Whole-genome fetal and maternal DNA methylation analysis using MeDIP-NGS for the identification of differentially methylated regions.
DNA methylation is an epigenetic marker that has been shown to vary significantly across different tissues. Taking advantage of the methylation differences between placenta-derived cell-free DNA and maternal blood, several groups employed different approaches for the discovery of fetal-specific biomarkers. The aim of this study was to analyse whole-genome fetal and maternal methylomes in order to identify and confirm the presence of differentially methylated regions (DMRs). We have initially utilized methylated DNA immunoprecipitation (MeDIP) and next-generation sequencing (NGS) to identify genome-wide DMRs between chorionic villus sampling (CVS) and female non-pregnant plasma (PL) and peripheral blood (WBF) samples. Next, using specific criteria, 331 fetal-specific DMRs were selected and confirmed in eight CVS, eight WBF and eight PL samples by combining MeDIP and in-solution targeted enrichment followed by NGS. Results showed higher enrichment in CVS samples as compared to both WBF and PL samples, confirming the distinct methylation levels between fetal and maternal DNA for the selected DMRs. We have successfully implemented a novel approach for the discovery and confirmation of a significant number of fetal-specific DMRs by combining for the first time MeDIP and in-solution targeted enrichment followed by NGS. The implementation of this double-enrichment approach is highly efficient and enables the detailed analysis of multiple DMRs by targeted NGS. Also, this is, to our knowledge, the first reported application of MeDIP on plasma samples, which leverages the implementation of our enrichment methodology in the detection of fetal abnormalities in maternal plasma.
Translational Genetics Team,The Cyprus Institute of Neurology and Genetics,Nicosia,Cyprus.
Anna
A
Keravnou
NIPD Genetics,Nicosia,Cyprus.
Marios
M
Ioannides
NIPD Genetics,Nicosia,Cyprus.
Kyriakos
K
Tsangaras
NIPD Genetics,Nicosia,Cyprus.
Charalambos
C
Loizides
Translational Genetics Team,The Cyprus Institute of Neurology and Genetics,Nicosia,Cyprus.
Michael D
MD
Hadjidaniel
Translational Genetics Team,The Cyprus Institute of Neurology and Genetics,Nicosia,Cyprus.
Elisavet A
EA
Papageorgiou
Translational Genetics Team,The Cyprus Institute of Neurology and Genetics,Nicosia,Cyprus.
Skevi
S
Kyriakou
NIPD Genetics,Nicosia,Cyprus.
Pavlos
P
Antoniou
NIPD Genetics,Nicosia,Cyprus.
Petros
P
Mina
NIPD Genetics,Nicosia,Cyprus.
Achilleas
A
Achilleos
Translational Genetics Team,The Cyprus Institute of Neurology and Genetics,Nicosia,Cyprus.
Maria
M
Neofytou
Translational Genetics Team,The Cyprus Institute of Neurology and Genetics,Nicosia,Cyprus.
Elena
E
Kypri
Department of Cytogenetics and Genomics,The Cyprus Institute of Neurology and Genetics,Nicosia,Cyprus.
Carolina
C
Sismani
Translational Genetics Team,The Cyprus Institute of Neurology and Genetics,Nicosia,Cyprus.
George
G
Koumbaris
Translational Genetics Team,The Cyprus Institute of Neurology and Genetics,Nicosia,Cyprus.
Philippos C
PC
Patsalis
D015415:Biomarkers / Q000032:analysis*; D015193:Chorionic Villi Sampling; D004247:DNA / Q000097:blood / Q000235:genetics*; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D005260:Female; D005315:Fetal Diseases / Q000097:blood / Q000175:diagnosis* / Q000235:genetics; D005333:Fetus / Q000378:metabolism; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D047468:Immunoprecipitation; D062145:Maternal Serum Screening Tests; D010920:Placenta / Q000378:metabolism; D011247:Pregnancy; D011248:Pregnancy Complications / Q000097:blood / Q000175:diagnosis* / Q000235:genetics; D011261:Pregnancy Trimester, First
D015415:Biomarkers; D004247:DNA