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Statistical Applications in Genetics and Molecular Biology

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Volume 16, Issue 3 (Jul 2017)

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Genetic association test based on principal component analysis

Zhongxue Chen
  • Department of Epidemiology and Biostatistics, School of Public Health, Indiana University Bloomington, 1025 E. 7th Street, Bloomington, IN 47405, USA
  • Other articles by this author:
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/ Shizhong Han
  • Department of Psychiatry, Carver College of Medicine, University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, USA
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/ Kai Wang
  • Corresponding author
  • Department of Biostatistics, N322 CPHB College of Public Health, University of Iowa, 145 N. Riverside Drive, Iowa City, IA 52242, USA
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Published Online: 2017-06-26 | DOI: https://doi.org/10.1515/sagmb-2016-0061

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

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About the article

Corresponding author: Kai Wang, PhD, Department of Biostatistics, N322 CPHB College of Public Health, University of Iowa, 145 N. Riverside Drive, Iowa City, IA 52242, USA


Published Online: 2017-06-26

Published in Print: 2017-07-26


Citation Information: Statistical Applications in Genetics and Molecular Biology, ISSN (Online) 1544-6115, ISSN (Print) 2194-6302, DOI: https://doi.org/10.1515/sagmb-2016-0061.

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