Linkage Disequilibrium (LD) Analysis
Background
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.
The data are collected using microarrays design to classify
millions of single nucleotide polymorphisms (SNPs) throughout the genome. The data from these microarrays can be
analyzed by a variety of bioinformatic tools and techniques.
Analysis
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.
Free demo accounts are available at http://www.simbiot.net.
Please also see more information about Simbiot Single User
Accounts and Private Server installations as well as a brief introduction to microarray analysis.
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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