Estimation of effect size distribution from genome-wide association studies and implications for future discoveries

Abstract

We report a set of tools to estimate the number of susceptibility loci and the distribution of their effect sizes for a trait on the basis of discoveries from existing genome-wide association studies (GWASs). We propose statistical power calculations for future GWASs using estimated distributions of effect sizes. Using reported GWAS findings for height, Crohn's disease and breast, prostate and colorectal (BPC) cancers, we determine that each of these traits is likely to harbor additional loci within the spectrum of low-penetrance common variants. These loci, which can be identified from sufficiently powerful GWASs, together could explain at least 15–20% of the known heritability of these traits. However, for BPC cancers, which have modest familial aggregation, our analysis suggests that risk models based on common variants alone will have modest discriminatory power (63.5% area under curve), even with new discoveries.

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Figure 1: Nonparametric estimates for distributions of effect sizes for susceptibility loci.
Figure 2: Receiver operating characteristic curves for genetic risk models.

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Acknowledgements

This work was supported by the intramural program of the National Cancer Institute, US National Institutes of Health. The research of N.C. and J.-H.P. was also partially funded by the Gene-Environment Initiative of the National Institutes of Health.

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J.-H.P. and N.C. developed the statistical methods and designed the analyses. J.-H.P. implemented the methods and carried out all analyses. N.C. and S.J.C. drafted the manuscript. S.W., M.H.G., K.B.J. and U.P. made important suggestions for presentation and interpretation of the results. All the authors participated in critically reviewing the paper and approved the final version of the manuscript.

Corresponding author

Correspondence to Nilanjan Chatterjee.

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The authors declare no competing financial interests.

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Supplementary Tables 1–7 and Supplementary Note. (PDF 544 kb)

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Park, J., Wacholder, S., Gail, M. et al. Estimation of effect size distribution from genome-wide association studies and implications for future discoveries. Nat Genet 42, 570–575 (2010). https://doi.org/10.1038/ng.610

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