Institute of Legal Medicine, Innsbruck Medical University, Austria.
Forensic Sci Int Genet. 2011 Mar;5(2):133-7. doi: 10.1016/j.fsigen.2010.10.003. Epub 2010 Nov 10.
The application of quasi-median networks provides an effective tool to check the quality of mtDNA data. Filtering of highly recurrent mutations prior to network analysis is required to simplify the data set and reduce the complexity of the network. The phylogenetic background determines those mutations that need to be filtered. While the traditional EMPOPspeedy filter was based on the worldwide mtDNA phylogeny, haplogroup-specific filters can more effectively highlight potential errors in data of the respective (sub)-continental region. In this study we demonstrate the performance of a new, west Eurasian filter EMPOPspeedyWE for the fine-tuned examination of data sets belonging to macrohaplogroup N that constitutes the main portion of mtDNA lineages in Europe. The effects on the resulting network of different database sizes, high-quality and flawed data, as well as the examination of a phylogenetically distant data set, are presented by examples. The analyses are based on a west Eurasian etalon data set that was carefully compiled from more than 3500 control region sequences for network purposes. Both, etalon data and the new filter file, are provided through the EMPOP database (www.empop.org).
拟中值网络的应用为检查 mtDNA 数据的质量提供了一种有效工具。在进行网络分析之前，需要对高度重复的突变进行过滤，以简化数据集并降低网络的复杂性。系统发生背景决定了需要过滤的突变。虽然传统的 EMPOPspeedy 过滤器基于全球 mtDNA 系统发生，但特定于单倍群的过滤器可以更有效地突出各自（亚）大陆区域数据中的潜在错误。在这项研究中，我们展示了一种新的、西部欧亚过滤器 EMPOPspeedyWE 的性能，该过滤器可用于对构成欧洲 mtDNA 谱系主要部分的主要单倍群 N 的数据集进行精细检查。通过示例展示了不同数据库大小、高质量和有缺陷的数据对生成网络的影响，以及对系统发生上遥远数据集的检查。分析基于一个精心编译的西部欧亚标准数据集，该数据集由 3500 多个控制区序列组成，用于网络目的。标准数据集和新的过滤器文件都通过 EMPOP 数据库（www.empop.org）提供。
