Background: A persistent high-risk HPV infection is a prerequisite to development of cervical cancer. However, among the 14 or so carcinogenic types, there are differences in absolute and attributable risks for cervical pre-cancer and cancer. HPV genotyping may be clinically useful in patient management.

The HPV persistence and progression (PaP) cohort study focuses on a population of screened women from Kaiser Permanente Northern California who have tested HPV positive. Residual specimens collected during routine care are saved for genotype testing.

The development of an integrated sample prep and real-time detection platform, the cobas® 4800 system, provides an opportunity for a streamlined workflow by using processed sample eluates with the HPV Linear Array Test.

Objectives: To evaluate the feasibility of HPV Genotyping using automated cobas® 4800 Sample Preparation and Linear Array detection.

Methods: Aliquots of 462 residual Hybrid Capture 2 specimens were processed using the HPV cobas® 4800. Eluted DNA from the cobas® 4800 is optimized for real-time PCR, necessitating a singly-modified protocol - addition of a solution to the PCR Master Mix for favorable Linear Array amplification conditions. Samples were analyzed with the cobas® 4800 HPV Test and genotyped using HPV Linear Array.

Results: Valid HPV results were obtained for 461 of 462 (99.8%) specimens. Observed agreement between HPV Linear Array® and cobas® 4800 was 97.4% with a Kappa of 0.94. Agreement for channel 1(12 HR HPV), channel 2 (HPV16) and channel 3 (HPV18) was 95.7 % (kappa of 0.91), 99.8 % with (kappa of 0.99) and 99% (kappa of 0.92) respectively. For LA positive samples, the average number of HPV types detected using the x480 was 2.01 for 348 specimens.

Conclusions: These results suggest sample preparation using the HPV cobas® 4800 test platform is suitable for HPV genotyping with the HPV Linear Array for the HPV PaP Cohort Study.