The mechanism underlying HLA-disease association is unclear. Many hypotheses have been postulated and generally fall into two categories.
(1) Those that blame "mistaken identity" in which an HLA allele appears to associate with the disease, although the actual culprit belongs to a different locus in the haplotype or associates through linkage disequilibrium
(2) Those that implicate immune reactivity to self-antigens due to abberant T cell repertoir selection, immune cross-reactivity with foreign antigens or immune attack on "altered self" antigens.
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