Establishing Best Practices for Clinical GWAS: Tackling Imputation and Data Quality Challenges

Genome-wide association studies (GWASs) play a central role in precision medicine, powering a range of clinical applications from pharmacogenomics to disease risk prediction. A critical component of GWASs is genotype imputation, a computational method used to infer untyped genetic variants. While imputation increases variant coverage by estimating genotypes at untyped loci, this expanded coverage can enhance the ability to detect genetic associations in some cases. However, imputation also introduces biases, particularly for rare variants and underrepresented populations, which may compromise clinical accuracy. This review examines the challenges and clinical implications of genotype imputation errors, including their impact on therapeutic decisions and predictive models, like polygenic risk scores (PRSs). In particular, the sources of imputation errors have been deeply explored, emphasizing the disparities in performance across ancestral populations and downstream effects on healthcare equity and addressing ethical considerations surrounding the access to equitable genomic resources. Based on the above, we propose evidence-based best practices for clinical GWAS implementation, including the direct genotyping of clinically actionable variants, the cross-population validation of imputation models, the transparent reporting of imputation quality metrics, and the use of ancestry-matched reference panels. As genomic data becomes increasingly adopted in healthcare systems worldwide, ensuring the accuracy and inclusivity of GWAS-derived insights is paramount. Here, we suggest a framework for the responsible clinical integration of imputed genetic data, paving the way for more reliable and equitable personalized medicine.