Amigo Jorge, Salas Antonio, Phillips Christopher, Carracedo Angel
Spanish National Genotyping Center (CeGen), Genomic Medicine Group, CIBERER, University of Santiago de Compostela, Galicia, Spain.
BMC Bioinformatics. 2008 Oct 10;9:428. doi: 10.1186/1471-2105-9-428.
In the last five years large online resources of human variability have appeared, notably HapMap, Perlegen and the CEPH foundation. These databases of genotypes with population information act as catalogues of human diversity, and are widely used as reference sources for population genetics studies. Although many useful conclusions may be extracted by querying databases individually, the lack of flexibility for combining data from within and between each database does not allow the calculation of key population variability statistics.
We have developed a novel tool for accessing and combining large-scale genomic databases of single nucleotide polymorphisms (SNPs) in widespread use in human population genetics: SPSmart (SNPs for Population Studies). A fast pipeline creates and maintains a data mart from the most commonly accessed databases of genotypes containing population information: data is mined, summarized into the standard statistical reference indices, and stored into a relational database that currently handles as many as 4 x 10(9) genotypes and that can be easily extended to new database initiatives. We have also built a web interface to the data mart that allows the browsing of underlying data indexed by population and the combining of populations, allowing intuitive and straightforward comparison of population groups. All the information served is optimized for web display, and most of the computations are already pre-processed in the data mart to speed up the data browsing and any computational treatment requested.
In practice, SPSmart allows populations to be combined into user-defined groups, while multiple databases can be accessed and compared in a few simple steps from a single query. It performs the queries rapidly and gives straightforward graphical summaries of SNP population variability through visual inspection of allele frequencies outlined in standard pie-chart format. In addition, full numerical description of the data is output in statistical results panels that include common population genetics metrics such as heterozygosity, Fst and In.
在过去五年中，出现了大量关于人类变异性的在线资源，尤其是HapMap、Perlegen和CEPH基金会。这些包含群体信息的基因型数据库充当了人类多样性的目录，并被广泛用作群体遗传学研究的参考来源。尽管通过单独查询数据库可以提取许多有用的结论，但缺乏将每个数据库内部和之间的数据进行组合的灵活性，无法计算关键的群体变异性统计数据。
我们开发了一种新颖的工具，用于访问和组合在人类群体遗传学中广泛使用的单核苷酸多态性（SNP）大规模基因组数据库：SPSmart（用于群体研究的SNP）。一个快速管道从最常用的包含群体信息的基因型数据库创建并维护一个数据集市：数据被挖掘、汇总为标准统计参考指标，并存储到一个关系数据库中，该数据库目前可处理多达4×10⁹个基因型，并且可以轻松扩展到新的数据库计划。我们还为数据集市构建了一个网络界面，允许按群体浏览基础数据并组合群体，从而直观、直接地比较群体。提供的所有信息都针对网络显示进行了优化，并且大多数计算已经在数据集市中进行了预处理，以加快数据浏览和任何所需的计算处理。
在实践中，SPSmart允许将群体组合成用户定义的组，同时可以通过单个查询中的几个简单步骤访问和比较多个数据库。它能快速执行查询，并通过以标准饼图格式概述的等位基因频率的视觉检查，给出SNP群体变异性的直接图形摘要。此外，数据的完整数值描述在统计结果面板中输出，其中包括常见的群体遗传学指标，如杂合度、Fst和In。
