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Genetic analysis of the Yavapai Native Americans from West-Central Arizona using the Illumina MiSeq FGx™ forensic genomics system.
Forensic Sci Int Genet. 2016 09; 24:18-23.FS

Abstract

Forensically-relevant genetic markers were typed for sixty-two Yavapai Native Americans using the ForenSeq™ DNA Signature Prep Kit.These data are invaluable to the human identity community due to the greater genetic differentiation among Native American tribes than among other subdivisions within major populations of the United States. Autosomal, X-chromosomal, and Y-chromosomal short tandem repeat (STR) and identity-informative (iSNPs), ancestry-informative (aSNPs), and phenotype-informative (pSNPs) single nucleotide polymorphism (SNP) allele frequencies are reported. Sequence-based allelic variants were observed in 13 autosomal, 3 X, and 3 Y STRs. These observations increased observed and expected heterozygosities for autosomal STRs by 0.081±0.068 and 0.073±0.063, respectively, and decreased single-locus random match probabilities by 0.051±0.043 for 13 autosomal STRs. The autosomal random match probabilities (RMPs) were 2.37×10-26 and 2.81×10-29 for length-based and sequence-based alleles, respectively. There were 22 and 25 unique Y-STR haplotypes among 26 males, generating haplotype diversities of 0.95 and 0.96, for length-based and sequencebased alleles, respectively. Of the 26 haplotypes generated, 17 were assigned to haplogroup Q, three to haplogroup R1b, two each to haplogroups E1b1b and L, and one each to haplogroups R1a and I1. Male and female sequence-based X-STR random match probabilities were 3.28×10-7 and 1.22×10-6, respectively. The average observed and expected heterozygosities for 94 iSNPs were 0.39±0.12 and 0.39±0.13, respectively, and the combined iSNP RMP was 1.08×10-32. The combined STR and iSNP RMPs were 2.55×10-58 and 3.02×10-61 for length-based and sequence-based STR alleles, respectively. Ancestry and phenotypic SNP information, performed using the ForenSeq™ Universal Analysis Software, predicted black hair, brown eyes, and some probability of East Asian ancestry for all but one sample that clustered between European and Admixed American ancestry on a principal components analysis. These data serve as the first population assessment using the ForenSeq™ panel and highlight the value of employing sequence-based alleles for forensic DNA typing to increase heterozygosity, which is beneficial for identity testing in populations with reduced genetic diversity.

Authors+Show Affiliations

Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd. Fort Worth, TX 76107, USA. Electronic address: Frank.Wendt@my.unthsc.edu.Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd. Fort Worth, TX 76107, USA.Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd. Fort Worth, TX 76107, USA.Institute of Applied Genetics, Department of Molecular and Medical Genetics, 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 of Applied Genetics, Department of Molecular and Medical Genetics, 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, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

Language

eng

PubMed ID

27243782

Citation

Wendt, Frank R., et al. "Genetic Analysis of the Yavapai Native Americans From West-Central Arizona Using the Illumina MiSeq FGx™ Forensic Genomics System." Forensic Science International. Genetics, vol. 24, 2016, pp. 18-23.
Wendt FR, Churchill JD, Novroski NMM, et al. Genetic analysis of the Yavapai Native Americans from West-Central Arizona using the Illumina MiSeq FGx™ forensic genomics system. Forensic Sci Int Genet. 2016;24:18-23.
Wendt, F. R., Churchill, J. D., Novroski, N. M. M., King, J. L., Ng, J., Oldt, R. F., McCulloh, K. L., Weise, J. A., Smith, D. G., Kanthaswamy, S., & Budowle, B. (2016). Genetic analysis of the Yavapai Native Americans from West-Central Arizona using the Illumina MiSeq FGx™ forensic genomics system. Forensic Science International. Genetics, 24, 18-23. https://doi.org/10.1016/j.fsigen.2016.05.008
Wendt FR, et al. Genetic Analysis of the Yavapai Native Americans From West-Central Arizona Using the Illumina MiSeq FGx™ Forensic Genomics System. Forensic Sci Int Genet. 2016;24:18-23. PubMed PMID: 27243782.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Genetic analysis of the Yavapai Native Americans from West-Central Arizona using the Illumina MiSeq FGx™ forensic genomics system. AU - Wendt,Frank R, AU - Churchill,Jennifer D, AU - Novroski,Nicole M M, AU - King,Jonathan L, 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 - 2016/05/17/ PY - 2016/02/15/received PY - 2016/05/10/revised PY - 2016/05/14/accepted PY - 2016/6/1/entrez PY - 2016/6/1/pubmed PY - 2017/6/15/medline KW - Allele frequencies KW - FGx™ system KW - ForenSeq™ DNA signature prep kit KW - Native american population KW - Population genetics KW - Yavapai SP - 18 EP - 23 JF - Forensic science international. Genetics JO - Forensic Sci Int Genet VL - 24 N2 - Forensically-relevant genetic markers were typed for sixty-two Yavapai Native Americans using the ForenSeq™ DNA Signature Prep Kit.These data are invaluable to the human identity community due to the greater genetic differentiation among Native American tribes than among other subdivisions within major populations of the United States. Autosomal, X-chromosomal, and Y-chromosomal short tandem repeat (STR) and identity-informative (iSNPs), ancestry-informative (aSNPs), and phenotype-informative (pSNPs) single nucleotide polymorphism (SNP) allele frequencies are reported. Sequence-based allelic variants were observed in 13 autosomal, 3 X, and 3 Y STRs. These observations increased observed and expected heterozygosities for autosomal STRs by 0.081±0.068 and 0.073±0.063, respectively, and decreased single-locus random match probabilities by 0.051±0.043 for 13 autosomal STRs. The autosomal random match probabilities (RMPs) were 2.37×10-26 and 2.81×10-29 for length-based and sequence-based alleles, respectively. There were 22 and 25 unique Y-STR haplotypes among 26 males, generating haplotype diversities of 0.95 and 0.96, for length-based and sequencebased alleles, respectively. Of the 26 haplotypes generated, 17 were assigned to haplogroup Q, three to haplogroup R1b, two each to haplogroups E1b1b and L, and one each to haplogroups R1a and I1. Male and female sequence-based X-STR random match probabilities were 3.28×10-7 and 1.22×10-6, respectively. The average observed and expected heterozygosities for 94 iSNPs were 0.39±0.12 and 0.39±0.13, respectively, and the combined iSNP RMP was 1.08×10-32. The combined STR and iSNP RMPs were 2.55×10-58 and 3.02×10-61 for length-based and sequence-based STR alleles, respectively. Ancestry and phenotypic SNP information, performed using the ForenSeq™ Universal Analysis Software, predicted black hair, brown eyes, and some probability of East Asian ancestry for all but one sample that clustered between European and Admixed American ancestry on a principal components analysis. These data serve as the first population assessment using the ForenSeq™ panel and highlight the value of employing sequence-based alleles for forensic DNA typing to increase heterozygosity, which is beneficial for identity testing in populations with reduced genetic diversity. SN - 1878-0326 UR - https://www.unboundmedicine.com/medline/citation/27243782/Genetic_analysis_of_the_Yavapai_Native_Americans_from_West_Central_Arizona_using_the_Illumina_MiSeq_FGx™_forensic_genomics_system_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S1872-4973(16)30077-1 DB - PRIME DP - Unbound Medicine ER -