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

Detecting genome wide haplotype sharing using SNP or microsatellite haplotype data.

Melanie Bahlo1, Jim Stankovich, Terence P Speed

  • 1The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, 3050 Parkville, VIC, Australia. bahlo@wehi.edu.au

Human Genetics
|December 20, 2005
PubMed
Summary

This study introduces a new algorithm for genome-wide association studies to detect disease susceptibility loci. It uses a chi2-based statistic to identify excess sharing of ancestral haplotypes, offering a computationally efficient first-pass analysis.

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

Somatic variation in multiple sclerosis: from blood to brain.

Current opinion in genetics & development·2026
Same author

Understanding <i>Plasmodium vivax</i> recurrent infections using an amplicon deep sequencing assay, identity-by-descent and model-based classification.

iScience·2026
Same author

Patient induced pluripotent stem cells identify specificities of a reticular pseudodrusen phenotype in age-related macular degeneration.

Genome medicine·2026
Same author

Genome sequencing boosts diagnostic yield for the developmental and epileptic encephalopathies.

medRxiv : the preprint server for health sciences·2026
Same author

Defining a tandem repeat catalog and variation clusters for genome-wide analyses and population databases.

American journal of human genetics·2026
Same author

PET-CT benchmarked detection and 5-year progression of asymptomatic tuberculosis: a longitudinal, prospective cohort study.

The Lancet. Respiratory medicine·2026

Area of Science:

  • Genetics
  • Bioinformatics
  • Statistical genomics

Background:

  • Genome-wide association studies (GWAS) face challenges in detecting disease signals.
  • Existing methods for haplotype association are limited and computationally intensive.
  • Linkage disequilibrium (LD) fine mapping focuses on locus identification, not signal detection.

Purpose of the Study:

  • To develop a novel algorithm for initial identification of disease susceptibility loci in GWAS.
  • To provide a computationally efficient method for genome-wide scanning of qualitative traits.
  • To serve as a first-pass analysis preceding more complex likelihood-based methods.

Main Methods:

  • A new chi2-based statistic detects excess sharing of ancestral haplotypes.
  • The algorithm performs genome-wide scanning for qualitative traits.

Related Experiment Videos

  • Statistical significance is assessed using permutation tests.

    • Main Results:

    • The method identifies candidate regions and susceptibility haplotypes.
    • It makes no assumptions about population history or LD patterns.
    • Demonstrated low type I error and greater power than single-marker tests in simulated and real data (cystic fibrosis, multiple sclerosis).

    Conclusions:

    • The developed algorithm offers an efficient and interpretable approach for initial GWAS analysis.
    • It effectively detects disease loci by identifying shared ancestral haplotypes.
    • The method shows promise for both simple and complex disease studies.