The human MHC region, located on the short arm of chromosome 6, is believed to contribute to the majority of common autoimmune and inflammatory disorders. It has been a difficult area of the genome to study in detail due to its inherent sequence characteristics. The region covers ~ 4 Mb and contains over 160 genes. Over 40% of the genes encode proteins involved in the immune system, including the human leukocyte antigen (HLA) membrane proteins. Linkage disequilibrium occurs at an unexpectedly high rate in the MHC.

CIDR performs MHC genotyping using the Illumina BeadArray technology on a BeadLab system. With this technology, 96 samples are assayed for up to 1,536 SNP loci in a single experiment.

The MHC marker panels developed at Illumina consist of two oligonucleotide assay pools, the MHC Mapping Panel and the MHC Exon-Centric Panel. The Mapping Panel was developed for use with a tag SNP approach to association mapping. The Exon-Centric Panel was developed for use with an approach focusing on SNPs near and within coding regions. The mean minor allele frequencies (MAF) are 0.26, 0.24, and 0.21, respectively for the CEU, HCB/JPT and YRI HapMap populations. All loci have a MAF greater than > 0.01 in at least one of the three populations.

Exon-Centric Panel (1,228 SNPs)

Mapping Panel (1,293 SNPs)

These two panels can be used independently or combined as a 2,360 SNP set with average 2 kb spacing for more comprehensive coverage.

Statistical Genetics Consultation
As an additional, unique option, CIDR offers to investigators the opportunity to consult regarding study design and statistical analysis issues. Investigators seeking consultation should contact Dr. Camilla Day at NHGRI. Such consultations need to be requested and planned well in advance. Collaboration with statistical genetics consultants incurs no additional charge for approved projects.