Barrett Jeffrey C, Cardon Lon R
Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.
Nat Genet. 2006 Jun;38(6):659-62. doi: 10.1038/ng1801. Epub 2006 May 21.
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.
目前正在开展涉及数千例病例和对照的数十万个单核苷酸多态性（SNP）的全基因组关联研究。这些研究中众多分析挑战的第一个涉及用于基因分型的SNP的选择。为每项研究构建不同的标签SNP面板并不实际，因此第一代全基因组扫描将使用预定义的、可商购的标记面板，这将部分决定其成败。我们比较了当今使用的不同方法，并表明尽管其中许多方法在非非洲人群中对常见变异提供了大量覆盖，但精确程度强烈依赖于感兴趣等位基因的频率以及研究设计的具体考量。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著差异，但第一代高通量平台都提供了相似水平的基因组覆盖。
