ArticleGenetics, selection, evolution : GSE2016
Assessing accuracy of imputation using different SNP panel densities in a multi-breed sheep population.
Article in Genetics, selection, evolution : GSE, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers, 1 of them a synthesis that pooled it.
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Who cites it
26 citing papers in PubMed, 1 synthesis or guideline pooled it.
- GWAS of Reproductive Traits in Large White Pigs on Chip and Imputed Whole-Genome Sequencing Data.International journal of molecular sciences · 2022Pooled it
- Assessing kinship detection: single nucleotide polymorphism array density and estimator comparison in white-tailed deer.G3 (Bethesda, Md.) · 2026Article
- Comparison between SNP array and imputed data to estimate population structure and ROH hotspots in horse breeds.BMC genomics · 2025Article
- Genomic analyses of withers height and linear conformation traits in German Warmblood horses using imputed sequence-level genotypes.Genetics, selection, evolution : GSE · 2024Article
- A cautionary tale of low-pass sequencing and imputation with respect to haplotype accuracy.Genetics, selection, evolution : GSE · 2024Article
- Accuracy of genotype imputation of a low-density SNP array for the Amazon fish Colossoma macropomum.Genetics and molecular biology · 2024Article
- Improving the accuracy of genomic prediction for meat quality traits using whole genome sequence data in pigs.Journal of animal science and biotechnology · 2023Article
- SNP- and haplotype-based single-step genomic predictions for body weight, wool, and reproductive traits in North American Rambouillet sheep.Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie · 2023Article
- Evaluation of low-density SNP panels and imputation for cost-effective genomic selection in four aquaculture species.Frontiers in genetics · 2023Article
- Impacts of additive, dominance, and inbreeding depression effects on genomic evaluation by combining two SNP chips in Canadian Yorkshire pigs bred in China.Genetics, selection, evolution : GSE · 2022Article
- Assessment of genotyping array performance for genome-wide association studies and imputation in African cattle.Genetics, selection, evolution : GSE · 2022Article
- Development and validation of a horse reference panel for genotype imputation.Genetics, selection, evolution : GSE · 2022Article
- Breeding of African sheep reared under low-input/output smallholder production systems for trypanotolerance.Veterinary world · 2022Review
- Genomic Selection for Milk Production Traits in Xinjiang Brown Cattle.Animals : an open access journal from MDPI · 2022Article
- Exploring the optimal strategy of imputation from SNP array to whole-genome sequencing data in farm animals.Frontiers in genetics · 2022Article
- SNPs in Sheep: Characterization of Lithuanian Sheep Populations.Animals : an open access journal from MDPI · 2021Article
- The Effect of Integrating Genomic Information into Genetic Evaluations of Chinese Merino Sheep.Animals : an open access journal from MDPI · 2020Article
- Genome wide association analysis on semen volume and milk yield using different strategies of imputation to whole genome sequence in French dairy goats.BMC genetics · 2020Article
- Development of a low-density panel for genomic selection of pigs in Russia.Translational animal science · 2020Article
- High imputation accuracy from informative low-to-medium density single nucleotide polymorphism genotypes is achievable in sheep1.Journal of animal science · 2019Article
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundGenotype imputation is a key element of the implementation of genomic selection within the New Zealand sheep industry, but many factors can influence imputation accuracy. Our objective was to provide practical directions on the implementation of imputation strategies in a multi-breed sheep population genotyped with three single nucleotide polymorphism (SNP) panels: 5K, 50K and HD (600K SNPs).
resultsImputation from 5K to HD was slightly better (0.6 %) than imputation from 5K to 50K. Two-step imputation from 5K to 50K and then from 50K to HD outperformed direct imputation from 5K to HD. A slight loss in imputation accuracy was observed when a large fixed reference population was used compared to a smaller within-breed reference (including all 50K genotypes on animals from different breeds excluding those in the validation set i.e. to be imputed), but only for a few animals across all imputation scenarios from 5K to 50K. However, a major gain in imputation accuracy for a large proportion of animals (purebred and crossbred), justified the use of a fixed and large reference dataset for all situations. This study also investigated the loss in imputation accuracy specifically for SNPs located at the ends of each chromosome, and showed that only chromosome 26 had an overall imputation (5K to 50K) accuracy for 100 SNPs at each end higher than 60 % (r
conclusionsImputation accuracy in sheep breeds can be improved by following a set of recommendations on SNP panels, software, strategies of imputation (one- or two-step imputation), and choice of the animals to be genotyped using both high- and low-density SNP panels. We present a method that predicts imputation accuracy for individual animals at the low-density level, before running imputation, which can be used to restrict genomic prediction only to the animals that can be imputed with sufficient accuracy.
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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.