HLAIb worldwide genetic diversity: New HLA-H alleles and haplotype structure description

Mol Immunol. 2019 Aug:112:40-50. doi: 10.1016/j.molimm.2019.04.017. Epub 2019 May 8.


The classical HLA class I genes (HLA Ia) were extensively studied because of their implication in clinical fields and anthropology. Less is known about worldwide genetic diversity and linkage disequilibrium for non-classical HLA class I genes (HLA Ib) and HLA pseudogenes. Notably, HLA-H, which is deleted in a fraction of the population, remains scarcely explored. The aims of this study were 1/ to get further insight into HLA-H genetic diversity and into how this variability potentially affects its expression and 2/ to define HLA Ib worldwide allelic diversity and linkage. Exome sequence data from the 1000 Genomes Project were used to define second field HLA-A, -E, -F, -G and -H typing using PolyPheMe software. Allelic and two-loci haplotype frequencies were estimated using Gene[Rate] software both at worldwide and continental levels. Eleven novel HLA-H alleles identified in exome data were validated by NGS performed on 25 genomic DNA samples from the same cohort. Phylogenetic analysis and frequency distribution of HLA-H alleles revealed three clades, each predominantly represented in Admixed American, European and East Asian populations, African populations and South Asian populations. Among these eleven novel alleles, two potentially encode complete transmembrane HLA proteins. We confirm the high LD between HLA-H and -A, and between HLA-H and -G, and show the three genes have distinct worldwide allelic distribution. Conversely, HLA-E and HLA-F both showed little LD, displayed restricted allelic diversity and practically no difference in their distribution across the planet. Our work thus reveals an unexpectedly high HLA-H genetic diversity, with alleles highly represented in Asia possibly encoding a functional HLA protein. Functional implication of these results remains to be explored, both in physiological and pathological contexts.

Keywords: Allele; Genetic diversity; HLA Ib; Haplotype; Next generation sequencing.

MeSH terms

  • Alleles
  • Asia
  • Asian People / genetics
  • Gene Frequency / genetics
  • Genes, MHC Class I / genetics
  • Genetic Variation / genetics*
  • HLA-DQ Antigens / genetics*
  • Haplotypes / genetics*
  • Hemochromatosis Protein / genetics*
  • Humans
  • Linkage Disequilibrium / genetics
  • Phylogeny


  • HFE protein, human
  • HLA-DQ Antigens
  • Hemochromatosis Protein