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.

The study subjects comprised 152 unrelated healthy Lebanese individuals of both sexes (90 males and 62 females), who were randomly collected from the five provinces and the six major religious groups of Lebanon. These comprised hospital and university staff, blood donors, and volunteers from the community. None of the study participants suffered from any acute or chronic disease, including neurologic, cardiac, or metabolic diseases, and were not on any medication at the time of specimen collection. The individuals were subjected to HLA class I and class II high-resolution genotyping and phylogenetic calculations. Low-resolution HLA-A, HLA-B, HLA-C, HLA-DRB1, and DQB1 typing was performed using generic polymerase chain reaction with sequence-specific primers (PCR-SSP) kits (One Lambda, Thousand Oaks, CA), while high-resolution typing was performed by PCR-SSP using SSP1L (class I) and SSP2L (class II) HLA genotyping kits according to the manufacturer’s specifications (Luminex–One Lambda, Canoga Park, CA).

The dataset contains HLA class I and class II profile of healthy (non-diseased) population.