Forensic evaluation of 101 identity-informative SNPs in a Filipino population using massively parallel sequencing

Area of Science:

• Forensic Genetics
• Population Genetics
• Human Identification

Background:

• Traditional DNA identification uses short tandem repeats (STRs), but single nucleotide polymorphisms (SNPs), especially identity-informative SNPs (iiSNPs), offer advantages for degraded DNA due to low mutation rates and short amplicons.
• Massively parallel sequencing (MPS) enables simultaneous analysis of numerous STRs and SNPs, enhancing forensic capabilities.
• Southeast Asian populations are underrepresented in forensic DNA databases.

Purpose of the Study:

• To characterize 101 iiSNPs in a Filipino population using two commercial MPS kits.
• To establish the first Filipino forensic iiSNP database and assess the forensic applicability of these markers.
• To contribute data from an underrepresented Southeast Asian population to global forensic databases.

Main Methods:

• Genotyping of 143 unrelated Filipino males using Precision ID and ForenSeq™ DNA Signature Prep Kits (MPS).
• Analysis of allele frequencies, forensic efficiency parameters, Hardy-Weinberg equilibrium (HWE), linkage disequilibrium (LD), population structure, and kinship performance.
• Comparison of iiSNP performance with existing autosomal STR (aSTR) data.

Main Results:

• 64 out of 101 evaluated iiSNPs met criteria for broad forensic applicability.
• iiSNP panels demonstrated strong individualization power, with combined match probabilities significantly lower than 23 aSTRs.
• Filipinos cluster with East Asian populations but show distinct genetic characteristics; iiSNPs performed comparably to aSTRs for first- and second-degree kinship analysis.

Conclusions:

• The study established the first Filipino forensic iiSNP database, validating the forensic utility of 101 iiSNPs for human identification in this population.
• Population-specific reference data is crucial, as Filipinos exhibit distinct genetic features.
• Future research should include diverse Philippine ethnic groups and explore higher-density iiSNP panels for improved forensic casework.