Non-invasive prenatal paternity testing by analysis of Y-chromosome mini-STR haplotype using next-generation sequencing

Abstract

Objectives To assess the efficacy of Y-chromosome mini-STR-based next-generation sequencing (NGS) for non-invasive prenatal paternity testing (NIPPT). Methods DNA was extracted from the plasma of 24 pregnant women, and cell-free fetal DNA (cffDNA) haplotyping was performed at 12 Y-chromosome mini-STR loci using the Illumina NextSeq 500 system. The cffDNA haplotype was validated by the paternal haplotype. Subsequentlly, the paternity testing parameters were attributed to each case quantitatively. Results The biological relationship between the alleged fathers and infants in all 24 family cases were confirmed by capillary electrophoresis (CE). The Y-chromosome mini-STR haplotypes of all 14 male cffDNA were obtained by NGS without any missing loci. The alleles of cffDNA and paternal genomic DNA were matched in 13 cases, and a mismatched allele was detected at the DYS393 locus in one case and considered as mutation. No allele was detected in the 10 female cffDNA. The combined paternity index (CPI) and probability of paternity calculation was based on 6 loci Y-haplotype distributions of a local population. The probability of paternity was 98.2699–99.8828% for the cases without mutation, and 14.8719% for the case harboring mutation. Conclusions Our proof-of-concept study demonstrated that Y-chromosome mini-STR can be used for NGS-based NIPPT with high accuracy in real cases, and is a promising tool for familial searching, paternity exclusion and sex selection in forensic and medical applications.

Insight into forensic efficiency and genetic structure of the Guizhou Dong group via a 64-plex panel

“…Nonetheless, there are still some defects for STRs in forensic practice. For example, the relatively high mutation rate of STRs may make incorrect conclusions in complex paternity analyses (Liu et al, 2021;Chandra et al, 2022); the large amplicon of STRs is not conducive to assessing outdated and degraded biological samples (Boelens et al, 2021;Song et al, 2022). To avoid these issues of STRs in practical application, SNPs are usually employed as supplemental genetic markers for forensic research because they have widespread in the human genome, show small amplicon, and possess low mutation rates.…”