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BMC Proc. 2011 Nov 29;5 Suppl 9:S98. doi: 10.1186/1753-6561-5-S9-S98.

Finding genes that influence quantitative traits with tree-based clustering.

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  • 1Institute of Genetic Medicine, Newcastle University, Newcastle NE3 1NB, UK. ian.wilson@ncl.ac.uk.


We present a new statistical method to identify genes in which one or more variants influence quantitative traits. We use the Genetic Analysis Workshop 17 (GAW17) data set of unrelated individuals as a test of the method on the raw GAW17 phenotypes and on residuals after fitting linear models to individual-based covariates. By performing appropriate randomization tests, we found many significant results for a proportion of the genes that contain variants that directly contribute to disease but that have an increased type I error for analyses of raw phenotypes. Power calculations show that our methods have the ability to reliably identify a subset of the loci contributing to disease. When we applied our method to derived phenotypes, we removed many false positives, giving appropriate type I error rates at little cost to power. The correlation between genome-wide heterozygosity and the value of the trait Q1 appears to drive much of the type I error in this data set.

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