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

Nature Genetics volume 42, pages 570575 (2010) | Download Citation


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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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.

Author information


  1. Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Rockville, Maryland, USA.

    • Ju-Hyun Park
    • , Sholom Wacholder
    • , Mitchell H Gail
    • , Stephen J Chanock
    •  & Nilanjan Chatterjee
  2. Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.

    • Ulrike Peters
  3. Core Genotyping Facility, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Gaithersburg, Maryland, USA.

    • Kevin B Jacobs
    •  & Stephen J Chanock


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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.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Nilanjan Chatterjee.

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