Exploring the efficacy of paternity and kinship testing based on single nucleotide polymorphisms

Area of Science:

• Forensic Genetics
• Human Identification
• Population Genetics

Background:

• Short tandem repeats (STRs) are standard for kinship analysis, but single nucleotide polymorphisms (SNPs) offer advantages for degraded samples.
• Next-generation sequencing (NGS) and multiplexing enable simultaneous analysis of numerous SNP loci.
• Limited research exists on kinship testing efficacy using solely SNP markers.

Purpose of the Study:

• To evaluate the efficacy of 90 autosomal human identity SNP loci for various kinship testing scenarios using NGS.
• To determine the number of SNP loci required for reliable discrimination in paternity, sibling, uncle-nephew, and cousin relationships.
• To assess the impact of including additional relatives on testing efficacy.

Main Methods:

• Genotyping of 90 autosomal human identity SNP loci using next-generation sequencing (NGS).
• Application of the likelihood ratio model to eight pedigree scenarios.
• In silico analysis to estimate the number of SNP loci needed for specific false testing levels (FTL).

Main Results:

• 90 SNPs were sufficient for paternity and full-sibling discrimination but insufficient for distant relatives.
• Estimated SNP loci required: 85 for paternity, 127 for full-sibling, 491 for half-sibling/uncle-nephew, and 1,858 for first-cousin (at 0.1% FTL).
• Including an uncle relative reduced SNP loci needed for half-sibling/nephew testing to ~320.

Conclusions:

• SNP-based kinship testing is feasible, particularly for close relationships.
• A substantial number of SNP loci are necessary for reliable identification of distant relatives.
• These findings provide a basis for developing SNP-based kinship testing strategies.