Investigation of SNPs in the Precision ID Identity Panel using next-generation sequencing in a Myanmar population

Abstract

Background—Single nucleotide polymorphisms (SNPs) have become popular in forensic genetics as an alternative to short tandem repeats (STRs) due to low mutation rates and small amplicon sizes. The Precision ID Identity Panel (Thermo Fisher Scientific), consisting of 90 autosomal SNPs and 34 Y-SNPs, was introduced for human identification by next-generation sequencing (NGS), enabling many studies on the global population; however, few reports are available on the Southeast Asian population.Methods and Results—A total of 96 unrelated male samples from Myanmar (Yangon) were analyzed with the Precision ID Identity Panel on a MiSeq (Illumina) using an in-house TruSeq compatible universal adapter. The sequencing performance was evaluated by locus balance and heterozygote balance, and the results were comparable to those of the Ion Torrent platform. For 90 autosomal SNPs, minor allele frequencies ranged between 0.068 and 0.500, and combined match probability (6.994×10−34) was lower than that of 22 PowerPlex Fusion autosomal STRs (3.130×10−26). Moreover, we identified 51 cryptic variations around the target SNPs using a custom variant caller, Visual SNP. For 34 Y-SNPs, 14 Y-haplogroups were observed—mostly O2 and O1b groups. Interpopulation analysis revealed that the Myanmar population is genetically closer to the East and Southeast Asian populations than the South Asian population.Conclusions—We demonstrate that the Precision ID Identity Panel can be successfully analyzed on a MiSeq using a custom data analysis pipeline and provide high discrimination power for human identification in the Myanmar population, while extending the accessibility of NGS analysis for SNPs in forensics.