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Genetics. 2015 Jun;200(2):483-94. doi: 10.1534/genetics.114.169490. Epub 2015 Apr 23.

The Causal Meaning of Genomic Predictors and How It Affects Construction and Comparison of Genome-Enabled Selection Models.

Author information

1
Department of Dairy Science, University of Wisconsin, Madison, Wisconsin 53706 Department of Animal Sciences, University of Wisconsin, Madison, Wisconsin 53706 bvalente@wisc.edu5.
2
Department of Animal Sciences, University of Wisconsin, Madison, Wisconsin 53706.
3
Department of Dairy Science, University of Wisconsin, Madison, Wisconsin 53706 Department of Animal Sciences, University of Wisconsin, Madison, Wisconsin 53706 Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, Wisconsin 53706.
4
Department of Dairy Science, University of Wisconsin, Madison, Wisconsin 53706.
5
Department of Animal Sciences, University of Wisconsin, Madison, Wisconsin 53706 Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, Wisconsin 53706.

Abstract

The term "effect" in additive genetic effect suggests a causal meaning. However, inferences of such quantities for selection purposes are typically viewed and conducted as a prediction task. Predictive ability as tested by cross-validation is currently the most acceptable criterion for comparing models and evaluating new methodologies. Nevertheless, it does not directly indicate if predictors reflect causal effects. Such evaluations would require causal inference methods that are not typical in genomic prediction for selection. This suggests that the usual approach to infer genetic effects contradicts the label of the quantity inferred. Here we investigate if genomic predictors for selection should be treated as standard predictors or if they must reflect a causal effect to be useful, requiring causal inference methods. Conducting the analysis as a prediction or as a causal inference task affects, for example, how covariates of the regression model are chosen, which may heavily affect the magnitude of genomic predictors and therefore selection decisions. We demonstrate that selection requires learning causal genetic effects. However, genomic predictors from some models might capture noncausal signal, providing good predictive ability but poorly representing true genetic effects. Simulated examples are used to show that aiming for predictive ability may lead to poor modeling decisions, while causal inference approaches may guide the construction of regression models that better infer the target genetic effect even when they underperform in cross-validation tests. In conclusion, genomic selection models should be constructed to aim primarily for identifiability of causal genetic effects, not for predictive ability.

KEYWORDS:

GenPred; causal inference; genomic selection; model comparison; prediction; selection; shared data resource

PMID:
25908318
PMCID:
PMC4492374
DOI:
10.1534/genetics.114.169490
[Indexed for MEDLINE]
Free PMC Article

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