| Title |
Assessing accuracy of imputation using different SNP panel densities in a multi-breed sheep population
|
|---|---|
| Published in |
Genetics Selection Evolution, September 2016
|
| DOI | 10.1186/s12711-016-0244-7 |
| Pubmed ID | |
| Authors |
Ricardo V. Ventura, Stephen P. Miller, Ken G. Dodds, Benoit Auvray, Michael Lee, Matthew Bixley, Shannon M. Clarke, John C. McEwan |
| Abstract |
Genotype 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). Imputation 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(2)). Most of the chromosomes displayed reduced imputation accuracy at least at one of their ends. Prediction of imputation accuracy based on the relatedness of low-density genotypes to those of the reference dataset, before imputation (without running an imputation software) was also investigated. FIMPUTE V2.2 outperformed BEAGLE 3.3.2 across all imputation scenarios. Imputation 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. |
X Demographics
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Geographical breakdown
| Country | Count | As % |
|---|---|---|
| United Kingdom | 1 | 100% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Members of the public | 1 | 100% |
Mendeley readers
The data shown below were compiled from readership statistics for 76 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Denmark | 1 | 1% |
| Unknown | 75 | 99% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Researcher | 14 | 18% |
| Student > Master | 11 | 14% |
| Student > Bachelor | 9 | 12% |
| Student > Ph. D. Student | 8 | 11% |
| Other | 7 | 9% |
| Other | 14 | 18% |
| Unknown | 13 | 17% |
| Readers by discipline | Count | As % |
|---|---|---|
| Agricultural and Biological Sciences | 35 | 46% |
| Veterinary Science and Veterinary Medicine | 8 | 11% |
| Biochemistry, Genetics and Molecular Biology | 8 | 11% |
| Medicine and Dentistry | 2 | 3% |
| Computer Science | 1 | 1% |
| Other | 2 | 3% |
| Unknown | 20 | 26% |
Attention Score in Context
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