Routine implementation of noninvasive prenatal paternity testing with STRs

Noninvasive Prenatal Paternity Testing: A Review on Genetic Markers

Noninvasive prenatal paternity testing (NIPPT) is a crucial tool in forensic contexts, particularly in cases involving post-rape pregnancies. It enables judicial authorities and victims to promptly address these situations by determining the paternity of the fetus within a few weeks of pregnancy. NIPPT relies on the analysis of cell-free fetal DNA (cffDNA) found in the maternal bloodstream. However, the abundance of maternal DNA presents a significant challenge in detecting fetal DNA. As a result, research has focused on improving methods for isolating or enriching fetal DNA and, specifically in the context of forensic genetics, on the development of suitable genetic markers. The use of Single Nucleotide Polymorphisms (SNPs) along with novel compound markers or composite multiplexes, has shown promising results. Despite significant advances, partly driven by the increased use of Massive Parallel Sequencing (MPS), challenges remain in validating markers-based NIPPT assays for forensic casework. Further studies are required to enhance the sensitivity of these tests, particularly during the early stages of pregnancy, such as the first trimester. Additionally, improving and standardizing statistical frameworks for result evaluation and interpretation is essential to ensure compatibility with forensic standards.

Noninvasive prenatal paternity determination using microhaplotypes: a pilot study

Background

The use of noninvasive techniques to determine paternity prenatally is increasing because it reduces the risks associated with invasive procedures. Current methods, based on SNPs, use the analysis of at least 148 markers, on average.

Methods

To reduce the number of regions, we used microhaplotypes, which are chromosomal segments smaller than 200 bp containing two or more SNPs. Our method employs massively parallel sequencing and analysis of microhaplotypes as genetic markers. We tested 20 microhaplotypes and ascertained that 19 obey Hardy–Weinberg equilibrium and are independent, and data from the 1000 Genomes Project were used for population frequency and simulations.

Results

We performed simulations of true and false paternity, using the 1000 Genomes Project data, to confirm if the microhaplotypes could be used as genetic markers. We observed that at least 13 microhaplotypes should be used to decrease the chances of false positives. Then, we applied the method in 31 trios, and it was able to correctly assign the fatherhood in cases where the alleged father was the real father, excluding the inconclusive results. We also cross evaluated the mother-plasma duos with the alleged fathers for false inclusions within our data, and we observed that the use of at least 15 microhaplotypes in real data also decreases the false inclusions.

Conclusions

In this work, we demonstrated that microhaplotypes can be used to determine prenatal paternity by using only 15 regions and with admixtures of DNA.