Flanking Region Variation of ForenSeq (TM) DNA Signature Prep Kit STR and SNP Loci in Yavapai Native Americans

• NCJ Number: 252446
• Journal: Forensic Science International-Genetics Volume: 28 Dated: May 2017 Pages: 146-154
• Author(s): Frank R, Wendt; Jonathan L. King; Nicole M. Novroski; Jennifer D. Churchill; Jillian Ng; Robert F. Oldt; Kelly L. McCulloh; Jessica A. Weise; David G. Smith; Sreetharan Kanthaswamy; Bruce Budowle
• Date Published: May 2017
• Length: 9 pages
• Grant Number(s): 2014-DN-BX-K024
• Agencies: NIJ-Sponsored
• Publication Type: Research (Applied/Empirical); Report (Study/Research); Report (Grant Sponsored); Program/Project Description
• Award: The Enhancement of the Native American CODIS STR Database for Use in Forensic Casework

Annotation

In this study, flanking region sequence variation in STR and single nucleotide polymorphism (SNP) loci in the Yavapai population were analyzed using the ForenSeq™ DNA Signature Prep Kit and STRait Razor v2s.

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. Although 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, but not for more isolated populations. In the current study, 7 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 ¡Ý5-percent increase in expected heterozygosity. The combined length- and sequence-based random match probabilities (RMPs) for 27 autosomal STRs were 6.11 ¡Á 10−26 and 2.79 ¡Á 10−29, respectively. When combined with 94 iiSNPs (a subset of which became microhaplotypes) the combined RMP was 5.49 ¡Á 10−63. Analysis of length-based and sequence-based autosomal STRs in STRUCTURE indicated that the Yavapai are most similar to the Hispanic population. Although 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. (Publisher abstract modified)