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arXiv 1503.08278stat.APstat.MEstat.OT
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基于递阶Dirichlet过程的种群结构建模

Modeling population structure under hierarchical Dirichlet processes

M. De Iorio, L. T. Elliott, S. Favaro, K. Adhikari, Y. W. Teh

摘要:

我们提出了一个贝叶斯非参数模型来推断人口混合,扩展了分层狄利克雷过程,使基因座之间的相关性,由于连锁不平衡。给定来自个体样本的多位点基因型数据,该模型允许推断将个体分类为未混合的或混合的,推断混合群体的祖先亚群的数量和染色体区域的起源群体。我们的模型不假设任何特定的突变过程,可以应用于大多数常用的遗传标记。我们提出了一个MCMC算法进行后验推理的模型和讨论的方法来总结MCMC输出的人口混合分析。我们证明了所提出的模型在模拟和实际应用中的性能,使用来自EDAR基因的遗传数据,由于众所周知的等位基因频率变化以及整个祖先的表型效应,该基因被认为是祖先信息。该数据集的结构分析导致在欧洲人中鉴定出一种罕见的单倍型。

英文摘要:

We propose a Bayesian nonparametric model to infer population admixture, extending the Hierarchical Dirichlet Process to allow for correlation between loci due to Linkage Disequilibrium. Given multilocus genotype data from a sample of individuals, the model allows inferring classifying individuals as unadmixed or admixed, inferring the number of subpopulations ancestral to an admixed population and the population of origin of chromosomal regions. Our model does not assume any specific mutation process and can be applied to most of the commonly used genetic markers. We present a MCMC algorithm to perform posterior inference from the model and discuss methods to summarise the MCMC output for the analysis of population admixture. We demonstrate the performance of the proposed model in simulations and in a real application, using genetic data from the EDAR gene, which is considered to be ancestry-informative due to well-known variations in allele frequency as well as phenotypic effects across ancestry. The structure analysis of this dataset leads to the identification of a rare haplotype in Europeans.

机构、总结、中文摘要均由AI分析而来,可能存在错误,请以论文正文为准。

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