title: Flanking region variation of ForenSeq™ DNA Signature Prep Kit STR and SNP loci in Yavapai Native Americans.
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 6.11×10-26and 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.
authors.affiliation: Institute for Molecular Medicine, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX, 76107, USA. Electronic address: Frank.Wendt@my.unthsc.edu.
authors.forename: Frank R
authors.initials: FR
authors.lastname: Wendt
authors.affiliation: Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA.
authors.forename: Jonathan L
authors.initials: JL
authors.lastname: King
authors.affiliation: Institute for Molecular Medicine, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX, 76107, USA.
authors.forename: Nicole M M
authors.initials: NMM
authors.lastname: Novroski
authors.affiliation: Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA.
authors.forename: Jennifer D
authors.initials: JD
authors.lastname: Churchill
authors.affiliation: Molecular Anthropology Laboratory, Department of Anthropology, University of California, One Shields Avenue, Davis, CA 95616, USA.
authors.forename: Jillian
authors.initials: J
authors.lastname: Ng
authors.affiliation: Molecular Anthropology Laboratory, Department of Anthropology, University of California, One Shields Avenue, Davis, CA 95616, USA.
authors.forename: Robert F
authors.initials: RF
authors.lastname: Oldt
authors.affiliation: Graduate Group in Forensic Science, University of California,One Shields Avenue, Davis, CA 95616, USA.
authors.forename: Kelly L
authors.initials: KL
authors.lastname: McCulloh
authors.affiliation: Graduate Group in Forensic Science, University of California,One Shields Avenue, Davis, CA 95616, USA.
authors.forename: Jessica A
authors.initials: JA
authors.lastname: Weise
authors.affiliation: Molecular Anthropology Laboratory, Department of Anthropology, University of California, One Shields Avenue, Davis, CA 95616, USA; Graduate Group in Forensic Science, University of California,One Shields Avenue, Davis, CA 95616, USA.
authors.forename: David Glenn
authors.initials: DG
authors.lastname: Smith
authors.affiliation: Molecular Anthropology Laboratory, Department of Anthropology, University of California, One Shields Avenue, Davis, CA 95616, USA; Graduate Group in Forensic Science, University of California,One Shields Avenue, Davis, CA 95616, USA.
authors.forename: Sreetharan
authors.initials: S
authors.lastname: Kanthaswamy
authors.affiliation: Institute for Molecular Medicine, 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 of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia.
authors.forename: Bruce
authors.initials: B
authors.lastname: Budowle
mesh_terms: D041321:Chromosomes, Human, X; D041322:Chromosomes, Human, Y; D016172:DNA Fingerprinting; D005787:Gene Frequency; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D007198:Indians, North American / Q000235:genetics*; D018895:Microsatellite Repeats; D020641:Polymorphism, Single Nucleotide
keywords: Flanking region; ForenSeq™ DNA Signature Prep Kit; Massively parallel sequencing; SNP; STR; STRait Razor v2s; Sequence variation