Genomic control

Devlin B, Roeder K. Genomic control for association studies. Biometrics 1999 55[4] 997—1004. 

Devlin, B., and Roeder, K. (1999) Genomic control for association studies. Biometrics. 55, 997-1004. Available at http //wpicr.wpic.pitt.eduAVPICCompGen/bayesian genomic control softwar.htm. 

Clayton, D.G., Watkerr, N.M., Smyth, Deborah., etal. (2005) Population structure, differential bias and genomic control in a large-scale, case-control association study. Nat. Genet. 37,1243-1246. 

The corrected / -values at any given locus can then be obtained using an adjusted distribution that accounts for any inflation observed. The structured association approach differs from the genomic approach in that it estimates the population structure while genomic control assumes a particular parametric distribution of the value of the test statistic (70). Compared with the structured association, the genomic control approach is computationally simple and can be applied to both scanning and validation stages. 

Devlin B, Bacanu SA, Roeder K. Genomic control to the extreme. Nature Genetics 2004 36 1129-1130. 

Genomic control Scar formation Cellular osmotic regulation... 

The many documented differences in structure and function between triazine resistant and susceptible biotypes may occur as a consequence of reduced PSII in resistant plants and thus, be due to pleiotropic effects of the chloroplast mutation. It is also possible that differential productivity between biotypes of the same species is the result of variation in other traits that are under nuclear, not chloroplast, control (22, 22). The role of the chloroplast genome in regulating growth and productivity of resistant plants is best determined by examining nuclear-isogenic susceptible and resistant biotypes, rather than field-collected ones, since differences between biotypes in nuclear genome-controlled traits may mask or even compensate for detrimental effects of the chloroplast mutation. 

In the field, natural selection acts to optimize the adaptations of a plant so as to maximize individual fitness. In triazine resistant weeds, coevolution of the less productive chloroplast with the nuclear genome could have resulted in compensatory mechanisms not present in susceptible plants. These mechanisms could optimize productivity and maximize the fitness of those individuals, within the constraints imposed by impaired PSII. Even slight differences in the chloroplast genome between susceptible and resistant biotypes could result in different responses to the same selection pressures in the environment, perhaps in the direction of overcoming limitations caused by the resistance mutation. Thus, after several generations of selection, many nuclear-genome controlled traits are likely to appear that could mask intrinsic differences between biotypes due to the chloroplast mutation. It is also possible that the alteration in PSII in resistant plants triggers developmental events that compensate in some way. Effects of the resistance mutation may be compensated for by other aspects of plant performance such as carbon allocation or rate of development. Resistant plants may not necessarily be less productive than susceptible ones when traits not directly linked with triazine resistance are considered. 

Decoding the genomic control of immune reactions. Wiley, Chichester (Novartis Foundation Symposium 281) p 2-24... 

Devlin and Roeder (1999) were the first to point out that this confounding problem may be addressed if there are many markers available on each individual and the overall genetic heterogeneity roughly has the same effects on all the markers. They proposed the genomic control method to realize this idea. The basic approach is as follows. First, a standard association test is conducted between the trait and each individual marker. Under the null hypothesis of no association, the distribution of all the test statistics should follow a specific distribution, for example, a chi-square distribution for a test based on a contingency table. With hundreds of thousands of markers, the asymptotic distribution should provide a very good... 

Genomic control A statistical approach to reducing the effect of sample heterogeneity through the use an... 

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