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Improving power in genetic-association studies via wavelet transformation.

ABSTRACT: A key to increasing the power of multilocus association tests is to reduce the number of degrees of freedom by suppressing noise from data. One of the difficulties is to decide how much noise to suppress. An often overlooked problem is that commonly used association tests based on genotype data cannot utilize the genetic information contained in spatial ordering of SNPs (see proof in the Appendix), which may prevent them from achieving higher power.We develop a score test based on wavelet transform with empirical Bayesian thresholding. Extensive simulation studies are carried out under various LD structures as well as using HapMap data from many different chromosomes for both qualitative and quantitative traits. Simulation results show that the proposed test automatically adjusts the level of noise suppression according to LD structures, and it is able to consistently achieve higher or similar powers than many commonly used association tests including the principle component regression method (PCReg).The wavelet-based score test automatically suppresses the right amount of noise and uses the information contained in spatial ordering of SNPs to achieve higher power.

SUBMITTER: Jiang R

PROVIDER: S-EPMC2759953 | biostudies-literature | 2009 Sep

REPOSITORIES: biostudies-literature

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Improving power in genetic-association studies via wavelet transformation.

Jiang Renfang R Dong Jianping J Dai Yilin Y

BMC genetics 20090911

<h4>Background</h4>A key to increasing the power of multilocus association tests is to reduce the number of degrees of freedom by suppressing noise from data. One of the difficulties is to decide how much noise to suppress. An often overlooked problem is that commonly used association tests based on genotype data cannot utilize the genetic information contained in spatial ordering of SNPs (see proof in the Appendix), which may prevent them from achieving higher power.<h4>Results</h4>We develop a ...[more]

PMID: 19747393

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Project description:BackgroundFeature selection is an approach to overcome the 'curse of dimensionality' in complex researches like disease classification using microarrays. Statistical methods are utilized more in this domain. Most of them do not fit for a wide range of datasets. The transform oriented signal processing domains are not probed much when other fields like image and video processing utilize them well. Wavelets, one of such techniques, have the potential to be utilized in feature selection method. The aim of this paper is to assess the capability of Haar wavelet power spectrum in the problem of clustering and gene selection based on expression data in the context of disease classification and to propose a method based on Haar wavelet power spectrum.ResultsHaar wavelet power spectra of genes were analysed and it was observed to be different in different diagnostic categories. This difference in trend and magnitude of the spectrum may be utilized in gene selection. Most of the genes selected by earlier complex methods were selected by the very simple present method. Each earlier works proved only few genes are quite enough to approach the classification problem 1. Hence the present method may be tried in conjunction with other classification methods. The technique was applied without removing the noise in data to validate the robustness of the method against the noise or outliers in the data. No special software or complex implementation is needed. The qualities of the genes selected by the present method were analysed through their gene expression data. Most of them were observed to be related to solve the classification issue since they were dominant in the diagnostic category of the dataset for which they were selected as features.ConclusionIn the present paper, the problem of feature selection of microarray gene expression data was considered. We analyzed the wavelet power spectrum of genes and proposed a clustering and feature selection method useful for classification based on Haar wavelet power spectrum. Application of this technique in this area is novel, simple, and faster than other methods, fit for a wide range of data types. The results are encouraging and throw light into the possibility of using this technique for problem domains like disease classification, gene network identification and personalized drug design.

Dataset Information

Improving power in genetic-association studies via wavelet transformation.

Publications

Improving power in genetic-association studies via wavelet transformation.

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