ships spectral hierarchical clustering for the inference of population structure in genetic studies船只光谱分级聚类基因研究人口结构的推理.pdfVIP

SHIPS: Spectral Hierarchical Clustering for the Inference of Population Structure in Genetic Studies 1,2 1 1 2 Matthieu Bouaziz *, Caroline Paccard , Mickael Guedj , Christophe Ambroise 1 Department of Biostatistics, Pharnext, Paris, France, 2 Statistics and Genome Laboratory, University of Evry Val d’Essonne, UMR CNRS 8071 - USC INRA, Evry, France Abstract Inferring the structure of populations has many applications for genetic research. In addition to providing information for evolutionary studies, it can be used to account for the bias induced by population stratification in association studies. To this end, many algorithms have been proposed to cluster individuals into genetically homogeneous sub-populations. The parametric algorithms, such as Structure, are very popular but their underlying complexity and their high computational cost led to the development of faster parametric alternatives such as Admixture. Alternatives to these methods are the non- parametric approaches. Among this category, AWclust has proven efficient but fails to properly identify population structure for complex datasets. We present in this article a new clustering algorithm called Spectral Hierarchical clustering for the Inference of Population Structure (SHIPS), based on a divisive hierarchical clustering strategy, allowing a progressive investigation of population structure. This method takes genetic data as input to cluster individuals into homogeneous sub- populations and with the use of the gap statistic estimates the optimal number of such sub-populations. SHIPS was applied to a set of simulated discrete and admixed datasets and to real SNP datasets, that are data from the HapMap and Pan-Asian SNP consortium. The programs Structure, Adm