Large-scale genotyping of complex DNA
Large-scale genotyping of complex DNA
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DOI：
10.1038/nbt869
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发表时间：
2003-10-01
影响因子：
46.9
通讯作者：
Jones, KW
中科院分区：
文献类型：
--
作者：
Kennedy, GC;Matsuzaki, H;Jones, KW
遗传学研究旨在了解复杂人类表型的分子基础，需要对大量个体中成千上万的单核苷酸多态性（snp）进行基因分型(1)。到目前为止，公众的努力已经确定了超过200万个常见的人类snp (2)；然而，这些snp的评分是劳动密集型的，需要大量的自动化。在这里，我们描述了一种简单而有效的方法，称为全基因组采样分析（WGSA），用于在没有位点特异性引物或自动化的情况下同时对复杂DNA样品中的数千个snp进行基因分型。我们的方法在多个DNA样本中扩增高度可重复的基因组部分，并以>99%的准确率调用基因型。我们在三个不同的人群中快速对14,548个snp进行了基因分型，并确定了其中一个子集在群体之间具有显着的等位基因频率差异。我们还通过黑猩猩和大猩猩DNA的基因分型确定了8,386个snp的祖先等位基因。WGSA具有高度可扩展性，可以创建用于遗传研究的超高密度SNP图谱。
Genetic studies aimed at understanding the molecular basis of complex human phenotypes require the genotyping of many thousands of single-nucleotide polymorphisms (SNPs) across large numbers of individuals(1). Public efforts have so far identified over two million common human SNPs(2); however, the scoring of these SNPs is labor-intensive and requires a substantial amount of automation. Here we describe a simple but effective approach, termed whole-genome sampling analysis (WGSA), for genotyping thousands of SNPs simultaneously in a complex DNA sample without locus-specific primers or automation. Our method amplifies highly reproducible fractions of the genome across multiple DNA samples and calls genotypes at >99% accuracy. We rapidly genotyped 14,548 SNPs in three different human populations and identified a subset of them with significant allele frequency differences between groups. We also determined the ancestral allele for 8,386 SNPs by genotyping chimpanzee and gorilla DNA. WGSA is highly scaleable and enables the creation of ultrahigh density SNP maps for use in genetic studies.