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

Open Access Proceedings

Detecting rare functional variants using a wavelet-based test on quantitative and qualitative traits

Renfang Jiang and Jianping Dong*

Author Affiliations

Department of Mathematical Sciences, Michigan Technological University, Fisher Hall, Room 319, 1400 Townsend Drive, Houghton, MI 49931-1295, USA

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BMC Proceedings 2011, 5(Suppl 9):S70  doi:10.1186/1753-6561-5-S9-S70

Published: 29 November 2011


We conducted a genome-wide association study on the Genetic Analysis Workshop 17 simulated unrelated individuals data using a multilocus score test based on wavelet transformation that we proposed recently. Wavelet transformation is an advanced smoothing technique, whereas the currently popular collapsing methods are the simplest way to smooth multilocus genotypes. The wavelet-based test suppresses noise from the data more effectively, which results in lower type I error rates. We chose a level-dependent threshold for the wavelet-based test to suppress the optimal amount of noise according to the data. We propose several remedies to reduce the inflated type I error rate: using a window of fixed size rather than a gene; using the Bonferroni correction rather than comparing to the maxima of test values for multiple testing corrections; and removing the influence of other factors by using residuals for the association test. A wavelet-based test can detect multiple rare functional variants. Type I error rates can be controlled using the wavelet-based test combined with the mentioned remedies.