PGG MHC

PGG MHC provides high-resolution HLA allele data and analytical functions derived from whole-genome and whole-exome sequencing to characterize MHC (HLA) diversity across global human populations.

Key Features:

• Extensive Data Archive: Contains high-resolution HLA allele information from 53,254 samples representing 190 populations across 66 countries.
• High-Quality Allele Frequencies: Provides allele frequency data for eight classical HLA loci: HLA-A, -B, -C, -DQA1, -DQB1, -DRB1, -DPA1, and -DPB1.
• Visualization Tools: Enables visualization of HLA allele prevalence at global, regional, and country-specific levels.
• Haplotype Structure Analysis: Reports haplotype structures for 134 populations to inform linkage and population-level patterns within MHC loci.
• HLA Imputation Tool: Infers HLA alleles from SNP genotyping data using reference panels.
• HLA Association Tool: Performs case/control association analyses between HLA alleles and phenotypes.
• East Asian-Specific Reference Panels: Provides specialized reference panels to improve HLA imputation accuracy in East Asian populations.

Scientific Applications:

• Population genetics and diversity mapping: Characterizes global and regional distribution of MHC alleles and haplotypes across human populations.
• Evolutionary studies: Investigates HLA polymorphism and haplotype structure to study selection and demographic history of MHC loci.
• Immunogenetics and disease association: Supports case/control analyses to identify associations between HLA alleles and disease susceptibility or immune-related phenotypes.
• Genotype imputation and cohort analysis: Enables inference of HLA alleles from SNP data using population-specific reference panels for large-scale genomic studies.

Methodology:

Leverages whole-genome and whole-exome sequencing to obtain high-resolution HLA allele information, computes allele frequencies for the eight classical HLA loci, analyzes haplotype structures across populations, performs HLA imputation from SNP genotyping using reference panels (including East Asian-specific panels), and conducts case/control HLA association analyses.