HLA genomics in the third millennium

The MHC region contains several unique characteristics that set it apart as the most important region in the vertebrate genome in relation to disease. Recent data fit with the long-held view that the polymorphism of this region is driven by resistance to infection, although this is not yet proven. Interestingly, the MHC gene complex is associated with most, if not all, of the common autoimmune conditions. It has been difficult to identify the precise MHC genes associated with infection and autoimmunity, mainly because of the strong linkage disequilibrium over the region. Over the past few years, tools have been developed in an attempt to overcome these problems, including multiple fully sequenced MHC haplotypes, which have led to high-density hapmaps. In conjunction with large well-documented patient/control groups and sophisticated statistical methods these advances are starting to provide a comprehensive view of the genetics of the HLA region and disease susceptibility.