The idea is to (pre- phase the assayed genotypre- phaseWAS datheet, then impute directly into the inferred hassayedes; this speeds up imputation by more than an order of magenotypest the cost of a small amount of accuracy (B. Howin and C. FuchsberGWAS unpublishedataset.
But some expressed discomfort at his practice of imputing thoughts directly to DiMaggio, who had refused to be interviewed for the book.
Both MACH and IMPUTE directly model genotypes on the set of haplotypes without clustering, and both of these methods appear to outperform fastPHASE and Beagle, which adopt haplotype clustering strategies [5], [27].
After post-imputation filtering there were 77 SNPs with significantly different (imputed v. directly typed) allele frequencies in the unQCed data compared with 67 significant SNPs in the QCed data.
The procedure includes genotype imputation based on the appropriate reference panel, testing the association per imputed and directly genotyped SNP in each GWA study, performing a meta-analysis to combine the association signals from different studies, and testing for between-study heterogeneity and correcting for this (32).
Concordance of imputed with directly genotyped SNPs was slightly lower than between genotyped SNPs alone, but the level of discordance was still quite low.
For the pollution levels estimated in the two decades before the MESA baseline exam, the imputed and directly observed PM10 levels are comparable, with the imputed levels slightly lower on average than the observed.
In the discovery stage imputed and directly genotyped autosomal single nucleotide polymorphism (SNPs) were assessed using a quality control (QC) procedure that is described in the online supplementary material (section 1.a).
While there are much less demanding methods which avoid the genotype imputation step by directly imputing SNP statistics, e.g. Directly Imputing summary STatistics (DIST) proposed by our group, their implicit assumptions make them applicable only to ethnically homogeneous cohorts.
Mixed-effects models use a likelihood-based approach to estimation and therefore made use of all available data without directly imputing missing outcome values.
