Wendt Frank R, Warshauer David H, Zeng Xiangpei, Churchill Jennifer D, Novroski Nicole M M, Song Bing, King Jonathan L, LaRue Bobby L, 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.
Promega Corporation, 2800 Woods Hollow Rd, Madison, WI, 53711, USA.
Forensic Sci Int Genet. 2016 Nov;25:198-209. doi: 10.1016/j.fsigen.2016.09.005. Epub 2016 Sep 20.
Short tandem repeat (STR) loci are the traditional markers used for kinship, missing persons, and direct comparison human identity testing. These markers hold considerable value due to their highly polymorphic nature, amplicon size, and ability to be multiplexed. However, many STRs are still too large for use in analysis of highly degraded DNA. Small bi-allelic polymorphisms, such as insertions/deletions (INDELs), may be better suited for analyzing compromised samples, and their allele size differences are amenable to analysis by capillary electrophoresis. The INDEL marker allelic states range in size from 2 to 6 base pairs, enabling small amplicon size. In addition, heterozygote balance may be increased by minimizing preferential amplification of the smaller allele, as is more common with STR markers. Multiplexing a large number of INDELs allows for generating panels with high discrimination power. The Nextera™ Rapid Capture Custom Enrichment Kit (Illumina, Inc., San Diego, CA) and massively parallel sequencing (MPS) on the Illumina MiSeq were used to sequence 68 well-characterized INDELs in four major US population groups. In addition, the STR Allele Identification Tool: Razor (STRait Razor) was used in a novel way to analyze INDEL sequences and detect adjacent single nucleotide polymorphisms (SNPs) and other polymorphisms. This application enabled the discovery of unique allelic variants, which increased the discrimination power and decreased the single-locus random match probabilities (RMPs) of 22 of these well-characterized INDELs which can be considered as microhaplotypes. These findings suggest that additional microhaplotypes containing human identification (HID) INDELs may exist elsewhere in the genome.
短串联重复序列（STR）位点是用于亲缘关系鉴定、失踪人员查找和直接比较个体身份检测的传统标记。由于其高度多态性、扩增子大小以及可进行多重分析的能力，这些标记具有重要价值。然而，许多STR对于高度降解的DNA分析来说仍然太大。小的双等位基因多态性，如插入/缺失（INDEL），可能更适合分析受损样本，并且它们的等位基因大小差异适合通过毛细管电泳进行分析。INDEL标记的等位基因状态大小范围为2至6个碱基对，使得扩增子较小。此外，通过尽量减少较小等位基因的优先扩增，可以提高杂合子平衡，这在STR标记中更为常见。对大量INDEL进行多重分析可以生成具有高鉴别力的面板。使用Nextera™快速捕获定制富集试剂盒（Illumina公司，加利福尼亚州圣地亚哥）和Illumina MiSeq上的大规模平行测序（MPS）对美国四个主要人群组中的68个特征明确的INDEL进行测序。此外，STR等位基因识别工具：Razor（STRait Razor）以一种新颖的方式用于分析INDEL序列并检测相邻的单核苷酸多态性（SNP）和其他多态性。该应用能够发现独特的等位基因变体，提高了鉴别力，并降低了其中22个可被视为微单倍型的特征明确的INDEL的单基因座随机匹配概率（RMP）。这些发现表明，基因组中其他地方可能存在包含人类身份识别（HID）INDEL的额外微单倍型。
