A high-resolution HLA and SNP haplotype map for disease association studies in the extended human MHC.

Journal Article (Journal Article)

The proteins encoded by the classical HLA class I and class II genes in the major histocompatibility complex (MHC) are highly polymorphic and are essential in self versus non-self immune recognition. HLA variation is a crucial determinant of transplant rejection and susceptibility to a large number of infectious and autoimmune diseases. Yet identification of causal variants is problematic owing to linkage disequilibrium that extends across multiple HLA and non-HLA genes in the MHC. We therefore set out to characterize the linkage disequilibrium patterns between the highly polymorphic HLA genes and background variation by typing the classical HLA genes and >7,500 common SNPs and deletion-insertion polymorphisms across four population samples. The analysis provides informative tag SNPs that capture much of the common variation in the MHC region and that could be used in disease association studies, and it provides new insight into the evolutionary dynamics and ancestral origins of the HLA loci and their haplotypes.

Full Text

Duke Authors

Cited Authors

  • de Bakker, PIW; McVean, G; Sabeti, PC; Miretti, MM; Green, T; Marchini, J; Ke, X; Monsuur, AJ; Whittaker, P; Delgado, M; Morrison, J; Richardson, A; Walsh, EC; Gao, X; Galver, L; Hart, J; Hafler, DA; Pericak-Vance, M; Todd, JA; Daly, MJ; Trowsdale, J; Wijmenga, C; Vyse, TJ; Beck, S; Murray, SS; Carrington, M; Gregory, S; Deloukas, P; Rioux, JD

Published Date

  • October 2006

Published In

Volume / Issue

  • 38 / 10

Start / End Page

  • 1166 - 1172

PubMed ID

  • 16998491

Pubmed Central ID

  • PMC2670196

International Standard Serial Number (ISSN)

  • 1061-4036

Digital Object Identifier (DOI)

  • 10.1038/ng1885


  • eng

Conference Location

  • United States