Noninvasive Prenatal Paternity Testing (NIPAT) through Maternal Plasma DNA Sequencing: A Pilot Study

Abstract

Short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) have been already used to perform noninvasive prenatal paternity testing from maternal plasma DNA. The frequently used technologies were PCR followed by capillary electrophoresis and SNP typing array, respectively. Here, we developed a noninvasive prenatal paternity testing (NIPAT) based on SNP typing with maternal plasma DNA sequencing. We evaluated the influence factors (minor allele frequency (MAF), the number of total SNP, fetal fraction and effective sequencing depth) and designed three different selective SNP panels in order to verify the performance in clinical cases. Combining targeted deep sequencing of selective SNP and informative bioinformatics pipeline, we calculated the combined paternity index (CPI) of 17 cases to determine paternity. Sequencing-based NIPAT results fully agreed with invasive prenatal paternity test using STR multiplex system. Our study here proved that the maternal plasma DNA sequencing-based technology is feasible and accurate in determining paternity, which may provide an alternative in forensic application in the future.

Detection of short tandem repeats at 5 loci and amelogenin with cell-free fetal DNA as a specimen in the development of prenatal paternity diagnostic tests

“…This rate is relatively high considering the circulating cell-free fetal DNA. The results of this study are in accordance with those of a study conducted by Jiang et al (Jiang et al 2016) which proved that maternal plasma DNA sequencing-based technology is feasible and accurate in determining paternity, possibly providing an alternative Fig. 1 Comparison of DNA concentration from circulating cell-free fetal DNA and maternal blood using T-test.…”

Noninvasive prenatal paternity testing using targeted massively parallel sequencing

“…According to the Bayesian model, a previously reported SNP‐based mathematical model for PI calculation for the effective loci (maternal homozygous SNPs) was used for paternity determination with minor adjustment. In fact, PI is a likelihood ratio that considers two competing and mutually exclusive hypotheses.…”

“…Currently, Illumina sequencers, based on the sequencing by synthesis (SBS) technology, and Ion Torrent sequencers, based on semiconductor technology, have become the predominant MPS platforms widely used in various life science fields. Recent studies based on the Illumina MiSeq platform (Illumina, Inc.) and Ion Torrent PGM platform (Thermo Fisher Scientific) have demonstrated the great potential of the MPS technology in the application of NIPAT . Meanwhile, several strategies for data interpretation in this field have been also developed.…”

“…Validation of this method in fetal tissues demonstrated that paternal alleles were accurately identified. Another study by Jiang and coworkers established a mathematical model for paternity index (PI) calculation for NIPAT based on Bayes' theorem, and the reliability of this strategy was initially validated in 17 real parentage cases in the second trimester. However, linkage analysis was not considered for the more than 5000 SNPs used in this study; therefore, the statistical results are controversial, especially for the combined paternity index (CPI) calculation.…”

An SNP panel for the analysis of paternally inherited alleles in maternal plasma using ion Torrent PGM

“…Based on the Illumina MiSeq platform (Illumina, Inc., San Diego, CA), a recent study by Jang et al demonstrates that targeted MPS technology using an insolution hybridization capture system allows the capture of foetus-and mother-derived DNA in the maternal plasma within a given genomic region with little bias [19]. The strategy has been systematically evaluated, and the reliability was validated in 17 real parentage cases in the second trimester, thus showing the feasibility of non-invasive prenatal paternity testing (NIPAT) [19].…”