Craig Ian, Meaburn Emma, Butcher Lee, Hill Linzy, Plomin Robert
SGDP Centre, Institute of Psychiatry, London, UK.
Methods Mol Biol. 2005;311:147-64. doi: 10.1385/1-59259-957-5:147.
To undertake partial, or complete, genome screens by association-based methodology for quantitative trait loci, multiple individuals have to be screened for large numbers of genetic markers. Consequently, much recent interest has focused on methods enabling accurate allele quantification in pooled deoxyribonucleic acid (DNA) samples. Microsatellites were the favored markers in initial studies, but the extraordinary wealth of data concerning single-nucleotide polymorphisms (SNPs) has turned attention to the quantification of SNP alleles in pools. All such approaches require accurate estimation of DNA concentrations, followed by the preparation of replicate pools, their validation, and application of procedures for determining allele frequencies. This chapter describes the important steps in preparing pools and surveys a variety of techniques that have been proposed for SNP detection. Finally, we describe the application of a generic approach using pooled DNA for detection of allele frequency differences between case and control populations based on primer extension protocols and outline a strategy for estimating SNP allele frequencies employing microarrays.
要通过基于关联的方法对数量性状基因座进行部分或全基因组筛选，就必须对多个个体进行大量遗传标记的筛选。因此，最近人们的兴趣大多集中在能够对混合脱氧核糖核酸（DNA）样本中的等位基因进行准确量化的方法上。微卫星是最初研究中青睐的标记，但有关单核苷酸多态性（SNP）的海量数据已将注意力转向混合样本中SNP等位基因的量化。所有这些方法都需要准确估计DNA浓度，随后制备重复样本池、对其进行验证，并应用确定等位基因频率的程序。本章描述了制备样本池的重要步骤，并概述了已提出的用于SNP检测的各种技术。最后，我们描述了一种基于引物延伸方案，利用混合DNA检测病例组和对照组群体之间等位基因频率差异的通用方法的应用，并概述了一种使用微阵列估计SNP等位基因频率的策略。
