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New Database for Studying MHC Diversity in Human Populations

A database for exploring the diversity of the major histocompatibility complex (MHC) in global human populations is described in Nucleic Acids Research this week. The MHC region harbors multiple class I and class II human leukocyte antigen (HLA) genes, which are associated with various diseases and play a role in transplantation since certain encoded HLA molecules can trigger immune responses that lead to transplant rejection. HLA genes are also highly polymorphic and display a high degree of diversity among populations and geographic regions. Using whole-genome and whole-exome sequencing data, a group led by Fudan University investigators built the Population Genomics and Genetics (PGG) of MHC — or PGG.MHC — an archive of high-resolution HLA alleles of 53,254 samples representing 190 populations spanning 66 countries. The freely available database features interfaces for querying allele frequency and affiliated populations, an interactive visualization of allele population prevalence and haplotype structure, and online analysis functions for genotype imputation and phenotype association. It also includes East Asian-specific reference panels for HLA imputation. "We expect that the PGG.MHC database can advance the understanding and facilitate applications of MHC genomic diversity in both evolutionary and medical studies," the developers write.