Whole-genome fetal and maternal DNA methylation analysis using MeDIP-NGS for the identification of differentially methylated regions

Abstract

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.

Fig. 1.

DMR methylation enrichment in CVS, WBF and PL samples. Overall, DMR methylation enrichment in CVS, WBF and PL samples using (a) the 1453 common fetalspecific DMRs following MeDIPNGS analysis and (b) a subset of 331 fetalspecific DMRs using MeDIP in combination with insolution targeted enrichment followed by NGS. Posthoc comparisons showed significant statistical differences between the three tissues (P < 2 × 10⁻¹⁶) with higher enrichment in CVS compared to maternal DNA, confirming the hypermethylation status of the fetal DNA (CVS) as compared to the maternal DNA (WBF and PL). CVS: chorionic villus sampling; PL: female nonpregnant plasma sample; WBF: female nonpregnant whole blood.