Division of Biological Traces, Netherlands Forensic Institute, The Hague, The Netherlands.
Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
Forensic Sci Int Genet. 2021 May;52:102489. doi: 10.1016/j.fsigen.2021.102489. Epub 2021 Feb 26.
The interpretation of short tandem repeat (STR) profiles can be challenging when, for example, alleles are masked due to allele sharing among contributors and/or when they are subject to drop-out, for instance from sample degradation. Mixture interpretation can be improved by increasing the number of STRs and/or loci with a higher discriminatory power. Both capillary electrophoresis (CE, 6-dye) and massively parallel sequencing (MPS) provide a platform for analysing relatively large numbers of autosomal STRs. In addition, MPS enables distinguishing between sequence variants, resulting in enlarged discriminatory power. Also, MPS allows for small amplicon sizes for all loci as spacing is not an issue, which is beneficial with degraded DNA. Altogether, MPS has the potential to increase the weights of evidence for true contributors to (complex) DNA profiles. In this study, likelihood ratio (LR) calculations were performed using STR profiles obtained with two different MPS systems and analysed using different settings: 1) MPS PowerSeq™ Auto System profiles analysed using FDSTools equipped with optimized settings such as noise correction, 2) ForenSeq™ DNA Signature Prep Kit profiles analysed using the default settings in the Universal Analysis Software (UAS), and 3) ForenSeq™ DNA Signature Prep Kit profiles analysed using FDSTools empirically adapted to cope with one-directional reads and provisional, basic settings. The LR calculations used genotyping data for two- to four-person mixtures varying for mixture proportion, level of drop-out and allele sharing and were generated with the continuous model EuroForMix. The LR results for the over 2000 sets of propositions were affected by the variation for the number of markers and analysis settings used in the three approaches. Nevertheless, trends for true and non-contributors, effects of replicates, assigned number of contributors, and model validation results were comparable for the three MPS approaches and alike the trends known for CE data. Based on this analogy, we regard the probabilistic interpretation of MPS STR data fit for forensic DNA casework. In addition, guidelines were derived on when to apply LR calculations to MPS autosomal STR data and report the corresponding results.
短串联重复序列（STR）谱的解释可能具有挑战性，例如，由于供体之间的等位基因共享以及/或者当它们受到例如样品降解的影响而导致等位基因丢失。通过增加具有更高鉴别力的 STR 和/或基因座的数量，可以改善混合物的解释。毛细管电泳（CE，6 染料）和大规模平行测序（MPS）都为分析相对大量的常染色体 STR 提供了平台。此外，MPS 能够区分序列变异体，从而提高鉴别力。此外，MPS 允许所有基因座的小扩增子大小，因为间距不是问题，这对于降解 DNA 是有益的。总之，MPS 有可能增加（复杂）DNA 谱中真实供体的证据权重。在这项研究中，使用两种不同的 MPS 系统获得的 STR 谱进行似然比（LR）计算，并使用不同的设置进行分析：1）使用配备了噪声校正等优化设置的 FDSTools 分析 MPS PowerSeq™ Auto System 谱，2）使用 Universal Analysis Software（UAS）中的默认设置分析 ForenSeq™ DNA Signature Prep Kit 谱，以及 3）使用 FDSTools 分析 ForenSeq™ DNA Signature Prep Kit 谱，该软件经过 empirically 适应，以应对单向读取和临时基本设置。LR 计算使用混合比例、缺失水平和等位基因共享变化的二至四人混合物的基因分型数据生成，生成模型为连续模型 EuroForMix。超过 2000 组提议的 LR 结果受到三种方法中所用标记数量和分析设置变化的影响。尽管如此，三种 MPS 方法的真实和非供体趋势、重复的影响、分配的供体数量以及模型验证结果是可比的，并且与 CE 数据的趋势相似。基于这种相似性，我们认为 MPS STR 数据的概率解释适用于法医 DNA 案例工作。此外，还得出了关于何时对 MPS 常染色体 STR 数据应用 LR 计算并报告相应结果的指南。
