Using Genetic Distance to Infer the Accuracy of Genomic Prediction
By Marco Scutari, I. Mackay, David J. Balding. 2015
124 citations recorded by the source corpus.
The prediction of phenotypic traits using high-density genomic data has many applications such as the selection of plants and animals of commercial interest; and it is expected to play an increasing role in medical diagnostics. Statistical models used for this task are usually tested using cross-validation, which implicitly assumes that new individuals (whose phenotypes we would like to predict) originate from the same population the genomic prediction model is trained on. In this paper we propose an approach based on clustering and resampling to investigate the effect of increasing genetic distance between training and target populations when predicting quantitative traits. This is important for plant and animal genetics, where genomic selection programs rely on the precision of predictions in future rounds of breeding. Therefore, estimating how quickly predictive accuracy decays is important in deciding which training population to use and how often the model has to be recalibrated. We find that the correlation between true and predicted values decays approximately linearly with respect to either FST or mean kinship between the training and the target populations. We illustrate this relationship using simulations and a collection of data sets from mice, wheat and human genetics.
Subfields: Genetics, Plant Science
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Citations in the corpus
- Geographic variation and bias in polygenic scores of complex diseases and traits in Finland (2018, background): “However, a major challenge is that the geographic distribution of PS is a complex function of population genetic differences between the GWAS data and the target samples, complicating its interpretation (Scutari et al. 2016; Martin et al. 2017; Reisberg et al. 2017; Martin et al. 2018a).”
- Comparative genetic architectures of schizophrenia in East Asian and European populations (2018, unknown): “However, previous studies have shown that prediction accuracy decays with increasing genetic divergence between the risk allele discovery and target datasets 20,21 .”