Application of single nucleotide polymorphisms (SNPs) to forensic casework in Malaysia

Abstract

The analysis of degraded DNA can be problematic. Recent advances in the identification and analysis of single nucleotide polymorphisms (SNPs) have demonstrated the advantage of these markers over short tandem repeats (STRs) in that they only require small amplicons. However, before applying to casework, it is important to develop allele frequency databases from relevant populations. The main aim of the study is to characterize three Malaysian major ethnic groups; Malay, Chinese and Indian, using 52 autosomal SNP markers that have been identified in the SNPforID project.

Sanchez et. al., 2006 reported a multiplex of 52 SNP markers in one PCR reaction with two single base reaction (SBE) in the detection of SNPs using capillary electrophoresis (CE). The amplicons for PCR ranged from 59 bp to 115 bp. Whilst for SBE reactions ranged from 16 nt to 92 nt. In their study, full complete profile was obtained from 500 pg DNA input. The study was carried out on three major populations: African, Asian and European.

As in this study, a total of 325 Malaysian samples (109 from Malays, 107 from Chinese and 109 from Indians) were genotyped. In order to genotype the population samples reliably and robustly, four sets of 13-plex SNPs were developed. Internal validation was carried out using both genetic analyzers, ABI PRISM® 310 and 3500 Genetic Analyzer. Sensitivity and reproducibility studies demonstrated that the assays were highly sensitive, requiring as little as 30 pg of DNA. Full, complete and clear profiles were generated. Data were collected and evaluated statistically for forensic usefulness.

Across the three ethnic groups, few significant departures from HWE, at p values <0.05 were observed at 3 SNP markers in Malays, 4 SNP markers in Chinese and 9 SNP markers in Indian samples. Five markers (rs2107612, rs722098, rs2076848, rs907100 and rs1528460) in the Indians and one marker (rs1528460) in the Chinese, showed the lowest p value, that is p=0.0. However, after Bonferroni correction at p <0.00096 significant deviation(s) from HWE was observed at 1 SNP marker (code marker 26) in the Malays, 2

SNP markers (code marker 46 and 54) in the Chinese and 5 SNP markers (code marker 12, 21, 36, 38 and 54) in the Indians. In addition, a pair of loci (at code markers 3 and 53) was found to be associated in the Malays after the Bonferroni correction (at p <0.0000377).

As for forensic parameters, the combined mean match probabilities for the 52 SNPs of Malay, Chinese, and Indian were 1 in 3.9654e-19, 5.3964e-18, and 1.7459e-19, corresponding to a combined power of discrimination of >99.99999999%, respectively. Paired Fst values obtained in the study showed, as expected, that Malay group is closely related to the Chinese population, with the Indian population being more distant.