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Primarily as a result of very low LD in wild A. Gambiae, LD-based association mapping is challenging, but is feasible at least for major effect variants, especially where LD is enhanced by selective sweeps.
Our data illustrate that association mapping is difficult but feasible for wild A. gambiae populations, at least for major effect variants and especially, where LD is enhanced by selective sweeps.
In contrast, we did detect with statistical confidence (P≈10−6) association of major effect variants in the insecticide target site gene, though this required combined analysis of the three subsamples.
The strongly inverse relationship between effect size and MAF we observed is in accord with recent model predictions advanced as an explanation for why the plethora of GWA studies has rarely detected major effect variants underlying common human diseases [36].
Therefore, whilst elucidation of the full genetic architecture of insecticide resistance and other medically important traits will likely have to wait until association mapping by whole genome sequencing becomes economically feasible for A. gambiae, major effect variants that will be of greatest utility for predictive diagnostic screening can be identified.
It is possible that future discoveries of rare, major effect variants may add new perspectives for pharmacogenetics in T2DM.
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Analysis of the family clustering of the extreme phenotype groups pinpointed to large multigenerational families (not shown) that are expected to be enriched for rare and major-effect variants.
This is consistent with the idea that transcripts may be valuable when sensitivity or resistance has a complex genetic basis with many minor-effect variants rather than one major-effect variant.
For such traits, we might expect the levels of interference during selection to be reduced from the values seen in our simulations, as the expected transit of the major-effect variant to high frequency will not interfere with selection at other QTL.
Major effect target site variants, especially kdr L1014F, are clearly of major importance in permethrin resistance, and it is noteworthy that in populations differing dramatically in both resistance levels and kdr L1014F frequencies this was the only consistently associated SNP.
Although a major effect of this genetic variant on cognitive and affective processing and hence an increased susceptibility to various psychiatric symptoms is plausible, many well-designed studies produced inconsistent results.
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