Comparison of human papillomavirus detection and typing by cycle sequencing, line blotting, and hybrid capture

We compared the results of human papillomavirus (HPV) detection and typing from 781 cervical samples assayed by three methods: LI consensus PCR follow ed by cycle sequencing, LI consensus PCR with biotinylated primers followed by hybridization to a Line blot, and Hybrid Capture assay. Both PCR assays used L1 consensus PCR with primers MY09 and MY11. We evaluated the amplifi cation efficiencies of both PCR assays and also compared the specific HPV t ypes detected by each method. The samples positive by the Hybrid Capture as say were compared to the specific types detected by the PCR-based assays. T he concordance between the tno PCR assays in producing an HPV amplicon visi ble by gel electrophoresis or in detecting any HPV type was moderate: kappa values were 0.61 (95% confidence interval [CI] = 0.56 to 0.67) and 0.51 (9 5% CI = 0.46 to 0.58), respectively. The McNemar test for correlated propor tions indicated that biotinylated PCR,vas less likely to produce a band (P = 0.001) and to detect an HPV type (P = 0.001) than the other PCR assay. In comparing the Hybrid Capture assay results with the HPV types detected by the PCR based assays, we found that positivity by the Hybrid Capture assay for a number of samples may be due to cross-hybridization with HPV types no t included in the Hybrid Capture assay probe cocktails.