Copyright © 2004 The American Society of Human Genetics. All rights reserved.
The American Journal of Human Genetics, Volume 74, Issue 4, 765-769, 1 April 2004
doi:10.1086/383251
Report
A Simple Correction for Multiple Testing for Single-Nucleotide Polymorphisms in Linkage Disequilibrium with Each Other
Dale R. Nyholt
, 
Address for correspondence and reprints: Dr. Dale R. Nyholt, Queensland Institute of Medical Research, Post Office Royal Brisbane Hospital, Brisbane QLD 4029, AustraliaAbstract
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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