Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2004 Apr;74(4):765-9.
doi: 10.1086/383251. Epub 2004 Mar 2.

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

Dale R Nyholt  1
Affiliations

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

Dale R Nyholt. Am J Hum Genet. 2004 Apr.

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.

PubMed Disclaimer

Figures

Figure 1
Figure 1
Probability (Pr) of a type I error plotted against the number of SNPs (in chromosomal order) tested in the Keavney et al. (1998) data. The graph shows the expected increase in the false-positive rate for completely independent SNPs [i.e., 1-(1-α)M] (thick dashed line), by use of an Meff-Šidák correction [i.e., 1-(1-α)Meff] (thin dashed line), and from 50,000 permutations (thick solid line), for α=0.05.
See this image and copyright information in PMC

References

Electronic-Database Information

    1. SNP Spectral Decomposition (SNPSpD) Web Interface, http://genepi.qimr.edu.au/general/daleN/SNPSpD/
    1. LDMAX Program (Part of the GOLD Command Line Tools Package [gold-1.1.0.tar.gz]), http://www.sph.umich.edu/csg/abecasis/GOLD/download/index.html
    1. TCR α/δ Locus Data of Moffatt et al. (2000), http://www.well.ox.ac.uk/asthma/public/TCR/index.shtml

References

    1. Abecasis GR, Cherny SS, Cookson WO, Cardon LR (2002) Merlin: rapid analysis of dense genetic maps using sparse gene flow trees. Nat Genet 30:97–101 10.1038/ng786 - DOI - PubMed
    1. Abecasis GR, Cookson WO (2000) GOLD: graphical overview of linkage disequilibrium. Bioinformatics 16:182–183 10.1093/bioinformatics/16.2.182 - DOI - PubMed
    1. Akey J, Jin L, Xiong M (2001) Haplotypes vs single marker linkage disequilibrium tests: what do we gain? Eur J Hum Genet 9:291–300 10.1038/sj.ejhg.5200619 - DOI - PubMed
    1. Bader JS (2001) The relative power of SNPs and haplotype as genetic markers for association tests. Pharmacogenomics 2:11–24 - PubMed
    1. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Statist Soc [Ser B] 57:289–300

Publication types