Journal
AMERICAN JOURNAL OF HUMAN GENETICS
Volume 74, Issue 4, Pages 765-769Publisher
CELL PRESS
DOI: 10.1086/383251
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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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