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PubMed · 14997420

A simple correction for multiple testing for single-nucleotide polymorphisms in linkage disequilibrium with each other.

Dale R Nyholt
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Abstract

In this report, we describe a simple correction for multiple testing of single-nucleotide polymorphisms (SNPs) in linkage disequilibrium (LD) with each other, on the basis of the spectral decomposition (SpD) of matrices of pairwise LD between SNPs. This method provides a useful alternative to more computationally intensive permutation tests. A user-friendly interface (SNPSpD) for performing this correction is available online (http://genepi.qimr.edu.au/general/daleN/SNPSpD/). Additionally, output from SNPSpD includes eigenvalues, principal-component coefficients, and factor "loadings" after varimax rotation, enabling the selection of a subset of SNPs that optimize the information in a genomic region.

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Gene FrequencyHaplotypesHumansInternetLinkage DisequilibriumPolymorphism, Single NucleotideProbabilityResearch DesignSoftwareJournal ArticleResearch Support, Non-U.S. Gov't

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Dale R Nyholt. 2004-03-02. A simple correction for multiple testing for single-nucleotide polymorphisms in linkage disequilibrium with each other.. https://doi.org/10.1086/383251

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