In a routine setting we analyzed DNA from 100 samples of various tissues with the automated procedure using the INNO-LiPA HPV Genotyping Extra II kit (Fujirebio, Malvern, PA, US) and compared the results with the performance of the manual, highly validated HPV genotyping protocol for Linear Array (Roche Diagnostics, Pleasanton, California, US).
Both methods are line probe assays based on PCR amplification of part of the L1 region of the human papillomavirus (HPV) genome. INNO-LiPA HPV Genotyping Extra II employs SPF10 primers and is designed for the identification of 28 different genotypes where the hybridization steps are performed on the Fujiberio automated platform. In contrast, the Linear Array targets 37 genotypes using PGMY09/11 primers and the hybridization steps are highly manual.
Based on our study, the two methods are highly comparable with 80% of the cases exhibiting complete agreement. This agreement was higher for single infections than for multiple infections. Ninety two percent of all samples were at least in partial agreement (concordant or compatible), however this number was higher for cervical (97%), than non-cervical tissues (80%). This discrepancy is best explained by the increased number of failed assays and/or lower sensitivity of the Linear Array compared to the INNO-LiPA method when FFPE samples are genotyped. Better performance of INNO-LiPA on often degraded FFPE samples is a logical outcome of its primer design, since Linear Array requires nearly 7 times longer DNA fragments for potential identification of HPV genotypes, than INNO-LiPA does. Moreover, Linear array was inferior in detecting HPV 52, probably due to its shared probe design.
Overall, the two methods are highly comparable regarding performance of HPV genotyping and although INNO-LiPA kit is more expensive, it requires substantial less hands-on work in addition to being superior in genotyping of low quality DNA often characteristic of FFPE specimens.