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Genetic model misspecification in genetic association studies.

Amadou Gaye1, Sharon K Davis2

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Genetic association studies may incorrectly model dominant genetic effects as additive, reducing statistical power and effect size. Researchers should use larger sample sizes or mitigation methods to account for this misspecification error in candidate gene studies.

Keywords:
Genetic association analysisIncorrect genetic modelStatistical power

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Area of Science:

  • Genetics
  • Statistical Genetics
  • Bioinformatics

Background:

  • Genetic association studies aim to identify genetic variants influencing traits.
  • The genetic model (e.g., dominant, additive) is often unknown a priori.
  • Misspecification of the genetic model can lead to erroneous conclusions.

Purpose of the Study:

  • To evaluate the impact of misspecifying a dominant genetic model as additive in candidate gene studies.
  • To determine the sample size needed to compensate for this misspecification error.
  • To compare statistical power, sample size, and effect size under true dominant and misspecified additive models.

Main Methods:

  • Power calculations were performed using both the correct dominant model and an incorrect additive model.
  • Empirical power, sample size, and effect size were compared between the two models.
  • Analyses considered rare, low-frequency, and common single nucleotide polymorphisms based on minor allele frequency.

Main Results:

  • Model misspecification significantly reduces statistical power and effect size across all minor allele frequencies.
  • The detrimental effects of misspecification are substantial and cannot be ignored.
  • A larger sample size is recommended to counteract the impact of model misspecification.

Conclusions:

  • Candidate gene studies must account for potential genetic model misspecification.
  • Increasing sample size is a recommended strategy to mitigate the effects of using an incorrect additive model.
  • When sample size cannot be increased, alternative methods to reduce the impact of misspecification should be employed.