High-Resolution (4th-Field) NGS-Based HLA Allele and Haplotype Frequencies in a Western Central Anatolian Turkish...

This study presents the first 4th-field high resolution HLA allele and multi-locus haplotype frequencies from a regional cohort in Western Central Anatolia, including Eskişehir and its surrounding provinces, providing new insights into Turkiye's genetic diversity. Next-generation sequencing (NGS) was used to genotype 138 unrelated healthy individuals for six HLA loci: -A, -B, -C, -DRB1, -DQB1 and -DPB1. MIA FORA NGS FLEX platform was used for genotyping and population genetic analyses were primarily conducted using the HLA-net GENE[RATE] pipeline, with PyPop applied for complementary analyses. Fifty-four HLA-A, 96 HLA-B, 62 HLA-C, 74 DRB1, 45 DQB1 and 33 DPB1 alleles were found at the 4th-field level. A*24:02:01:01 (15.5%), B*51:01:01:01 (6.9%), C*06:02:01:01 (8.7%), DRB1*11:04:01:01 (10.8%), DQB1*03:01:01:02 (18.5%) and DPB1*04:01:01:01 (17.7%) were the most common alleles. The study also identified several rare alleles and haplotypes. This finding highlights the significance of 4th-field resolution in revealing fine-scale diversity. Haplotype analyses observed population-specific combinations with strong linkage disequilibrium, especially between DRB1 and DQB1 (D' = 0.9702). All reported multi-locus haplotypes were validated through significant pairwise LD (standardised residual > 2) between neighbouring loci. For instance, the LD-supported haplotype A*01:01:01:01 ~ B*08:01:01 ~ DRB1*03:01:01:01 (1.45%). When compared to lower-field (2nd-field) data, a considerable amount of sub-allelic diversity was obscured. These results underline the significance of high-resolution HLA genotyping for clinical and population-based applications, as well as Türkiye's distinct immunogenetic structure as a genetic bridge connecting Europe, Asia and the Middle East.