Japan Bioinformatics

In population genetics, linkage disequilibrium (LD) is the non-random association of alleles at two or more loci, not necessarily on the same chromosome.  Linkage disequilibrium describes a situation in which some combinations of alleles or genetic markers occur more or less frequently in a population than would be expected from a random formation of haplotypes from alleles based on their frequencies.  Numerically, it is the difference between observed and expected (assuming random distributions) allelic frequencies.

Simbiot provides functionality to perform LD analysis on data generated using Affymetrix and Illumina SNP microarrays.  The analysis is implemented using the algorithm published in the Bioconductor (Gentleman, Carey et al. 2004) snpMatrix (Clayton and Leung 2007) library.

 

References

Clayton, D. and H. T. Leung (2007). “An R package for analysis of whole-genome association studies.” Hum Hered 64(1): 45-51.

Gentleman, R. C., V. J. Carey, et al. (2004). “Bioconductor: open software development for computational biology and bioinformatics.” Genome Biol 5(10): R80.

 

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