The sheer number of inter-individual differences, mostly rare, to be detected by whole-genome sequencing (roughly 0.4% of 3 billion base pairs51) also raises the question of finding appropriate comparison subjects, or allelic matches, because people carrying rare variants at some loci may have important differences in ancestry or other factors from a general population. To reduce the number of variants that must be considered in a case-control comparison it would be useful to implement chromosomal-region-specific matching throughout the genome, to select closely related alleles and regions from the comparison population, thereby greatly reducing the number of incidental allelic differences from cases.
