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This article is part of the supplement: Genetic Analysis Workshop 17: Unraveling Human Exome Data

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Treating phenotype as given: a simple resampling method for genome-wide association studies

Kai Wang1* and Jian Huang12

Author Affiliations

1 Department of Biostatistics, University of Iowa, Iowa City, IA 52242, USA

2 Department of Statistics and Actuarial Sciences, University of Iowa, Iowa City, IA 52242, USA

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BMC Proceedings 2011, 5(Suppl 9):S60  doi:10.1186/1753-6561-5-S9-S60

Published: 29 November 2011


Significance of genetic association to a marker has been traditionally evaluated through statistics that are standardized such that their null distributions conform to some known ones. Distributional assumptions are often required in this standardization procedure. Based on the observation that the phenotype remains the same regardless of the marker being investigated, we propose a simple statistic that does not need such standardization. We propose a resampling procedure to assess this statistic’s genome-wide significance. This method has been applied to replicate 2 of the Genetic Analysis Workshop 17 simulated data on unrelated individuals in an attempt to map phenotype Q2. However, none of the selected SNPs are in genes that are disease-causing. This may be due to the weak effect that each genetic factor has on Q2.