一种使用连锁不平衡标准进行标签单核苷酸多态性选择的高效综合搜索算法。
An efficient comprehensive search algorithm for tagSNP selection using linkage disequilibrium criteria.
作者信息
Qin Zhaohui S, Gopalakrishnan Shyam, Abecasis Gonçalo R
机构信息
Center for Statistical Genetics, Department of Biostatistics, School of Public Health, University of Michigan 1420 Washington Heights, Ann Arbor, MI 48109-2029, USA.
出版信息
Bioinformatics. 2006 Jan 15;22(2):220-5. doi: 10.1093/bioinformatics/bti762. Epub 2005 Nov 3.
MOTIVATION
Selecting SNP markers for genome-wide association studies is an important and challenging task. The goal is to minimize the number of markers selected for genotyping in a particular platform and therefore reduce genotyping cost while simultaneously maximizing the information content provided by selected markers.
RESULTS
We devised an improved algorithm for tagSNP selection using the pairwise r(2) criterion. We first break down large marker sets into disjoint pieces, where more exhaustive searches can replace the greedy algorithm for tagSNP selection. These exhaustive searches lead to smaller tagSNP sets being generated. In addition, our method evaluates multiple solutions that are equivalent according to the linkage disequilibrium criteria to accommodate additional constraints. Its performance was assessed using HapMap data.
AVAILABILITY
A computer program named FESTA has been developed based on this algorithm. The program is freely available and can be downloaded at http://www.sph.umich.edu/csg/qin/FESTA/
动机
为全基因组关联研究选择单核苷酸多态性（SNP）标记是一项重要且具有挑战性的任务。目标是在特定平台上尽量减少用于基因分型的标记数量，从而降低基因分型成本，同时使所选标记提供的信息含量最大化。
结果
我们设计了一种使用成对r(2)标准进行标签SNP选择的改进算法。我们首先将大型标记集分解为不相交的片段，在这些片段中，更详尽的搜索可以替代用于标签SNP选择的贪心算法。这些详尽的搜索导致生成更小的标签SNP集。此外，我们的方法评估根据连锁不平衡标准等效的多个解决方案，以适应额外的约束条件。使用HapMap数据评估了其性能。
可用性
基于此算法开发了一个名为FESTA的计算机程序。该程序可免费获取，可从http://www.sph.umich.edu/csg/qin/FESTA/下载。
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