Genomic regions exhibiting positive selection identified from dense genotype data
Genomic regions exhibiting positive selection identified from dense genotype data
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DOI：
10.1101/gr.4326505
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发表时间：
2005-11-01
期刊：
影响因子：
7
通讯作者：
Nickerson, DA
中科院分区：
文献类型：
--
作者：
Carlson, CS;Thomas, DJ;Nickerson, DA
DNA序列中多态性的等位基因频谱可以用来测试自然选择的特征，这些特征偏离了中性理论下的预期频谱。我们观察到完整重测序数据中的Tajima's D检验统计量与密集的全基因组179个基因型多态性数据集中的Tajima's D之间存在显著相关性（P = 0.001）。在此基础上，我们对人类基因组中的田岛D进行了滑动窗口分析，以确定推定受强烈、近期、选择性扫描影响的区域。本研究在非洲裔人群（AD）、欧洲裔人群（ED）和中国裔人群（XD）中分别确定了7个田岛D减少区（CRTRs）、23个田岛D减少区（CRTRs）。种群之间只有4个CRTR重叠：ED和XD之间有3个，AD和ED之间有1个。对6个CRTR中8个基因的全重测序表明，每个CRTR中至少有一个基因的频谱与中性预期不一致。鉴定每个CRTR中负责选择性扫描的功能多态性（和/或单倍型）可能为人类基因组在最近的进化史上所经历的最强选择压力提供有趣的见解。
The allele frequency spectrum of polymorphisms in DNA sequences can be used to test for signatures of natural selection that depart from the expected frequency spectrum under the neutral theory. We observed a significant (P = 0.001) correlation between the Tajima's D test statistic in full resequencing data and Tajima's D in a dense, genome-wide data set of genotyped polymorphisms for a set of 179 genes. Based on this, we used a sliding window analysis of Tajima's D across the human genome to identify regions putatively subject to strong, recent, selective sweeps. This survey identified seven Contiguous Regions of Tajima's D Reduction (CRTRs) in an African-descent population (AD), 23 in a European-descent population (ED), and 29 in a Chinese-descent population (XD). Only four CRTRs overlapped between Populations: three between ED and XD and one between AD and ED. Full resequencing of eight genes within six CRTRs demonstrated frequency spectra inconsistent with neutral expectations for at least one gene within each CRTR. Identification of the functional polymorphism (and/or haplotype) responsible for the selective sweeps within each CRTR may provide interesting insights into the strongest selective pressures experienced by the human genome over recent evolutionary history.