OpenADAM: an open source genome-wide association data management system for Affymetrix SNP arrays
OpenADAM: an open source genome-wide association data management system for Affymetrix SNP arrays
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DOI：
10.1186/1471-2164-9-636
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发表时间：
2008-12-31
期刊：
影响因子：
4.4
通讯作者：
Cherny, S. S.
中科院分区：
文献类型：
--
作者：
Yeung, J. M. Y.;Sham, P. C.;Cherny, S. S.
背景：自从高通量基因分型平台的引入，大规模的全基因组关联研究变得流行起来。描述：我们已经开发了一个开源的基于网络的数据管理系统，用于处理从AffytechnologyGeneChip（R）Mapping Array和AffytechnologyGenome-Wide Human SNP Array平台生成的大量基因型数据。该数据库支持使用由Affytechnic Power Tools提供的DM、BRLMM、BRLMM-P或Birdseed算法进行基因型调用。基因型和相应的谱系数据存储在关系数据库中，用于有效的下游数据操作和分析，例如等位基因和基因型频率的计算、样品身份检查和以各种文件格式导出基因型数据，用于使用常用软件进行分析。利用HapMap项目中的连锁不平衡信息，实现了一种新的基因分型错误估计方法。所有功能都可以通过基于Web的用户界面访问。结论：OpenADAM提供了一个开源数据库系统来管理Affymetrix全基因组关联SNP数据。
Background: Large scale genome-wide association studies have become popular since the introduction of high throughput genotyping platforms. Efficient management of the vast array of data generated poses many challenges.Description: We have developed an open source web-based data management system for the large amount of genotype data generated from the Affymetrix GeneChip (R) Mapping Array and Affymetrix Genome-Wide Human SNP Array platforms. The database supports genotype calling using DM, BRLMM, BRLMM-P or Birdseed algorithms provided by the Affymetrix Power Tools. The genotype and corresponding pedigree data are stored in a relational database for efficient downstream data manipulation and analysis, such as calculation of allele and genotype frequencies, sample identity checking, and export of genotype data in various file formats for analysis using commonly-available software. A novel method for genotyping error estimation is implemented using linkage disequilibrium information from the HapMap project. All functionalities are accessible via a web-based user interface.Conclusion: OpenADAM provides an open source database system for management of Affymetrix genome-wide association SNP data.