Currently, the gold standard in prenatal diagnosis involves invasive procedures for the collection of fetal material through amniocentesis and chorionic villus sampling (CVS). These procedures are associated with a considerable risk fetal loss, estimated at 0.1–0.2%. For this reason scientists have focused their attention on the development of non-invasive approaches for the detection of fetal aneuploidies that carry no risk for the pregnancy. The aim of the project was the development of a novel, disease related, fetal specific epigenetic biomarker panel that can be used in Non-Invasive Prenatal Testing (NIPT).
For the purposes of this study we initially employed Methylated mRNA immunoprecipitation (MeRIP) followed by NGS on fetal and maternal samples for the discovery of fetal specific differentially methylated regions (DMRs). This resulted in the identification of hundreds of DMRs that can potentially be used in NIPT for the detection of fetal aneuploidies. A subset of these DMRs were then characterized and confirmed on multiple fetal and maternal tissues utilizing MeRIP-Targeted NGS method, which is a double enrichment approach that allows simultaneous analysis of hundreds of DMRs in a single assay. Using an in-house developed bioinformatics pipeline and novel statistical tools specifically designed for this project, more than 60 fetal specific DMRs, located in 23 gens were discovered and validated.
Overall the following has been achieved towards the project’s objectives:
1. We discovered hundreds of potential fetal specific differentially methylated regions, based on RNA-methylation differences between fetal and maternal tissues.
2. We confirmed the methylation differences of a subset of fetal specific biomarkers on multiple fetal and maternal tissues.
3. We developed a double enrichment method, new bioinformatics pipelines and statistical analysis models for the confirmation of fetal specific DMRs.
To our knowledge, this is the first study to investigate fetal-specific methylated, RNA-based biomarkers towards their implementation in NIPT for the detection of chromosomal abnormalities such as Down syndrome. Additional large scale studies are necessary to thoroughly characterize the discovered biomarkers and assess their viability for non-invasive prenatal diagnosis.
Every year an estimated 7.9 million infants (6% of worldwide births) are born with serious birth defects, in part due to genetic abnormalities (WHO). Epidemiological studies have shown that chromosomal aneuploidies account for more than 0.3% of live births. This number is substantially higher in developed countries, where due to socioeconomic reasons maternal age has increased. The development of novel non-invasive prenatal tests that offer a safe alternative to the existing invasive tests will have a tremendously positive social impact. We envision that our novel RNA-based biomarkers will be utilized towards the development of a safe, accurate NIPT that will be available to all pregnant women independent from social and economic status while eliminating the risk of miscarriage associated with invasive tests.
