NIPT-Immunoprecipitation methods based on differential DNA methylation (MeDIP-qPCR)

Immunoprecipitation methods based on differential DNA methylation (MeDIP-qPCR) method for aneuploidy detection:  ANEUPLOIDY DETECTION/NON-INVASIVE PRENATAL TESTING? digital polymerase chain reactions (PCR) and massively parallel sequencing (MPS) won’t help in detecting aneuploidies of foetus.  The uses of cfDNA analysis are technically less challenging because in both fetal sexing and RhD determination the DNA is being interrogated to find genes that would otherwise not be present in the mother.

However, using cfDNA for the detection of fetal aneuploidy is more difficult as one is trying to establish a quantitative difference in the fetal contribution, amongst the cfDNA reservoir which also contains the maternal DNA as the majority (80%) . In these circumstances, such as a woman carrying a fetus with trisomy 21, one would expect the total amount of cfDNA originating from chromosome 21 would be higher than expected due to the additional fetal chromosome 21, however, this relative excess would be small because fetal DNA is only the minority of DNA present . A very precise technique for making these counts is therefore required to detect these small differences reliably and/or a technique is required to enrich the fetal cfDNA fraction.

Fetal cfDNA enrichment

A range of approaches have been attempted to selectively enrich the fetal cfDNA fraction. Firstly, there appears to be a physiological enrichment of cfDNA in pregnancies with Down’s syndrome fetuses ,and artificial enrichment methods have included attempts to separate fetal and maternal DNft on the basis that fetal DNA fragments are typically smaller in size Chemical purification techniques have also been attempted , as well as immunoprecipitation methods based on differential DNA methylation (MeDIP-qPCR)

. Further investigation is preparing such methods for clinical use in larger validation

Early work focused on the detection of genes known only to be present in the fetus. These included identifying genes on the Y chromosome from a male fetus, or other alleles present in the fetus alone, such as identifying a fetus which is rhesus positive in a rhesus negative mother.