Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria.
Forensic Sci Int Genet. 2013 Sep;7(5):543-9. doi: 10.1016/j.fsigen.2013.06.003. Epub 2013 Jul 23.
Insights into the human mitochondrial phylogeny have been primarily achieved by sequencing full mitochondrial genomes (mtGenomes). In forensic genetics (partial) mtGenome information can be used to assign haplotypes to their phylogenetic backgrounds, which may, in turn, have characteristic geographic distributions that would offer useful information in a forensic case. In addition and perhaps even more relevant in the forensic context, haplogroup-specific patterns of mutations form the basis for quality control of mtDNA sequences. The current method for establishing (partial) mtDNA haplotypes is Sanger-type sequencing (STS), which is laborious, time-consuming, and expensive. With the emergence of Next Generation Sequencing (NGS) technologies, the body of available mtDNA data can potentially be extended much more quickly and cost-efficiently. Customized chemistries, laboratory workflows and data analysis packages could support the community and increase the utility of mtDNA analysis in forensics. We have evaluated the performance of mtGenome sequencing using the Personal Genome Machine (PGM) and compared the resulting haplotypes directly with conventional Sanger-type sequencing. A total of 64mtGenomes (>1 million bases) were established that yielded high concordance with the corresponding STS haplotypes (<0.02% differences). About two-thirds of the differences were observed in or around homopolymeric sequence stretches. In addition, the sequence alignment algorithm employed to align NGS reads played a significant role in the analysis of the data and the resulting mtDNA haplotypes. Further development of alignment software would be desirable to facilitate the application of NGS in mtDNA forensic genetics.
人类线粒体系统发生的研究主要通过测序完整的线粒体基因组（mtGenome）来实现。在法医学遗传学中（部分）mtGenome 信息可用于将单倍型分配到其系统发生背景中，这些背景可能具有特征性的地理分布，从而在法医学案件中提供有用的信息。此外，在法医学背景下，可能更为相关的是，单倍型特异性突变模式为 mtDNA 序列的质量控制提供了基础。目前建立（部分）mtDNA 单倍型的方法是桑格型测序（STS），这种方法既费力、耗时又昂贵。随着新一代测序（NGS）技术的出现，可用 mtDNA 数据的数量有可能更快、更具成本效益地扩展。定制的化学、实验室工作流程和数据分析软件包可以支持社区，并提高 mtDNA 分析在法医学中的实用性。我们使用个人基因组机（PGM）评估了 mtGenome 测序的性能，并直接将得到的单倍型与传统的桑格型测序进行了比较。总共建立了 64 个 mtGenome（超过 100 万个碱基对），与相应的 STS 单倍型高度一致（<0.02%的差异）。大约三分之二的差异发生在或围绕着高度同源序列延伸处。此外，用于对齐 NGS 读取的序列比对算法在数据分析和得到的 mtDNA 单倍型中起着重要作用。进一步开发对齐软件将有助于 NGS 在 mtDNA 法医遗传学中的应用。
