ArticleVeterinary medicine and science2024
The effects of case/control ratio and sample size on genome-wide association studies: A simulation study.
Article in Veterinary medicine and science, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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8 citing papers in PubMed.
- Bayesian Genome-Wide Association Study of Feed Efficiency Traits in Pigs.Animals : an open access journal from MDPI · 2026Article
- Imputed whole genome sequence based association pinpoints genetic architecture of labour dystocia of pigs using multi-breed populations.Genetics, selection, evolution : GSE · 2026Article
- The Utility of Genome-Wide Association Studies in Inherited Arrhythmias and Cardiomyopathies.Genes · 2025Review
- Sex-Specific Polygenic Risk Scores and Replication in a Model-Free Analysis of Schizophrenia Data.Genes · 2025Article
- Article
- Multitrait GWAS of non-suicidal self-injury and the polygenetic effects on child psychopathology and brain structures.Cell reports. Medicine · 2025Article
- Data simulation to optimize frameworks for genome-wide association studies in diverse populations.Frontiers in genetics · 2025Article
- The effects of case/control ratio and sample size on genome-wide association studies: A simulation study.Veterinary medicine and science · 2024Article
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Abstract
backgroundGenome-wide association studies (GWAS) is a useful tool for the detection of disease or quantitative trait-related genetic variations in the veterinary field. For a binary trait, a case/control experiment is designed in GWAS. However, there is limited information on the optimal case/control and sample size in GWAS.
objectivesIn this study, it was aimed to detect the effects of case/control ratio and sample size for GWAS using computer simulation under certain assumptions.
methodUsing the PLINK software, we simulated three different disease scenarios. In scenario 1, we simulated 10 different case/control ratios with increasing ratio of cases to controls. In scenario 2, we did versa of scenario 1 with the increasing ratio of controls to cases. In scenarios 1 and 2, sample size gradually was increased with the change case/control ratios. In scenario 3, the total sample size was fixed to 2000 to see real effects of case/control ratio on the number of disease-related single nucleotide polymorphisms (SNPs).
resultsThe results showed that the number of disease-related SNPs were the highest when the case/control ratio is close to 1:1 in scenarios 1 and 2 and did not change with an increase in sample size. Similarly, the number of disease-related SNPs was the highest in case/control ratios 1:1 in scenario 3. However, unbalanced case/control ratio caused the detection of lower number of disease-related SNPs in scenario 3. The estimated average power of SNPs was highest when case/control ratio is 1:1 in all scenarios.
conclusionsAll findings led to the conclusion that an increase in sample size may enhance the statistical power of GWAS when the number of cases is small. In addition, case/control ratio 1:1 may be the optimal ratio for GWAS. These findings may be valuable not only for veterinary field but also for human clinical experiments.
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