HLA diversity in the Russian population assessed by next generation sequencing

Хамаганова, Е Г; Leonov, Evgeny A; Abdrakhimova, Alena R; Хижинский, С. П.; Гапонова, Т. В.; Савченко, В Г

doi:10.15789/1563-0625-hdi-2182

Cited by 8 publications

(12 citation statements)

References 23 publications

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“…Russians from this study share several common haplotypes with European and Russian populations, but the frequency differs somewhat. Thus, HLA‐A*01:01:01‐C*07:01:01‐B*08:01:01‐DRB1*03:01:01‐DQB1*02:01:01 , a frequent haplotype in this study (3.53%) was found at comparable frequencies in Russians from NRCH Registry (3.9%) 14 . On the other hand, this haplotype was seen at higher frequencies in donors from Southern Ireland (11.5%), North West England (9.5%), Poland (5.9%), Italy (4.7%) 25 …”

Section: Discussionsupporting

confidence: 64%

“…Moreover, 12 new HLA alleles were found (Table 3). In the study by Khamaganova et al ( n = 1510) 14 a total of 82, 156, 85, 45 and 18 alleles were detected at the HLA‐A, ‐B, ‐C, ‐DRB1 and ‐DQB1 loci, accordingly. A greater number of identified alleles of class I loci is because of the level of resolution of the 4‐fields.…”

Section: Discussionmentioning

confidence: 95%

“…HLA‐B*07:02:01 (13.18%) is utmost common HLA‐B allele within the studied population/It was frequent in donors from Finland (14.40%), 25 England (13.30%), 25 Poland (11.50%) 25 and Russian from NRCH Registry (13.34%), 14 but less frequent in donors from Czech Republic (6.60%) 25 . HLA‐C*07:02:01 (14.98%), a frequent allele in our study, was found at comparable frequencies in Russians from NRCH Registry (14.74%), 14 in donors from England (14.8%) and Poland (12.3%).…”

Section: Discussionmentioning

confidence: 98%

“…As expected, our data showed that the Russians from the European part of Russia share HLA allelic commonality with comparable frequencies with European and Russian populations. For example, HLA‐A*02:01:01 (26.74%), was also common among donors from England (30.30%), 25 Bulgaria (30.00%), 26 Poland (28.50%), 25 Madeira (24.6%) 25 and Russian from NRCH (National Research Center of Hematology) Registry (28.02%) 14 . HLA‐A*34:02:01 and HLA‐A*74:03:01 alleles identified in two and one individual, accordingly, were not detected in the study by Khamaganova et al 14 perhaps this is because of the smaller sample size of donors.…”

Section: Discussionmentioning

confidence: 99%

“…To date, in Russian population, the most studies are devoted to the distribution of HLA alleles and haplotypes evaluated in low‐resolution and serological polymorphisms of HLA‐A, HLA‐B, HLA‐C and HLA‐DRB1 10–13 . There has been only one report of HLA class I and class II genes for allele polymorphisms, where were 1510 subjects 14 . The objective of this study was to evaluate the HLA‐A, ‐B, ‐C, ‐DRB1 and ‐DQB1 alleles and haplotypes in 3‐fields resolution of a registry population from 3341 healthy Russians, who has been recruited in the European part of Russia from 2019 to 2021, using next generation DNA sequencing (NGS).…”

Section: Introductionmentioning

confidence: 99%

See 4 more Smart Citations

Distributions of HLA‐A, ‐B, ‐C, ‐DRB1 and ‐DQB1 alleles typed by next generation sequencing in Russian volunteer donors

Smirnova

Loginova

Druzhinina

et al. 2023

HLA

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HLA genes play a major role for successful hematopoietic stem cell transplantation (HSCT). While the success of HSCT depends on a HLA compatibility between donor and patient, finding a suitable donor remains challenging because of the high polymorphic nature of HLA genes. In this study, HLA‐A, ‐B, ‐C, ‐DRB1 and ‐DQB1 alleles were genotyped at the 3‐fields resolution level using MiSeq Illumina of 3341 Russian volunteers from the Kirov bone marrow Registry. Full gene of HLA‐A, ‐B and ‐C, exons 2–4 of HLA‐DRB1 and exons 1–5 of HLA‐DQB1 were amplified by multiplex long‐range polymerase chain reaction (PCR) and each allele was determined by matching the targeted regions and the reference sequence consisting of the IPD‐IMGT/HLA Database. A total of 79 alleles of HLA‐A, 115 alleles of HLA‐B, 67 alleles of HLA‐C, 71 alleles of HLA‐DRB1 and 34 alleles of HLA‐DQB1 were identified. According to common, intermediate and well‐documented catalogs, 38 alleles in HLA‐A, 69 in HLA‐B, 39 in HLA‐C, 48 in HLA‐DRB1 and 21 in HLA‐DQB1 locus were common alleles, and 5, 7, 7, 7, 2 kinds, accordingly, to written above were well‐documented alleles. A total of 12 novel alleles including 3 alleles in HLA‐A, 3 alleles in HLA‐B, 1 allele in HLA‐C, 2 alleles in HLA‐DRB1 and 3 alleles in HLA‐DQB1 loci were found. Six haplotypes with a frequency of more than 1.0% accounted for 13.19% of the total haplotype frequencies. This information on rare and novel alleles found by HLA typing with NGS may be helpful for unrelated HSCT among Russians.

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Section: Discussionsupporting

confidence: 64%

Section: Discussionmentioning

confidence: 95%

Section: Discussionmentioning

confidence: 98%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Distributions of HLA‐A, ‐B, ‐C, ‐DRB1 and ‐DQB1 alleles typed by next generation sequencing in Russian volunteer donors

Smirnova

Loginova

Druzhinina

et al. 2023

HLA

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Candidate genes for IgA nephropathy in pediatric patients: exome-wide association study

Buianova

Proskura

Cheranev

et al. 2023

Preprint

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IgA nephropathy (IgAN) is an autoimmune disorder that commonly manifests during adolescence. This disease is believed to be a non-monogenic disorder related to variations in multiple genes involved in various biological pathways. We performed the exome-wide association study of 70 children with IgAN confirmed by renal biopsy and 637 healthy donors to identify gene associations responsible for the disease. The HLA allele frequencies between the patients and healthy donors from the bone marrow registry of the Pirogov University were compared. We tested 78,020 gene markers for association, performed the functional enrichment analysis and the transcription factor binding preference detection. We detected 333 genetic variants, employing three inheritance models. The most significant association with the disorder was observed for rs143409664 (PRAG1) in case of the additive and dominant models (PBONF= 1.808 × 10−15and PBONF= 1.654 × 10−15, respectively) and for rs13028230 (UBR3) in case of the recessive model (PBONF = 1.545 × 10−9). Enrichment analysis indicated the strongly overrepresented "immune system" and "kidney development" terms. The HLA-DQA1*01:01:01G allele (P = 0.0076; OR, 2.021 [95% CI, 1.322-3.048]) was significantly the most frequent among IgAN patients. Here we characterized, for the first time, the genetic background of the Russian IgAN patients identifying the risk alleles typical of the population. The most prominent signals were detected in previously undescribed loci.

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Association between the HLA-A, HLA-B, HLA-C and HLA-DRB1 gene alleles and Sjögren's syndrome with anti-Ro/SSA and anti-La/SSB autoantibodies production

Guseva,

Chanyshev,

Torgashina

et al. 2024

Sovremennaâ revmatologiâ

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Literature data suggest that HLA alleles may be associated with the development of Sjögren's syndrome (SS) and the production of autoantibodies against the Ro/SSA and La/SSB antigens. However, such studies have not been conducted in Russia.Objective: to study the association between alleles of the HLA-A, HLA-B, HLA-C and HLA-DRB1 genes and the risk of developing SS and the production of autoantibodies.Material and methods. The study included 80 patients with SS or Sjögren's disease (SD). All patients met the ACR/EULAR criteria, 2016. AntiRo/SSA and anti-La/SSB autoantibodies were detected in 67 patients (83.8%), 37 patients had the combination anti-Ro/SSA/anti-La/SSB, 30 patients had only anti-Ro/SSA, and 13 patients did not have these antibodies. The control group consisted of 160 healthy blood donors without autoimmune diseases and without a family history of autoimmune diseases, who were comparable in gender and age to the patient group. High-throughput sequencing of the alleles of the HLA-A, HLA-B, HLA-C and HLA-DRB1 genes was performed on the Illumina MiSeq platform using the MiSeq Reagent Kit v3. To amplify the exons of the HLA-A, HLA-B, HLA-C and HLA-DRB1 genes, 56 specially designed primers containing Illumina adapters at the 5’ ends for subsequent indexing were used. Statistical data processing, including comparison of the frequencies of HLA alleles in the group of patients with SS/SD and in the control group, was performed in the Python software environment using the Numpy, Pandas and scikit-learn libraries.Results and discussion. In the group of patients compared to the control group we observed an increase in frequency for the alleles HLA-A*01:01:01 (OR=3.28, 95% CI [1.90–5.67], p <0.001), B*08:01:01 (OR=5.41, 95% CI [3.00–9.82], p<0.001), C*07:01:01 (OR=5.12, 95% CI [2.57– 10.19], p<0.001). In addition, all 2-, 3- and 4-allele combinations were significantly more frequent in the patient group compared to the controls. The most significant combinations of alleles as risk markers for the development of SS were the 2-allele haplotype B*08:01:01-DRB1*03:01:01 (OR=6.65, 95% CI [3.37–13.14], p<0.001) and the 4-allele haplotype A*01:01- B*08:01-C*07:01-DRB1*03:01 (OR=6.05, 95% CI [2.71–13.51], p <0.001). The most significant correlation between the production of two autoantibodies anti-Ro/SSA/anti-La/SSB was found for the haplotypes B*08:01:01-DRB1*03:01:01 (OR=9.50, 95% CI [4.16–21.70], p<0.001) and A*01:01:01-B*08:01:01-C*07:01:01-DRB1*03:01:01 (OR=7.20, 95% CI [2.81–18.43], p <0.001). In the group of 30 patients who only produced anti-Ro/SSA, the association with the above-mentioned haplotypes was less pronounced, although it remained high. Small sample of patients without anti-Ro/SSA and anti-La/SSB (13 patients), did not allow to determine statistically significant associations with HLA alleles/haplotypes.Conclusion. A statistically significant association was found between several HLA alleles/haplotypes belonging to ancestral haplotype 8.1 (AH 8.1) as markers of susceptibility to SS and the production of Ro/SSA and La/SSB autoantibodies.

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HLA diversity in the Russian population assessed by next generation sequencing

Cited by 8 publications

References 23 publications

Distributions of HLA‐A, ‐B, ‐C, ‐DRB1 and ‐DQB1 alleles typed by next generation sequencing in Russian volunteer donors

Distributions of HLA‐A, ‐B, ‐C, ‐DRB1 and ‐DQB1 alleles typed by next generation sequencing in Russian volunteer donors

Candidate genes for IgA nephropathy in pediatric patients: exome-wide association study

Association between the HLA-A, HLA-B, HLA-C and HLA-DRB1 gene alleles and Sjögren's syndrome with anti-Ro/SSA and anti-La/SSB autoantibodies production

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