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Comparative evaluation of different DNA extraction methods for HPV genotyping by linear array and INNO‐LiPA
Author(s) -
Donà Maria Gabriella,
Benevolo Maria,
Pimpinelli Fulvia,
Battista Mara,
Rollo Francesca,
Stivali Francesca,
Moscarelli Antonella,
Giuliani Massimo,
Di Carlo Aldo,
Vocaturo Amina
Publication year - 2011
Publication title -
journal of medical virology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.782
H-Index - 121
eISSN - 1096-9071
pISSN - 0146-6615
DOI - 10.1002/jmv.22088
Subject(s) - genotyping , dna extraction , concordance , dna , biology , microbiology and biotechnology , virology , chromatography , genotype , polymerase chain reaction , chemistry , genetics , gene
In order to investigate the influence of DNA extraction on two PCR‐based HPV genotyping tests (Linear Array, Roche and INNO‐LiPA Extra , Innogenetics), three different procedures were used to purify DNA from 28 cervico‐vaginal samples tested previously by the Hybrid Capture 2: the AmpliLute Liquid Media Extraction kit (Roche), the QIAamp DNA Blood mini kit (QIAGEN), and the NucliSENS EasyMAG automated platform (bioMérieux). All HC2‐positive samples were found positive by both assays, independently of the extract used. Type‐specific concordance (i.e., identical HPV type‐specific profile in all the extracts of the same sample) was observed in 55% and 75% of the cases testing samples by the Linear Array and the INNO‐LiPA, respectively. Using the DNA extracted with the two manual methods the results were concordant in 75% of the cases both for the Linear Array and the INNO‐LiPA. When comparing the Linear Array results obtained on either of the two manual extracts with those obtained following automated extraction, 65% of the samples showed type‐specific concordance in both cases. The INNO‐LiPA results were concordant in 80% of the cases comparing the AmpliLute versus the automated extract, while concordant results were observed in 90% of the cases when comparing the QIAGEN versus the automated extract. In conclusion, the Linear Array and INNO‐LiPA results are affected by the method of DNA extraction. Consequently, different HPV type‐specific profiles may be observed using different extracts of the same sample. The use of consistent protocols for DNA purification is a priority to guarantee intra‐assay reproducibility over time. J. Med. Virol. 83:1042–1047, 2011. © 2011 Wiley‐Liss, Inc.