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- Introduction
- FineMap is a computer program for refining the location of a disease
- gene beyond the bounds provided by linkage analysis. Many scientists
- use the pattern of linkage disequilibrium between the disease allele
- and alleles at nearby markers. FineMap seeks to
- refine location by analysis of `disease' and `normal' haplotypes,
- thereby using multivariate information about linkage disequilibrium.
- Assuming the disease mutation occurs in a specific gap between
- adjacent markers, FineMap first combines parsimony and likelihood
- to build an evolutionary tree of disease haplotypes with each node
- (haplotype) separated by a single mutational or recombinational step
- from its parent. If required, latent nodes (unobserved haplotypes)
- are incorporated to complete the tree. Once the tree is built, its
- likelihood is computed from probabilities of mutation and
- recombination. When each gap between adjacent markers is evaluated in
- this fashion, and these results are combined with prior information,
- they yield a posterior probability distribution to guide the search
- for the disease mutation.
- FineMap was written by Johnny Lam. It runs in any UNIX environment
- Lam, J.C, Roeder, K. and Devlin, B. (2000)
- Haplotype fine-mapping by evolutionary trees,
- American Journal of Human Genetics, in press
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