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J Clin Virol. 2016 Jul;80:36-9. doi: 10.1016/j.jcv.2016.04.016. Epub 2016 Apr 27.

Validation of a standardized extraction method for formalin-fixed paraffin-embedded tissue samples.

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Department of Laboratory Medicine, Karolinska Institutet, F56 Huddinge, 14188 Stockholm, Sweden.
Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
Department of Laboratory Medicine, Karolinska Institutet, F56 Huddinge, 14188 Stockholm, Sweden; Medical Epidemiology & Biostatistics, Karolinska Institutet, SE-17177 Stockholm, Sweden. Electronic address:



Formalin-fixed paraffin-embedded (FFPE) samples can be DNA-extracted and used for human papillomavirus (HPV) genotyping. The xylene-based gold standard for extracting FFPE samples is laborious, suboptimal and involves health hazards for the personnel involved.


To compare extraction with the standard xylene method to a xylene-free method used in an HPV LabNet Global Reference Laboratory at the Centers for Disease Control (CDC); based on a commercial method with an extra heating step.


Fifty FFPE samples were randomly selected from a national audit of all cervical cancer cases diagnosed in Sweden during 10 years. For each case-block, a blank-block was sectioned, as a control for contamination. For xylene extraction, the standard WHO Laboratory Manual protocol was used. For the CDC method, the manufacturers' protocol was followed except for an extra heating step, 120°C for 20min. Samples were extracted and tested in parallel with β-globin real-time PCR, HPV16 real-time PCR and HPV typing using modified general primers (MGP)-PCR and Luminex assays.


For a valid result the blank-block had to be betaglobin-negative in all tests and the case-block positive for beta-globin. Overall, detection was improved with the heating method and the amount of HPV-positive samples increased from 70% to 86% (p=0.039). For all samples where HPV type concordance could be evaluated, there was 100% type concordance.


A xylene-free and robust extraction method for HPV-DNA typing in FFPE material is currently in great demand. Our proposed standardized protocol appears to be generally useful.


DNA-extraction; Formalin-Fixed paraffin-Embedded (FFPE); Genotyping; Human papillomavirus (HPV); Xylene

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