Cross comparison of AmpFire HPV genotyping assay and Roche human papillomavirus (HPV) linear array for HPV genotyping of anal swab samples.

Abstract Although anal cancers represent just 0.5% of all new cancer cases in U.S., rates have increased markedly, with highest rates in HIV-infected MSM. American Cancer Society estimates there will be ∼9,090 new cases and ∼1,420 deaths in 2021. We compared Roche Linear Array HPV Genotyping (Roche) and AmpFire HPV Genotyping (AmpFire) assays for concordance and agreement to detect 15 HR-HPV types from 151 anal specimens. Within run precision of AmpFire was assessed on 50 anal specimens. Specimens with Roche Combo-positive and HPV33, HPV35 and/or HPV58-positive results were further tested using HPV52-specific TaqMan assay. AmpFire generated valid results on 149/151 (98.7%) specimens; 135/149 (90.6%) and 134/149 (89.9%) had detectable HR-HPV DNA by AmpFire or Roche, respectively. Overall concordance was 89.8% (2007/2235, κ = 0.65). HPV16 showed highest overall concordance at 93.3% (139/149, κ = 0.84). HPV68 had lowest overall concordance at 77.2% (115/149, κ = 0.28). Kappa values were interpreted as being moderate or good for all other HR-HPV types. Within run precision generated 744/750 concordant results; R2 value = 0.97 (p