The framework we have proposed can serve as a general approach for using reference data in current and future imputation studies, and we expect that it will spur additional methods development in this area.
Future imputation strategies might also consider making use of textual information in the address field to better inform the weighting scheme.
As in the HapMap 3 comparisons, our main goal in designing a cross-validation experiment was to provide guidance on how to use existing and future imputation reference panels.
Finally, we leverage the genotypes obtained from next-generation sequencing to identify SNPs that are at high linkage disequilibrium with sub-population-specific deletions, allowing their imputation in future studies of matched cohorts.
Such an approach of contextually ordering the reference sequence assisted by GBS maps will, in turn, enable better SNP calling in future GBS datasets and haplotypic imputation of missing data (Poland et al. 2012; Tortereau et al. 2012).
If wrong map assignment and genotypic error of SNPs have a significant effect on the accuracy of imputation process is not known, but should be considered in future studies.
Nevertheless, we attempted to assess whether a subset of these SNPs tag common CNVs in this population, which could be useful for imputation of Arab-population CNVs from genetic data using this or similar arrays in future studies.
We now record transfers out and reasons for transfers systematically in IeDEA, allowing the imputation of survival times separately for patients lost to follow-up and patients transferred out in future analyses.
In addition to the reference population size, the relatedness among animals in the reference and test population also affects the imputation accuracy; although we did not consider it in this research, it can be done in future studies.
In total, 1980 SNPs had high imputation error rates in several breeds, which is probably due to genome assembly errors, and we recommend to discard these in future studies.
