Microarray-Based Analysis of Methylation Status of CpGs in Placental DNA and Maternal Blood DNA--Potential New Epigenetic Biomarkers for Cell Free Fetal DNA-Based Diagnosis

PLoS One. 2015 Jul 31;10(7):e0128918. doi: 10.1371/journal.pone.0128918. eCollection 2015.

Abstract

Epigenetic markers for cell free fetal DNA in the maternal blood circulation are highly interesting in the field of non-invasive prenatal testing since such markers will offer a possibility to quantify the amount of fetal DNA derived from different chromosomes in a maternal blood sample. The aim of the present study was to define new fetal specific epigenetic markers present in placental DNA that can be utilized in non-invasive prenatal diagnosis. We have conducted a high-resolution methylation specific beadchip microarray study assessing more than 450.000 CpG sites. We have analyzed the DNA methylation profiles of 10 maternal blood samples and compared them to 12 1st trimesters chorionic samples from normal placentas, identifying a number of CpG sites that are differentially methylated in maternal blood cells compared to chorionic tissue. To strengthen the utility of these differentially methylated CpG sites to be used with methyl-sensitive restriction enzymes (MSRE) in PCR-based NIPD, we furthermore refined the list of selected sites, containing a restriction sites for one of 16 different methylation-sensitive restriction enzymes. We present a list of markers on chromosomes 13, 18 and 21 with a potential for aneuploidy testing as well as a list of markers for regions harboring sub-microscopic deletion- or duplication syndromes.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell-Free System
  • CpG Islands*
  • DNA / blood*
  • DNA Methylation*
  • Epigenesis, Genetic*
  • Female
  • Fetus / metabolism*
  • Humans
  • Oligonucleotide Array Sequence Analysis*
  • Placenta / metabolism*
  • Pregnancy
  • Pregnancy Trimester, First

Substances

  • DNA

Grants and funding

Funding was provided by the University of Southern Denmark(LH), Jørgen Werner Schous Fond(AB), Det Videnskabelige Fond ved Horsens Sygehus(SS), Familien Hede-Nielsens Fond(LH), and Aase og Ejner Danielsens Fond(LH). These funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.