTICLE; FEMALE; GENOTYPE; HPV GENOTYPING ASSAY; HUMAN; HUMAN PAPILLOMAVIRUS DNA TEST; INTERMETHOD COMPARISON; MAJOR CLINICAL STUDY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; MULTIPLEX POLYMERASE CHAIN REACTION; NONHUMAN; NUCLEOTIDE SEQUENCE; POPULATION RESEARCH; PRIORITY JOURNAL; RECEIVER OPERATING CHARACTERISTIC; SENSITIVITY AND SPECIFICITY; UTERINE CERVIX CARCINOMA IN SITU; VALIDATION STUDY; VIRUS CULTURE; WART VIRUS;

CERVICAL CANCER SCREENING; HPV GENOTYPING TEST; ION TORRENT PGM; MISEQ; NEXT-GENERATION SEQUENCING (NGS); SELF-SAMPLING;

ALPHAPAPILLOMAVIRUS; CARCINOMA, SQUAMOUS CELL; CERVICAL INTRAEPITHELIAL NEOPLASIA; DNA, VIRAL; EARLY DETECTION OF CANCER; FEMALE; GENOTYPING TECHNIQUES; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMAN PAPILLOMAVIRUS DNA TESTS; HUMANS; MULTIPLEX POLYMERASE CHAIN REACTION; PAPILLOMAVIRUS INFECTIONS; ROC CURVE; SENSITIVITY AND SPECIFICITY; SPECIMEN HANDLING; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION; UTERINE CERVICAL NEOPLASMS; VAGINAL SMEARS;

EID: 84904467759     PISSN: 00029173     EISSN: 19437722     Source Type: Journal    
DOI: 10.1309/AJCP9P2KJSXEKCJB     Document Type: Article

References (24)

1. International Agency for Research on Cancer. Globocon 2012: Estimated Cancer Incidence, Mortality, and Prevalence Worldwide in 2012. Available at: http://globocan.iarc.fr. Accessed October 30, 2011.
2. Ferlay J, Shin HR, Bray F, et al. Estimates of worldwide burden of cancer in 2008: GLOBOCAN 2008. Int J Cancer. 2010;127:2893-2917.
3. Kjaer SK, van den Brule AJ, Pauli G, et al. Type specific persistence of high risk human papillomavirus (HPV) as indicator of high grade cervical squamous intraepithelial lesions in young women: population based prospective follow up study. BMJ. 2002;325:572.
4. Muñoz N, Bosch FX, de Sanjosé S, et al. Epidemiologic classification of human papillomavirus types associated with cervical cancer. N Engl J Med. 2003;348:518-527. (Pubitemid 36159887)
5. Castle PE, Gravitt PE, Solomon D, et al. Comparison of linear array and line blot assay for detection of human papillomavirus and diagnosis of cervical precancer and cancer in the atypical squamous cell of undetermined significance and low-grade squamous intraepithelial lesion triage study. J Clin Microbiol. 2008;46:109-117.
6. Qiao YL, Sellors JW, Eder PS, et al. A new HPV-DNA test for cervical cancer screening in developing regions: a crosssectional study of clinical accuracy in rural China. Lancet Oncol. 2008;9:929-936.
7. Sankaranarayanan R, Nene BM, Shastri SS, et al. HPV screening for cervical cancer in rural India. N Engl J Med. 2009;360:1385-1394.
8. Ronco G, Giorgi-Rossi P, Carozzi F, et al. Efficacy of human papillomavirus testing for the detection of invasive cervical cancers and cervical intraepithelial neoplasia: a randomized controlled trial. Lancet Oncol. 2010;11:249-257.
9. Zhao FH, Lin MJ, Chen F, et al. Performance of high-risk human papillomavirus DNA testing as a primary screen for cervical cancer: a pooled analysis of individual patient data from 17 population-based studies from China. Lancet Oncol. 2010;11:1160-1171.
10. Belinson JL, Wu R, Belinson SE, et al. Population based clinical trial comparing endocervical high-risk HPV testing using Hybrid Capture II and Cervista from the SHENCCAST II study. Am J Clin Pathol. 2011;135:790-795.
11. Belinson J, Qiao YL, Pretorius R, et al. Shanxi Province Cervical Cancer Screening Study: a cross-sectional comparative trial of multiple techniques to detect cervical neoplasia. Gynecol Oncol. 2011;83:439-444.
12. Belinson JL, Qiao YL, Pretorius RG, et al. Province Cervical Cancer Screening study II: self-sampling for high-risk human papillomavirus compared to direct sampling for HPV and liquid based cervical cytology. Int J Gyn Cancer. 2003;13:1-8.
13. Gravitt PE, Belinson JL, Salmeron J, et al. Looking ahead: a case for HPV testing of self-sampled vaginal specimens as a cervical cancer screening strategy. Int J Cancer. 2011;129:517-527.
14. Belinson JL, Hu S, Niyazi M, et al. Prevalence of type-specific human papillomavirus in endocervical, upper and lower vaginal, perineal, and vaginal self-collected specimens; implications for vaginal self-collection. Int J Gyn Cancer. 2010;127:1151-1157.
15. Belinson JL, Du H, Yang B, et al. Improved sensitivity of vaginal self-collection and high-risk human papillomavirus testing. Int J Cancer. 2012;130:1855-1860.
16. Du H, Yi J, Wu R, et al. A new PCR based mass spectrometry system for high-risk HPV part II: clinical trial. Am J Clin Pathol. 2011;136:920-923.
17. Loman NJ, Misra RV, Dallman TJ, et al. Performance comparison of benchtop high-throughput sequencing platforms. Nat Biotechnol. 2012;30:434-439.
18. Jiang B, Song K, Ren J, et al. Comparison of next-generation sequencing systems. J Biomed Biotechnol. 2012;251364.
19. Quail MA, Smith M, Coupland P, et al. A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics. 2012;13:341.
20. Clavel C, Masure M, Bory JP, et al. Hybrid Capture II-based human papillomavirus detection, a sensitive test to detect in routine high-grade cervical lesions: a preliminary study on 1518 women. Br J Cancer. 1999;80:1306-1311. (Pubitemid 29308597)
21. Yi X, Li JJ, Yu S, et al. A new PCR-based mass spectrometry system for high-risk HPV, part 1: methods. Am J Clin Pathol. 2011;136:913-919.
22. Barzon L, Militello V, Lavezzo E, et al. Human papillomavirus genotyping by 454 next generation sequencing technology. J Clin Virol. 2011;52:93-97.
23. Meiring TL, Salimo AT, Coetzee B, et al. Next-generation sequencing of cervical DNA detects human papillomavirus types not detected by commercial kits. Virol J. 2012;9:164.
24. Castle PE, Solomon D, Wheeler CM, et al. Human papillomavirus genotype specificity of hybrid capture 2. J Clin Microbiol. 2008;46:2595-2604.