Hanchard Neil A, Rockett Kirk A, Spencer Chris, Coop Graham, Pinder Margaret, Jallow Muminatou, Kimber Martin, McVean Gil, Mott Richard, Kwiatkowski Dominic P
Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom.
Am J Hum Genet. 2006 Jan;78(1):153-9. doi: 10.1086/499252. Epub 2005 Nov 16.
There is growing interest in the use of haplotype-based methods for detecting recent selection. Here, we describe a method that uses a sliding window to estimate similarity among the haplotypes associated with any given single-nucleotide polymorphism (SNP) allele. We used simulations of natural selection to provide estimates of the empirical power of the method to detect recently selected alleles and found it to be comparable in power to the popular long-range haplotype test and more powerful than methods based on nucleotide diversity. We then applied the method to a recently selected allele--the sickle mutation at the HBB locus--and found it to have a signal of selection that was significantly stronger than that of simulated models both with and without strong selection. Using this method, we also evaluated >4,000 SNPs on chromosome 20, indicating the applicability of the method to regional data sets.
人们对使用基于单倍型的方法来检测近期选择的兴趣与日俱增。在此，我们描述了一种方法，该方法使用滑动窗口来估计与任何给定单核苷酸多态性（SNP）等位基因相关的单倍型之间的相似性。我们通过自然选择模拟来估计该方法检测近期选择等位基因的经验功效，发现其功效与流行的长程单倍型检验相当，且比基于核苷酸多样性的方法更强大。然后，我们将该方法应用于一个近期选择的等位基因——HBB基因座上的镰状突变，发现其选择信号明显强于有强选择和无强选择的模拟模型。使用这种方法，我们还评估了20号染色体上的4000多个SNP，表明该方法适用于区域数据集。
