The Genographic Project public participation mitochondrial DNA database.
The Genographic Project public participation mitochondrial DNA database.
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DOI：
10.1371/journal.pgen.0030104
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发表时间：
2007-06
期刊：
影响因子：
4.5
通讯作者：
Genographic Consortium
中科院分区：
文献类型：
--
作者：
Behar DM;Rosset S;Blue-Smith J;Balanovsky O;Tzur S;Comas D;Mitchell RJ;Quintana-Murci L;Tyler-Smith C;Wells RS;Genographic Consortium
Genographic Project正在研究古代人类迁徙的基因特征，并创建一个开源研究数据库。它允许公众参与实时人类学遗传学研究，提交个人样本进行分析，并将遗传结果捐赠给数据库。我们报告了公众参与基因组计划的前18个月的经验，在此期间，我们创建了有史以来收集的最大的标准化人类线粒体DNA（mtDNA）数据库，包括78，590种基因型。在这里，我们详细介绍了我们的基因分型和质量保证方案，包括线粒体DNA HVS-I的直接测序、22个编码区SNP的基因分型以及一系列基于系统发育原则的计算质量检查。这个数据库是非常翔实的mtDNA单倍型发生和突变动力学方面，它的大小允许我们开发一个最近邻为基础的方法预测的基础上HVS-I模体是上级经典的基于规则的方法。我们向科学界和公众提供了两个新的资源：一个定期更新的数据库，包括参与者捐赠的所有数据，以及最近邻单倍群预测工具。基因地理项目于2005年启动，以遗传学为工具，在全球范围内解决人类学问题。样品以两种方式收集。首先，该项目由来自世界各地的10个科学团队组成，由一个核心伦理和科学框架联合起来，负责各自区域的样本收集和分析。第二，该项目促进世界各国的公众参与，任何人都可以通过购买参与工具包参与（视频S1）。女性参与者的线粒体DNA（mtDNA）是从母亲那里遗传的，没有重组，特别是关于母系血统的信息。在公众参与该项目的前18个月里，我们建立了迄今为止最大的mtDNA变异数据库，包含来自世界各地的78，590个条目。在这里，我们描述了用于生成，管理和分析遗传数据的程序，以及从中获得的第一个见解。我们可以了解mtDNA树结构的新方面，并开发出更好的mtDNA分类方法。因此，我们现在发布这个数据集和我们开发的新方法，并将随着更多人加入基因组计划而继续更新它们。
The Genographic Project is studying the genetic signatures of ancient human migrations and creating an open-source research database. It allows members of the public to participate in a real-time anthropological genetics study by submitting personal samples for analysis and donating the genetic results to the database. We report our experience from the first 18 months of public participation in the Genographic Project, during which we have created the largest standardized human mitochondrial DNA (mtDNA) database ever collected, comprising 78,590 genotypes. Here, we detail our genotyping and quality assurance protocols including direct sequencing of the mtDNA HVS-I, genotyping of 22 coding-region SNPs, and a series of computational quality checks based on phylogenetic principles. This database is very informative with respect to mtDNA phylogeny and mutational dynamics, and its size allows us to develop a nearest neighbor–based methodology for mtDNA haplogroup prediction based on HVS-I motifs that is superior to classic rule-based approaches. We make available to the scientific community and general public two new resources: a periodically updated database comprising all data donated by participants, and the nearest neighbor haplogroup prediction tool. The Genographic Project was launched in 2005 to address anthropological questions on a global scale using genetics as a tool. Samples are collected in two ways. First, the project comprises a consortium of ten scientific teams from around the world united by a core ethical and scientific framework that is responsible for sample collection and analysis in their respective region. Second, the project promotes public participation in countries around the world and anyone can participate by purchasing a participation kit (Video S1). The mitochondrial DNA (mtDNA), typed in female participants, is inherited from the mother without recombining, being particularly informative with respect to maternal ancestry. Over the first 18 months of public participation in the project we have built up the largest to date database of mtDNA variants, containing 78,590 entries from around the world. Here, we describe the procedures used to generate, manage, and analyze the genetic data, and the first insights from them. We can understand new aspects of the structure of the mtDNA tree and develop much better ways of classifying mtDNA. We therefore now release this dataset and the new methods we have developed, and will continue to update them as more people join the Genographic Project.
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影响因子：
2.1
作者：
Brandstätter, A;Peterson, CT;Parsons, TJ
通讯作者：
Parsons, TJ
影响因子：
2.1
作者：
Bandelt, HJ;Salas, A;Lutz-Bonengel, S
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Lutz-Bonengel, S
影响因子：
2.1
作者：
Bandelt, HJ;Lahermo, P;Macaulay, V
通讯作者：
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影响因子：
9.8
作者：
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通讯作者：
Kalaydjieva, L
影响因子：
5.2
作者：
Behar, DM;Hammer, MF;Skorecki, K
通讯作者：
Skorecki, K