Wendt Frank R, Churchill Jennifer D, Novroski Nicole M M, King Jonathan L, Ng Jillian, Oldt Robert F, McCulloh Kelly L, Weise Jessica A, Smith David Glenn, Kanthaswamy Sreetharan, Budowle Bruce
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.
Forensic Sci Int Genet. 2016 Sep;24:18-23. doi: 10.1016/j.fsigen.2016.05.008. Epub 2016 May 17.
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.
使用ForenSeq™ DNA Signature Prep试剂盒对62名雅瓦派印第安原住民进行了法医相关基因标记分型。由于美国主要人群中，印第安部落之间的基因差异大于其他细分群体，这些数据对人类身份识别领域而言价值非凡。本文报告了常染色体、X染色体和Y染色体短串联重复序列（STR）以及身份信息单核苷酸多态性（iSNP）、祖先信息单核苷酸多态性（aSNP）和表型信息单核苷酸多态性（pSNP）的等位基因频率。在13个常染色体、3个X染色体和3个Y染色体STR中观察到基于序列的等位基因变异。这些观察结果使常染色体STR的观察杂合度和期望杂合度分别增加了0.081±0.068和0.073±0.063，并使13个常染色体STR的单基因座随机匹配概率降低了0.051±0.043。基于长度和基于序列的等位基因的常染色体随机匹配概率（RMP）分别为2.37×10-26和2.81×10-29。26名男性中分别有22种和25种独特的Y-STR单倍型，基于长度和基于序列的等位基因的单倍型多样性分别为0.95和0.96。在生成的26种单倍型中，17种被归为Q单倍群，3种归为R1b单倍群，E1b1b和L单倍群各2种，R1a和I1单倍群各1种。基于序列的男性和女性X-STR随机匹配概率分别为为3.28×10-7和1.22×10-6。94个iSNP的平均观察杂合度和期望杂合度分别为0.39±0.12和0.39±0.13，iSNP组合RMP为1.08×10-32。基于长度和基于序列的STR等位基因的STR和iSNP组合RMP分别为2.55×10-58和3.02×！0-61。使用ForenSeq™通用分析软件进行的祖先和表型SNP信息分析预测，除了一个在主成分分析中聚类于欧洲和混合美洲祖先之间的样本外，所有样本均为黑发、棕眼，且有一定概率具有东亚血统。这些数据是使用ForenSeq™检测板进行的首次群体评估，突出了使用基于序列的等位基因进行法医DNA分型以增加杂合度的价值，这有利于在遗传多样性降低的人群中进行身份测试。
