title: Development and evaluation of a liquid bead microarray assay for genotyping genital human papillomaviruses.
abstract: We developed a liquid bead microarray (LBMA) assay for genotyping genital human papillomaviruses (HPVs) based on the MY09-MY11-HMB01 PCR system and the reverse line blot (RLB) assay probe sequences. Using individual HPV plasmids, we were able to detect as few as 50 copies per reaction. In two separate retrospective studies, the LBMA assay was compared to the RLB assay and to the Hybrid Capture II (hc2) assay. Testing was performed without knowledge of other assay results. In the first study, 614 cervical swab samples (enriched for HPV infection) from 160 young women were tested for HPV DNA, and 360 (74.8%) type-specific HPV infections were detected by both assays, 71 (14.8%) by the LBMA assay only, and 50 (10.4%) by the RLB assay only. Type-specific agreement for the two assays was excellent (99.1%; kappa=0.85; 95% confidence interval [95% CI], 0.82 to 0.88). Samples with discrepant LBMA and RLB test results tended to have low viral loads by a quantitative type-specific PCR assay. In the second study, cervical swab samples from 452 women (including 54 women with histologically confirmed cervical-intraepithelial neoplasia grade 2 or worse [>or= CIN2]) were tested initially by the hc2 and subsequently by the LBMA assay. The estimated sensitivities for >or= CIN2 were similar for the LBMA and hc2 assays (98.4% [95% CI, 95.0 to 100%] and 95.6% [95% CI, 89.2 to 100%], respectively). The percentages of negative results among 398 women without >or= CIN2 were similar for the LBMA and hc2 assays (45% and 50%, respectively). The repeat test reproducibility for 100 samples was 99.1% (kappa=0.92; 95% CI, 0.90 to 0.95). We conclude that the new LBMA assay will be useful for clinical and epidemiological research.
authors.affiliation: Department of Pathology, University of Washington, School of Public Health and Community Medicine, Seattle, Washington 98109, USA. qf@u.washington.edu
authors.forename: Qinghua
authors.initials: Q
authors.lastname: Feng
authors.forename: Stephen
authors.initials: S
authors.lastname: Cherne
authors.forename: Rachel L
authors.initials: RL
authors.lastname: Winer
authors.forename: Akhila
authors.initials: A
authors.lastname: Balasubramanian
authors.forename: Shu-Kuang
authors.initials: SK
authors.lastname: Lee
authors.forename: Stephen E
authors.initials: SE
authors.lastname: Hawes
authors.forename: Nancy B
authors.initials: NB
authors.lastname: Kiviat
authors.forename: Laura A
authors.initials: LA
authors.lastname: Koutsky
mesh_terms: D000293:Adolescent; D000328:Adult; D002584:Cervix Uteri / Q000821:virology; D004279:DNA, Viral / Q000235:genetics; D005260:Female; D005838:Genotype; D006801:Humans; D046228:Microarray Analysis / Q000379:methods*; D008863:Microspheres; D009693:Nucleic Acid Hybridization / Q000379:methods; D027383:Papillomaviridae / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D030361:Papillomavirus Infections / Q000175:diagnosis* / Q000821:virology*; D016133:Polymerase Chain Reaction / Q000379:methods; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D055815:Young Adult
chemical_list: D004279:DNA, Viral