HLA‐A, ‐B, ‐C, ‐DRB1 and ‐DQB1 allele and haplotype frequencies in Saudis using next generation sequencing technique

Abstract

Next generation sequencing (NGS) is a promising technique that can reveal the entire gene sequences and to the highest possible resolution without any phase ambiguities. We have used this technique to investigate the frequencies of HLA-A, -B, -C, -DRB1 and -DQB1 in a Saudi cohort of healthy individuals. We used NGS using the 454 genome sequence (GS) FLX System and Conexio assign atf 454 software to human leukocyte antigen (HLA) genotype eight class I and class II loci. A total of 158 healthy Saudi adults were analyzed. The most frequently observed allele for HLA-A was HLA-A*02:01:01:01 (13.6%); for HLA-B, HLA-B*50:01:01 (15.8%); for HLA-C, HLA-C*06:02:01:01 (18.7%); for HLA-DRB1, HLA-DRB1*07:01:01:01 (26.6%); and for HLA-DQB1, HLA-DQB1*02:01:01 (20.3%). The most common four loci haplotypes in the Saudi population were HLA-A*24:02:01:01-B*08:01:01-C*07:02:01:01-DRB1*03:01:01:01 and HLA-A*23:01:01-B*50:01:01-C*06:02:01:01-DRB1*07:01:01:01.. We have used a highly informative technique for HLA typing of a Saudi healthy cohort to establish allele and haplotype frequencies. These results should prove useful for population studies, disease associations and future planning of the unrelated bone marrow donor registry.

HLA class II polymorphism in Saudi patients with multiple sclerosis

“…Control data were obtained from previously published data . Only HLA alleles present in the MS group were presented for the control group.…”

“…HLA typing on controls were obtained from our previously published data . Control group included 158 Saudi individuals with age ranging between 21 and 81 years (mean: 39.5 years; median: 38 years).…”

HLA‐A, B, C, DRB1 and DQB1 allele and haplotype frequencies in volunteer bone marrow donors from Eastern Region of Saudi Arabia

“…Allele and haplotype frequencies were estimated using an expectation‐maximization (EM) algorithm. The frequencies of HLA Class I and HLA Class II alleles were examined in the study group (Eastern region) and compared with the published data from the Central region . The allele frequencies of the Eastern region were compared with the Central region using χ 2 test (2 × 2 contingency table).…”

The Relevance ofHLASequencing in Population Genetics Studies

“…The proportion of nonsynonymous is known to exceed that of synonymous substitutions in the PBR (providing evidence of balancing selection) [29–31], but the number of known synonymous substitutions is also becoming quite substantial. Although the number of alleles defined by such silent mutations (i.e., the third field alleles) is still limited (Table 1), many of them are detected in population samples typed by high-throughput sequencing (e.g., [32]). Actually, this may even change to a large extent the overall HLA allele repertoire: among the 2127 new HLA -A, -B, and -C alleles recently discovered by SBT sequencing in a large set of potential haematopoietic stem cell donors from Germany, United States, and Poland [33], as many as 28–30% of them were defined by synonymous substitutions.…”