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The causative role of HPV infection in a wide range of diseases is well established, highlighting the importance of accurate HPV genotyping techniques applicable to various tissue types and conservation methods. This study compared the performance of the automated INNO-LiPA HPV Genotyping Extra II and the manual Linear Array HPV genotyping assays in diagnostically relevant specimens. Samples with discrepant results were also tested with Anyplex II HPV28 detection assay. DNA from 120 samples, primarily from anogenital and head-neck FFPE tissues and cervical cytology specimens, were analysed. Interclass correlation efficiencies between the assays and percentage and kappa agreements for individual genotypes were calculated. Overall, a high agreement was found between the two genotyping methods (>0.95), however, INNO-LiPA was more likely to identify genotypes in samples indicating low viral load and/or originating from FFPE tissues. Specifically, INNO-LiPA detected more genotypes in FFPE material harbouring multiple HPV infections; in particular HPV51 and 52 were the most affected high-risk genotypes. In contrast, Linear Array identified more low-risk HPV54 infections in both cytology and FFPE specimens. The discrepant genotypes detected by Anyplex resembled more the results of Linear Array than that of INNO-LiPA. We conclude that the assays are highly comparable, but differences may arise in a context dependent manner.

A comparison of the Linear Array and the Automated INNO-LiPA HPV Genotyping Systems on Pathological Specimens