The effects of case/control ratio and sample size on genome-wide association studies: A simulation study

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dc.authoridKoca, Davut/0000-0002-7962-6959
dc.contributor.authorTurgut, Ali Osman
dc.contributor.authorKoca, Davut
dc.date.accessioned2024-12-24T19:24:22Z
dc.date.available2024-12-24T19:24:22Z
dc.date.issued2024
dc.departmentSiirt Üniversitesi
dc.description.abstractBackgroundGenome-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. An increase in sample size may enhance the statistical power of GWAS when the number of cases is small. 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. image
dc.identifier.doi10.1002/vms3.1444
dc.identifier.issn2053-1095
dc.identifier.issue3
dc.identifier.pmid38581306
dc.identifier.scopus2-s2.0-85189447075
dc.identifier.scopusqualityQ1
dc.identifier.urihttps://doi.org/10.1002/vms3.1444
dc.identifier.urihttps://hdl.handle.net/20.500.12604/5946
dc.identifier.volume10
dc.identifier.wosWOS:001197471400001
dc.identifier.wosqualityN/A
dc.indekslendigikaynakWeb of Science
dc.indekslendigikaynakScopus
dc.indekslendigikaynakPubMed
dc.language.isoen
dc.publisherWiley
dc.relation.ispartofVeterinary Medicine and Science
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanı
dc.rightsinfo:eu-repo/semantics/openAccess
dc.snmzKA_20241222
dc.subjectcase/control ratio
dc.subjectdiseases
dc.subjectGWAS
dc.subjectsample size
dc.subjectsimulation
dc.titleThe effects of case/control ratio and sample size on genome-wide association studies: A simulation study
dc.typeArticle

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