Genetic association test based on principal component analysis

Chen Zhongxue, Han Shizhong and Wang Kai ()
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Chen Zhongxue: Department of Epidemiology and Biostatistics, School of Public Health, Indiana University Bloomington, 1025 E. 7th Street, Bloomington, IN 47405, USA
Han Shizhong: Department of Psychiatry, Carver College of Medicine, University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, USA
Wang Kai: Department of Biostatistics, N322 CPHB College of Public Health, University of Iowa, 145 N. Riverside Drive, Iowa City, IA 52242, USA

Statistical Applications in Genetics and Molecular Biology, 2017, vol. 16, issue 3, 189-198

Abstract: Many gene- and pathway-based association tests have been proposed in the literature. Among them, the SKAT is widely used, especially for rare variants association studies. In this paper, we investigate the connection between SKAT and a principal component analysis. This investigation leads to a procedure that encompasses SKAT as a special case. Through simulation studies and real data applications, we compare the proposed method with some existing tests.

Keywords: gene-based association; pathway-based association; rare variants (search for similar items in EconPapers)
Date: 2017
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DOI: 10.1515/sagmb-2016-0061

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