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All enrichments were computed with respect to the background defined by the 2,204 loci under study, so as to avoid biases due to possible functional enrichments of the latter gene list.
In our analysis, each pseudocase or pseudocontrol haplotype in the table was defined over the complete sequence of DNA loci under study.
This can be interpreted as showing considerable among-farm differences in frequency and composition of alleles at the 15 loci under study.
Thus, we next combined data from 1st generation GWAS genotyping by BeadChip, re-genotyping by MALDI-TOF and TaqMan® MGB, and imputation based on this combined set of genotypes to comprehensively saturate all 14 candidate gene loci under study with 566 tagging SNPs as well as previously associated SNPs (figure 4 and table S2).
Importantly, none of these estimates require knowledge of mutation rates of the loci under study.
Of course, indirect estimates of gene flow apply only to the loci under study.
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The difference between the two offspring genotype vectors has an expected value of zero at each locus, under the null hypothesis of no linkage or no association with the disease locus under study.
Throughout the paper, we assumed that the marker locus under study is the actual QTL.
Assuming neutrality selection at the locus under study, these results can be interpreted as a signature of a demographic expansion.
For the present illustration, however, we assume that the locus under study is the QTL itself and not a marker in linkage disequilibrium with the QTL.
Nevertheless, the accuracy of the imputation is not 100%, depending on the ethnicity of the population and the HLA locus under study [ 34].
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