Hecker2023FPGWAS

Title

Fallacies and Pitfalls in Genome-Wide Association Studies
View PDF | Save PDF

Authors

Julian Hecker, Adam Craig, Andrew Hughes, Julie Neidich, Carl Taswell, Nan Laird

Affiliations

Harvard University, Boston, MA; Washington University St Louis, St Louis, MO; Brain Health Alliance Virtual Institute, Ladera Ranch, CA 92694 USA

Abstract

Since the first genome-wide association study (GWAS) identifying variants associated with myocardial infarction was published over 20 years ago, GWASs have emerged as a powerful tool for exploring the genetic basis of complex traits. To date, hundreds of thousands of statistically significant associations have been reported across thousands of human phenotypes. Nevertheless, the design, implementation, and analysis of GWASs remain complex, and the results are easily misinterpreted. Common mistakes include 1) assuming that variants with the strongest statistical associations are causal instead of correlative, 2) believing that associated loci act through nearby genes, and 3) overemphasizing the contribution of individual loci to the total variability of particular traits. Clinical assays have been designed using the results of GWAS that rely on the contribution of such erroneous data interpretations to predict clinical phenotypes, reactions to medications or foods, and/or propensity to develop diseases. The failure to recognize these errors due to fallacies in logical reasoning and statistical inference presents problems for both the scientific community when the wrong targets may be prioritized in future research studies, as well as for communication with the general public when our understanding of the genetic basis of important traits may be misrepresented and overstated. Here, we review statistical data quality, analysis, and meta-analysis, of GWAS results with an emphasis on accurate and reliable interpretation. Placed in the appropriate context, GWASs enable genome-wide discovery of loci associated with diverse traits, but they constitute only a first step towards understanding the biological mechanism(s) underlying the observed associations. Scientific elucidation of these biological mechanisms must be required to establish causality with biochemical and pathophysiological explanations for any putative statistical correlations.

Keywords

Genome-wide association studies (GWAS), correlation-causation fallacy, meta-analysis, random effects model, fixed effects model, population stratification, family-based association studies (FBAS).

Citation

Brainiacs Journal 2023 Volume 4 Issue 2 Edoc GFA4E8812
DOI: 10.48085/GFA4E8812
PDP: /Nexus/Brainiacs/Hecker2023FPGWAS
URL: BrainiacsJournal.org/arc/pub/Hecker2023FPGWAS

Dates

Created 2023-10-01, received 2023-10-03, presented 2023-10-09, updated 2023-12-21, published 2023-12-21, endorsed 2023-12-30.