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Daetwyler et al. [ 22] also pointed out that results of association studies that are based on imputed sequences should be interpreted with caution, since SNPs with slightly higher P values than the most significant SNPs from multiple-testing can also be considered as potential causative mutations, particularly if there is strong supporting functional evidence.
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Our objective was to investigate the reliability of genomic prediction based on imputed whole-genome sequence genotypes versus high-density SNP genotypes using real cattle data.
Results presented here are based on imputed data.
We therefore display results based on imputed data.
We only present results based on imputed datasets.
‡Treatment effects are ratios of means based on imputed data.
Since results of analyses based on imputed datasets were comparable to the results found in complete case analyses, we only show results based on imputed data.
Similarly, coefficients from models based on imputed data replicated findings from the complete case analysis.
These results were similar to the estimations based on imputed data, see Table 3.
All analyses will use the intention-to-treat [ 153] principle based on imputed data.
The GEBV accuracy based on 12k genotypes was higher than that based on imputed 50k genotypes with low accuracy.
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