High-density map of short tandem repeats across the human major histocompatibility complex

The human genome contains one short tandem repeat (STR) roughly every 2,000 base pairs. They are particularly useful markers for gene mapping and disease association studies due to their high degree of polymorphism and ubiquitous frequency throughout the genome. The major histocompatibility complex (MHC) has been the focus of many disease association studies, and the recent availability of the entire sequence of the complex has logarithmically expanded the density of potential markers for fine mapping disease loci. Here we present a complete assessment of the available STRs within a 3.8-Mb genomic segment encompassing the MHC. Of 443 potential STRs identified by computer analysis and tested for variation in a single sample containing pooled DNA from 36 individuals, 249 polymorphic STRs located throughout the complex were identified. The class of repeat (di-, tri-, etc.), precise nucleotide position, position relative to known genes, PCR conditions, and D6S numbers for the 249 polymorphic STRs are provided as a resource for selecting appropriate markers to use in future studies of MHC molecular genetics and disease association.