The Isothermal Amplification AmpFire Assay for Human Papillomavirus (HPV) Detection and Genotyping in Formalin-Fixed, Paraffin-Embedded Oropharyngeal Cancer Samples

J Mol Diagn. 2022 Jan;24(1):79-87. doi: 10.1016/j.jmoldx.2021.10.008. Epub 2021 Nov 18.


Human papillomavirus (HPV)-related oropharyngeal squamous cell carcinomas (OPSCCs) represent a distinct clinical entity compared with HPV-negative tumors with particular regard to treatment response and survival outcome. The aim of this study was to assess the AmpFire Multiplex HR-HPV tests, for the detection and genotyping of 15 high-risk (HR) HPV types in formalin-fixed, paraffin-embedded (FFPE) samples and identify HPV-driven OPSCC. DNA from 160 OPSCC FFPE specimens plus 23 samples from other head and neck primary sites was tested. Results were compared with those obtained using Linear Array HPV-DNA Genotyping Test. Linear Array and AmpFire Multiplex HR-HPV tests showed, for all samples and specifically for OPSCCs, an overall concordance agreement of 98.9% and 99.4% and a Cohen κ coefficient of 0.972 and 0.984, respectively. A concordance of 100% for HPV16 and HPV18 was observed. The overall agreement between p16INK4a overexpression and HPV detection by the AmpFire Multiplex HR-HPV assay in 145 OPSCC samples was 93.8%, with a Cohen κ coefficient of 0.848. The AmpFire HPV Tests are simple assays for detection and genotyping of HPV-DNA in OPSCC FFPE samples and can be easily implemented in the clinical practice setting for HPV-DNA detection.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alphapapillomavirus* / genetics
  • DNA, Viral / genetics
  • Formaldehyde
  • Genotype
  • Head and Neck Neoplasms*
  • Humans
  • Oropharyngeal Neoplasms* / diagnosis
  • Oropharyngeal Neoplasms* / genetics
  • Oropharyngeal Neoplasms* / pathology
  • Papillomaviridae / genetics
  • Papillomavirus Infections* / diagnosis
  • Papillomavirus Infections* / genetics
  • Paraffin Embedding


  • DNA, Viral
  • Formaldehyde