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
N1 - Funding Information:
This study was partly supported by a National Institute of Justice grant 2014-DN-BX-K024 to SK and DGS and a research grant to KM from the UC Davis Forensic Science Graduate Program . Additionally, the authors would like to thank Illumina for kindly providing library preparation and sequencing reagents.
Publisher Copyright:
© 2016 Elsevier Ireland Ltd. All rights reserved.
PY - 2016/9/1
Y1 - 2016/9/1
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.
AB - 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.
KW - Allele frequencies
KW - FGx™ system
KW - ForenSeq™ DNA signature prep kit
KW - Native American population
KW - Population genetics
KW - Yavapai
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U2 - 10.1016/j.fsigen.2016.05.008
DO - 10.1016/j.fsigen.2016.05.008
M3 - Article
C2 - 27243782
AN - SCOPUS:84971317361
SN - 1872-4973
VL - 24
SP - 18
EP - 23
JO - Forensic Science International: Genetics
JF - Forensic Science International: Genetics
ER -