Initially, we imputed on the basis of no SNP-level QC, including all directly typed SNPs, regardless of MAF, call rate and HWE.
Each individual was imputed initially from haplotypes in the same panel, then from reference sets that cumulatively added panels in the order shown in the plot legends, reading from bottom to top.
David et al. imputed income, initially using global residual draws [ 10], setting k to the number of observations with x observed.
This same variant had also been reported in another genome-wide association study in the Northern Finland Birth Cohort (p = 6.97e-29) [12], and a meta analysis of three genome-wide association studies initially comprising 8,656 individuals and ∼2,261,000 imputed and/or genotyped SNPs (p = 2.8e-19 2.8e-19followed by validation in six European cohorts totaling 11,569 individuals (p = 6.4e-43) [16].
It is interesting to note that initially as a few pseudo-positive cases were imputed into the training cases the precision of the called positive peaks decreased but later became stable after 75 iterations.
Using the CNVhap algorithm, copy number variation was also imputed in 40 samples that were not initially sequenced as their aCGH scores were below the selection threshold (ADM2, threshold 4).
In this model we imputed 40 completed datasets including all children initially randomised.
First, we analysed the imputed UK|CC cohort for the 36 SNPs initially genotyped in the UK SLE trio cohort.
Irrespectively of the existing spectrum of techniques, the results of imputation are commonly numeric meaning that once the data have been imputed they are not distinguishable from the original data being initially available prior to imputation.
To analyze cDNA datasets, we initially filtered out missing values when the percentage of missing values was greater than 30%, imputed missing values by the k-nearest neighbor method, merged replicate probes by an average value, and finally mean-centered each gene.
