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

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 ID: 14997420

Authors

  • Nyholt DR

Journal

American journal of human genetics

Publication Data

April 16, 2004

Associated Grants

None

Mesh Terms

  • Gene Frequency
  • Haplotypes
  • Humans
  • Internet
  • Linkage Disequilibrium
  • Polymorphism, Single Nucleotide
  • Probability
  • Research Design
  • Software