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

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 genotyping test, was introduced and is compared here with a sequencing-based HPV genotyping system.

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 array genotyping assay.

The sequence analysis revealed the presence of 80 single high-risk types and 22 single low-risk 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.

The Roche Linear array 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.