The Association between SNPs and a Quantitative Trait: Power Calculation
Robert Delongchamp 1 2, Mohammed F. Faramawi 1 2 * , Eleanor Feingold 3, Dongjun Chung 4, Saly Abouelenein 2
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1 Department of Epidemiology, College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR, USA2 Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, USA3 Department of Human Genetics- Graduate School of Public Health, University of Pittsburgh, PA, USA4 Department of Public Health Sciences - Medical University of South Carolina, SC, USA* Corresponding Author

Abstract

A power calculation for a study with a quantitative outcome requires information on the outcome distribution under the alternative hypothesis.  Researchers face challenges when they concisely specify alternative distributions in genetic studies because power depends on genotype frequencies and the average effect of each genotype.  In GWAS, investigators evaluate hundreds of thousands of associations; therefore it is unrealistic to specify gene frequencies and gene effects for each test and some simplification is needed.  Software packages are available to calculate power, but many of them have limited flexibility and / or may have a steep learning curve. In this review, we describe to researchers and graduate students the essentials of a power calculation for testing for an association between a quantitative trait and genotypes.  In addition, we provide them with the codes of the different available software packages—free and commercial—to calculate this power.  The calculations can be carried out using virtually any computer language that computes the cumulative distribution function of a non-central F-distribution.

License

This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Article Type: Research Article

EUR J ENV PUBLIC HLT, Volume 2, Issue 2, 2018, Article No: 10

https://doi.org/10.20897/ejeph/3925

Publication date: 16 Oct 2018

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