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.

中文翻译：

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使用MeDIP-NGS进行全基因组胎儿和母体DNA甲基化分析，以鉴定差异甲基化区域。

DNA甲基化是一种表观遗传标记，已显示在不同组织之间存在显着差异。利用胎盘来源的无细胞DNA和母体血液之间的甲基化差异，几个小组采用了不同的方法来发现胎儿特异性生物标记物。这项研究的目的是分析全基因组胎儿和母亲的甲基化组，以鉴定和确认差异甲基化区域（DMR）的存在。我们最初利用甲基化的DNA免疫沉淀（MeDIP）和下一代测序（NGS）来鉴定绒毛膜绒毛取样（CVS）与女性非妊娠血浆（PL）和外周血（WBF）样本之间的全基因组DMR。接下来，使用特定标准，选择了331个胎儿特定DMR，并在8个CVS中进行了确认，通过结合MeDIP和溶液内靶向富集，再结合NGS，可得到8个WBF和8个PL样品。结果显示，与WBF和PL样品相比，CVS样品具有更高的富集度，这证实了所选DMR的胎儿和母体DNA之间存在明显的甲基化水平。通过首次结合MeDIP和溶液内靶向富集，然后结合NGS，我们已经成功地实现了发现和确认大量胎儿特异性DMR的新颖方法。这种双重富集方法的实施非常高效，并且可以通过目标NGS对多个DMR进行详细分析。而且，据我们所知，这是MeDIP在血浆样品上的首次报道应用，