Multiple imputation analysis adjusting the imputed values downwards by a range of values will assess the sensitivity of the analysis to the missing at random assumption [ 61].
†Multiple imputation analysis based on 50 imputed datasets and estimates combined using Rubin's method.
Imputation analysis in this dataset found strong associations for imputed SNPs, including some SNPs in regulatory regions which may be good candidates for the causal SNP.
Where minimum value imputation analysis was performed, our results were additionally validated by a stability analysis imputing changing fractions of the minimum values obtained for each response, which confirmed our main analysis.
Potential limitations highlighted by the WTCCC GWA study are discussed, including problems associated with massive genotype imputation, analysis of pooled national samples, shared controls, and the critical role of interactions.
Multiple imputation involves three steps, namely, imputation, analysis, and pooling as determined by [56].
However, in imputation analysis, inserting zero or median in place of missing data did not affect the overall results.
The 80-kb LD block showing the association corresponds to the second intron of BICD1 as revealed by the imputation analysis shown in Figure 3b (Table S3).
We performed genotype imputation analysis for each set of samples by utilizing a Hidden Markov model as programmed in MACH version 1.0 (http://www.sph.umich.edu/csg/abecasis/mach/index.html).html
Imputation analysis also revealed modest association at SNPs located near to or on the FOXQ1 gene suggesting it to be one of the causative genes for pancreatic cancer (Figure 3a and Table S3).
Given that none of the SNPs in the imputed association analyses from the HapMap data was in exons of the NTSR1 gene, the current imputation analysis did not help us to find causative exon SNPs with WM performance.
