Genetic epidemiology aims to identify genetic variation related to risk for disease. Because it is currently not feasible to fully sequence the genomes of every person in a sample, the field has traditionally relied on genetic markers with known locations to act as surrogate information for the surrounding sequence. These markers are typically called polymorphisms to reflect the concept that they are locations in the genome with variability within and across individuals (i.e., they have multiple forms or ‘spellings’). The ability for markers to act as surrogates for surrounding sequence is a function of a genetic property called linkage and a related concept of linkage disequilibrium, which results in correlation between polymorphisms and surrounding sequence. Because markers are often simply proxies for unmeasured sequences ...

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