Increasing the Discrimination Power of Ancestry- and Identity-Informative SNP Loci Within the ForenSeg

• NCJ Number: 253289
• Journal: Forensic Science International-Genetics Volume: 36 Dated: September 2018 Pages: 60-76
• Author(s): Jonathan L. King; Jennifer D. Churchill; Nicole M.m. Novroski; Xiangpei Zeng; David H. Warshauer; Lay-hong Seah; Bruce Budowle
• Date Published: September 2018
• Length: 17 pages
• Grant Number(s): 2012-DN-BX-K033; 2015-DN-BX-K067
• Agencies: NIJ-Sponsored
• Publication Type: Research (Applied/Empirical); Report (Study/Research); Report (Grant Sponsored); Program/Project Description
• Award: Development of Reference Sample DNA Profiling for Databases Using Next Generation Sequencing Technologies; Enhancing Mixture Interpretation with Highly Informative STRs

Annotation

In this study, 714 individuals from four major populations (African American, AFA; East Asian, ASN; US Caucasian, CAU; and Southwest US Hispanic, HIS) previously reported by Churchill et al. [Forensic Sci Int Genet. 30 (2017) 81-92; DOI: https://doi.org/10.1016/j.fsigen.2017.06.004] were assessed using STRait Razor v2s to determine the level of diversity in the flanking regions of these amplicons.

Abstract

The use of single nucleotide polymorphisms (SNPs) in forensic genetics has been limited to challenged samples with low template and/or degraded DNA. The recent introduction of massively parallel sequencing (MPS) technologies has expanded the potential applications of these markers and increased the discrimination power of well-established loci by considering variation in the flanking regions of target loci. The ForenSeq Signature Preparation Kit contains 165 SNP amplicons for ancestry- (aiSNPs), identity- (iiSNPs), and phenotype-inference (piSNPs). The current study found that nearly 70 percent of loci showed some level of flanking region variation with 22 iiSNPs and 8 aiSNPs categorized as microhaplotypes in this study. The heterozygosities of these microhaplotypes approached, and in one instance surpassed, those of some core STR loci. Also, the impact of the flanking region on other forensic parameters (e.g., power of exclusion and power of discrimination) was examined. Sixteen of the 94 iiSNPs had an effective allele number greater than 2.00 across the four populations. To assess what effect the flanking region information had on the ancestry inference, genotype probabilities and likelihood ratios were determined. In addition, concordance with the ForenSeq UAS and Nextera Rapid Capture was evaluated, and patterns of heterozygote imbalance were identified. Pairwise comparison of the iiSNP diplotypes determined the probability of detecting a mixture (i.e., observing less than or equal to 3 haplotypes) using these loci alone was 0.9952. The improvement in random match probabilities for the full regions over the target iiSNPs was found to be significant. When combining the iiSNPs with the autosomal STRs, the combined match probabilities ranged from 6.4010 -73 (ASN) to 1.0210 -79 (AFA). (publisher abstract modified)