title: Genetic analysis of completely sequenced disease-associated MHC haplotypes identifies shuffling of segments in recent human history.
abstract: The major histocompatibility complex (MHC) is recognised as one of the most important genetic regions in relation to common human disease. Advancement in identification of MHC genes that confer susceptibility to disease requires greater knowledge of sequence variation across the complex. Highly duplicated and polymorphic regions of the human genome such as the MHC are, however, somewhat refractory to some whole-genome analysis methods. To address this issue, we are employing a bacterial artificial chromosome (BAC) cloning strategy to sequence entire MHC haplotypes from consanguineous cell lines as part of the MHC Haplotype Project. Here we present 4.25 Mb of the human haplotype QBL (HLA-A26-B18-Cw5-DR3-DQ2) and compare it with the MHC reference haplotype and with a second haplotype, COX (HLA-A1-B8-Cw7-DR3-DQ2), that shares the same HLA-DRB1, -DQA1, and -DQB1 alleles. We have defined the complete gene, splice variant, and sequence variation contents of all three haplotypes, comprising over 259 annotated loci and over 20,000 single nucleotide polymorphisms (SNPs). Certain coding sequences vary significantly between different haplotypes, making them candidates for functional and disease-association studies. Analysis of the two DR3 haplotypes allowed delineation of the shared sequence between two HLA class II-related haplotypes differing in disease associations and the identification of at least one of the sites that mediated the original recombination event. The levels of variation across the MHC were similar to those seen for other HLA-disparate haplotypes, except for a 158-kb segment that contained the HLA-DRB1, -DQA1, and -DQB1 genes and showed very limited polymorphism compatible with identity-by-descent and relatively recent common ancestry (<3,400 generations). These results indicate that the differential disease associations of these two DR3 haplotypes are due to sequence variation outside this central 158-kb segment, and that shuffling of ancestral blocks via recombination is a potential mechanism whereby certain DR-DQ allelic combinations, which presumably have favoured immunological functions, can spread across haplotypes and populations.
authors.affiliation: Department of Pathology, Immunology Division, University of Cambridge, Cambridge, United Kingdom.
authors.forename: James A
authors.initials: JA
authors.lastname: Traherne
authors.forename: Roger
authors.initials: R
authors.lastname: Horton
authors.forename: Anne N
authors.initials: AN
authors.lastname: Roberts
authors.forename: Marcos M
authors.initials: MM
authors.lastname: Miretti
authors.forename: Matthew E
authors.initials: ME
authors.lastname: Hurles
authors.forename: C Andrew
authors.initials: CA
authors.lastname: Stewart
authors.forename: Jennifer L
authors.initials: JL
authors.lastname: Ashurst
authors.forename: Alexey M
authors.initials: AM
authors.lastname: Atrazhev
authors.forename: Penny
authors.initials: P
authors.lastname: Coggill
authors.forename: Sophie
authors.initials: S
authors.lastname: Palmer
authors.forename: Jeff
authors.initials: J
authors.lastname: Almeida
authors.forename: Sarah
authors.initials: S
authors.lastname: Sims
authors.forename: Laurens G
authors.initials: LG
authors.lastname: Wilming
authors.forename: Jane
authors.initials: J
authors.lastname: Rogers
authors.forename: Pieter J
authors.initials: PJ
authors.lastname: de Jong
authors.forename: Mary
authors.initials: M
authors.lastname: Carrington
authors.forename: John F
authors.initials: JF
authors.lastname: Elliott
authors.forename: Stephen
authors.initials: S
authors.lastname: Sawcer
authors.forename: John A
authors.initials: JA
authors.lastname: Todd
authors.forename: John
authors.initials: J
authors.lastname: Trowsdale
authors.forename: Stephan
authors.initials: S
authors.lastname: Beck
mesh_terms: D002874:Chromosome Mapping; D022202:Chromosomes, Artificial, Bacterial; D003001:Cloning, Molecular; D019143:Evolution, Molecular; D014644:Genetic Variation; D006684:HLA-DR Antigens / Q000235:genetics; D006239:Haplotypes / Q000235:genetics*; D006801:Humans; D008285:Major Histocompatibility Complex; D011110:Polymorphism, Genetic; D020641:Polymorphism, Single Nucleotide; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA
chemical_list: D006684:HLA-DR Antigens