Genomic selection using regularized linear regression models: ridge regression, lasso, elastic net and their extensions
TLDR
The elastic net, lasso, adaptive lasso and the adaptive elastic net all had similar accuracies but outperformed ridge regression and ridge regression BLUP in terms of the Pearson correlation between predicted GEBVs and the true genomic value as well as the root mean squared error.Abstract:
Background
Genomic selection (GS) is emerging as an efficient and cost-effective method for estimating breeding values using molecular markers distributed over the entire genome. In essence, it involves estimating the simultaneous effects of all genes or chromosomal segments and combining the estimates to predict the total genomic breeding value (GEBV). Accurate prediction of GEBVs is a central and recurring challenge in plant and animal breeding. The existence of a bewildering array of approaches for predicting breeding values using markers underscores the importance of identifying approaches able to efficiently and accurately predict breeding values. Here, we comparatively evaluate the predictive performance of six regularized linear regression methods-- ridge regression, ridge regression BLUP, lasso, adaptive lasso, elastic net and adaptive elastic net-- for predicting GEBV using dense SNP markers.read more
Citations
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References
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Hui Zou,Trevor Hastie +1 more
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The Elements of Statistical Learning
TL;DR: Chapter 11 includes more case studies in other areas, ranging from manufacturing to marketing research, and a detailed comparison with other diagnostic tools, such as logistic regression and tree-based methods.