Cited by 1,699Genetic Associations and EpidemiologyGenetic Mapping and Diversity in Plants and AnimalsForensic and Genetic Research

A Simple Correction for Multiple Testing for Single-Nucleotide Polymorphisms in Linkage Disequilibrium with Each Other

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Nyholt, Dale R.·2004·The American Journal of Human Genetics

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.

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Crossref · 10.1086/383251

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  • Before meta-analysis, all study-specific files underwent quality control procedures to check for completeness and plausible descriptive statistics on all variables as well as for compliance of allele frequencies with HapMap.

    “Before meta-analysis, all study-specific files underwent quality control procedures to check for completeness and plausible descriptive statistics on all variables as well as for compliance of allele frequencies with HapMap59.”

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Authors
Nyholt, D. R.
Affiliations
QIMR Berghofer Medical Research Institute (AU)
Corresponding author
Nyholt, Dale R.
Venue
The American Journal of Human Genetics
Publisher
Elsevier BV
Published
2004-04
Volume
74
Issue
4
Pages
765-769
ISSN
0002-9297 (ISSN-L)
OpenAlex
W2030705868
Cited by
1,699
References
30
Citations by year
2026: 27 · 2025: 36 · 2024: 42 · 2023: 37 · 2022: 40 · 2021: 71 · 2020: 58 · 2019: 56 · 2018: 67 · 2017: 49 · 2016: 81 · 2015: 101 · 2014: 106 · 2013: 111 · 2012: 136
FWCI
38.08
Type
journal article
Language
en
Open access
Locations
  • The American Journal of Human Genetics (publishedVersion)
  • Europe PMC (PubMed Central) (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
  • Faculty of Health; Institute of Health and Biomedical Innovation
Funders
  • National Health and Medical Research Council
  • National Medical Research Council
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
Keywords
multiple testing correction, single nucleotide polymorphisms, linkage disequilibrium, spectral decomposition, principal component analysis, factor analysis, varimax rotation
MeSH terms
Gene Frequency, Haplotypes, Humans, Probability, Research Design, Software, Linkage Disequilibrium, Internet, Polymorphism, Single Nucleotide

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