Our cross-validation experiments have provided a wealth of information about how to use existing imputation resources like HapMap 3, but these datasets do not capture the full range of features that will be present in future reference panels.
Imputation for resource use was undertaken using the uvis command in STATA V.11, based on a single imputed dataset, and assuming a non-normal distribution for each dependent variable.
The 1000 Genomes panel is a much more comprehensive and powerful resource for imputation, comprising more than 37 million autosomal SNPs present in 1,094 individuals from different populations around the world.
The GoNL imputation reference set is a resource of sequenced data from the Netherlands, where a group of 250 trio's from all Dutch provinces was sequenced at a depth of ~12 13×.
Missing data were imputed using ICE (imputation using chained equations) in Stata version 11.1 (Stata, College Station, Tex., USA) [ 26] for each missing item of resource use versus total cost.
CGDSNPdb was constructed primarily as a resource to support the imputation and mouse diversity array projects, however, it is being made available as a somewhat reduced size, but high confidence, collection of mouse SNPs.
There are numerous approaches for building imputation reference panels from publicly available resources.
Mean substitution techniques (for individual-item missing resource use data) and multiple imputation techniques (resource use data) will be carried out to ensure that all trial participants are included in the final analysis.
Patterns of imputation quality by chromosome are shown in Online Resource 6.
In the multiple imputation analysis all participants with partial information on resource usage and outcomes will be included.
