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Open Access Methodology article

A new association test based on disease allele selection for case–control genome-wide association studies

Zhongxue Chen

Author Affiliations

Department of Epidemiology and Biostatistics, School of Public Health, Indiana University Bloomington, 1025 E. 7th street, PH C104, Bloomington, IN 47405, USA

BMC Genomics 2014, 15:358  doi:10.1186/1471-2164-15-358

Published: 12 May 2014



Current robust association tests for case–control genome-wide association study (GWAS) data are mainly based on the assumption of some specific genetic models. Due to the richness of the genetic models, this assumption may not be appropriate. Therefore, robust but powerful association approaches are desirable.


In this paper, we propose a new approach to testing for the association between the genotype and phenotype for case–control GWAS. This method assumes a generalized genetic model and is based on the selected disease allele to obtain a p-value from the more powerful one-sided test. Through a comprehensive simulation study we assess the performance of the new test by comparing it with existing methods. Some real data applications are also used to illustrate the use of the proposed test.


Based on the simulation results and real data application, the proposed test is powerful and robust.

Generalized genetic model; Robust test; Single-nucleotide polymorphism