Sentence examples for based on imputed genotypes from inspiring English sources

The genotype probabilities provide an implicit measure of uncertainty in the imputation that can be taken into account in further analyses based on imputed genotypes, such as GWAS or genomic prediction.

Although reliability of GEBV was not evaluated in the present study, it is plausible to assume that the reliability of GEBV of Nelore cattle based on imputed genotypes from a chip with approximately 15 K SNPs, for which the imputation accuracy was around 0.98, would be similar to that of GEBV obtained with the HD chip.

The accuracy of genomic prediction decreased by 15.9 to 21.9 % across the three traits when it was based on imputed genotypes with very low accuracy (on average equal to 0.68 and 0.57, respectively).

Genomic evaluation based on imputed genotypes in selection candidates can be implemented at a fraction of the cost of a genomic evaluation using observed genotypes and still yield virtually the same accuracy.

If imputation procedures have been used, it is useful to know the method, accuracy thresholds for acceptable imputation, how imputed genotypes were handled or weighted in the analysis, and whether any associations based on imputed genotypes were also verified on the basis of direct genotyping at a subsequent stage.

However, there were 133 SNPs that gave stronger evidence based on imputed genotypes (all with imputation r > 0.90); an intronic single-base deletion in AKAP9 (chr7:91681597), located 51 kb from rs6964587, was the best imputed hit (P = 4.4 × 10−7, compared with 1.7 × 10−6 for rs6964587 in the same dataset).

The GEBV accuracy based on 12k genotypes was higher than that based on imputed 50k genotypes with low accuracy.

Then, accuracies of genomic prediction based on imputed 50k genotypes that had different accuracies, were compared with those based on observed 50 and 12k genotypes.

Accuracy of genomic prediction based on imputed 50k genotypes but with relatively moderate to high accuracies (ranging from 0.73 to 0.96, with an average of 0.885), was up to 4.0%% less than that using observed 50k genotypes, but it was still higher than the accuracy based on observed 12k genotypes.

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.

performing association tests on imputed genotypes.