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Molecular epistasis also changes the marginal effects and the power for single locus test of association.
In contrast to haplotype-based methods, the main advantage of the single locus test is that it does not necessitate information of SNP positions and reconstruction haplotypes of multiple SNP loci.
Uncorrected single locus test and PCRCox are the most powerful approaches, having however the worst performance in terms of false positives.
We used the software written by Jody Hey (Rutgers University (http://genfaculty.rutgers.edu/hey/software), which allows a multiple locus test with varying sample sizes.
Effect sizes for SNPs identified with the multi-locus models when analyzed using a single locus test were nearly two-fold lower than those detected only in the single-marker models (average R = 0.015).
An additive model does not have direct interaction between the loci's effects, but even so, the presence of multiple effect loci means that the data looks noisier to a single locus test.
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Indeed, four brewery isolates are heterozygous at every locus tested.
Single locus tests of association identified one significant single locus effect (Table 2a) in IL12B at SNP rs3212227 for the allelic test of association (p = 0.04).
Single locus tests of association in The Gambia identified a significant allelic association at IL12B SNP rs11574790 (Table 2a) (p = 0.05).
All the samples were re-sequenced to assess the genotype at each locus tested.
We repeated the same process at each locus tested in this study as well as for the autosomal loci previously reported.
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