Analyses of related individuals provide the intuition behind genotype imputation: whenever a particular stretch of chromosome is examined in detail in at least one individual, we learn about the genotypes of many other individuals who inherit that same stretch “identical-by-descent”. When studying samples of apparently unrelated individuals, the exact same approach can be utilized. The major difference is that, when studying apparently unrelated individuals, shared haplotype stretches will be much shorter (because common ancestors are more distant) and thus may be harder to identify with confidence. The intuition that short stretches of haplotype provide useful information about untyped genetic markers provides the justification for the potential power gains suggested for many proposed haplotype analysis strategies (22, 60, 91, 115).
