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Related Experiment Videos

Linkage disequilibrium mapping using single nucleotide polymorphisms--which population?

A Collins1

  • 1Department of Human Genetics, University of Southampton, Southampton General Hospital. arc@soton.ac.uk

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
|July 21, 2000
PubMed
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Single nucleotide polymorphisms (SNPs) are valuable for mapping complex traits. Useful linkage disequilibrium exists between SNP pairs and SNP-oligogene pairs, even in small populations, aiding genetic mapping efforts.

Area of Science:

  • Genetics
  • Population Genetics
  • Bioinformatics

Background:

  • Complex traits are influenced by multiple genes of small effect (oligogenes).
  • Single nucleotide polymorphisms (SNPs) are common genetic variations with potential for trait mapping.
  • Limited data exist on linkage disequilibrium (LD) between SNP pairs and SNP-oligogene pairs in diverse populations.

Purpose of the Study:

  • To evaluate the extent of linkage disequilibrium (LD) between SNP pairs and SNP-oligogene pairs.
  • To assess the utility of common polymorphisms, like blood groups, as surrogates for SNPs in LD studies.
  • To compare LD patterns in isolated versus large populations for genetic mapping.

Main Methods:

  • Developed and applied a novel approach to evaluate association (rho) in SNP haplotypes.

Related Experiment Videos

  • Utilized extensive data from Rhesus and MNS blood group systems as surrogates for SNP-SNP and SNP-oligogene pairs.
  • Analyzed linkage disequilibrium in both large populations and isolates.

    • Main Results:

    • Found significant linkage disequilibrium (LD) between the MN-Ss locus pair (0.195 cM apart) in both population types.
    • Observed little difference in LD patterns between isolates and large populations, with few exceptions.
    • Demonstrated useful LD for mapping, exceeding expectations from recent simulations.

    Conclusions:

    • Linkage disequilibrium mapping is feasible using common polymorphisms like blood groups as SNP surrogates.
    • Population structure has a limited impact on detectable LD for genetic mapping purposes.
    • The findings suggest a more favorable landscape for LD-based mapping than previously simulated.