The HLA system and the analysis of multifactorial genetic disease

Trends Genet. 1995 Dec;11(12):493-8. doi: 10.1016/s0168-9525(00)89159-3.


The human leukocyte antigen (HLA) system comprises closely linked genes controlling highly polymorphic proteins involved in the presentation of peptides to the T-cell receptor. Specific alleles at HLA loci are associated with diseases, often those suspected to be of autoimmune aetiology. Many of these associations result from linkage disequilibrium between the HLA gene studied and other HLA genes or non-HLA genes close by. Owing to its high level of polymorphism and its candidate role in many diseases, HLA was the first system used in many techniques of genetic mapping, such as affected-sib-pair analysis and association (linkage disequilibrium) studies. Much remains unknown about the reasons why diseases are associated with HLA. Experience gained from HLA has, however, shown how other loci involved in complex traits can be identified by studying families with multiple affected cases or sib pairs, followed by linkage-disequilibrium mapping and then analysis of candidate genes.

Publication types

  • Review

MeSH terms

  • Autoimmune Diseases / genetics
  • Autoimmune Diseases / immunology
  • Chromosome Mapping
  • Diabetes Mellitus, Type 1 / genetics
  • Diabetes Mellitus, Type 1 / immunology
  • Genes, MHC Class I
  • Genes, MHC Class II
  • Genetic Diseases, Inborn / genetics*
  • Genetic Diseases, Inborn / immunology
  • Genetic Markers
  • HLA Antigens / genetics*
  • Humans
  • Linkage Disequilibrium
  • Major Histocompatibility Complex*
  • Pseudogenes


  • Genetic Markers
  • HLA Antigens