Tsui Circe, Coleman Laura E, Griffith Jacqulyn L, Bennett E Andrew, Goodson Summer G, Scott Jason D, Pittard W Stephen, Devine Scott E
Department of Biochemistry, Center for Bioinformatics, Emory University School of Medicine, Atlanta, GA 30322, USA.
Nucleic Acids Res. 2003 Aug 15;31(16):4910-6. doi: 10.1093/nar/gkg664.
An international effort is underway to generate a comprehensive haplotype map (HapMap) of the human genome represented by an estimated 300,000 to 1 million 'tag' single nucleotide polymorphisms (SNPs). Our analysis indicates that the current human SNP map is not sufficiently dense to support the HapMap project. For example, 24.6% of the genome currently lacks SNPs at the minimal density and spacing that would be required to construct even a conservative tag SNP map containing 300,000 SNPs. In an effort to improve the human SNP map, we identified 140,696 additional SNP candidates using a new bioinformatics pipeline. Over 51,000 of these SNPs mapped to the largest gaps in the human SNP map, leading to significant improvements in these regions. Our SNPs will be immediately useful for the HapMap project, and will allow for the inclusion of many additional genomic intervals in the final HapMap. Nevertheless, our results also indicate that additional SNP discovery projects will be required both to define the haplotype architecture of the human genome and to construct comprehensive tag SNP maps that will be useful for genetic linkage studies in humans.
一项国际合作正在进行中，旨在生成一份涵盖约30万至100万个“标签”单核苷酸多态性（SNP）的人类基因组综合单倍型图谱（HapMap）。我们的分析表明，当前的人类SNP图谱密度不足，无法支持HapMap计划。例如，目前基因组中有24.6%的区域缺乏构建包含30万个SNP的保守标签SNP图谱所需的最小密度和间距的SNP。为了改进人类SNP图谱，我们使用新的生物信息学流程鉴定了另外140,696个SNP候选位点。其中超过51,000个SNP定位到人类SNP图谱中最大的空白区域，使这些区域得到了显著改善。我们发现的SNP将立即对HapMap计划有用，并将使最终的HapMap能够纳入更多的基因组区间。然而，我们的结果也表明，还需要开展更多的SNP发现项目，以确定人类基因组的单倍型结构，并构建对人类遗传连锁研究有用的综合标签SNP图谱。
