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Flanking region variation of ForenSeq™ DNA Signature Prep Kit STR and SNP loci in Yavapai Native Americans.
Forensic Sci Int Genet. 2017 05; 28:146-154.FS

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.

Authors+Show Affiliations

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.Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA.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.Molecular Anthropology Laboratory, Department of Anthropology, University of California, One Shields Avenue, Davis, CA 95616, USA.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.Graduate Group in Forensic Science, University of California,One Shields Avenue, Davis, CA 95616, USA.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.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.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.

Pub Type(s)

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

Language

eng

PubMed ID

28273507

Citation

Wendt, Frank R., et al. "Flanking Region Variation of ForenSeq™ DNA Signature Prep Kit STR and SNP Loci in Yavapai Native Americans." Forensic Science International. Genetics, vol. 28, 2017, pp. 146-154.
Wendt FR, King JL, Novroski NMM, et al. Flanking region variation of ForenSeq™ DNA Signature Prep Kit STR and SNP loci in Yavapai Native Americans. Forensic Sci Int Genet. 2017;28:146-154.
Wendt, F. R., King, J. L., Novroski, N. M. M., Churchill, J. D., Ng, J., Oldt, R. F., McCulloh, K. L., Weise, J. A., Smith, D. G., Kanthaswamy, S., & Budowle, B. (2017). Flanking region variation of ForenSeq™ DNA Signature Prep Kit STR and SNP loci in Yavapai Native Americans. Forensic Science International. Genetics, 28, 146-154. https://doi.org/10.1016/j.fsigen.2017.02.014
Wendt FR, et al. Flanking Region Variation of ForenSeq™ DNA Signature Prep Kit STR and SNP Loci in Yavapai Native Americans. Forensic Sci Int Genet. 2017;28:146-154. PubMed PMID: 28273507.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Flanking region variation of ForenSeq™ DNA Signature Prep Kit STR and SNP loci in Yavapai Native Americans. AU - Wendt,Frank R, AU - King,Jonathan L, AU - Novroski,Nicole M M, AU - Churchill,Jennifer D, AU - Ng,Jillian, AU - Oldt,Robert F, AU - McCulloh,Kelly L, AU - Weise,Jessica A, AU - Smith,David Glenn, AU - Kanthaswamy,Sreetharan, AU - Budowle,Bruce, Y1 - 2017/02/27/ PY - 2016/12/16/received PY - 2017/02/01/revised PY - 2017/02/24/accepted PY - 2017/3/9/pubmed PY - 2017/7/8/medline PY - 2017/3/9/entrez KW - Flanking region KW - ForenSeq™ DNA Signature Prep Kit KW - Massively parallel sequencing KW - SNP KW - STR KW - STRait Razor v2s KW - Sequence variation SP - 146 EP - 154 JF - Forensic science international. Genetics JO - Forensic Sci Int Genet VL - 28 N2 - 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. SN - 1878-0326 UR - https://www.unboundmedicine.com/medline/citation/28273507/Flanking_region_variation_of_ForenSeq™_DNA_Signature_Prep_Kit_STR_and_SNP_loci_in_Yavapai_Native_Americans_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S1872-4973(17)30043-1 DB - PRIME DP - Unbound Medicine ER -