Once and Again—Issues Surrounding Replication in Genetic Association Studies

Over the last 15 yr, genes responsible for hundreds of inherited human diseases have been identified, enabling clinical diagnosis and the potential for therapeutic intervention. Until very recently, however, success has been limited to so-called monogenic disorders, diseases in which mutation of a single gene is both necessary and sufficient to cause disease in any given individual. Because such mutations are strictly co-inherited with disease, it is possible to use linkage analysis to identify their chromosomal location by analyzing which of a genome-wide set of markers segregates with disease in families. Genes contained within such linked regions become positional “candidates” and are next examined for mutations in affected individuals. For any such candidate gene, proof of causality typically depends on two additional lines of evidence. First, the putative causal changes should be found only in affected individuals. Second, one hopes for a “smoking gun”—that the disease-associated mutations are obviously deleterious to protein function (due to truncation or deletion of a coding region or alteration of a highly conserved residue). Success is typically declared when these criteria are all satisfied: the putative disease gene 1) is located in a chromosomal region that co-segregates with disease in affected families, 2) contains multiple independent mutations that are perfectly associated with disease status in the families, and 3) whose characteristics obviously alter protein function.