Tags

Type your tag names separated by a space and hit enter

Increasing the discrimination power of ancestry- and identity-informative SNP loci within the ForenSeq™ DNA Signature Prep Kit.
Forensic Sci Int Genet. 2018 09; 36:60-76.FS

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).

Authors+Show Affiliations

Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX, 76107, USA. Electronic address: jonathan.king@unthsc.edu.Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX, 76107, USA.Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX, 76107, USA.Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX, 76107, USA.Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX, 76107, USA.Department of Chemistry Malaysia, Kuching Branch, Lot 3148, Block 14, Jalan Sultan Tengah, 93050 Petra Jaya, Kuching, Malaysia.Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX, 76107, USA.

Pub Type(s)

Journal Article
Research Support, U.S. Gov't, Non-P.H.S.

Language

eng

PubMed ID

29935396

Citation

King, Jonathan L., et al. "Increasing the Discrimination Power of Ancestry- and Identity-informative SNP Loci Within the ForenSeq™ DNA Signature Prep Kit." Forensic Science International. Genetics, vol. 36, 2018, pp. 60-76.
King JL, Churchill JD, Novroski NMM, et al. Increasing the discrimination power of ancestry- and identity-informative SNP loci within the ForenSeq™ DNA Signature Prep Kit. Forensic Sci Int Genet. 2018;36:60-76.
King, J. L., Churchill, J. D., Novroski, N. M. M., Zeng, X., Warshauer, D. H., Seah, L. H., & Budowle, B. (2018). Increasing the discrimination power of ancestry- and identity-informative SNP loci within the ForenSeq™ DNA Signature Prep Kit. Forensic Science International. Genetics, 36, 60-76. https://doi.org/10.1016/j.fsigen.2018.06.005
King JL, et al. Increasing the Discrimination Power of Ancestry- and Identity-informative SNP Loci Within the ForenSeq™ DNA Signature Prep Kit. Forensic Sci Int Genet. 2018;36:60-76. PubMed PMID: 29935396.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Increasing the discrimination power of ancestry- and identity-informative SNP loci within the ForenSeq™ DNA Signature Prep Kit. AU - King,Jonathan L, AU - Churchill,Jennifer D, AU - Novroski,Nicole M M, AU - Zeng,Xiangpei, AU - Warshauer,David H, AU - Seah,Lay-Hong, AU - Budowle,Bruce, Y1 - 2018/06/06/ PY - 2017/12/11/received PY - 2018/05/03/revised PY - 2018/06/05/accepted PY - 2018/6/24/pubmed PY - 2018/12/12/medline PY - 2018/6/24/entrez KW - Bioinformatics KW - FGx KW - ForenSeq KW - Massively parallel sequencing KW - Microhaplotypes KW - SNPs SP - 60 EP - 76 JF - Forensic science international. Genetics JO - Forensic Sci Int Genet VL - 36 N2 - 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). SN - 1878-0326 UR - https://www.unboundmedicine.com/medline/citation/29935396/Increasing_the_discrimination_power_of_ancestry__and_identity_informative_SNP_loci_within_the_ForenSeq™_DNA_Signature_Prep_Kit_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S1872-4973(17)30283-1 DB - PRIME DP - Unbound Medicine ER -