Elwick Kyleen, Bus Magdalena M, King Jonathan L, Chang Joseph, Hughes-Stamm Sheree, Budowle Bruce
Department of Forensic Science, Sam Houston State University, Huntsville, TX, USA.
Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, USA.
Leg Med (Tokyo). 2019 Nov;41:101623. doi: 10.1016/j.legalmed.2019.08.001. Epub 2019 Aug 14.
Often in missing persons' and mass disaster cases, the samples remaining for analysis are hard tissues such as bones, teeth, nails, and hair. These remains may have been exposed to harsh environmental conditions, which pose challenges for downstream genotyping. Short tandem repeat analysis (STR) via capillary electrophoresis (CE) is still the gold standard for DNA typing; however, a newer technology known as massively parallel sequencing (MPS) could improve upon our current techniques by typing different and more markers in a single analysis, and consequently improving the power of discrimination. In this study, bone and tooth samples exposed to a variety of DNA insults (cremation, embalming, decomposition, thermal degradation, and fire) were assessed and sequenced using the Precision ID chemistry and a custom AmpliSeq™ STR and iiSNP panel on the Ion S5™ System, and the ForenSeq DNA Signature Prep Kit on the MiSeq FGx™ system, as well as the GlobalFiler™ PCR Amplification Kit on the 3500™ Genetic Analyzer. The results demonstrated that using traditional CE-based genotyping performed as expected, producing a partial or full DNA profile for all samples, and that both sequencing chemistries and platforms were able to recover sufficient STR and SNP information from a majority of the same challenging samples. Run metrics including profile completeness and mean read depth produced good results with each system, considering the degree of damage of some samples. Most sample insults (except decomposed) produced similar numbers of alleles for both MPS systems. Comparable markers produced full concordance between the two platforms.
在失踪人员和大规模灾难案件中，通常留存用于分析的样本是骨骼、牙齿、指甲和毛发等硬组织。这些遗骸可能已暴露于恶劣的环境条件下，这给下游的基因分型带来了挑战。通过毛细管电泳（CE）进行的短串联重复序列分析（STR）仍是DNA分型的金标准；然而，一种名为大规模平行测序（MPS）的新技术可以通过在单次分析中对更多不同的标记进行分型来改进我们目前的技术，从而提高鉴别能力。在本研究中，使用Precision ID化学方法以及Ion S5™ 系统上的定制AmpliSeq™ STR和iiSNP panel、MiSeq FGx™ 系统上的ForenSeq DNA Signature Prep试剂盒以及3500™ 基因分析仪上的GlobalFiler™ PCR扩增试剂盒，对遭受各种DNA损伤（火化、防腐、分解、热降解和火灾）的骨骼和牙齿样本进行了评估和测序。结果表明，使用基于传统CE的基因分型按预期进行，所有样本均产生了部分或完整的DNA图谱，并且两种测序化学方法和平台都能够从大多数同样具有挑战性的样本中获得足够的STR和SNP信息。考虑到一些样本的损伤程度，包括图谱完整性和平均读深度在内的运行指标在每个系统上都产生了良好的结果。大多数样本损伤（除分解外）在两个MPS系统中产生的等位基因数量相似。两个平台上的可比标记完全一致。
