Detection of fetal cfDNA in maternal blood

An NGS-based assay was developed to determine the presence or absence of paternally inherited genetic variants in cfDNA derived from the fetus in the plasma of pregnant women. This assay can be used in connection with NGS-based prenatal prediction of fetal blood groups in immunised pregnant women. The purpose of the assay is to minimise the risk of a false-negative outcome in the situation with a prediction of the absence of a blood group allele from the fetus.

The underlying principle was to examine genetic markers, with each single marker giving a small contribution to the probability of differentiating between individuals (woman and fetus) and combining several markers into one multiplex PCR assay with enough discerning power to determine whether cfDNA from a fetus was present in maternal plasma. If only maternal cfDNA was detected, a prediction of the absence of a fetal blood group might be due to a false-negative result based on insufficient amounts of fetal cfDNA.

The assay did not require knowledge of maternal or paternal genotypes. The genetic markers were deletion or insertion variants and were selected using an SQL algorithm searching all autosomes from gnomAD v 3 on the Google Cloud Platform and included alleles with a frequency close to 0.5 in four different ethnic populations, including several other criteria. The final assay consisted of a multiplex PCR amplification of 22 different biallelic delin markers, each located on a separate chromosome. The assay is informative in >99% of cases with at least one primer set. After experimental testing, an algorithm for scoring test results was defined, and the cut-off was set at <0.15%.

Per sample, the control assay required one extra dedicated multiplex PCR, which was eventually spiked into the sequencing reaction. The assay estimated the presence of non-self-genetic variation and may have applications beyond control for the presence of fetal cfDNA.