US Population Data for 94 Identity-Informative SNP Loci.

Area of Science:

• Forensic Science
• Genetics
• Molecular Biology

Background:

• Traditional short tandem repeat (STR) markers are standard in forensic DNA profiling.
• Degraded DNA samples pose challenges for amplification using existing STR markers.
• Advancements in sequencing technology enable the use of single nucleotide polymorphisms (SNPs) for individual identification.

Purpose of the Study:

• To evaluate the efficacy of 94 single nucleotide polymorphisms (SNPs) for individual identification (iiSNPs) across diverse US population groups.
• To explore the potential of microhaplotypes, formed by combining targeted SNPs with flanking variants, to increase discriminatory power.
• To compare the forensic statistical power of iiSNPs and microhaplotypes against established CODIS core STR markers.

Main Methods:

• Analysis of 1036 DNA samples from four major US population groups (African American, Asian American, Caucasian, Hispanic).
• Genotyping of 94 single nucleotide polymorphisms (SNPs) for individual identification.
• Examination of flanking SNP regions to identify and form microhaplotypes.
• Calculation of allele frequencies and forensic statistics (e.g., match probability) for iiSNPs and microhaplotypes.
• Comparison of performance metrics against 20 CODIS core STR markers.

Main Results:

• iiSNPs demonstrated high discriminatory power, with an estimated average match probability of 1.7 × 10^-38 across 94 SNPs.
• Microhaplotypes, combining targeted SNPs with flanking variants, showed heterozygosity increases greater than 15% in four amplicons.
• The forensic discrimination of iiSNPs was significantly higher (4-10 orders of magnitude lower match probability) than STR markers, even when considering internal sequence variation or capillary electrophoresis length-based genotypes.

Conclusions:

• Single nucleotide polymorphisms (SNPs) represent a powerful tool for individual identification in forensic science.
• The development of microhaplotypes further enhances the discriminatory capacity of SNP-based forensic analysis.
• iiSNPs and microhaplotypes offer superior performance compared to traditional STR markers, particularly for degraded DNA samples.