Comparison of DNA sequencing and Roche Linear array (R) in human papillomavirus (HPV) genotyping

Background: Human papillomavirus (HPV) is the etiological agent of cervical cancer. HPV genotyping is important to determine the presence of high-risk types. Recently, a new HPV genotyping method, the Roche Linear array (R) genotyping test, was introduced and is compared here with a sequencing-based HPV genotyping system. Materials and Methods: A series of 102 women (age range 30-55 years) shown to be HPV DNA-positive by PCR were typed by sequencing and the Linear at-ray genotyping assay. Results: The sequence analysis revealed the presence of 80 single high-risk types and 22 single low-fisk types. With the Linear array, single infections were found in 46 cases, double infections in 37 cases, triple infections in 12 cases, and more than three in 6 cases. One case positive by sequencing gave a negative result by Linear array. Altogether, a concordant single genotype was found in 93 (91.2%) out of the 102 cases and the single-type concordance between the two assays was significant (Spearman rho=0.849, p=0.0001; intraclass correlation coefficient (ICC) (ICC=0.924, 95%CI 0.888-0.949) (p=0.0001). The majority of the disparate results were due to the detection of multiple types by the Linear array. Conclusion: The Roche Linear array (R) is a highly accurate assay for HPV genotyping. This is particularly true in the presence of multiple infections which DNA sequencing is unable to resolve.