ArticleMammalian genome : official journal of the International Mammalian Genome Society2016
Genotype imputation in the domestic dog.
Article in Mammalian genome : official journal of the International Mammalian Genome Society, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
36 citing papers in PubMed, 52 citations in OpenAlex.
- High Imputation Accuracy Can Be Achieved Using a Small Reference Panel in a Natural Population With Low Genetic Diversity.Molecular ecology resources · 2025Article
- Performance Comparison of Genomic Best Linear Unbiased Prediction and Four Machine Learning Models for Estimating Genomic Breeding Values in Working Dogs.Animals : an open access journal from MDPI · 2025Article
- Technical note: anomaly detection for breed purity analysis in pigs using a single breed genotype panel.Journal of animal science · 2025Article
- Breeding values and index creation for health and behavior traits in Labrador Retriever guide dogs.Frontiers in veterinary science · 2025Article
- A NovelJournal of fungi (Basel, Switzerland) · 2024Article
- GWAS using low-pass whole genome sequence reveals a novel locus in canine congenital idiopathic megaesophagus.Mammalian genome : official journal of the International Mammalian Genome Society · 2023Article
- Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture.Genome biology · 2023Article
- Canine models of Charcot-Marie-Tooth: MTMR2, MPZ, and SH3TC2 variants in golden retrievers with congenital hypomyelinating polyneuropathy.Neuromuscular disorders : NMD · 2023Article
- Best practices for analyzing imputed genotypes from low-pass sequencing in dogs.Mammalian genome : official journal of the International Mammalian Genome Society · 2022Article
- Genome-wide imputation using the practical haplotype graph in the heterozygous crop cassava.G3 (Bethesda, Md.) · 2022Article
- Use of whole genome analysis to identify shared genomic variants across breeds in canine mitral valve disease.Human genetics · 2021Article
- Improving the resolution of canine genome-wide association studies using genotype imputation: A study of two breeds.Animal genetics · 2021Article
- Article
- A defect in the NOG gene increases susceptibility to spontaneous superficial chronic corneal epithelial defects (SCCED) in boxer dogs.BMC veterinary research · 2021Article
- A novel missense mutation of the NAT10 gene in a juvenile Schnauzer dog with chronic respiratory tract infections.Journal of veterinary internal medicine · 2021Article
- Identification of common predisposing loci to hematopoietic cancers in four dog breeds.PLoS genetics · 2021Article
- A novel canine reference genome resolves genomic architecture and uncovers transcript complexity.Communications biology · 2021Article
- Biologically Enhanced Genome-Wide Association Study Provides Further Evidence for Candidate Loci and Discovers Novel Loci That Influence Risk of Anterior Cruciate Ligament Rupture in a Dog Model.Frontiers in genetics · 2021Article
- X-linked CD40 ligand deficiency in a 1-year-old male Shih Tzu with secondary Pneumocystis pneumonia.Journal of veterinary internal medicine · 2021Article
- The Genetic Basis of Obesity and Related Metabolic Diseases in Humans and Companion Animals.Genes · 2020Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Application of imputation methods to accurately predict a dense array of SNP genotypes in the dog could provide an important supplement to current analyses of array-based genotyping data. Here, we developed a reference panel of 4,885,283 SNPs in 83 dogs across 15 breeds using whole genome sequencing. We used this panel to predict the genotypes of 268 dogs across three breeds with 84,193 SNP array-derived genotypes as inputs. We then (1) performed breed clustering of the actual and imputed data; (2) evaluated several reference panel breed combinations to determine an optimal reference panel composition; and (3) compared the accuracy of two commonly used software algorithms (Beagle and IMPUTE2). Breed clustering was well preserved in the imputation process across eigenvalues representing 75 % of the variation in the imputed data. Using Beagle with a target panel from a single breed, genotype concordance was highest using a multi-breed reference panel (92.4 %) compared to a breed-specific reference panel (87.0 %) or a reference panel containing no breeds overlapping with the target panel (74.9 %). This finding was confirmed using target panels derived from two other breeds. Additionally, using the multi-breed reference panel, genotype concordance was slightly higher with IMPUTE2 (94.1 %) compared to Beagle; Pearson correlation coefficients were slightly higher for both software packages (0.946 for Beagle, 0.961 for IMPUTE2). Our findings demonstrate that genotype imputation from SNP array-derived data to whole genome-level genotypes is both feasible and accurate in the dog with appropriate breed overlap between the target and reference panels.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.