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Increasing the discrimination power of ancestry- and identity-informative SNP loci within the ForenSeq™ DNA Signature Prep Kit
- Source :
- Forensic science international. Genetics. 36
- Publication Year :
- 2017
-
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). 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. The results show that nearly 70% 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. Additionally, 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 ≥ 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 6.40 × 10−73 (ASN) to 1.02 × 10-79 (AFA).
- Subjects :
- 0301 basic medicine
Forensic Genetics
Concordance
Single-nucleotide polymorphism
Biology
Polymorphism, Single Nucleotide
Pathology and Forensic Medicine
03 medical and health sciences
0302 clinical medicine
Gene Frequency
Genotype
Genetics
SNP
Humans
030216 legal & forensic medicine
Allele
Likelihood Functions
Principal Component Analysis
Massive parallel sequencing
Haplotype
Racial Groups
High-Throughput Nucleotide Sequencing
Sequence Analysis, DNA
Amplicon
DNA Fingerprinting
030104 developmental biology
Haplotypes
Microsatellite Repeats
Subjects
Details
- ISSN :
- 18780326
- Volume :
- 36
- Database :
- OpenAIRE
- Journal :
- Forensic science international. Genetics
- Accession number :
- edsair.doi.dedup.....a03302c6afa67a3af0cc6a17d74a1060