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.
Human Phenome Institute, Zhangjiang Fudan International Innovation Center, and Ministry of Education Key Laboratory of Contemporary Anthropology, FudanUniversity, Shanghai 201203, China.
Nucleic Acids Res. 2023 Jan 6;51(D1):D1102-D1108. doi: 10.1093/nar/gkac997.
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.
人类白细胞抗原 (HLA) 系统，或人类主要组织相容性复合体 (MHC) 的版本，以其极端的多态性和高度的异质性而闻名。利用全基因组和外显子组测序数据，我们开发了 PGG.MHC，为探索亚洲以及全球人群中 MHC 的多样性提供了一个平台。PGG.MHC 目前存储了代表来自 66 个国家的 190 个群体的 53254 个样本的高分辨率 HLA 等位基因。PGG.MHC 提供：(i) 八个经典 HLA 基因座（HLA-A、-B、-C、-DQA1、-DQB1、-DRB1、-DPA1 和 -DPB1）的高质量等位基因频率；(ii) 在全球、区域和国家级水平上显示 HLA 等位基因的人群流行率；(iii) 134 个群体的单倍型结构；(iv) 包括“HLA 推断”的两个在线分析工具，用于从 SNP 基因分型数据推断 HLA 等位基因，以及“HLA 关联”，用于针对 HLA 相关表型进行病例/对照研究；(v) HLA 推断的东亚特定参考面板。配备高质量的频率数据和用户友好的计算机工具，我们希望 PGG.MHC 数据库能够推进对 MHC 基因组多样性的理解，并促进其在进化和医学研究中的应用。PGG.MHC 数据库可通过 https://pog.fudan.edu.cn/pggmhc 或 https://www.pggmhc.org/pggmhc 免费访问。
