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Nat Genet DOI:10.1038/ng1885

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

Publication TypeJournal Article
Year of Publication2006
Authorsde 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, SShaw, Carrington, M, Gregory, S, Deloukas, P, Rioux, JD
JournalNat Genet
Date Published2006 Oct
KeywordsContinental Population Groups, Genetic Predisposition to Disease, Genetics, Medical, Haplotypes, Histocompatibility Antigens, HLA Antigens, Humans, Polymorphism, Genetic, Polymorphism, Single Nucleotide

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.


Alternate JournalNat. Genet.
PubMed ID16998491
PubMed Central IDPMC2670196
Grant List077011 / / Wellcome Trust / United Kingdom
/ / Intramural NIH HHS / United States
U19 AI050864 / AI / NIAID NIH HHS / United States
G9800943 / / Medical Research Council / United Kingdom
N01CO12400 / CA / NCI NIH HHS / United States
/ / Wellcome Trust / United Kingdom
N01-CO-12400 / CO / NCI NIH HHS / United States