Several authors have investigated imputation error rates obtained when genotypes were imputed from this or other low-density panels to the Illumina BovineSNP50 chips.
For the calculation of groupings, analyte missing values for cases and controls were imputed from control measurement data using the previously described imputation procedure, with the exception that the LOD was specified as the lower limit for imputed values.
Measurements below the limit of detection were imputed from a log-normal probability distribution via a multiple imputation procedure.
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.
In 8 patients, who missed their 12 month study visit, any missing data for frequency, medication, or questionnaire data were imputed from the preceding 9 month study visit.
In addition, 1785 SNPs in six genes (HEPH, MGST1, SERPINA, SLC25A45, SLC39A11 and UGT1A) were imputed from the 1000 Genomes Project and examined for association with INV EOC in white-European subjects.
In the replication, we also expanded our investigation to include those SNPs that were not genotyped in either array, but were imputed from their respective arrays.
Among the final 23,294 individuals of verified European ancestry, genotypes for a total of 2,608,509 SNPs were imputed from the experimental genotypes and LD relationships implicit in the HapMap r. 22 CEU samples.
Genotypes in WGHS were imputed from GWA data based on the HumanHap300 Duo "+" chips or a combination of the HumanHuman300 Duo and iSelect chips (Illumina, San Diego, CA) with the Infinium II protocol [20].
Whenever possible, these were imputed from other summary statistics [ 44].
For 60 participants, noise values were imputed from isophone bands.
