Genomics Inform.  2016 Dec;14(4):149-159. 10.5808/GI.2016.14.4.149.

Prediction of Quantitative Traits Using Common Genetic Variants: Application to Body Mass Index

Affiliations
  • 1Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 08826, Korea. tspark@stats.snu.ac.kr
  • 2Bioinformatics and Biostatistics Lab, Seoul National University, Seoul 08826, Korea.
  • 3Department of Statistics, Seoul National University, Seoul 08826, Korea.

Abstract

With the success of the genome-wide association studies (GWASs), many candidate loci for complex human diseases have been reported in the GWAS catalog. Recently, many disease prediction models based on penalized regression or statistical learning methods were proposed using candidate causal variants from significant single-nucleotide polymorphisms of GWASs. However, there have been only a few systematic studies comparing existing methods. In this study, we first constructed risk prediction models, such as stepwise linear regression (SLR), least absolute shrinkage and selection operator (LASSO), and Elastic-Net (EN), using a GWAS chip and GWAS catalog. We then compared the prediction accuracy by calculating the mean square error (MSE) value on data from the Korea Association Resource (KARE) with body mass index. Our results show that SLR provides a smaller MSE value than the other methods, while the numbers of selected variables in each model were similar.

Keyword

body mass index; clinical prediction rule; genome-wide association study; penalized regression models; variable selection
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