title: Detection of alpha human papillomaviruses in archival formalin-fixed, paraffin-embedded (FFPE) tissue specimens.
abstract: Formalin-fixed, paraffin-embedded (FFPE) tissue specimens stored in pathology departments worldwide are an invaluable source for diagnostic purposes when fresh clinical material is unavailable as well as for retrospective molecular and epidemiological studies, especially when dealing with rare clinical conditions for which prospective collection is not feasible. Accurate detection of HPV infection in these specimens is particularly challenging because nucleic acids are often degraded and therefore, not suitable for amplification of larger fragments of the viral genome or viral gene transcripts. This review provides a brief summary of molecular methods for detecting alpha-HPV DNA/RNA in FFPE tissue specimens. We specifically address the key procedural and environmental factors that have the greatest impact on the quality of nucleic acids extracted from FFPE tissue specimens, and describe some solutions that can be used to increase their integrity and/or amplifiability. Moreover, commonly used methods for HPV DNA/RNA detection in FFPE tissue specimens are presented and discussed, focusing on studies using polymerase chain reaction as an HPV detection method and published after 1999. Finally, we briefly summarize our 22 years of experience with HPV detection in FFPE tissue specimens.
authors.affiliation: Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia.
authors.forename: Boštjan J
authors.initials: BJ
authors.lastname: Kocjan
authors.affiliation: Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia.
authors.forename: Lea
authors.initials: L
authors.lastname: Hošnjak
authors.affiliation: Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia; European Society of Clinical Microbiology and Infectious Diseases (ESCMID), Study Group for Forensic and Postmortem Microbiology (ESGFOR), Basel, Switzerland. Electronic address: mario.poljak@mf.uni-lj.si.
authors.forename: Mario
authors.initials: M
authors.lastname: Poljak
mesh_terms: D052685:Alphapapillomavirus / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D004279:DNA, Viral / Q000235:genetics / Q000302:isolation & purification*; D005260:Female; D005404:Fixatives / Q000737:chemistry; D005557:Formaldehyde / Q000737:chemistry; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D061809:Human Papillomavirus DNA Tests; D006801:Humans; D030361:Papillomavirus Infections / Q000150:complications / Q000175:diagnosis* / Q000821:virology; D016612:Paraffin Embedding / Q000379:methods; D016133:Polymerase Chain Reaction / Q000379:methods; D012367:RNA, Viral / Q000235:genetics / Q000302:isolation & purification*; D016707:Tissue Fixation / Q000379:methods; D002583:Uterine Cervical Neoplasms / Q000150:complications / Q000175:diagnosis* / Q000821:virology; D002578:Uterine Cervical Dysplasia / Q000150:complications / Q000175:diagnosis* / Q000821:virology
chemical_list: D004279:DNA, Viral; D005404:Fixatives; D012367:RNA, Viral; D005557:Formaldehyde
keywords: Achival tissues specimens; FFPE; Formalin fixed; HPV; Human papillomaviruses; Paraffin-embedded tissue