title: HPV Genotyping from the high risk mRNA Aptima assay- a direct approach using DNA from Aptima sample tubes.
abstract: The underlying cause of cervical cancer is an infection with the human papilloma virus (HPV) and HPV testing can be used for cervical cancer screening. The Aptima HPV assay from Hologic is an mRNA HPV test used to identify clinically relevant infections but the method does not discriminate between the different high risk genotypes. The aim of the current study was to evaluate if analyzed Aptima sample transfer tubes could be used as a source for HPV genotyping, using sample DNA. Study samples (n=108); were HPV-tested with mRNA Aptima assay and in parallel DNA was extracted and genotyped with Anyplex II HPV28. Analyzed mRNA Aptima tubes were thereafter used as source for a second DNA extraction and genotyping. Using mRNA Aptima result as reference, 90% of the samples (35/39) were high risk positive with the Anyplex II HPV28. Cohen's kappa 0.78 (95% CI: 0.66-0.90), sensitivity 0.90 (95% CI: 0.76-0.97) and specificity 0.90 (95% CI: 0.80-0.96). Two discordant samples carried low-risk genotypes (HPV 82 and HPV 44) and two were negative. DNA-genotyping results, in parallel to and after mRNA testing, were compared and differed significantly (McNemar test: P=0.021) possibly due to sample extraction volume difference. Cohen's kappa 0.81 (95% CI: 0.70-0.92), sensitivity 0.85 (95% CI: 0.74-0.93) and specificity 0.98 (95% CI: 0.88-1.00). In conclusion, analyzed mRNA Aptima sample tubes could be used as a source for DNA HPV genotyping. The sample volume used for extraction needs to be further explored.
authors.affiliation: Dept. of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, SE- 701 82 Örebro, Sweden. Electronic address: gabriella.lillsunde-larsson@regionorebrolan.se.
authors.forename: G
authors.initials: G
authors.lastname: Lillsunde Larsson
authors.affiliation: Dept. of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, SE- 701 82 Örebro, Sweden.
authors.forename: M
authors.initials: M
authors.lastname: Kaliff
authors.affiliation: Dept. of Women's health, Faculty of Medicine and Health, Örebro University, SE-701 82 Örebro, Sweden.
authors.forename: L
authors.initials: L
authors.lastname: Bergengren
authors.affiliation: Dept. of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, SE- 701 82 Örebro, Sweden.
authors.forename: M G
authors.initials: MG
authors.lastname: Karlsson
authors.affiliation: Dept. of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, SE- 701 82 Örebro, Sweden.
authors.forename: G
authors.initials: G
authors.lastname: Helenius
mesh_terms: D004279:DNA, Viral / Q000235:genetics; D055088:Early Detection of Cancer / Q000379:methods; D005260:Female; D005838:Genotype; D061809:Human Papillomavirus DNA Tests / Q000379:methods*; D006801:Humans; D025202:Molecular Diagnostic Techniques; D027383:Papillomaviridae / Q000235:genetics*; D030361:Papillomavirus Infections / Q000175:diagnosis* / Q000821:virology; D012333:RNA, Messenger / Q000235:genetics* / Q000302:isolation & purification; D012367:RNA, Viral / Q000235:genetics; D012680:Sensitivity and Specificity; D002583:Uterine Cervical Neoplasms / Q000175:diagnosis / Q000821:virology; D002578:Uterine Cervical Dysplasia / Q000175:diagnosis / Q000821:virology
chemical_list: D004279:DNA, Viral; D012333:RNA, Messenger; D012367:RNA, Viral
keywords: DNA-testing; Genotype; HPV; mRNA testing