title: Systematic identification of placental epigenetic signatures for the noninvasive prenatal detection of Edwards syndrome.
abstract: BACKGROUND
  Noninvasive prenatal diagnosis of fetal aneuploidy by maternal plasma analysis is challenging owing to the low fractional and absolute concentrations of fetal DNA in maternal plasma. Previously, we demonstrated for the first time that fetal DNA in maternal plasma could be specifically targeted by epigenetic (DNA methylation) signatures in the placenta. By comparing one such methylated fetal epigenetic marker located on chromosome 21 with another fetal genetic marker located on a reference chromosome in maternal plasma, we could infer the relative dosage of fetal chromosome 21 and noninvasively detect fetal trisomy 21. Here we apply this epigenetic-genetic (EGG) chromosome dosage approach to detect Edwards syndrome (trisomy 18) in the fetus noninvasively.
  
  
  RESULTS
  We have systematically identified methylated fetal epigenetic markers on chromosome 18 by methylated DNA immunoprecipitation (MeDIP) and tiling array analysis with confirmation using quantitative DNA methylation assays. Methylated DNA sequences from an intergenic region between the VAPA and APCDD1 genes (the VAPA-APCDD1 DNA) were detected in pre-delivery, but not post-delivery, maternal plasma samples. The concentrations correlated positively with those of an established fetal genetic marker, ZFY, in pre-delivery maternal plasma. The ratios of methylated VAPA-APCDD1(chr18) to ZFY(chrY) were higher in maternal plasma samples of 9 male trisomy 18 fetuses than those of 27 male euploid fetuses (Mann-Whitney test, P=0.029). We defined the cutoff value for detecting trisomy 18 fetuses as mean+1.96 SD of the EGG ratios of the euploid cases. Eight of 9 trisomy 18 and 1 of 27 euploid cases showed EGG ratios higher than the cutoff value, giving a sensitivity of 88.9% and a specificity of 96.3%.
  
  
  CONCLUSIONS
  Our data have shown that the methylated VAPA-APCDD1 DNA in maternal plasma is predominantly derived from the fetus. We have demonstrated that this novel fetal epigenetic marker in maternal plasma is useful for the noninvasive detection of fetal trisomy 18.
authors.affiliation: The Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China.
authors.forename: Dana W Y
authors.initials: DW
authors.lastname: Tsui
authors.forename: Y M Doris
authors.initials: YM
authors.lastname: Lam
authors.forename: Wing S
authors.initials: WS
authors.lastname: Lee
authors.forename: Tak Y
authors.initials: TY
authors.lastname: Leung
authors.forename: Tze K
authors.initials: TK
authors.lastname: Lau
authors.forename: Elizabeth T
authors.initials: ET
authors.lastname: Lau
authors.forename: Mary H Y
authors.initials: MH
authors.lastname: Tang
authors.forename: Ranjit
authors.initials: R
authors.lastname: Akolekar
authors.forename: Kypros H
authors.initials: KH
authors.lastname: Nicolaides
authors.forename: Rossa W K
authors.initials: RW
authors.lastname: Chiu
authors.forename: Y M Dennis
authors.initials: YM
authors.lastname: Lo
authors.forename: Stephen S C
authors.initials: SS
authors.lastname: Chim
mesh_terms: D002887:Chromosomes, Human, Pair 18 / Q000235:genetics*; D018899:CpG Islands / Q000235:genetics; D004247:DNA / Q000097:blood / Q000235:genetics; D019175:DNA Methylation; D057890:Epigenomics; D005260:Female; D006801:Humans; D047908:Intracellular Signaling Peptides and Proteins; D051741:Kruppel-Like Transcription Factors / Q000235:genetics; D008562:Membrane Glycoproteins / Q000235:genetics; D008565:Membrane Proteins; D010920:Placenta / Q000378:metabolism*; D016133:Polymerase Chain Reaction / Q000379:methods; D011247:Pregnancy; D011296:Prenatal Diagnosis / Q000379:methods; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D013577:Syndrome; D014314:Trisomy / Q000175:diagnosis / Q000235:genetics*; D033921:Vesicular Transport Proteins / Q000235:genetics
chemical_list: C549624:APCDD1 protein, human; D047908:Intracellular Signaling Peptides and Proteins; D051741:Kruppel-Like Transcription Factors; D008562:Membrane Glycoproteins; D008565:Membrane Proteins; C114051:VAPA protein, human; D033921:Vesicular Transport Proteins; C054430:ZFY protein, human; D004247:DNA