ArticleJournal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie2019
Significance testing and genomic inflation factor using high-density genotypes or whole-genome sequence data.
Article in Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers, 1 of them a synthesis that pooled it.
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Who cites it
37 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-Analysis for Epigenome-Wide Association Studies.Methods in molecular biology (Clifton, N.J.) · 2022Pooled it
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- Genomic prediction of beef quality using GWAS-prioritized markers.Translational animal science · 2026Article
- Genome-Wide Detection of Copy Number Variation and Association Studies With Physiological and Anatomical Indicators of Heat Stress Response in Lactating Sows.Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie · 2026Article
- Genome-wide association study of gestation length in German Holsteins.Archives animal breeding · 2026Article
- Claudin and Rab proteins are key molecular components involved in coccidiosis resistance in Portuguese Merino sheep.Genetics, selection, evolution : GSE · 2025Article
- Agricultural copper pesticide exposure and DNA methylation in Central Valley of California residents with and without Parkinson's disease.Environmental research · 2025Article
- Mapping genes for resilient dairy cows by means of across-breed genome-wide association analysis.BMC genomics · 2025Article
- Genotypic and phenotypic consequences of domestication in dogs.bioRxiv : the preprint server for biology · 2025Article
- Single-variant genome-wide association study and regional heritability mapping of protein efficiency and performance traits in Large White pigs.Genetics, selection, evolution : GSE · 2025Article
- Associations between circulating metabolites and pca: a bidirectional two-sample Mendelian randomization study.Discover oncology · 2025Article
- Article
- A lethal disease of the European bison - posthitis is conditionally determined by its genomics.Scientific reports · 2025Article
- Sequence-based GWAS in 180,000 German Holstein cattle reveals new candidate variants for milk production traits.Genetics, selection, evolution : GSE · 2025Article
- Targeted analysis of dyslexia-associated regions on chromosomes 6, 12 and 15 in large multigenerational cohorts.PloS one · 2025Article
- Changes in allele frequencies and genetic architecture due to selection in two pig populations.Genetics, selection, evolution : GSE · 2024Article
- Extreme-Phenotype Genome-Wide Association Analysis for Growth Traits in Spotted Sea Bass (Animals : an open access journal from MDPI · 2024Article
- An overview of recent technological developments in bovine genomics.Veterinary and animal science · 2024Review
- Genomic regions, candidate genes, and pleiotropic variants associated with physiological and anatomical indicators of heat stress response in lactating sows.BMC genomics · 2024Article
- Mendelian randomization analysis of 34,497 German Holstein cows to infer causal associations between milk production and health traits.Genetics, selection, evolution : GSE · 2024Article
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5 authors.
Funding
Abstract
Significance testing for genome-wide association study (GWAS) with increasing SNP density up to whole-genome sequence data (WGS) is not straightforward, because of strong LD between SNP and population stratification. Therefore, the objective of this study was to investigate genomic control and different significance testing procedures using data from a commercial pig breeding scheme. A GWAS was performed in GCTA with data of 4,964 Large White pigs using medium density, high density or imputed whole-genome sequence data, fitting a genomic relationship matrix based on a leave-one-chromosome-out approach to account for population structure. Subsequently, genomic inflation factors were assessed on whole-genome level and the chromosome level. To establish a significance threshold, permutation testing, Bonferroni corrections using either the total number of SNPs or the number of independent chromosome fragments, and false discovery rates (FDR) using either the Benjamini-Hochberg procedure or the Benjamini and Yekutieli procedure were evaluated. We found that genomic inflation factors did not differ between different density genotypes but do differ between chromosomes. Also, the leave-one-chromosome-out approach for GWAS or using the pedigree relationships did not account appropriately for population stratification and gave strong genomic inflation. Regarding different procedures for significance testing, when the aim is to find QTL regions that are associated with a trait of interest, we recommend applying the FDR following the Benjamini and Yekutieli approach to establish a significance threshold that is adjusted for multiple testing. When the aim is to pinpoint a specific mutation, the more conservative Bonferroni correction based on the total number of SNPs is more appropriate, till an appropriate method is established to adjust for the number of independent tests.
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