Improving population-specific allele frequency estimates by adapting supplemental data: an empirical Bayes approach

Estimation of the allele frequency at genetic markers is a key ingredient in biological and biomedical research, such as studies of human genetic variation or of the genetic etiology of heritable traits. As genetic data becomes increasingly available, investigators face a dilemma: when should data from other studies and population subgroups be pooled with the primary data? Pooling additional samples will generally reduce the variance of the frequency estimates; however, used inappropriately, pooled estimates can be severely biased due to population stratification. Because of this potential bias, most investigators avoid pooling, even for samples with the same ethnic background and residing on the same continent. Here, we propose an empirical Bayes approach for estimating allele frequencies of single nucleotide polymorphisms. This procedure adaptively incorporates genotypes from related samples, so that more similar samples have a greater influence on the estimates. In every example we have considered, our estimator achieves a mean squared error (MSE) that is smaller than either pooling or not, and sometimes substantially improves over both extremes. The bias introduced is small, as is shown by a simulation study that is carefully matched to a real data example. Our method is particularly useful when small groups of individuals are genotyped at a large number of markers, a situation we are likely to encounter in a genome-wide association study.Comment: Published in at http://dx.doi.org/10.1214/07-AOAS121 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

The ν\nuTHDM with the Inverse Seesaw Mechanisms

In this paper, we combine the $\nu$-Two-Higgs-Doublet-Model ($\nu$THDM) with the inverse seesaw mechanisms. In this model, the Yukawa couplings involving the sterile neutrinos and the exotic Higgs bosons can be of order one in the case of a large $\tan \beta$. We calculated the corrections to the Z-resonance parameters $R_{l_i}$, $A_{l_i}$, $N_{\nu}$, together with the $l_1 \rightarrow l_2 \gamma$ branching ratios, and the muon anomalous $g-2$. Compared with the current bounds and plans for the future colliders, we find that the corrections to the electroweak parameters can be contrained or discovered in much of the parameter space