Sequence based HLA-DRB1,-DQB1 and-DPB1 allele and haplotype frequencies in The Gambia

Class II HLA loci DRB1, DQB1 and DPB1 were typed for a total of 939 Gambian participants by locus-specific amplicon sequencing. Participants were from multiple regions of The Gambia and drawn from two studies: a family study aiming to identify associations between host genotype and trachomatous scarring (N = 796) and a cohort study aiming to identify correlates of immunity to trachoma (N = 143). All loci deviated from HardyWeinberg equilibrium, likely due to the family-based nature of the study: 608 participants had at least one other family member included in the study population. The most common alleles for HLA-DRB1, DQB1 and DPB1 respectively were DRB1*13:04 (18.8 %), DQB1*03:19 (27.9 %) and DPB1*01:01 (25.4 %). Participants belonged to a variety of ethnicities, including the Mandinka, Fula, Wolof and Jola ethnic groups.

Automated summary

HLA DRB1, DQB1, and DPB1 alleles were determined for 939 Gambian individuals using locus-specific amplicon sequencing. The participants were from various regions of The Gambia and divided into two studies: a family study investigating the relationship between host genotype and trachomatous scarring (N = 796) and a cohort study identifying correlates of trachoma immunity (N = 143). Deviation from Hardy-Weinberg equilibrium was observed in all loci, likely due to the inclusion of family members in the study population. The most common alleles for HLA-DRB1, DQB1, and DPB1 were DRB1*13:04 (18.8%), DQB1*03:19 (27.9%), and DPB1*01:01 (25.4%), respectively. The participants belonged to different ethnic groups, including Mandinka, Fula, Wolof, and Jola.