Systematic Identification of Placental Epigenetic Signatures for the Noninvasive Prenatal Detection of Edwards Syndrome

Dana W Y Tsui,Wing S Lee,Kypros H Nicolaides,Ranjit Akolekar,Stephen S C Chim,Rossa W K Chiu,Mary H Y Tang,Tak Y Leung,Y M Dennis Lo,Elizabeth T Lau,Y M Doris Lam,Tze K Lau,Iris Schrijver

doi:10.1371/journal.pone.0015069

Abstract

BackgroundNoninvasive 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.Principal FindingsWe 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%.ConclusionsOur 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.

Highlights

Fetal chromosomal aneuploidies are the main reasons for pregnant women to seek prenatal diagnosis [1]
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

Summary

Introduction

Fetal chromosomal aneuploidies are the main reasons for pregnant women to seek prenatal diagnosis [1]. To detect fetal Down syndrome noninvasively, we and other researchers have applied massively parallel genomic sequencing to determine the proportional amounts of chromosome 21 DNA molecules in maternal plasma [6,7,8] This approach entails the analysis of millions of DNA molecules, derived from both the mother and the fetus, in maternal plasma. We demonstrated for the first time that fetal DNA in maternal plasma could be 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. We apply this epigenetic-genetic (EGG) chromosome dosage approach to detect Edwards syndrome (trisomy 18) in the fetus noninvasively

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