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Am J Hum Genet. 2004 Apr;74(4):765-9. Epub 2004 Mar 2.

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

Author information

1
Genetic Epidemiology Laboratory, Queensland Institute of Medical Research, Brisbane, Queensland, Australia. daleN@qimr.edu.au

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.

PMID:
14997420
PMCID:
PMC1181954
DOI:
10.1086/383251
[Indexed for MEDLINE]
Free PMC Article

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