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In the last years GWA studies have successfully identified common SNPs associated with complex diseases. However, most of the variants found this way account for only a small portion of the trait variance. This fact leads researchers to focus on rare-variant mapping with large scale sequencing, which can be facilitated by using linkage information. The question arises why linkage analysis often fails to identify genes when analyzing complex diseases. Using simulations we have investigated the power of parametric and nonparametric linkage statistics (KC-LOD, NPL, LOD and MOD scores), to detect the effect of genes responsible for complex diseases using different pedigree structures.
Pubmed ID: 22862841
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Software application that carries out single-point and multipoint analyses of pedigree data, including IBD and kinship calculations, nonparametric and variance component linkage analyses, error detection and information content mapping. For multipoint analyses in dense maps, Merlin allows the user to impose constraints on the number of recombinants between consecutive markers. Merlin estimates haplotypes by finding the most likely path of gene flow or by sampling paths of gene flow at all markers jointly. It can also list all possible nonrecombinant haplotypes within short regions. Finally, Merlin provides swap-file support for handling very large numbers of markers as well as gene-dropping simulations for estimating empirical significance levels. (entry from Genetic Analysis Software)
View all literature mentionsA set of useful accessory programs to the LINKAGE package. It simplifies the performance of a large array of parametric and nonparametric tests for linkage and association on data entered in LINKAGE format pedigree and parameter files. (entry from Genetic Analysis Software)
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