ArticleGenetics, selection, evolution : GSE2019
Family-specific genotype arrays increase the accuracy of pedigree-based imputation at very low marker densities.
Article in Genetics, selection, evolution : GSE, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- Genomic inbreeding coefficients using imputed genotypes: assessing differences among SNP panels in Holstein-Friesian dairy cows.Frontiers in veterinary science · 2023Article
- Evaluation of low-density SNP panels and imputation for cost-effective genomic selection in four aquaculture species.Frontiers in genetics · 2023Article
- An imputed whole-genome sequence-based GWAS approach pinpoints causal mutations for complex traits in a specific swine population.Science China. Life sciences · 2022Article
- Accuracy of whole-genome sequence imputation using hybrid peeling in large pedigreed livestock populations.Genetics, selection, evolution : GSE · 2020Article
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3 authors.
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Abstract
backgroundIn this paper, we evaluate the performance of using family-specific low-density genotype arrays to increase the accuracy of pedigree-based imputation. Genotype imputation is a widely used tool that decreases the costs of genotyping a population by genotyping the majority of individuals on a low-density array and using statistical regularities between the low-density and high-density individuals to fill in the missing genotypes. Previous work on population-based imputation has found that it is possible to increase the accuracy of imputation by maximizing the number of informative markers on an array. In the context of pedigree-based imputation, where the informativeness of a marker depends only on the genotypes of an individual's parents, it may be beneficial to select the markers on each low-density array on a family-by-family basis.
resultsIn this paper, we examined four family-specific low-density marker selection strategies and evaluated their performance in the context of a real pig breeding dataset. We found that family-specific or sire-specific arrays could increase imputation accuracy by 0.11 at one marker per chromosome, by 0.027 at 25 markers per chromosome and by 0.007 at 100 markers per chromosome.
conclusionsThese results suggest that there may be room to use family-specific genotyping for very-low-density arrays particularly if a given sire or sire-dam pairing have a large number of offspring.
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