1. ¹Division of Clinical Immunology and Rheumatology, Department of Medicine, The University of Alabama at Birmingham (UAB), Birmingham, AL, USA
2. ²Section on Statistical Genetics, Department of Biostatistics, School of Public Health, University of Alabama at Birmingham (UAB), Birmingham, AL, USA

Correspondence: Professor Dr SL Bridges Jr, Department of Medicine, The University of Alabama at Birmingham (UAB), 1530 3rd Avenue South, 210 SHEL, Birmingham, AL 35294-2182, USA. E-mail: LBridges@uab.edu

Received 20 November 2007; Revised 21 January 2008; Accepted 25 January 2008; Published online 28 February 2008.

Abstract

The major histocompatibility complex (MHC) (Chromosome 6p21.3) is a dynamic, immune gene-rich region that is associated with multiple diseases. Haplotype-tagging single-nucleotide polymorphism (htSNP) panels for the MHC can aid association studies but have only been reported for African, Asian and Caucasian populations to date. We genotyped 2154 SNPs spanning a 3.8-Mb region of the classical MHC in 94 healthy African Americans using Illumina BeadArray technology. We describe the haplotype structure of the MHC in African Americans, calculate the recombination rate (0.35 cM Mb^{- 1}) across the region, identify recombination hot spots and develop a panel of htSNPs for future genetic association studies in this population. We conclude that while patterns of LD and recombination are similar within the MHC to that reported in other populations, differences in minor allele frequency at specific markers necessitates an htSNP panel unique to African Americans, which we provide here for use in future genetic association studies.