Variability of ffDNA in maternal plasma does not prevent correct classification of trisomy 21 using MeDIP-qPCR methodology

ABSTRACT Objective The goal of this study is to evaluate the amount of free fetal DNA (ffDNA), total DNA, and ‘fetal fraction’ found in maternal plasma and whether these influence the enrichment ratios of differentially methylated regions (DMRs) and the correct classification of trisomy 21 using the methylated DNA immunoprecipitation‐quantitative polymerase chain reaction (MeDIP‐qPCR)‐based noninvasive prenatal diagnostic methodology applied in peripheral blood. Methods Absolute quantification of ffDNA using DYS14 and total DNA using β ‐globin was applied in 83 maternal plasma samples. The quantification values for all 83 samples were correlated with the enrichment ratios of all seven DMRs and D‐values that were obtained from the diagnostic formula of MeDIP‐qPCR method. Results Our analysis concluded that trisomy 21 samples had significantly higher ffDNA and total DNA levels compared with those of normal samples. Enrichment ratios of the majority of DMRs studied exhibited no association with ffDNA, total DNA, and ‘fetal fraction’, and only a small portion of DMRs exhibited moderate association. Correlation studies of ffDNA, total DNA, and fetal fraction with the diagnostic D‐value showed weak to no association but without affecting the classification of trisomy 21. Conclusion Overall, the variability of ffDNA and total DNA among maternal samples does not affect the correct trisomy 21 classification using MeDIP‐qPCR methodology applied in peripheral blood. © 2013 John Wiley & Sons, Ltd.