ArticleGenetics, selection, evolution : GSE2012
A phasing and imputation method for pedigreed populations that results in a single-stage genomic evaluation.
Article in Genetics, selection, evolution : GSE, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 77 papers, 1 of them a synthesis that pooled it.
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Who cites it
77 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Data Integration, Imputation, and Meta-analysis for Genome-Wide Association Studies.Methods in molecular biology (Clifton, N.J.) · 2022Pooled it
- Integrating longitudinal metabolite profiles improves phenotype prediction in pigs in a trait- and timepoint-dependent manner.Genetics, selection, evolution : GSE · 2026Article
- Benchmarking imputation accuracy in the presence or absence of a reference panel.Molecular biology and evolution · 2026Article
- Establishing Best Practices for Clinical GWAS: Tackling Imputation and Data Quality Challenges.International journal of molecular sciences · 2025Review
- Evaluating regional heritability mapping methods for identifying QTLs in a wild population of Soay sheep.Heredity · 2025Article
- Inclusion of imputed genotypes from non-genotyped dairy cattle in a Thai multibreed genomic-polygenic evaluation.Animal bioscience · 2025Article
- Empirical versus estimated accuracy of imputation: optimising filtering thresholds for sequence imputation.Genetics, selection, evolution : GSE · 2024Article
- An overview of recent technological developments in bovine genomics.Veterinary and animal science · 2024Review
- Purifying and balancing selection on embryonic semi-lethal haplotypes in a wild mammal.Evolution letters · 2024Article
- Using residual regressions to quantify and map signal leakage in genomic prediction.Genetics, selection, evolution : GSE · 2023Article
- Genomic inbreeding coefficients using imputed genotypes: assessing differences among SNP panels in Holstein-Friesian dairy cows.Frontiers in veterinary science · 2023Article
- A Pipeline for Phasing and Genotype Imputation on Mixed Human Data (Parents-Offspring Trios and Unrelated Subjects) by Reviewing Current Methods and Software.Life (Basel, Switzerland) · 2022Review
- The impact of SNP density on quantitative genetic analyses of body size traits in a wild population of Soay sheep.Ecology and evolution · 2022Article
- PolyHaplotyper: haplotyping in polyploids based on bi-allelic marker dosage data.BMC bioinformatics · 2022Article
- Genomic prediction with whole-genome sequence data in intensely selected pig lines.Genetics, selection, evolution : GSE · 2022Article
- Vitamin D status is heritable and under environment-dependent selection in the wild.Molecular ecology · 2022Article
- Rare and population-specific functional variation across pig lines.Genetics, selection, evolution : GSE · 2022Article
- Mendelian imputation of parental genotypes improves estimates of direct genetic effects.Nature genetics · 2022Article
- Imputation of non-genotyped F1 dams to improve genetic gain in swine crossbreeding programs.Journal of animal science · 2022Article
- Improving the accuracy of genomic predictions in an outcrossing species with hybrid cultivars between heterozygote parents: a case study of oil palm (Elaeis guineensis Jacq.).Molecular genetics and genomics : MGG · 2022Article
17 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
Funding
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Abstract
backgroundEfficient, robust, and accurate genotype imputation algorithms make large-scale application of genomic selection cost effective. An algorithm that imputes alleles or allele probabilities for all animals in the pedigree and for all genotyped single nucleotide polymorphisms (SNP) provides a framework to combine all pedigree, genomic, and phenotypic information into a single-stage genomic evaluation.
methodsAn algorithm was developed for imputation of genotypes in pedigreed populations that allows imputation for completely ungenotyped animals and for low-density genotyped animals, accommodates a wide variety of pedigree structures for genotyped animals, imputes unmapped SNP, and works for large datasets. The method involves simple phasing rules, long-range phasing and haplotype library imputation and segregation analysis.
resultsImputation accuracy was high and computational cost was feasible for datasets with pedigrees of up to 25 000 animals. The resulting single-stage genomic evaluation increased the accuracy of estimated genomic breeding values compared to a scenario in which phenotypes on relatives that were not genotyped were ignored.
conclusionsThe developed imputation algorithm and software and the resulting single-stage genomic evaluation method provide powerful new ways to exploit imputation and to obtain more accurate genetic evaluations.
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