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As detailed in the Methods section, this model relies on the estimation, through a logistic regression, of both a "locus effect" and a "population effect" on genetic differentiation.
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We tested for a mixture of three normal distributions consistent with population genetics for a major locus effect in which the proportion of normal homozygotes is p2; of heterozygotes, 2pq; of affected homozygotes, q2; and in which p+q = 1.
The homozygosity correlation was not due to a single locus effect (F = 1.13, df = 14, P = 0.36; see Appendix S1).
The results indicate that it is unlikely that there is a major locus effect of one of the genes on aggression in the Golden Retrievers that we studied.
Second, the untargeted insertion can provoke an unpredictable locus effect.
The BOADICEA model allows for a polygenic modifier locus effect in which several low-penetrance genes have joint effects [ 19].
Hence, relying on an infinite Wright island model with drift and migration at equilibrium, Beaumont and Balding [10] proposed a Bayesian modeling of allele frequencies involving both a "locus" and a "population" effects on genetic differentiation.
We simulate data under a variety of disease locus effect size and linkage disequilibrium patterns.
We have thus only tested for a very strong major locus effect.
We have investigated the performance of several penalized logistic regression approaches, simulating data under a variety of disease locus effect size and linkage disequilibrium patterns.
A marginal effect was defined as a single-locus effect with a chi-squared (1 df) statistic larger than 3.84 (p-value <.05).
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