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Zhang et al. (2013) showed, using simulated sequence data and data from the 1000 Genomes Project, that by using the maximum-PD panel, higher imputation accuracy is obtained, and more sites are imputed as polymorphic in the sample population, than if the reference panel consists of randomly selected haplotypes.
Missing data will be imputed using available data from that same center if for any matching variable, the proportion of missing values per center is <30% for the INDICATED population; if higher, imputation will not be done.
The locally elevated LD level caused by the low MAF in low LD regions, results in much higher imputation AR than that attained with high MAF.
FImpute resulted in higher imputation accuracies for the different chips and validation sets than BEAGLE.
Hence, using the hybrid method may achieve higher imputation performance than a single type approach only.
However, we noted a very small proportion of the SNPs with higher imputation error than expected.
Similar(26)
The imputed SNPs had a high imputation quality score.
The majority of the imputed SNPs had a high imputation quality score (MACH-R> 0.6).
All of the imputed SNPs had a high imputation quality score.
We verified that the imputed markers included in genomic risk scores had high imputation accuracy (r > 0.8) in the training data.
These results demonstrated high imputation quality, even though nearly 10,000 SNPs within this 6-Mb region were imputed from the Affy 5.0 chip.
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