Sasaki T, Tahira T, Suzuki A, Higasa K, Kukita Y, Baba S, Hayashi K
Division of Genome Analysis, Institute of Genetic Information, Kyushu University, Fukuoka 812-8582, Japan.
Am J Hum Genet. 2001 Jan;68(1):214-8. doi: 10.1086/316928. Epub 2000 Nov 14.
We show that single-nucleotide polymorphisms (SNPs) of moderate to high heterozygosity (minor allele frequencies >10%) can be efficiently detected, and their allele frequencies accurately estimated, by pooling the DNA samples and applying a capillary-based SSCP analysis. In this method, alleles are separated into peaks, and their frequencies can be reliably and accurately quantified from their peak heights (SD <1.8%). We found that as many as 40% of publicly available SNPs that were analyzed by this method have widely differing allele frequency distributions among groups of different ethnicity (parents of Centre d'Etude Polymorphisme Humaine families vs. Japanese individuals). These results demonstrate the effectiveness of the present pooling method in the reevaluation of candidate SNPs that have been collected by examination of limited numbers of individuals. The method should also serve as a robust quantitative technique for studies in which a precise estimate of SNP allele frequencies is essential-for example, in linkage disequilibrium analysis.
我们表明，通过汇集DNA样本并应用基于毛细管的单链构象多态性（SSCP）分析，可以有效地检测中度至高度杂合性（次要等位基因频率>10%）的单核苷酸多态性（SNP），并准确估计其等位基因频率。在该方法中，等位基因被分离成峰，并且可以根据其峰高可靠且准确地定量其频率（标准差<1.8%）。我们发现，通过该方法分析的多达40%的公开可用SNP在不同种族群体（人类多态性研究中心家庭的父母与日本个体）之间具有广泛不同的等位基因频率分布。这些结果证明了当前汇集方法在重新评估通过检查有限数量个体收集的候选SNP方面的有效性。该方法还应作为一种强大的定量技术，用于对SNP等位基因频率进行精确估计至关重要的研究，例如连锁不平衡分析。
