Flanking region variation of ForenSeq™ DNA Signature Prep Kit STR and SNP loci in Yavapai Native Americans. (May 2017)

• Record Type: Journal Article
• Authors: Wendt, Frank R.; King, Jonathan L.; Novroski, Nicole M.M.; Churchill, Jennifer D.; Ng, Jillian; Oldt, Robert F.; McCulloh, Kelly L.; Weise, Jessica A.; Smith, David Glenn; Kanthaswamy, Sreetharan; Budowle, Bruce
• Is Part Of: Forensic science international. Volume 28(2017)
• Page Start: 146
• Page End: 154
• Publication Date: 2017-05
• Subjects: Sequence variation -- STR -- SNP -- Flanking region -- ForenSeq™ DNA Signature Prep Kit -- Massively parallel sequencing -- STRait Razor v2s; Forensic genetics -- Periodicals; Génétique légale -- Périodiques; Forensic genetics; Electronic journals; Periodicals; 614.1
• DOI: 10.1016/j.fsigen.2017.02.014
• Languages: English
• ISSNs: 1872-4973

Abstract

Highlights: Flanking region variation of ForenSeq™ DNA Signature Prep Kit loci was analyzed in a sample population of Yavapai with STRait Razor v2s. The number of alleles increased in twenty-one autosomal STRs and iiSNPs due to flanking region sequence variation in the Yavapai population. Three autosomal STRs and four identity-informative SNPs exhibited ≥5% increase in expected heterozygosity due to flanking region data. Yavapai STR allele frequencies are different compared with those from major population groups. Identity-, ancestry-, and phenotype-informative SNP string sequence information is reported. Abstract: Massively parallel sequencing (MPS) offers advantages over current capillary electrophoresis-based analysis of short tandem repeat (STR) loci for human identification testing. In particular STR repeat motif sequence information can be obtained, thereby increasing the discrimination power of some loci. While sequence variation within the repeat region is observed relatively frequently in some of the commonly used STRs, there is an additional degree of variation found in the flanking regions adjacent to the repeat motif. Repeat motif and flanking region sequence variation have been described for major population groups, however, not for more isolated populations. Flanking region sequence variation in STR and single nucleotide polymorphism (SNP) loci in the Yavapai population was analyzed using the ForenSeq™ DNA Signature Prep Kit and STRait Razor v2s. Seven and 14 autosomal STRs and identity-informative single nucleotide polymorphisms (iiSNPs), respectively, had some degree of flanking region variation. Three and four of these identity-informative loci, respectively, showed ≥5% increase in expected heterozygosity. The combined length- and sequence-based random match probabilities (RMPs) for 27 autosomal STRs were 6.11 × 10 −26 and 2.79 × 10 −29, respectively. When combined with 94 iiSNPs (a subset of which became microhaplotypes) the combined RMP was 5.49 × 10 −63 . Analysis of length-based and sequence-based autosomal STRs in STRUCTURE indicated that the Yavapai are most similar to the Hispanic population. While producing minimal increase in X- and Y-STR discrimination potential, access to flanking region data enabled identification of one novel X-STR and three Y-STR alleles relative to previous reports. Five ancestry-informative SNPs (aiSNPs) and two phenotype-informative SNPs (piSNPs) exhibited notable flanking region variation.