180 J. A. Traherne 1997; Yamazaki & Beauchamp, 2007). Despite medical progress, pathogen-imposed selectivity must be high as infectious disease causes 50% of global mortality among those below the age of 45 (Kapp, 1999). Characterization of HLA loci was initially motivated by their importance in transplantation. Subsequently, the typing of classical HLA genes and microsatellites, followed by variation at non-HLA candidate loci, was exploited to study MHC involvement in disease. Over time, conﬁdence that the HLA genes act as predominant disease determinants within the MHC was established, although a small number of non-HLA genes have been identiﬁed as directly causative of some diseases. However, uncertainty still remains to which HLA genes are primarily important and to whether, or to what extent, non-HLA loci contribute to disease phenotypes. Recently, systematic DNA sequence analyses between haplotypes have yielded information on polymorphisms and ﬁne-structure linkage disequilibrium (LD) across the complete MHC. This information provides pools of sequence variants for disease association analysis. It also showed insight into the evolutionary dynamics and ancestral origins of common HLA loci and their haplo- types. However, there is an increasing ‘postgenomic’ appreciation of the intricacies of genome structure in modulating gene activities. Novel areas of research include chromatin modiﬁcations and microRNAs. The challenge now is to determine the role of these control mechanisms in the cellular development of a disease. This review surveys the genetic architecture of the MHC, its relationship with disease, and how it impacts on strategies to identify variants contributing to common, multifactorial disorders. MHC diversity With HLA coding variation well characterized, attention has turned to the MHC region as a whole for additional information on variability relevant to disease. Recently, four independent re-sequencing projects have signiﬁcantly expanded our knowledge of variation within the MHC (Raymond et al., 2005; Shiina et al., 2006; Smith et al., 2006; Horton et al., 2008). The aims, target area, haplotype depth and strategies differed between projects. The strategies included shotgun sequencing of fosmid and bacterial artiﬁcial chromosome (BAC) libraries, as well as polymerase chain reaction (PCR)-based, direct sequencing, allowing detection of rare variants. The MHC haplotype project (Horton et al., 2008) determined the sequences of eight common and disease-associated MHC haplotypes. These serve as single haplotype reference sequences and can be viewed in the context of current genome annotation through the VEGA genome browser (Fig. 1). The comprehensive catalogue of variation generated by these projects allowed the construction of high-resolution LD maps (Miretti et al., 2005; de Bakker et al., 2006b) and facilitated precise mapping of susceptibility loci for multiple sclerosis (Yeo et al., 2007) and type I diabetes (Nejentsev et al., 2007). The amassed data also draw a detailed picture of the degree and distribution of variation across the MHC as well as allowing genealogical relation- ships between haplotypes to be deﬁned. Divergence between some pairs of haplotypes over parts of class I and class II can be 20-fold higher than the rest of the genome, consistent with independent haplotype evolution over tens of millions of years (assuming normal mutation rates). These extreme levels of haplotype divergence remain unprecedented in the human genome. Remarkably, human–human pairwise divergences within the MHC can be higher than human–primate comparisons (Raymond et al., 2005). Typically, regions of the MHC distant from classical HLA genes show the lowest levels of variation, in line with the average across the genome. However, areas of exceptional divergence (> 3%) are not limited to HLA loci, but spread over tens of thousands of base pairs into the surrounding regions. The observed broad peaks of variation may have arisen from the combined effects of balancing selection acting on the peptide-binding domains of HLA loci with hitchhiking of neighbouring neutral mutations. A novel, but untested, hypothesis proposes that some MHC-linked diseases are a conse- quence of hitchhiked deleterious mutations within nearby genes (Shiina et al., 2006). A recent study suggests that new alleles in HLA loci are being recurrently created by gene conversion (von Salome et al., 2007). Regulatory regions of MHC genes may also be subject to natural selection (Liu et al., 2006; Loisel et al., 2006; Yamazaki & Beauchamp, 2007), where sequence variants conferring differential levels of expression among dif- ferent cells or in different developmental stages may be the selected factors. It is predicted from recent large-scale expression analyses that variants in regulatory regions may play a greater contribution to complex disease than previously thought (Spielman et al., 2007). Genetic vari- ants that modify HLA-DR, HLA-DQ, HLA-DP, HLA-A and HLA-C have been identiﬁed (Dixon et al., 2007). The strength of the observed effects implies that associations of MHC class I and II polymorphism with disease may relate to the level of gene expression as much as the restriction of response to antigen. Characterization of regulatory region architecture and transcriptional regulation of MHC genes may therefore elucidate the molecular basis for some MHC associations to diseases and particular immune responses (Eagle et al., 2006; Baena et al., 2007; Rodriguez-Rodero et al., 2007; Venkataraman et al., 2007). Moreover, other variation not associated with the peptide-binding grooves, such as that affecting the cyto- plasmic tail of HLA molecules, may be critical as it alters their export to the cell surface (Boyle et al., 2006). MHC genetic variation also affects alternative splicing, which expands the information content and versatility of the transcriptome through the expression of multiple different mRNAs from individual genes (Rollinger- Holzinger et al., 2000; Boyle et al., 2007; Greetham et al., 2007). Current annotation of the MHC reference sequence (PGF) indicates that the total number of splice variants is almost fourfold higher than the total number of © 2008 The Author Journal compilation © 2008 Blackwell Publishing Ltd, International Journal of Immunogenetics 35, 179–192