HaploGrep: A Fast and Reliable Algorithm for Automatic Classification of Mitochondrial DNA Haplogroups
HaploGrep: A Fast and Reliable Algorithm for Automatic Classification of Mitochondrial DNA Haplogroups
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DOI：
10.1002/humu.21382
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发表时间：
2011-01-01
期刊：
影响因子：
3.9
通讯作者：
Kronenberg, Florian
中科院分区：
文献类型：
--
作者：
Kloss-Brandstaetter, Anita;Pacher, Dominic;Kronenberg, Florian
线粒体DNA （mtDNA）研究中一个持续的争议来源是基于对mtDNA谱中大量错误的检测，这些错误导致了错误的结论和错误的疾病关联。如果考虑到样本的单倍群状态，这些争议大多可以避免。了解mtDNA单倍群隶属关系是研究人类进化机制和发现复杂疾病相关基因的关键前提，而利用单倍群分类验证系统发育一致性是质量控制的重要一步。然而，尽管有定期更新的全球mtDNA变异分类树Phylotree，单倍群分类的过程仍然是耗时且容易出错的，因为研究人员必须手动将种群样本中发现的多态性与Phylotree中总结的多态性进行比较，一个多态性一个多态性，一个样本一个样本。我们提出了HaploGrep，一个快速、可靠和直接的算法，在一个Web应用程序中实现，用于确定数千个mtDNA基因型的单倍群隶属关系，用于整个mtDNA或其任何部分。HaploGrep使用最新版本的Phylotree，为临床遗传学、群体遗传学和法医学中mtDNA谱的质量评估提供了一个一体化的解决方案。HaploGrep可以在http://haplogrep.uibk.ac.at免费访问。Hum Mutat 32:25-32, 2011。(C) 2010 Wiley-Liss, Inc。
An ongoing source of controversy in mitochondrial DNA (mtDNA) research is based on the detection of numerous errors in mtDNA profiles that led to erroneous conclusions and false disease associations. Most of these controversies could be avoided if the samples' haplogroup status would be taken into consideration. Knowing the mtDNA haplogroup affiliation is a critical prerequisite for studying mechanisms of human evolution and discovering genes involved in complex diseases, and validating phylogenetic consistency using haplogroup classification is an important step in quality control. However, despite the availability of Phylotree, a regularly updated classification tree of global mtDNA variation, the process of haplogroup classification is still time-consuming and error-prone, as researchers have to manually compare the polymorphisms found in a population sample to those summarized in Phylotree, polymorphism by polymorphism, sample by sample. We present HaploGrep, a fast, reliable and straight-forward algorithm implemented in a Web application to determine the haplogroup affiliation of thousands of mtDNA profiles genotyped for the entire mtDNA or any part of it. HaploGrep uses the latest version of Phylotree and offers an all-in-one solution for quality assessment of mtDNA profiles in clinical genetics, population genetics and forensics. HaploGrep can be accessed freely at http://haplogrep.uibk.ac.at. Hum Mutat 32:25-32, 2011. (C) 2010 Wiley-Liss, Inc.