Reliable heritability estimation using sparse regularization in ultrahigh dimensional genome-wide association studies

Minimax Rates of ℓp-Losses for High-Dimensional Linear Errors-in-Variables Models over ℓq-Balls

In this paper, the high-dimensional linear regression model is considered, where the covariates are measured with additive noise. Different from most of the other methods, which are based on the assumption that the true covariates are fully obtained, results in this paper only require that the corrupted covariate matrix is observed. Then, by the application of information theory, the minimax rates of convergence for estimation are investigated in terms of the ℓp(1≤p<∞)-losses under the general sparsity assumption on the underlying regression parameter and some regularity conditions on the observed covariate matrix. The established lower and upper bounds on minimax risks agree up to constant factors when p=2, which together provide the information-theoretic limits of estimating a sparse vector in the high-dimensional linear errors-in-variables model. An estimator for the underlying parameter is also proposed and shown to be minimax optimal in the ℓ2-loss.

Boosting heritability: estimating the genetic component of phenotypic variation with multiple sample splitting

Background

Heritability is a central measure in genetics quantifying how much of the variability observed in a trait is attributable to genetic differences. Existing methods for estimating heritability are most often based on random-effect models, typically for computational reasons. The alternative of using a fixed-effect model has received much more limited attention in the literature.

Results

In this paper, we propose a generic strategy for heritability inference, termed as “boosting heritability”, by combining the advantageous features of different recent methods to produce an estimate of the heritability with a high-dimensional linear model. Boosting heritability uses in particular a multiple sample splitting strategy which leads in general to a stable and accurate estimate. We use both simulated data and real antibiotic resistance data from a major human pathogen, Sptreptococcus pneumoniae, to demonstrate the attractive features of our inference strategy.

Conclusions

Boosting is shown to offer a reliable and practically useful tool for inference about heritability.