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

Paul I.W. De Bakker, Gil McVean, Pardis C. Sabeti, Marcos M. Miretti, Todd Green, Jonathan Marchini, Xiayi Ke, Alienke J. Monsuur, Pamela Whittaker, Marcos Delgado, Jonathan Morrison, Angela Richardson, Emily C. Walsh, Xiaojiang Gao, Luana Galver, John Hart, David A. Hafler, Margaret Pericak-Vance, John A. Todd, Mark J. DalyJohn Trowsdale, Cisca Wijmenga, Tim J. Vyse, Stephan Beck, Sarah Shaw Murray, Mary Carrington, Simon Gregory, Panos Deloukas, John D. Rioux

Research output: Contribution to journalArticlepeer-review

573 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)1166-1172
Number of pages7
JournalNature genetics
Issue number10
StatePublished - Oct 2006
Externally publishedYes

ASJC Scopus subject areas

  • Genetics


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