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Haplotype fine mapping by evolutionary trees.

J C Lam1, K Roeder, B Devlin

  • 1Department of Statistics, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA.

American Journal of Human Genetics
|March 21, 2000
PubMed
Summary
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This study introduces FineMap, a novel method for pinpointing disease gene locations using linkage disequilibrium and haplotype analysis. FineMap refines genetic disease mapping by analyzing evolutionary trees of haplotypes.

Area of Science:

  • Genetics
  • Bioinformatics
  • Computational Biology

Background:

  • Linkage analysis is used to locate disease genes.
  • Linkage disequilibrium (LD) patterns between disease alleles and nearby markers refine gene location.
  • Multivariate haplotype analysis offers a more refined approach to LD.

Purpose of the Study:

  • To develop and evaluate a novel method for refining disease gene location using multivariate linkage disequilibrium information.
  • To improve the precision of disease gene mapping beyond traditional linkage analysis.

Main Methods:

  • The FineMap method analyzes "disease" and "normal" haplotypes to leverage multivariate LD information.
  • It constructs an evolutionary tree of disease haplotypes using parsimony and likelihood, incorporating latent nodes if necessary.

Related Experiment Videos

  • The likelihood of the tree is calculated using mutation and recombination probabilities, with results combined with prior information to generate a posterior probability distribution.

    • Main Results:

    • Evolutionary simulations demonstrated that FineMap significantly refines the location of disease mutations and provides excellent coverage.
    • Application to hereditary hemochromatosis haplotypes showed FineMap's robustness to genetic heterogeneity.

    Conclusions:

    • The FineMap method offers a powerful approach to enhance the resolution of disease gene mapping.
    • It effectively utilizes haplotype information and linkage disequilibrium patterns for precise gene localization, even in the presence of genetic heterogeneity.