Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

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

Dale R Nyholt1

  • 1Genetic Epidemiology Laboratory, Queensland Institute of Medical Research, Brisbane, Queensland, Australia. daleN@qimr.edu.au

American Journal of Human Genetics
|March 5, 2004
PubMed
Summary

We present a straightforward method for multiple testing correction in genetic studies involving single-nucleotide polymorphisms (SNPs) that are in linkage disequilibrium (LD). This spectral decomposition approach offers a computationally efficient alternative to permutation tests.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Genome-Wide and Locus-Level Analyses Reveal Modest, Heterogeneous Genetic Sharing Between Alzheimer's Disease and Myasthenia Gravis.

International journal of molecular sciences·2026
Same author

Decoding chronic pain: integrating genetics, neuroimaging, and AI for precision management.

Frontiers in pain research (Lausanne, Switzerland)·2026
Same author

Shared genetic risk and causal associations between Post-traumatic stress disorder and migraine with antithrombotic agents and other medications.

Neurobiology of stress·2025
Same author

Publisher Correction: Understanding the genetic complexity of puberty timing across the allele frequency spectrum.

Nature genetics·2024
Same author

Understanding the genetic complexity of puberty timing across the allele frequency spectrum.

Nature genetics·2024
Same author

CpG methylation changes in human mesenchymal and neural stem cells in response to in vitro niche modifications.

Biochimie·2024

Area of Science:

  • Genetics
  • Statistical Genetics
  • Bioinformatics

Background:

  • Multiple testing is a common challenge in genetic association studies.
  • Single-nucleotide polymorphisms (SNPs) are often in linkage disequilibrium (LD), meaning they are inherited together, complicating statistical analysis.
  • Existing methods for correcting multiple testing in the presence of LD can be computationally intensive.

Purpose of the Study:

  • To introduce a simple and computationally efficient method for correcting multiple testing of SNPs in linkage disequilibrium (LD).
  • To provide a user-friendly tool for implementing this correction method.
  • To facilitate the selection of informative SNPs within a genomic region.

Main Methods:

  • The study utilizes spectral decomposition (SpD) of matrices representing pairwise LD between SNPs.

Related Experiment Videos

  • A user-friendly interface, SNPSpD, was developed for performing the correction.
  • The method's output includes eigenvalues, principal-component coefficients, and factor loadings after varimax rotation.

    • Main Results:

    • A simple correction for multiple testing of SNPs in LD was developed.
    • The spectral decomposition (SpD) method is computationally less intensive than permutation tests.
    • The SNPSpD tool provides additional outputs for selecting informative SNPs.

    Conclusions:

    • The described spectral decomposition method offers a practical and efficient solution for multiple testing correction in the context of SNP LD.
    • The SNPSpD tool is a valuable resource for genetic researchers.
    • The method aids in optimizing information extraction from genomic regions by enabling informed SNP selection.