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Although we believe that this is a likely consequence of the differences in detailed linkage disequilibrium between the SNP markers and the actual pathogenic allelic variants at many of these chromosomal loci, some of these phase differences are also likely to reflect results that co-occur in the two independent samples by chance.
Our quantitative-genetic approach is uniquely able to discern modifier effects that depend simultaneously on variants at many loci.
However, the mechanisms through which genetic variants at many disease-associated loci affect disease susceptibility remain to be determined.
However, with complex traits selection may occur through polygenic adaptation, where adaptation occurs by simultaneous selection on variants at many loci.
More recently, it has been argued that the greater part of cancer predisposition may be due to a combination of weak genetic variants at many different loci rather than to single high penetrance genes (Balmain et al, 2003).
It is expected that simultaneous selection of variants at many loci (i.e., polygenic adaptation) will result in subtle variation in allelic frequencies on several covarying loci, yielding a combined effect greater than the effect of individual loci on the phenotype (McKay and Latta 2002; Pritchard et al. 2010; Le Corre and Kremer 2012; Bourret et al. 2014; Pavey et al. 2015).
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Doing so, deletes variants called at many positions, calling into question many basic conclusions from a sequencing experiment.
The low coverage prevented immediate and reliable variant calling at many sites.
In the case of functional pleiotropy, we suppose there are multiple genetic variants (at least as many variants as there are risk factors) which have different magnitudes of effect on the risk factors.
The use of PCA in population genetics has a long history, including early work of Cavalli-Sforza and colleagues [1], [2], who considered high dimensional genetic variants from population samples at many different continental locations and used the top PCs to summarize the genetic variation across space.
Although "reactive" genotyping for pharmacogenomic variants can be ordered at many sites, turnaround is often slow and uptake low.
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