Evaluating coverage of genome-wide association studies
Evaluating coverage of genome-wide association studies
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DOI：
10.1038/ng1801
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发表时间：
2006-06-01
期刊：
影响因子：
30.8
通讯作者：
Cardon, Lon R.
中科院分区：
文献类型：
--
作者：
Barrett, Jeffrey C.;Cardon, Lon R.
目前正在进行全基因组关联研究，涉及数千个病例和对照中的数十万个 SNP。这些研究中的许多分析挑战中的第一个涉及到基因型 SNP 的选择。为每项研究构建不同的标签 SNP 面板是不切实际的，因此第一代全基因组扫描将使用预定义的、市售的标记面板，这将在一定程度上决定其成功或失败。我们比较了当今使用的不同方法，结果表明，尽管其中许多方法基本上覆盖了非非洲人群中的常见变异，但精确范围在很大程度上取决于感兴趣的等位基因的频率和研究设计的具体考虑因素。总体而言，尽管基因分型技术、标记选择策略和检测的标记数量存在显着差异，但第一代高通量平台均提供相似水平的基因组覆盖率。
Genome-wide association studies involving hundreds of thousands of SNPs in thousands of cases and controls are now underway. The first of many analytical challenges in these studies involves the choice of SNPs to genotype. It is not practical to construct a different panel of tag SNPs for each study, so the first generation of genome-wide scans will use predefined, commercially available marker panels, which will in part dictate their success or failure. We compare different approaches in use today, and show that although many of them provide substantial coverage of common variation in non-African populations, the precise extent is strongly dependent on the frequencies of alleles of interest and on specific considerations of study design. Overall, despite substantial differences in genotyping technologies, marker selection strategies and number of markers assayed, the first-generation high-throughput platforms all offer similar levels of genome coverage.