Machine learning methods and predictive ability metrics for genome-wide prediction of complex traits

Genome-wide prediction of complex traits has become increasingly important in animal and plant breeding, and is receiving increasing attention in human genetics. Most common approaches are whole-genome regression models where phenotypes are regressed on thousands of markers concurrently, applying different prior distributions to marker effects. While use of shrinkage or regularization in SNP regression models has delivered improvements in predictive ability in genome-based evaluations, serious over-fitting problems may be encountered as the ratio between markers and available phenotypes continues increasing. Machine learning is an alternative approach for prediction and classification, capable of dealing with the dimensionality problem in a computationally flexible manner. In this article we provide an overview of non-parametric and machine learning methods used in genome wide prediction, discuss their similarities as well as their relationship to some well-known parametric approaches. Although the most suitable method is usually case dependent, we suggest the use of support vector machines and random forests for classification problems, whereas Reproducing Kernel Hilbert Spaces regression and boosting may suit better regression problems, with the former having the more consistently higher predictive ability. Neural Networks may suffer from over-fitting and may be too computationally demanded when the number of neurons is large. We further discuss on the metrics used to evaluate predictive ability in model comparison under cross-validation from a genomic selection point of view. We suggest use of predictive mean squared error as a main but not only metric for model comparison. Visual tools may greatly assist on the choice of the most accurate model. (C) 2014 Elsevier B.V. All rights reserved.