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The resulting distributions of marker frequency from the small randomly chosen groups were plotted and compared to the results from the analysis performed on the complete set of 50 individuals.
Sample dimension was then estimated, assuming a frequency of the predisposing allele of 0.15, a disease prevalence of 0.4 (prevalence of asthma in the allergic population is ≥40%) [21], a genotype relative risk of 1.7 (for both the homozygote and heterozygote), and a marker frequency of 0.2 (taken from Affymetrix product description).
Results: The method accurately reproduces complex marker frequency trajectories.
SBI-06 had the lowest multicopy marker frequency (1.1%).
The LCT C/T-13910 marker frequency shows strong population differences.
Its genotype is indicated at the bottom of each marker frequency data.
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Note that the effect of locus frequencies in association mapping studies differs from typical QTL linkage mapping in experimental populations, where marker frequencies are under experimental control due to breeding designs and are often equal among alleles.
Graph of the first three principal components based on marker frequencies.
In addition, we assumed no decay of linkage disequilibrium (LD) or change in marker frequencies.
This final correction yielded estimates even closer to the true marker frequencies (discussed further below).
Fisher's exact tests were performed, using Genepop v. 4 (Raymond and Rousset 1995; Rousset 2008), on marker frequencies at each locus between all pairs of populations to determine whether significant differences in marker frequencies existed between groups of individuals.
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