Noninvasive Prenatal Paternity Testing with a Combination of Well-Established SNP and STR Markers Using Massively Parallel Sequencing

Abstract

Cell-free fetal DNA (cffDNA) from maternal plasma has made it possible to develop noninvasive prenatal paternity testing (NIPPT). However, most studies have focused on customized single nucleotide polymorphism (SNP) typing systems and few have used conventional short tandem repeat (STR) markers. Based on massively parallel sequencing (MPS), this study used a widely-accepted forensic multiplex assay system to evaluate the effect of noninvasive prenatal paternity testing with a combination of well-established SNP and STR markers. Using a ForenSeq DNA Signature Prep Kit, NIPPT was performed in 17 real parentage cases with monovular unborn fetuses at 7 to 24 gestational weeks. Different analytical strategies for the identification of paternally inherited allele (PIA) were developed to deal with SNPs and STRs. Combined paternity index (CPI) for 17 real trios as well as 272 unrelated trios was calculated. With the combination of SNPs and A-STRs, 82.35% (14/17), 88.24% (15/17), 94.12% (16/17), and 94.12% (16/17) of real trios could be accurately determined when the likelihood ratio (LR) threshold for paternity inclusion was set to 10,000, 1000, 100, and 10, respectively. This reveals that simultaneous surveys of SNP and STR markers included in the ForenSeq DNA Signature Prep Kit offer a promising method for NIPPT using MPS technology.

Set of 15 SNP-SNP Markers for Detection of Unbalanced Degraded DNA Mixtures and Noninvasive Prenatal Paternity Testing

“…In addition, current research towards cffDNA detection is still in the exploratory stage. Preliminary shows that MPS combines microhaplotypes and mature SNPs and STR kit has certain application potential in NIPPT ( Bai et al, 2020 ; Ou and Qu 2020 ; Ou and Bai 2021 ; Shen et al, 2021 ). In this study, based on the CE platform, the 15 SNP-SNPs, provide a new and cost-effective strategy for NIPPT.…”

Recent advances in forensic biology and forensic DNA typing: INTERPOL review 2019–2022

“…The potential for MPS methods to assist with environmental trace analysis was reviewed in terms of forensic soil analysis, forensic botany, and human identification utilizing the skin microbiome [ 403 ]. The possibility of non-invasive prenatal paternity testing using cell-free fetal DNA from maternal plasma was explored with the Precision ID Identity Panel [ 404 ] and the ForenSeq DNA Signature Prep Kit [ 405 ]. Pairwise kinship analysis was also examined using the ForenSeq DNA Signature Prep Kit and multi-generational family pedigrees [ 406 , 407 ].…”

Forensic Investigation Approaches of DNA Analysis and Criminal Investigation

“…To our knowledge, no male relative has ever been mistakenly identified using familial searches and reported as such. In the United States, strict guidelines, such as a list of specific and limited criminal types, an approval procedure, and an affirmative statement from particular stakeholders are often included that use familial searching [24].…”