"This has been going on since the age of the Romantics, but I think that gets exaggerated to the point of imputing good qualities onto the person..
Imputed SNPs with a quality score of <0.4 (info in Impute versus 2) or 0.3 (Rsq in MACH 1.0), respectively, were excluded from the meta-analysis.
16 It was not possible to impute stable quality of life estimates up to 42 days, so the analysis focused on the first 28 days after surgery (14 EQ-5D scores).
These criteria were: (1) without any filtering options on SNPs, (2) filtering on the imputation quality of R > 0.8, leaving only the high quality imputed SNPs and (3) filtering with R > 0.8 and MAF > 0.01, additionally excluding alleles with low minor allele frequency.
Imputed genotypes were passed through quality control filters of a minor allele frequency ≥0.01, a SNP missingness rate≤10%, and a Hardy-Weinberg test p-value ≥0.001.
After Quality Control, we analysed 430,000 autosomal SNPs together with an additional 1.2 million SNPs imputed with high quality from the Hap Map CEU samples.
Rating-scale measures of inattention and hyperactive-impulsive symptoms were extracted, study authors were contacted to obtain missing data, studies not reporting negative findings had these data imputed, and study quality was assessed using the Jadad system plus other indicators.
In order to identify duplicate samples that are not annotated as such by ENA we selected the high-quality imputed genotypes.
Imputation-based genomic coverage is calculated as the number of imputed variants with quality scores above the threshold value (info score ≥ 0.8) divided by the total number of variants in the reference panel [ 24].
The data did not support this hypothesis since the variance explained by individual SNPs in KORA-F3 was very low also for SNPs which were either genotyped or imputed with high quality (see Supplementary Material, Tables S2 and S3).
Of the 10 SNPs that could not be imputed with high quality, only one had P assoc < 10−5 in the original Levine data; we therefore genotyped this SNP (rs11771429) using KASPar in our cases and controls.
