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

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.

journal_name

Am J Hum Genet

authors

Nyholt DR

doi

10.1086/383251

subject

Has Abstract

pub_date

2004-04-01 00:00:00

pages

765-9

issue

4

eissn

0002-9297

issn

1537-6605

pii

S0002-9297(07)61903-X

journal_volume

74

pub_type

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