Genotyping a single marker in a gene of interest no longer reflects current practice in genetics. The field of genetics has been revolutionized by the discovery and mapping of genetic markers across the human genome. In October of 2002, the International HapMap Project1 was initiated as a collaboration among scientists across multiple countries with the goal of developing a haplotype map of the human genome to describe the common patterns of human DNA sequence variation. With data from the HapMap project, we now know something about the LD structure (i.e., correlation pattern across alleles) for most genes in the human genome (Manolio et al., 2008). Further, there are many polymorphic markers available across most genes of interest. It is possible that multiple polymorphic sites exist in a gene that lead to differential function of that gene and contribute to differential susceptibility to an outcome (McClellan and King, 2010). This is already well-known in Mendelian traits, where >1000 different mutations have been identified in the gene causing cystic fibrosis.
