HLA-A, -B, -C, -DRB1 and -DQB1 allele and haplotype frequencies in Lebanese and their relatedness to neighboring and distant populations

BACKGROUND: This study examined the origin of present-day Lebanese using high-resolution HLA class I and class II allele and haplotype distributions. The study subjects comprised 152 unrelated individuals, and their HLA class I and class II alleles and two-locus and five-locus haplotypes were compared with those of neighboring and distant communities using genetic distances, neighbor-joining dendrograms, correspondence, and haplotype analyses. HLA class I (A, B, C) and class II (DRB1, DQB1) were genotyped at a high-resolution level by PCR-SSP. RESULTS: In total, 76 alleles across the five HLA loci were detected: A*03:01 (17.1%), A*24:02 (16.5%), B*35:01 (25.7%), C*04:01 (25.3%), and C*07:01 (20.7%) were the most frequent class I alleles, while DRB1*11:01 (34.2%) and DQB1*03:01 (43.8%) were the most frequent class II alleles. All pairs of HLA loci were in significant linkage disequilibrium. The most frequent two-locus haplotypes recorded were DRB1*11:01 ~ DQB1*03:01 (30.9%), B*35:01-C*04:01 (20.7%), B*35:01 ~ DRB1*11:01 (13.8%), and A*24:02 ~ B*35:01 (10.3%). Lebanese appear to be closely related to East Mediterranean communities such as Levantines (Palestinians, Syrians, and Jordanians), Turks, Macedonians, and Albanians. However, Lebanese appear to be distinct from North African, Iberian, and Sub-Saharan communities. CONCLUSIONS: Collectively, this indicates a limited genetic contribution of Arabic-speaking populations (from North Africa or the Arabian Peninsula) and Sub-Saharan communities to the present-day Lebanese gene pool. This confirms the notion that Lebanese population are of mixed East Mediterranean and Asian origin, with a marked European component. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-022-08682-7.