Detection and Genotyping of Human Papillomaviruses from Archival Formalin-Fixed Tissue Samples

Curr Protoc Microbiol. 2016 Nov 18:43:14B.9.1-14B.9.20. doi: 10.1002/cpmc.16.


Pathology departments routinely process and store formalin-fixed, paraffin-embedded (FFPE) tissue samples for clinical diagnosis. These collections often contain decades' worth of samples and represent a treasure trove of specimens that can be analyzed for retrospective epidemiological studies, diagnostics, and pathogen discovery. Accurate amplification and sequencing of DNA from these samples is critical for the usability of these FFPE samples. Here we present a collection of protocols that describe extraction of DNA from FFPE tissues, PCR amplification of human papillomavirus DNA, and subsequent genotyping of the infecting virus. © 2016 by John Wiley & Sons, Inc.

Keywords: FFPE; HPV; PCR; cancer; cervix; degenerate primers; formalin; neoplasia; papillomavirus; sequencing.

Publication types

  • Research Support, N.I.H., Intramural

MeSH terms

  • Cloning, Molecular / methods*
  • DNA, Viral / genetics
  • Genotype
  • Humans
  • Papillomaviridae / chemistry
  • Papillomaviridae / genetics
  • Papillomaviridae / isolation & purification*
  • Papillomaviridae / physiology
  • Papillomavirus Infections / virology*
  • Polymerase Chain Reaction / methods*
  • Tissue Embedding / methods*
  • Tissue Fixation / methods*


  • DNA, Viral