In Scenario B, the study individuals genotyped on a larger number of SNPs can be used as an unphased, or “diploid”, reference panel for imputation in the remaining samples (which do not necessarily have to be cases). As before, we approach such a dataset by partitioning the SNPs into disjoint sets, named with reference to the study sample: a set U1 that is untyped in the study sample and typed only in the haploid reference panel, a set U2 that is untyped in the study sample and typed in both the haploid and diploid reference panels, and a set T that is typed in all samples.
