PGG.MHC: toward understanding the diversity of major histocompatibility complexes in human populations

Xiaohan Zhao; Sen Ma; Baonan Wang; Xuetong Jiang; The Han100K Initiative; Shuhua Xu

doi:10.1093/nar/gkac997

PGG.MHC: toward understanding the diversity of major histocompatibility complexes in human populations

Nucleic Acids Res. 2023 Jan 6;51(D1):D1102-D1108. doi: 10.1093/nar/gkac997.

Authors

Xiaohan Zhao^{1

2}, Sen Ma³, Baonan Wang^{1

2}, Xuetong Jiang¹; The Han100K Initiative; Shuhua Xu^{1

2

4}

Affiliations

¹ State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, FudanUniversity, Shanghai 200438, China.
² Human Phenome Institute, Zhangjiang Fudan International Innovation Center, and Ministry of Education Key Laboratory of Contemporary Anthropology, FudanUniversity, Shanghai 201203, China.
³ Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy ofSciences, Shanghai 200031, China.
⁴ Department of Liver Surgery and Transplantation Liver Cancer Institute, Zhongshan Hospital, FudanUniversity, Shanghai 200032, China.

Abstract

The human leukocyte antigen (HLA) system, or the human version of the major histocompatibility complex (MHC), is known for its extreme polymorphic nature and high heterogeneity. Taking advantage of whole-genome and whole-exome sequencing data, we developed PGG.MHC to provide a platform to explore the diversity of the MHC in Asia as well as in global populations. PGG.MHC currently archives high-resolution HLA alleles of 53 254 samples representing 190 populations spanning 66 countries. PGG.MHC provides: (i) high-quality allele frequencies for eight classical HLA loci (HLA-A, -B, -C, -DQA1, -DQB1, -DRB1, -DPA1 and -DPB1); (ii) visualization of population prevalence of HLA alleles on global, regional, and country-wide levels; (iii) haplotype structure of 134 populations; (iv) two online analysis tools including 'HLA imputation' for inferring HLA alleles from SNP genotyping data and 'HLA association' to perform case/control studies for HLA-related phenotypes and (v) East Asian-specific reference panels for HLA imputation. Equipped with high-quality frequency data and user-friendly computer tools, 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 PGG.MHC database is freely accessible via https://pog.fudan.edu.cn/pggmhc or https://www.pggmhc.org/pggmhc.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Alleles
Databases, Genetic*
Gene Frequency
HLA Antigens / genetics
Haplotypes
Histocompatibility Antigens Class I / genetics
Histocompatibility Antigens Class II / genetics
Humans
Major Histocompatibility Complex* / genetics

Substances

Histocompatibility Antigens Class I
Histocompatibility Antigens Class II
HLA Antigens