Sentence examples for based on genotype imputation from inspiring English sources
A range of approaches are available for follow-up, ranging from in silico approaches (based on genotype imputation) to targeted genotyping or targeted sequencing.
AMGP methods based on genotype imputation on a national scale were developed, and the most accurate method, GLDLA0BLUP, combined linkage and linkage disequilibrium information.
Animal model genomic prediction methods based on genotype imputation on a national scale were developed, and the most accurate method, GLDLA0BLUP, combined linkage and linkage analysis information.
After imputation, 222,888 SNPs with MAF > .05 passed quality control based on genotyping or imputation in all cohorts and were eligible for analysis.
These p-value thresholds are useful reference for GWAS based on the genotype imputation using genotypes from HapMap and 1000 Genomes as reference sample.
Imputation accuracy based on genotypes of randomly selected reference animals was slightly, albeit consistently lower (Table 6).
Imputation of genotypes from low-density to higher density chips is a cost-effective method to obtain high-density genotypes for many animals, based on genotypes of only a relatively small subset of animals (reference population) on the high-density chip.
Genotype imputation based on parental genotypes or genotypes from the general population is already in usage when lower density SNP panels are used [ 54, 55].
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 effectiveness of the method was assessed based on (1) the genotype imputation error rates and the correlation between true and predicted genotypes, and (2) a utilitarian measure given by the accuracy of GEBV derived with the imputed genotypes.
The "best guess" genotypes based on the imputation were used in the analysis.
