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

Area of Science:

• Genetics
• Molecular Biology
• Forensic Science

Background:

• Noninvasive prenatal paternity testing currently utilizes short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs).
• Existing methods often involve PCR with capillary electrophoresis or SNP typing arrays.
• Maternal plasma DNA analysis offers a noninvasive approach to genetic testing.

Purpose of the Study:

• To develop and evaluate a novel noninvasive prenatal paternity testing (NIPAT) method based on maternal plasma DNA sequencing.
• To assess the influence of factors like minor allele frequency (MAF), SNP count, fetal fraction, and sequencing depth on test performance.
• To validate the accuracy and feasibility of sequencing-based NIPAT in clinical cases.

Main Methods:

• Development of a NIPAT method utilizing targeted deep sequencing of selective single nucleotide polymorphisms (SNPs) from maternal plasma DNA.
• Evaluation of key influencing factors including MAF, total SNP number, fetal fraction, and effective sequencing depth.
• Design of three distinct selective SNP panels for performance verification.
• Application of an informative bioinformatics pipeline to calculate the combined paternity index (CPI) for paternity determination.

Main Results:

• Sequencing-based NIPAT demonstrated full agreement with results from invasive prenatal paternity tests using STR multiplex systems in 17 clinical cases.
• The study identified and evaluated critical factors influencing the accuracy of SNP typing from maternal plasma DNA.
• The developed method proved feasible and accurate for determining paternity noninvasively.

Conclusions:

• Maternal plasma DNA sequencing offers a feasible and accurate approach for noninvasive prenatal paternity testing.
• This sequencing-based NIPAT method provides a reliable alternative to existing techniques.
• The technology holds potential for future applications in forensic science.