HLA-A, -B, -C, -DRB1, -DQA1, and -DQB1 allele and haplotype frequencies defined by next generation sequencing in a population of East Croatia blood donors

Abstract

Next-generation sequencing (NGS) is increasingly used in transplantation settings, but also as a method of choice for in-depth analysis of population-specific HLA genetic architecture and its linkage to various diseases. With respect to complex ethnic admixture characteristic for East Croatian population, we aimed to investigate class-I (HLA-A,-B,-C) and class-II (HLA-DRB1,-DQA1,-DQB1) HLA diversity at the highest, 4-field resolution level in 120 healthy, unrelated, blood donor volunteers. Genomic DNA was extracted and HLA genotypes of class I and DQA1 genes were defined in full-length,-DQB1 from intron 1 to 3′ UTR, and-DRB1 from intron 1 to intron 4 (Illumina MiSeq platform, Omixon Twin algorithms, IMGT/HLA release 3.30.0_5). Linkage disequilibrium statistics, Hardy-Weinberg departures, and haplotype frequencies were inferred by exact tests and iterative Expectation-Maximization algorithm using PyPop 0.7.0 and Arlequin v3.5.2.2 software. Our data provide first description of 4-field allele and haplotype frequencies in Croatian population, revealing 192 class-I and class-II alleles and extended haplotypic combinations not apparent from the existing 2-field HLA reports from Croatia. This established reference database complements current knowledge of HLA diversity and should prove useful in future population studies, transplantation settings, and disease-associated HLA screening. Croatia is a Mediterranean, crescent-shaped south European country bordering Slovenia in the northwest, Hungary in the northeast, Serbia in the east, Bosnia and Herzegovina and Montenegro in the southeast, and Italy along the maritime border. Croatia consists of three major geomorphologic areas, which can be further broken down into five traditional districts based on history, topography, and economy; Istria and Dalmatia in the northern and southern Croatian littoral, Gorski Kotar in country's mountainous area, central continental Croatia, and Slavonia in the Pannonian basin in the east (Fig. 1). Slavonia territory was originally populated by the southern branch of the Indo-European Slavic populations in the 7 th century 1 , and has been a witness of significant population admixture ever since, including the Hungarian migration to Slavonia in 10 th century, and the influx of Islamic and Orthodox Balkan and Asian populations during the Ottoman conquest in 16 th century, causing at the same time, the continuous shift of Catholics from Bosnia to Slavonia during several centuries 2. Under the auspices of Habsburg monarchy, the settlement of Germans and Austrians in Slavonian urban areas peaks between 18 th and 19 th century, while Orthodox Vlachs from Bosnia, immigrating Czechs, Slovaks, Ukrainians, Italians, and

Exome Sequencing Reveals a Putative Role for HLA-C*03:02 in Control of HIV-1 in African Pediatric Populations

“…We then examined global pairwise LD between the loci as a way of understanding the underlying HLA haplotype structure in our cohort. As expected, HLA-B and C loci were in strong LD (D = 0.867, Table 2), although quantitatively lower than reported in European ancestry cohorts (D = 0.928) (Cao et al, 2001;Tokić et al, 2020), this is consistent with LD in healthy African populations. In our combined cohort, the strongest LD was observed between HLA-B * 42:01 and C * 17:01 (r 2 = 0.65, Figure 2A).…”

“…Despite the enrichment for exonic regions in the genome during exome sequencing, the high polymorphism in the HLA region makes such data less reliable, potentially leading to misclassification. Current evidence, however, suggests that this may not be as significant a concern as initially feared (Duke et al, 2016;Sverchkova et al, 2019;Tokić et al, 2020), and we observed a high degree of concordance between inferred and allelotyped alleles in our validation experiments. While HWE checks are useful for validating genotypes/genotyping in diseasefree controls, we did not have access to suitably matched healthy cohorts and deviations from HWE are not always sufficiently sensitive to case ascertainment status, particularly with dense datasets.…”

Common Risk Variants in AHI1 Are Associated With Childhood Steroid Sensitive Nephrotic Syndrome

“…Significant association with SSNS was detected in 6 classical HLA alleles, including 3 previously reported subtypes associated with SSNS in Europeans: DQB1∗02:01 , DQA1∗01 , and DQA1∗02:01 3 ( Table 2 3 , 26 , 27 ). The strongest association was observed in DQB1∗02:01 , which was a risk haplotype.…”

Human Leukocyte Antigen (HLA) System: Genetics and Association with Bacterial and Viral Infections

“…HLA data from various populations have been collected, but populations of African and Asian descent have limited representation to provide insight into HLA disease associations [ 105 ]. HLA genetic diversity among Europeans is well documented [ 106 – 108 ]. Hurley et al recently reported global frequencies of common, intermediate, and well-documented HLA alleles and highlighted the HLA diversity in world populations [ 109 ].…”