title: 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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.
authors.forename: Skevi
authors.initials: S
authors.lastname: Kyriakou
authors.forename: Elena
authors.initials: E
authors.lastname: Kypri
authors.forename: Christiana
authors.initials: C
authors.lastname: Spyrou
authors.forename: Evdokia
authors.initials: E
authors.lastname: Tsaliki
authors.forename: Voula
authors.initials: V
authors.lastname: Velissariou
authors.forename: Elisavet A
authors.initials: EA
authors.lastname: Papageorgiou
authors.forename: Philippos C
authors.initials: PC
authors.lastname: Patsalis
mesh_terms: D004247:DNA / Q000097:blood*; D019175:DNA Methylation; D004314:Down Syndrome / Q000175:diagnosis* / Q000235:genetics; D005260:Female; D005333:Fetus / Q000737:chemistry; D005820:Genetic Testing / Q000379:methods*; D006801:Humans; D047468:Immunoprecipitation; D008297:Male; D011247:Pregnancy; D011296:Prenatal Diagnosis / Q000379:methods*; D060888:Real-Time Polymerase Chain Reaction / Q000379:methods*; D055544:beta-Globins / Q000032:analysis
chemical_list: D055544:beta-Globins; D004247:DNA