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Letter

Ancient haplotypes of the HLA Class II region

¹ University of Washington Genome Center, Department of Medicine, University of Washington, Seattle, Washington 98195, USA

Allelic variation in codons that specify amino acids that line the peptide-binding pockets of HLA's Class II antigen-presenting proteins is superimposed on strikingly few deeply diverged haplotypes. These haplotypes appear to have been evolving almost independently for tens of millions of years. By complete resequencing of 20 haplotypes across the 100-kbp region that spans the HLA-DQA1, -DQB1, and -DRB1 genes, we provide a detailed view of the way in which the genome structure at this locus has been shaped by the interplay of selection, gene-gene interaction, and recombination.

³ Corresponding author.
E-mail mvo{at}u.washington.edu; fax (206) 616-5242.

[Supplemental material is available online at www.genome.org. The sequence data from this study have been submitted to GenBank under accession nos. AY663393-AY663415.]

Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.3554305.

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