Molecular geneticists are developing the third generation human genome map with single nucleotide polymorphisms (SNPs), which can be assayed through chip-based microarrays. One use of these SNP markers is to locate loci that may be responsible for complex traits through linkage/linkage-disequilibrium analysis. We describe a semiparametric method for combined linkage/linkage-disequilibrium analysis using SNP markers. Asymptotic results are obtained for the estimated parameters, and the finite sample properties are evaluated through a simulation study. We also applied this technique to a simulated genome scan experiment for mapping a complex trait with two major genes. This experiment shows that separate linkage and linkage-disequilibrium analyses correctly detected the signals of both major genes, but the rates of false positive signals seem high. Combining linkage and linkage-disequilibrium signals, the analysis yielded much stronger and clearer signals for the presence of two major genes than two separate analyses.
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Zhao, L., Aragaki, C., Hsu, L. et al. Mapping complex traits with single nucleotide polymorphisms. Nat Genet 23 (Suppl 3), 84 (1999). https://doi.org/10.1038/14434
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DOI: https://doi.org/10.1038/14434