Novroski Nicole M M, King Jonathan L, Churchill Jennifer D, Seah Lay Hong, 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 Nov;25:214-226. doi: 10.1016/j.fsigen.2016.09.007. Epub 2016 Sep 28.
Massively parallel sequencing (MPS) can identify sequence variation within short tandem repeat (STR) alleles as well as their nominal allele lengths that traditionally have been obtained by capillary electrophoresis. Using the MiSeq FGx Forensic Genomics System (Illumina), STRait Razor, and in-house excel workbooks, genetic variation was characterized within STR repeat and flanking regions of 27 autosomal, 7 X-chromosome and 24 Y-chromosome STR markers in 777 unrelated individuals from four population groups. Seven hundred and forty six autosomal, 227 X-chromosome, and 324 Y-chromosome STR alleles were identified by sequence compared with 357 autosomal, 107 X-chromosome, and 189 Y-chromosome STR alleles that were identified by length. Within the observed sequence variation, 227 autosomal, 156 X-chromosome, and 112 Y-chromosome novel alleles were identified and described. One hundred and seventy six autosomal, 123 X-chromosome, and 93 Y-chromosome sequence variants resided within STR repeat regions, and 86 autosomal, 39 X-chromosome, and 20 Y-chromosome variants were located in STR flanking regions. Three markers, D18S51, DXS10135, and DYS385a-b had 1, 4, and 1 alleles, respectively, which contained both a novel repeat region variant and a flanking sequence variant in the same nucleotide sequence. There were 50 markers that demonstrated a relative increase in diversity with the variant sequence alleles compared with those of traditional nominal length alleles. These population data illustrate the genetic variation that exists in the commonly used STR markers in the selected population samples and provide allele frequencies for statistical calculations related to STR profiling with MPS data.
大规模平行测序（MPS）能够识别短串联重复序列（STR）等位基因内的序列变异及其传统上通过毛细管电泳获得的标称等位基因长度。使用MiSeq FGx法医基因组学系统（Illumina）、STRait Razor和内部Excel工作簿，对来自四个群体的777名无关个体的27个常染色体、7个X染色体和24个Y染色体STR标记的STR重复和侧翼区域内的遗传变异进行了表征。通过序列鉴定出746个常染色体、227个X染色体和324个Y染色体STR等位基因，与之相比，通过长度鉴定出357个常染色体、107个X染色体和189个Y染色体STR等位基因。在观察到的序列变异中，鉴定并描述了227个常染色体、156个X染色体和112个Y染色体新等位基因。176个常染色体、123个X染色体和93个Y染色体序列变异位于STR重复区域内，86个常染色体、39个X染色体和20个Y染色体变异位于STR侧翼区域。三个标记D18S51、DXS10135和DYS385a - b分别有1个、4个和1个等位基因，它们在同一核苷酸序列中既包含新的重复区域变异又包含侧翼序列变异。有50个标记与传统标称长度等位基因相比，其变异序列等位基因的多样性相对增加。这些群体数据说明了所选群体样本中常用STR标记存在的遗传变异，并为与MPS数据的STR分析相关的统计计算提供了等位基因频率。
