MHC Mapping Panel

The MHC Mapping Panel can be used to map variants in the MHC region. This region is proposed to contain genomic sequences that contribute to the majority of autoimmune and inflammatory disorders, including multiple sclerosis (MS), Type-1 diabetes, and rheumatoid arthritis. Exploration of this region can provide information to determine the gene associations that lead to disease susceptibility.

The MHC region is one of the most difficult areas of the genome to study due to its inherent sequence characteristics. Located on the short (p) arm of chromosome 6, this gene-dense region spans ~4 Mb and encodes over 160 genes. Approximately 40% of these genes encode proteins involved in the immune system, including the human leukocyte antigen (HLA) membrane glycoproteins that mediate T-lymphocyte signaling. The MHC Panel Set interrogates genomic areas both inside and outside the HLA regions.

The MHC Mapping Panel employs a commonly used approach for association mapping genetic regions of interest that utilizes interrogation of evenly-spaced SNPs, an approach that has an emphasis on tag SNPs. This panel also has excellent coverage with respect to linkage disequilibrium (LD - non-random allele pairing). LD occurs at an unexpectedly high rate in the MHC region, influenced principally by low recombination rates and often involving extended haplotypes.

• The Mapping Panel consists of 1,293 SNPs, evenly spaced across the MHC region with an average 3.8 kb between each one
• Approximately half of the SNPs in the Mapping Panel are tag SNPs
• The Mapping Panel is included on the MHC Panel Set along with the MHC Exon-Centric Panel