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Tao S, Norman PJ, You X, Kichula KM, Dong L, Chen N, He Y, Chen C, Zhang W, Zhu F. High-resolution KIR and HLA genotyping in three Chinese ethnic minorities reveals distinct origins. HLA 2024; 103:e15482. [PMID: 38625090 PMCID: PMC11027949 DOI: 10.1111/tan.15482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 03/05/2024] [Accepted: 04/02/2024] [Indexed: 04/17/2024]
Abstract
Polymorphism of killer-cell immunoglobulin-like receptors (KIRs) and their HLA class I ligands impacts the effector activity of cytotoxic NK cell and T cell subsets. Therefore, understanding the extent and implications of KIR and HLA class I genetic polymorphism across various populations is important for immunological and medical research. In this study, we conducted a high-resolution investigation of KIR and HLA class I diversity in three distinct Chinese ethnic minority populations. We studied the She, Yugur, and Tajik, and compared them with the Zhejiang Han population (Zhe), which represents the majority Southern Han ethnicity. Our findings revealed that the Tajik population exhibited the most diverse KIR copy number, allele, and haplotype diversity among the four populations. This diversity aligns with their proposed ancestral origin, closely resembling that of Iranian populations, with a relatively higher presence of KIR-B genes, alleles, and haplotypes compared with the other Chinese populations. The Yugur population displayed KIR distributions similar to those of the Tibetans and Southeast Asians, whereas the She population resembled the Zhe and other East Asians, as confirmed by genetic distance analysis of KIR. Additionally, we identified 12.9% of individuals across the three minority populations as having KIR haplotypes characterized by specific gene block insertions or deletions. Genetic analysis based on HLA alleles yielded consistent results, even though there were extensive variations in HLA alleles. The observed variations in KIR interactions, such as higher numbers of 2DL1-C2 interactions in Tajik and Yugur populations and of 2DL3-C1 interactions in the She population, are likely shaped by demographic and evolutionary mechanisms specific to their local environments. Overall, our findings offer valuable insights into the distribution of KIR and HLA diversity among three distinct Chinese ethnic minority populations, which can inform future clinical and population studies.
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Affiliation(s)
- Sudan Tao
- Blood Center of Zhejiang Province, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, Zhejiang, People’s Republic of China
| | - Paul J. Norman
- Division of Biomedical Informatics and Personalized Medicine, and Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, United States
| | - Xuan You
- Blood Center of Zhejiang Province, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, Zhejiang, People’s Republic of China
| | - Katherine M. Kichula
- Division of Biomedical Informatics and Personalized Medicine, and Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, United States
| | - Lina Dong
- Blood Center of Zhejiang Province, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, Zhejiang, People’s Republic of China
| | - Nanying Chen
- Blood Center of Zhejiang Province, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, Zhejiang, People’s Republic of China
| | - Yizhen He
- Blood Center of Zhejiang Province, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, Zhejiang, People’s Republic of China
| | - Chen Chen
- Blood Center of Zhejiang Province, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, Zhejiang, People’s Republic of China
| | - Wei Zhang
- Blood Center of Zhejiang Province, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, Zhejiang, People’s Republic of China
| | - Faming Zhu
- Blood Center of Zhejiang Province, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, Zhejiang, People’s Republic of China
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2
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Madbouly A, Bolon YT. Race, ethnicity, ancestry, and aspects that impact HLA data and matching for transplant. Front Genet 2024; 15:1375352. [PMID: 38560292 PMCID: PMC10978785 DOI: 10.3389/fgene.2024.1375352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 02/29/2024] [Indexed: 04/04/2024] Open
Abstract
Race, ethnicity, and ancestry are terms that are often misinterpreted and/or used interchangeably. There is lack of consensus in the scientific literature on the definition of these terms and insufficient guidelines on the proper classification, collection, and application of this data in the scientific community. However, defining groups for human populations is crucial for multiple healthcare applications and clinical research. Some examples impacted by population classification include HLA matching for stem-cell or solid organ transplant, identifying disease associations and/or adverse drug reactions, defining social determinants of health, understanding diverse representation in research studies, and identifying potential biases. This article describes aspects of race, ethnicity and ancestry information that impact the stem-cell or solid organ transplantation field with particular focus on HLA data collected from donors and recipients by donor registries or transplant centers.
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Affiliation(s)
- Abeer Madbouly
- Center for International Blood and Marrow Transplant Research (CIBMTR), Minneapolis, MN, United States
| | - Yung-Tsi Bolon
- Center for International Blood and Marrow Transplant Research (CIBMTR), Minneapolis, MN, United States
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3
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Masmoudi HC, Afify N, Alnaqbi H, Alhalwachi Z, Tay GK, Alsafar H. HLA pharmacogenetic markers of drug hypersensitivity from the perspective of the populations of the Greater Middle East. Pharmacogenomics 2022; 23:695-708. [PMID: 35971864 DOI: 10.2217/pgs-2022-0078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Specific HLA associations with drug hypersensitivity may vary between geographic regions and ethnic groups. There are little to no data related to HLA-drug hypersensitivity on populations who reside in the Greater Middle East (GME), a vast region spanning from Morocco in the west to Pakistan in the east. In this review, the authors intended to summarize the significant HLA alleles associated with hypersensitive drug reactions induced by different drugs, as have been found in different populations, and to summarize the prevalence of these alleles in the specific and diverse populations of the GME. For example, HLA-B*57:01 allele prevalence, associated with abacavir-induced hypersensitivity, ranges from 1% to 3%, and HLA-DPB1*03:01 prevalence, associated with aspirin-induced asthma, ranges from 10% to 14% in the GME population. Studying pharmacogenomic associations in the ethnic groups of the GME may allow the discovery of new associations, confirm ones found with a low evidence rate and enable cost-effectiveness analysis of allele screening before drug use.
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Affiliation(s)
- Hend Chaker Masmoudi
- Center for Biotechnology, Khalifa University of Science & Technology, Abu Dhabi, United Arab Emirates.,Pharmaceutical Sciences Department, Faculty of Pharmacy of Monastir, Monastir, 5000, Tunisia.,Department of Histology & Cytogenetics, Institute Pasteur de Tunis, Tunis, 1002, Tunisia
| | - Nariman Afify
- College of Medicine & Health Sciences, Khalifa University of Science & Technology, Abu Dhabi, P.O. Box 127788, United Arab Emirates
| | - Halima Alnaqbi
- Center for Biotechnology, Khalifa University of Science & Technology, Abu Dhabi, United Arab Emirates.,Department of Biomedical Engineering, Khalifa University of Science & Technology, Abu Dhabi, P.O. Box 127788, United Arab Emirates
| | - Zainab Alhalwachi
- Center for Biotechnology, Khalifa University of Science & Technology, Abu Dhabi, United Arab Emirates
| | - Guan K Tay
- Center for Biotechnology, Khalifa University of Science & Technology, Abu Dhabi, United Arab Emirates.,Faculty of Health & Medical Sciences, UWA Medical School, University of Western Australia, Perth, 6009, Western Australia.,School of Medical & Health Sciences, Edith Cowan University, Joondalup, 6027, Western Australia
| | - Habiba Alsafar
- Center for Biotechnology, Khalifa University of Science & Technology, Abu Dhabi, United Arab Emirates.,College of Medicine & Health Sciences, Khalifa University of Science & Technology, Abu Dhabi, P.O. Box 127788, United Arab Emirates.,Department of Biomedical Engineering, Khalifa University of Science & Technology, Abu Dhabi, P.O. Box 127788, United Arab Emirates
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4
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Dashti M, Al-Matrouk A, Channanath A, Hebbar P, Al-Mulla F, Thanaraj TA. Distribution of HLA-B Alleles and Haplotypes in Qatari: Recommendation for Establishing Pharmacogenomic Markers Screening for Drug Hypersensitivity. Front Pharmacol 2022; 13:891838. [PMID: 36003520 PMCID: PMC9393242 DOI: 10.3389/fphar.2022.891838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 06/14/2022] [Indexed: 11/18/2022] Open
Abstract
Human leukocyte antigen (HLA) proteins are present at the cellular surface of antigen-presenting cells and play a crucial role in the adaptive immune response. Class I genes, specifically certain HLA-B alleles, are associated with adverse drug reactions (ADRs) and are used as pharmacogenetic markers. Although ADRs are a common causes of hospitalization and mortality, the data on the prevalence of HLA-B pharmacogenetics markers in Arab countries are scarce. In this study, we investigated the frequencies of major HLA-B pharmacogenomics markers in the Qatari population. Next-generation sequencing data from 1,098 Qatari individuals were employed for HLA-B typing using HLA-HD version 1.4.0 and IPD-IMGT/HLA database. In addition, HLA-B pharmacogenetics markers were obtained from the HLA Adverse Drug Reaction Database. In total, 469 major HLA-B pharmacogenetic markers were identified, with HLA-B*51:01 being the most frequent pharmacogenetic marker (26.67%) in the Qatari population. Moreover, HLA-B*51:01 is associated with phenytoin- and clindamycin-induced ADRs. The second most frequent pharmacogenetic marker was the HLA-B*58:01 allele (6.56%), which is associated with allopurinol-induced ADRs. The third most frequent pharmacogenetic marker was the HLA-B*44:03 allele, which is associated with phenytoin-induced ADRs. The establishment of a pharmacogenetics screening program in Qatar for cost effective interventions aimed at preventing drug-induced hypersensitivity can be aided by the highly prevalent HLA-B pharmacogenetic markers detected here.
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Affiliation(s)
- Mohammed Dashti
- Genetics and Bioinformatics Department, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Abdullah Al-Matrouk
- Narcotic and Psychotropic Department, Ministry of Interior, Farwaniya, Kuwait
| | - Arshad Channanath
- Genetics and Bioinformatics Department, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Prashantha Hebbar
- Genetics and Bioinformatics Department, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Fahd Al-Mulla
- Genetics and Bioinformatics Department, Dasman Diabetes Institute, Kuwait City, Kuwait
- *Correspondence: Fahd Al-Mulla, ; Thangavel Alphonse Thanaraj,
| | - Thangavel Alphonse Thanaraj
- Genetics and Bioinformatics Department, Dasman Diabetes Institute, Kuwait City, Kuwait
- *Correspondence: Fahd Al-Mulla, ; Thangavel Alphonse Thanaraj,
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Chentoufi AA, Uyar FA, Chentoufi HA, Alzahrani K, Paz M, Bahnassy A, Elyamany G, Elghazaly A. HLA Diversity in Saudi Population: High Frequency of Homozygous HLA Alleles and Haplotypes. Front Genet 2022; 13:898235. [PMID: 35754807 PMCID: PMC9218871 DOI: 10.3389/fgene.2022.898235] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
Human leukocyte antigens (HLA) diversity has a tremendous impact on shaping the transplantation practices, transfusion-associated graft versus host disease prevention strategies, and host-pathogen interactions. Here, we conducted a retrospective study of HLA class I and class II homozygosity at allelic and haplotype levels in unrelated individuals genotyped from 2012 to 2016 in a tertiary hospital in the capital of Saudi Arabia. Among 5,000 individuals, 2,773 individuals meet inclusion criteria and were retrospectively analyzed for HLA-A, -B, -C-DRB1, and -DQB1 homozygosity at allelic and haplotype levels. HLA molecular typing was performed using a commercial reverse sequence-specific oligonucleotide (rSSO) kit. We were able to identify 15 HLA-A, 20 HLA-B, 11 HLA-C, 13 HLA-DRB1, and five HLA-DQB1 homozygous alleles demonstrating a very low genetic diversity in the Saudi population. The highest homozygosity in HLA class I was found in locus C followed by A and B (20.3% > 16.1% > 15.5%; p < 0.001) where the most homozygote alleles were A*02 (9.2%), B*51 and B*50 (5.7% and 3.7%), and C*07, C*06, and C*15 (7.2%, 5.48%, and 3.3%) and in HLA class II, the highest homozygosity was found in locus DQB1 compared to DRB1 (31.71% > 19.2%; p < 0.001), with the most common homozygote alleles being DRB1*07 and DRB1*04 (5.33% and 4.2%) and DQB1*02, DQB1*06, and DQB1*03 (13.55%, 7.92%, and 7.64%). The frequency of finding an individual with one homozygote allele was (24.6%), two homozygote alleles (13.5%), three homozygote alleles (4.7%), four homozygote alleles (3.4%), and five alleles were (4.8%). The most frequent homozygote haplotypes are A*23∼C*06∼B*50∼DRB1*07∼DQB1*02 and A*02∼C*06∼B*50∼DRB1*07∼DQB1*02. This study shows low diversity of both class I and II alleles and haplotypes in the Saudi population, which would have a significant impact on shaping the transplantation practices, transfusion-associated graft versus host disease prevention strategies, and host-pathogen interactions.
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Affiliation(s)
- Aziz Alami Chentoufi
- King Fahad Medical City, Riyadh, Saudi Arabia.,Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - F Aytül Uyar
- Department of Physiology, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey
| | | | | | - Maria Paz
- King Fahad Medical City, Riyadh, Saudi Arabia
| | | | - Ghaleb Elyamany
- Department of Central Military Laboratory and Blood Bank, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Assem Elghazaly
- King Fahad Medical City, Riyadh, Saudi Arabia.,Department of Hematology/Oncology, King Saud Medical City, Riyadh, Saudi Arabia
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6
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Choe W, Chae JD, Yang JJ, Hwang SH, Choi SE, Oh HB. Identification of 8-Digit HLA-A, -B, -C, and -DRB1 Allele and Haplotype Frequencies in Koreans Using the One Lambda AllType Next-Generation Sequencing Kit. Ann Lab Med 2021; 41:310-317. [PMID: 33303716 PMCID: PMC7748103 DOI: 10.3343/alm.2021.41.3.310] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 05/13/2020] [Accepted: 11/26/2020] [Indexed: 12/02/2022] Open
Abstract
Background Recent studies have successfully implemented next-generation sequencing (NGS) in HLA typing. We performed HLA NGS in a Korean population to estimate HLA-A, -B, -C, and -DRB1 allele and haplotype frequencies up to an 8-digit resolution, which might be useful for an extended application of HLA results. Methods A total of 128 samples collected from healthy unrelated Korean adults, previously subjected to Sanger sequencing for 6-digit HLA analysis, were used. NGS was performed for HLA-A, -B, -C, and -DRB1 using the AllType NGS kit (One Lambda, West Hills, CA, USA), Ion Torrent S5 platform (Thermo Fisher Scientific, Waltham, MA, USA), and Type Steam Visual NGS analysis software (One Lambda). Results Eight HLA alleles showed frequencies of ≥10% in the Korean population, namely, A*24:02:01:01 (19.5%), A*33:03:01 (15.6%), A*02:01:01:01 (14.5%), A*11:01:01:01 (13.3%), B*15:01:01:01 (10.2%), C*01:02:01 (19.9%), C*03:04:01:02 (11.3%), and DRB1*09:01:02 (10.2%). Nine previous 6-digit HLA alleles were further identified as two or more 8-digit HLA alleles. Of these, eight alleles (A*24:02:01, B*35:01:01, B*40:01:02, B*55:02:01, B*58:01:01, C*03:02:02, C*07:02:01, and DRB1*07:01:01) were identified as two 8-digit HLA alleles, and one allele (B*51:01:01) was identified as three 8-digit HLA alleles. The most frequent four-loci haplotype was HLA-A*33:03:01-B*44:03:01:01-C*14:03-DRB1*13:02:01. Conclusions We identified 8-digit HLA-A, -B, -C, and -DRB1 allele and haplotype frequencies in a healthy Korean population using NGS. These new data can be used as a representative Korean data for further disease-related HLA type analysis.
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Affiliation(s)
- Wonho Choe
- Department of Laboratory Medicine, Eulji University School of Medicine, Seoul, Korea
| | - Jeong-Don Chae
- Department of Laboratory Medicine, Eulji University School of Medicine, Seoul, Korea
| | - John Jeongseok Yang
- Department of Laboratory Medicine, University of Ulsan College of Medicine and Asan Medical Center, Seoul, Korea
| | - Sang-Hyun Hwang
- Department of Laboratory Medicine, University of Ulsan College of Medicine and Asan Medical Center, Seoul, Korea
| | - Sung-Eun Choi
- Department of Statistics, Dongguk University, Seoul, Korea
| | - Heung-Bum Oh
- Department of Laboratory Medicine, University of Ulsan College of Medicine and Asan Medical Center, Seoul, Korea
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7
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Naemi FMA, Al-Adwani S, Al-Nazawi A, Al-Khatabi H. Association between HLA genotype and ferritin levels in COVID-19 infection: a study of a Saudi cohort. Infect Dis (Lond) 2021; 53:891-899. [PMID: 34304676 DOI: 10.1080/23744235.2021.1955149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND An elevation in serum ferritin levels through an unknown mechanism was observed in COVID-19 infected patients. This study examined the association between patients' HLA genotype and serum ferritin level modulation and also assessed the effect of serum ferritin levels on infection severity/mortality. MATERIALS AND METHODS One hundred and thirty-six COVID-19 Saudi patients were divided into two groups according to their ferritin levels: group 1 (<500 ng/mL, N = 67) and group 2 (>500 ng/mL, N = 69). HLA genotyping (class I and II) was carried out through the rPCR-SSO method. RESULTS High serum ferritin levels were associated with a significant increase in infection severity, as 75% of ICU patients showed high levels of ferritin compared to 43% of patients with moderate symptoms, p = .002. This elevation indicated a gender skew in that 56% of the infected male patients displayed high ferritin levels compared to 36.6% of the female patients, p = .03. In terms of mortality, 74% of patients with fatal outcomes had a high level of serum ferritin compared to 47% of recovered patients, p = .039. There was a significant difference in the HLA frequency between the two groups, with a predominance of HLA-A*01 in the low-ferritin group (19.4 vs. 6.5%, p = .002, pc = .016) and predominance of C*03 in the high ferritin group (10.9 vs. 3%, p = .047, pc = .27). CONCLUSION High serum ferritin levels are associated with an increase in COVID-19 severity, which may be affected by HLA polymorphism.
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Affiliation(s)
- Fatmah M A Naemi
- Histocompatibility and Immunogenetics Laboratory, King Fahd General Hospital, Ministry of Health, Jeddah, Saudi Arabia
| | - Shurooq Al-Adwani
- Histocompatibility and Immunogenetics Laboratory, King Fahd General Hospital, Ministry of Health, Jeddah, Saudi Arabia
| | | | - Heba Al-Khatabi
- Center of Excellence in Genomic Medicine Research, King Fahd Medical Research Center, King Abdul-Aziz University, Jeddah, Saudi Arabia
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8
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Tay GK, Al Naqbi H, Mawart A, Baalfaqih Z, Almaazmi A, Deeb A, Alsafar H. Segregation Analysis of Genotyped and Family-Phased, Long Range MHC Classical Class I and Class II Haplotypes in 5 Families With Type 1 Diabetes Proband in the United Arab Emirates. Front Genet 2021; 12:670844. [PMID: 34276777 PMCID: PMC8278101 DOI: 10.3389/fgene.2021.670844] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 06/09/2021] [Indexed: 12/16/2022] Open
Abstract
The classical Human Leucocyte Antigen (HLA) class II haplotypes of the Major Histocompatibility Complex (MHC) that are associated with type 1 diabetes (T1D) were identified in five families from the United Arab Emirates (UAE). Segregation analyses were performed on these 5 families with the disease, 3 with one child and 2 with 2 children diagnosed with T1D. Three HLA-DR4 haplotypes were identified: HLA- DRB1∗04:01:01-DQB1∗03:02:01:01; HLA- DRB1∗04:02:01- DQB1∗03:02:01; and HLA -DRB1∗04:05:01-DQB1∗02:02:01:02. All have previously been identified to be associated with T1D in studies of the Arabian population. In the 10 parents from the 5 families, 9 had at least one HLA-DR4 and HLA-DR3 haplotype which potentially increases the risk of T1D. Of these 9 parents, 3 were heterozygous for HLA-DR4/HLA-DR3 and one was homozygous for HLA-DR3. Two haplotypes that were identified here extend to the HLA class I region were previously designated AH8.2 (HLA -A∗26-B∗08-DRB1∗03) and AH50.2 (HLA -C∗06-B∗50-DRB1∗03:01-DQ∗02) and associated with diabetes in neighboring North Indian populations. This study provides examples of MHC haplotype analysis in pedigrees to improve our understanding of the genetics of T1D in the understudied population of the UAE.
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Affiliation(s)
- Guan K Tay
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.,Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.,Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.,Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.,Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Halima Al Naqbi
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Aurélie Mawart
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Zahrah Baalfaqih
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Anoud Almaazmi
- College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Asma Deeb
- Department of Endocrinology, Mafraq Hospital, Abu Dhabi, United Arab Emirates
| | - Habiba Alsafar
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.,Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.,College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
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9
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Pham TTH, Tran QB, Sukasem C, Nguyen VD, Chu CH, Do TQN, Tran NPM, Phung TH. A Novel Allele-Specific PCR Protocol for the Detection of the HLA-C*03:02 Allele, a Pharmacogenetic Marker, in Vietnamese Kinh People. APPLICATION OF CLINICAL GENETICS 2021; 14:27-35. [PMID: 33603436 PMCID: PMC7881795 DOI: 10.2147/tacg.s278652] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 01/18/2021] [Indexed: 12/18/2022]
Abstract
Background Allopurinol, a common anti-hyperuricemia drug, is well known as an inducer of severe cutaneous adverse drug reactions (SCARs). One of the most well-defined risk factors of allopurinol-induced SCARs is the presence of polymorphic alleles of human leukocyte antigen (HLA) genes, such as HLA-B*58:01 and HLA-C*03:02 alleles. There is no commercial test or published in-house protocol for the specific detection of the HLA-C*03:02 allele. In this article, we established for the first time a simple allele-specific (AS) PCR method to identify HLA-C*03:02 allele carriers, and at the same time, determine their zygosities. Methods A two-step AS-PCR protocol, using four primer sets, was designed to specifically amplify and differentiate the HLA-C*03:02 allele from 17 other HLA-C alleles found in Vietnamese people. The protocol was validated with PCR-sequencing-based typing (SBT) of 100 samples of unknown genotypes. Results The PCR protocol can detect the HLA-C*03:02 allele and determine the zygosity. The results of this protocol were highly consistent with those of the SBT (ĸ = 0.98, p < 0.001). Regarding the specific detection of the HLA-C*03:02 allele, the PCR protocol had a sensitivity of 100% (95% CI: 91.61-100%) and specificity of 98.3% (95% CI: 90.9-99.7%). The protocol was used to determine the distribution of the HLA-C*03:02 allele in 810 unrelated Vietnamese Kinh people, 14.2% of which were HLA-C*03:02 carriers, the allele frequency was 7.5%. Conclusion A novel AS-PCR protocol with a sensitivity of 100% for the detection of the HLA-C*03:02 allele was established. The protocol can be used for personalized treatment with allopurinol in order to minimize the risk of SCARs in Vietnamese people as well as in other Asian populations with similar genetic characteristics.
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Affiliation(s)
| | | | - Chonlaphat Sukasem
- Division of Pharmacogenomics and Personalized Medicine, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.,Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center (SDMC), Ramathibodi Hospital, Bangkok, Thailand.,The Thai Severe Cutaneous Adverse Drug Reaction (THAI-SCAR) Research Group, Bangkok, Thailand
| | - Van Dinh Nguyen
- Respiratory, Allergy and Clinical Immunology Unit, Internal Medicine Department, Vinmec Times City International Hospital, Vinmec Healthcare System, Hanoi, Vietnam.,College of Health Sciences, VinUniversity, Hanoi, Vietnam
| | - Chi Hieu Chu
- Center of Allergology and Clinical Immunology, Bach Mai Hospital, Hanoi, Vietnam
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10
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Alfraih F, Alawwami M, Aljurf M, Alhumaidan H, Alsaedi H, El Fakih R, Alotaibi B, Rasheed W, Bernas SN, Massalski C, Heidl A, Sauter J, Lange V, Schmidt AH. High-resolution HLA allele and haplotype frequencies of the Saudi Arabian population based on 45,457 individuals and corresponding stem cell donor matching probabilities. Hum Immunol 2020; 82:97-102. [PMID: 33388178 DOI: 10.1016/j.humimm.2020.12.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 12/09/2020] [Accepted: 12/10/2020] [Indexed: 11/20/2022]
Abstract
We estimated HLA allele and haplotype frequencies of the Saudi Arabian population from a sample of 45,457 registered stem cell donors. The most frequent HLA alleles were A*02:01g (18.5%), C*06:02g (16.1%), B*51:01g (14.1%), DRB1*07:01g (16.2%), DQB1*02:01g (30.5%), and DPB1*04:01g (33.6%). The most frequent 5-locus haplotypes were A*02:05g~C*06:02g~B*50:01g~DRB1*07:01g~DQB1*02:01g (1.73%), A*02:01g~C*06:02g~B*50:01g~DRB1*07:01g~DQB1*02:01g (1.66%), and A*26:01g~C*07:02g~B*08:01g~DRB1*03:01g~DQB1*02:01g (1.38%). Furthermore, we used the calculated haplotype frequencies to estimate stem cell donor matching probabilities for Saudi Arabian donor and patient populations under various matching requirements. These results are relevant for strategic donor registry planning in the Kingdom of Saudi Arabia.
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Affiliation(s)
- Feras Alfraih
- King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Moheeb Alawwami
- King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Mahmoud Aljurf
- King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Hind Alhumaidan
- King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Hawazen Alsaedi
- King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Riad El Fakih
- King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Bander Alotaibi
- King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Walid Rasheed
- King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
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Eltayeb-Elsheikh N, Khalil E, Mubasher M, AlJurayyan A, AlHarthi H, Omer WH, Elghazali I, Sherbeeni SM, Alghofely MA, Ilonen J, Elghazali G. Association of HLA-DR-DQ alleles, haplotypes, and diplotypes with type 1 diabetes in Saudis. Diabetes Metab Res Rev 2020; 36:e3345. [PMID: 32418312 DOI: 10.1002/dmrr.3345] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 03/14/2020] [Accepted: 04/22/2020] [Indexed: 12/31/2022]
Abstract
AIMS Type 1 diabetes (T1D) is an autoimmune disease that affects many children worldwide. Genetic factors and environmental triggers play crucial interacting roles in the aetiology. This study aimed to assess the contribution of HLA-DRB1-DQA1-DQB1 alleles, haplotypes, and genotypes to the risk of T1D among Saudis. METHODS A total of 222 children with T1D and 342 controls were genotyped for HLA-DRB1, -DQA1, and -DQB1 using reverse sequence-specific oligonucleotide (rSSO) Lab Type high definition (HD) kits. Alleles, haplotypes, and diplotypes were compared between cases and controls using the SAS statistical package. RESULTS DRB1*03:01-DQA1*05:01-DQB1*02:01 (32.4%; OR = 3.68; Pc < .0001), DRB1*04:05-DQA1*03:02-DQB1*03:02 (6.6%; OR = 6.76; Pc < .0001), DRB1*04:02-DQA1*03:01-DQB1*03:02 (6.0%; OR = 3.10; Pc = .0194), DRB1*04:01-DQA1*03:01-DQB1*03:02 (3.7%; OR = 4.22; Pc = .0335), and DRB1*04:05-DQA1*03:02-DQB1*02:02 (2.7%; OR = 6.31; Pc = .0326) haplotypes were significantly increased in cases compared to controls, whereas DRB1*07:01-DQA1*02:01-DQB1*02:02 (OR = 0.41; Pc = .0001), DRB1*13:01-DQA1*01:03-DQB1*06:03 (OR = 0.05; Pc < .0001), DRB1*15:01-DQA1*01:02-DQB1*06:02 (OR = 0.03; Pc < .0001), and DRB1*11:01-DQA1*05:05-DQB1*03:01 (OR = 0.07; Pc = .0291) were significantly decreased. Homozygous DRB1*03:01-DQA1*05:01-DQB1*02:01 genotypes and combinations of DRB1*03:01-DQA1*05:01-DQB1*02:01 with DRB1*04:05-DQA1*03:02-DQB1*03:02, DRB1*04:02-DQA1*03:01-DQB1*03:02, and DRB1*04:01-DQA1*03:01-DQB1*03:02 were significantly increased in cases than controls. Combinations of DRB1*03:01-DQA1*05:01-DQB1*02:01 with DRB1*07:01-DQA1*02:01-DQB1*02:02 and DRB1*13:02-DQA1*01:02-DQB1*06:04 showed low OR values but did not remain significantly decreased after Bonferroni correction. CONCLUSIONS HLA-DRB1-DQA1-DQB1 alleles, haplotypes, and diplotypes in Saudis with T1D are not markedly different from those observed in Western and Middle-Eastern populations but are quite different than those of East Asians.
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Affiliation(s)
- Nezar Eltayeb-Elsheikh
- Department of Pathology and Clinical Laboratory Medicine, King Fahad Medical City, Riyadh, Kingdom of Saudi Arabia
| | - Eltahir Khalil
- Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
| | - Mohamed Mubasher
- Biostatistics & Data Management Core, Morehouse School of Medicine, Atlanta, Georgia, USA
| | - Abdullah AlJurayyan
- Department of Pathology and Clinical Laboratory Medicine, King Fahad Medical City, Riyadh, Kingdom of Saudi Arabia
| | - Hanan AlHarthi
- Department of Pathology and Clinical Laboratory Medicine, King Fahad Medical City, Riyadh, Kingdom of Saudi Arabia
| | - Waleed H Omer
- Division of Human Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Inas Elghazali
- Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | - Suphia M Sherbeeni
- Endocrinology Department, King Fahad Medical City, Riyadh, Kingdom of Saudi Arabia
| | - Mohammed A Alghofely
- Endocrinology Department, King Fahad Medical City, Riyadh, Kingdom of Saudi Arabia
| | - Jorma Ilonen
- Immunogenetics Laboratory, Institute of Biomedicine, University of Turku and Clinical Microbiology Laboratory, Turku University Hospital, Turku, Finland
| | - Gehad Elghazali
- Department of Immunology, Sheikh Khalifa Medical City, Abu Dhabi, United Arab Emirates
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12
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Barquera R, Zuniga J, Flores-Rivera J, Corona T, Penman BS, Hernández-Zaragoza DI, Soler M, Jonapá-Gómez L, Mallempati KC, Yescas P, Ochoa-Morales A, Barsakis K, Aguilar-Vázquez JA, García-Lechuga M, Mindrinos M, Yunis M, Jiménez-Alvarez L, Mena-Hernández L, Ortega E, Cruz-Lagunas A, Tovar-Méndez VH, Granados J, Fernández-Viña M, Yunis E. Diversity of HLA Class I and Class II blocks and conserved extended haplotypes in Lacandon Mayans. Sci Rep 2020; 10:3248. [PMID: 32094421 PMCID: PMC7039995 DOI: 10.1038/s41598-020-58897-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 01/22/2020] [Indexed: 12/18/2022] Open
Abstract
Here we studied HLA blocks and haplotypes in a group of 218 Lacandon Maya Native American using a high-resolution next generation sequencing (NGS) method. We assessed the genetic diversity of HLA class I and class II in this population, and determined the most probable ancestry of Lacandon Maya HLA class I and class II haplotypes. Importantly, this Native American group showed a high degree of both HLA homozygosity and linkage disequilibrium across the HLA region and also lower class II HLA allelic diversity than most previously reported populations (including other Native American groups). Distinctive alleles present in the Lacandon population include HLA-A*24:14 and HLA-B*40:08. Furthermore, in Lacandons we observed a high frequency of haplotypes containing the allele HLA-DRB1*04:11, a relatively frequent allele in comparison with other neighboring indigenous groups. The specific demographic history of the Lacandon population including inbreeding, as well as pathogen selection, may have elevated the frequencies of a small number of HLA class II alleles and DNA blocks. To assess the possible role of different selective pressures in determining Native American HLA diversity, we evaluated the relationship between genetic diversity at HLA-A, HLA-B and HLA-DRB1 and pathogen richness for a global dataset and for Native American populations alone. In keeping with previous studies of such relationships we included distance from Africa as a covariate. After correction for multiple comparisons we did not find any significant relationship between pathogen diversity and HLA genetic diversity (as measured by polymorphism information content) in either our global dataset or the Native American subset of the dataset. We found the expected negative relationship between genetic diversity and distance from Africa in the global dataset, but no relationship between HLA genetic diversity and distance from Africa when Native American populations were considered alone.
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Affiliation(s)
- Rodrigo Barquera
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History (MPI-SHH), Jena, Germany
- Laboratory of Molecular Genetics, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico
| | - Joaquin Zuniga
- Department of Immunology, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas (INER), Mexico City, Mexico
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Mexico City, Mexico
| | - José Flores-Rivera
- Clinical Laboratory of Neurodegenerative Diseases, Instituto Nacional de Neurología y Neurocirugía "Manuel Velasco Suárez", Mexico City, Mexico
| | - Teresa Corona
- Clinical Laboratory of Neurodegenerative Diseases, Instituto Nacional de Neurología y Neurocirugía "Manuel Velasco Suárez", Mexico City, Mexico
| | - Bridget S Penman
- University of Warwick, School of Life Sciences, Coventry, United Kingdom
| | - Diana Iraíz Hernández-Zaragoza
- Laboratory of Molecular Genetics, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico
- Immunogenetics Unit, Técnicas Genéticas Aplicadas a la Clínica (TGAC), Mexico City, Mexico
| | - Manuel Soler
- Department of Transplantation, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán (INCMSZ), Mexico City, Mexico
| | | | - Kalyan C Mallempati
- Histocompatibility, Immunogenetics and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA
- Biology Department, University of Crete, Heraklion, Greece
| | - Petra Yescas
- Department of Neurogenetics and Molecular Biology, Instituto Nacional de Neurología y Neurocirugía "Manuel Velasco Suárez", Mexico City, Mexico
| | - Adriana Ochoa-Morales
- Department of Neurogenetics and Molecular Biology, Instituto Nacional de Neurología y Neurocirugía "Manuel Velasco Suárez", Mexico City, Mexico
| | - Konstantinos Barsakis
- Histocompatibility, Immunogenetics and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA
- Department of Pathology, Stanford University, CA, USA
| | - José Artemio Aguilar-Vázquez
- Clinical Analysis Laboratory, Unidad Médica Familiar (UMF) No. 23, Instituto Mexicano del Seguro Social (IMSS), Tuxtla Gutiérrez, Chiapas, Mexico
| | - Maricela García-Lechuga
- Department of Transplantation, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán (INCMSZ), Mexico City, Mexico
| | | | - María Yunis
- Department of Cancer Immunology and Virology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Luis Jiménez-Alvarez
- Department of Immunology, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas (INER), Mexico City, Mexico
| | - Lourdes Mena-Hernández
- Department of Transplantation, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán (INCMSZ), Mexico City, Mexico
| | - Esteban Ortega
- The William Harvey Research Institute, Barts and London School of Medicine, Queen Mary University of London, London, United Kingdom
| | - Alfredo Cruz-Lagunas
- Department of Immunology, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas (INER), Mexico City, Mexico
| | - Víctor Hugo Tovar-Méndez
- Department of Transplantation, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán (INCMSZ), Mexico City, Mexico
| | - Julio Granados
- Department of Transplantation, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán (INCMSZ), Mexico City, Mexico.
| | | | - Edmond Yunis
- Department of Cancer Immunology and Virology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
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13
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Ameen R, Al Shemmari SH, Marsh SGE. HLA Haplotype Frequencies and Genetic Profiles of the Kuwaiti Population. Med Princ Pract 2020; 29:39-45. [PMID: 30870850 PMCID: PMC7024892 DOI: 10.1159/000499593] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 03/14/2019] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVE The aim of this study was to assess the HLA haplotype frequencies and genetic profiles of the Kuwaiti population. MATERIALS AND METHODS Whole venous blood was obtained from 595 healthy, unrelated Kuwaiti volunteers. The study population was genotyped for HLA class I (HLA-A, HLA-B, and HLA-C) and class II (HLA-DRB1 and HLA-DQB1) loci using sequence-specific oligonucleotide (SSO) probe-based hybridization and high-resolution HLA genotyping. Haplotype frequencies were estimated using an implementation of the expectation maximization algorithm that resolves both phase and allelic ambiguity. The Kuwaiti population was compared with other populations from the US National Marrow Donor Program (NMDP), by running a principal component analysis (PCA) on the relevant haplotype frequencies. RESULTS The most common HLA class I alleles in Kuwait were HLA-A*02:01g, HLA-C*06:02g, and HLA-B*50:01g with frequencies of 16, 14, and 12%, respectively. The most common HLA class II alleles in Kuwait were HLA-DQB1*02:01g and HLA-DRB1*07:01 with frequencies of 29.7 and 16.5%, respectively. The most common Kuwaiti haplotype observed was HLA-A*02:01g∼HLA-C*06:02g∼HLA-B*50:01g∼HLA-DRB1*07:01∼HLA-DQB1*02:01g at a frequency of 2.3%. The PCA demonstrated close genetic proximity of the Kuwaiti population with Middle Eastern, Southeast Asian, and North African populations in the NMDP. CONCLUSION Identifying the haplotype diversity in the Kuwaiti population will contribute to the selection of an HLA-match for HSCT, disease associations, pharmacogenomics, and knowledge of pop-ulation HLA diversity.
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Affiliation(s)
- Reem Ameen
- Medical Laboratory Department, Health Sciences Center, Kuwait University, Kuwait City, Kuwait,
| | - Salem H Al Shemmari
- Medicine Department, Health Sciences Center, Kuwait University, Kuwait City, Kuwait
| | - Steven G E Marsh
- Anthony Nolan Research Institute and UCL Cancer Institute, Royal Free Campus, London, United Kingdom
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14
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Moutaouakkil Y, Adouani B, Cherrah Y, Lamsaouri J, Bousliman Y. Diagnostic Utility of Human Leukocyte Antigen B*15:02 Screening in Severe Carbamazepine Hypersensitivity Syndrome. Ann Indian Acad Neurol 2019; 22:377-383. [PMID: 31736555 PMCID: PMC6839291 DOI: 10.4103/aian.aian_492_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 12/10/2018] [Accepted: 12/12/2018] [Indexed: 12/19/2022] Open
Abstract
Background Despite many studies suggesting an association between human leukocyte antigen (HLA)-B*15:02 and carbamazepine (CBZ)-induced severe cutaneous adverse drug reactions essentially toxic epidermal necrolysis (TEN) and Stevens-Johnson syndrome (SJS), the evidence of association in different populations and the degree of association remain uncertain. Materials and Methods The primary analysis was based on population control studies. Data were pooled by means of a random-effects model, and sensitivity, specificity, positive and negative likelihood ratios (LR+ and LR-), diagnostic odds ratios (DOR), and areas under the summary receiver operating characteristic curve (AUC) were calculated. Results In 23 population control studies, HLA-B*15:02 was measured in 373 patients with CBZ-induced TEN/SJS and 3452 patients without CBZ-induced TEN/SJS. The pooled sensitivity, specificity, LR+, LR-, DOR, and AUC were 0.67 (95% confidence interval [CI] = 0.63-0.72), 0.98 (95% CI = 0.98-0.99), 19.73 (95% CI = 10.54-36.92), 0.34 (95% CI = 0.23-0.49), 71.38 (95% CI = 34.89-146.05), and 0.96 (95% CI = 0.92-0.98), respectively. Subgroup analyses for Han Chinese, Thai, and Malaysian populations yielded similar findings. Specifically, racial/ethnic subgroup analyses revealed similar findings with respect to DOR for Han Chinese (99.28; 95% CI = 22.20-443.88), Thai (61.01; 95% CI = 23.05-161.44), and Malaysian (30; 95% CI = 7.08-126.68) populations, which are similar to the pooled DOR for the relationship between the HLA-B*15:02 allele and CBZ-induced TEN/SJS across all populations (71.38; 95% CI = 34.89-146.05). Conclusions The present study reveals that CBZ is the leading cause of TEN/SJS in many countries. Screening of HLA-B*15:02 may help patients to prevent the occurrence of CBZ-induced TEN/SJS, especially in populations with a higher (≥5%) risk allele frequency.
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Affiliation(s)
- Youssef Moutaouakkil
- Laboratory of Pharmacology-Toxicology, Faculty of Medicine and Pharmacy, Rabat Institute University Mohamed V, Rabat, Morocco
| | - Badr Adouani
- Laboratory of Pharmacology-Toxicology, Faculty of Medicine and Pharmacy, Rabat Institute University Mohamed V, Rabat, Morocco
| | - Yahia Cherrah
- Laboratory of Pharmacology-Toxicology, Faculty of Medicine and Pharmacy, Rabat Institute University Mohamed V, Rabat, Morocco
| | - Jamal Lamsaouri
- Laboratory of Medicinal Chemistry, Faculty of Medicine and Pharmacy, Rabat Institute University Mohamed V, Rabat, Morocco
| | - Yassir Bousliman
- Laboratory of Pharmacology-Toxicology, Faculty of Medicine and Pharmacy, Rabat Institute University Mohamed V, Rabat, Morocco
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15
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Bishara A, Halagan M, Brautbar C, Israel S, Maiers M, Madbouly A. High resolution HLA allele and haplotype frequencies for Arab donors in the Hadassah bone marrow donor registry. Hum Immunol 2019; 80:823-827. [DOI: 10.1016/j.humimm.2019.05.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 04/29/2019] [Accepted: 05/10/2019] [Indexed: 01/10/2023]
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16
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Jawdat D, Al-Zahrani M, Al-Askar A, Fakhoury H, Uyar FA, Hajeer A. HLA-A, B, C, DRB1 and DQB1 allele and haplotype frequencies in volunteer bone marrow donors from Eastern Region of Saudi Arabia. HLA 2019; 94:49-56. [PMID: 30903680 DOI: 10.1111/tan.13533] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 03/18/2019] [Accepted: 03/20/2019] [Indexed: 11/29/2022]
Abstract
We analyzed HLA allele and haplotype frequencies from donors from the Eastern region of Saudi Arabia. A cross-sectional study was performed on 2405 bone marrow donors from the Eastern region. HLA typing was carried out by sequencing. The most common HLA allele groups were HLA-A*02:01:01G (11.08%), A*01:01:01G (10.40%), HLA-B*52:01:01G (8.79%), B*18:01:01G (8.07%), HLA-C*04:01:01G (17.88%), C*12:03:01G (10.23%), HLA-DRB1*10:01 (14.89%), DRB1*03:01:01G (14.10%), HLA-DQB1*02:01:01G (24.53%) and DQB1*05:01:01G (20.17%). The most frequent HLA-A~ C~ B~ DRB1~ DQB1 haplotypes were HLA-A*01:03~ C*15:05:01G~ B*73:01~ DRB1*10:01:01~ DQB1*05:01:01G (3.11%) and HLA-A*01:01:01G~ C*12:02:01G~ B*52:01:01G~ DRB1*15:02:01~ DQB1*06:01:01G (2.25%). When comparing the allele and haplotype frequencies of the Eastern regions' population to those from the Central region we found significant differences in several allele frequencies including A*01:01:01G (P ≤ 0.0001), B*52:01:01G (P ≤ 0.0001), B*18:01:01G (P = 0.0001), C*12:03:01G (P < 0.0001), DRB1*10:01:01 (P < 0.0001) and DQB1*05:01:01G (P < 0.0001). Our data confirms genetic heterogeneity among the Saudi population.
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Affiliation(s)
- Dunia Jawdat
- Cord Blood Bank, King Abdullah International Medical Research Center/College of Science and Health Professions, King Saud Bin Abdulaziz University for Health Sciences/King Abdulaziz Medical City-Riyadh, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia.,Saudi Stem Cells Donor Registry, King Abdullah International Medical Research Center/King Saud Bin Abdulaziz University for Health Sciences/King Abdulaziz Medical City-Riyadh, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Mohsen Al-Zahrani
- Saudi Stem Cells Donor Registry, King Abdullah International Medical Research Center/King Saud Bin Abdulaziz University for Health Sciences/King Abdulaziz Medical City-Riyadh, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia.,Division of Adult Hematology and HSCT, Department of Oncology, King Abdulaziz Medical City-Riyadh, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Ahmed Al-Askar
- King Abdullah International Medical Research Center/King Saud Bin Abdulaziz University for Health Sciences/King Abdulaziz Medical City-Riyadh, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia.,Division of Adult Hematology and HSCT, Department of Oncology, King Abdulaziz Medical City-Riyadh, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Hana Fakhoury
- Department of Biochemistry and Molecular Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Fatma Aytül Uyar
- Department of Physiology, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey
| | - Ali Hajeer
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City-Riyadh, Ministry of National Guard Health Affairs/College of Medicine, King Saud bin Abdulaziz University for Health Sciences/King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
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17
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Kulski JK, AlSafar HS, Mawart A, Henschel A, Tay GK. HLA class I allele lineages and haplotype frequencies in Arabs of the United Arab Emirates. Int J Immunogenet 2019; 46:152-159. [PMID: 30892829 DOI: 10.1111/iji.12418] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 11/29/2018] [Accepted: 01/03/2019] [Indexed: 12/18/2022]
Abstract
The high degree of polymorphism of the HLA system provides suitable genetic markers to study the diversity and migration of different world populations and is beneficial for forensic identification, anthropology, transplantation and disease associations. Although the United Arab Emirates (UAE) population of about nine million people is heterogeneous, information is limited for the HLA class I allele and haplotype frequencies of the Bedouin ethnic group. We performed low-resolution PCR-SSP genotyping of three HLA class I loci at HLA-A, -B and -C for 95 unrelated healthy Bedouins from the cities of Al Ain and Abu Dhabi in the UAE. A total of 54 HLA allele lineages were detected; the most frequent low-resolution allele lineages at each HLA locus were A*02 (0.268), B*51 (0.163) and C*07 (0.216). The inferred estimates for the two most frequent HLA-A and HLA-B haplotypes were HLA-A*02 ~ HLA-B*50 (0.070) and HLA-A*02 ~ HLA-B*51 (0.051), and the most frequent 3-locus haplotype was HLA-A*02 ~ HLA-B*50 ~ HLA-C*06 (0.068). The HLA allele lineage frequencies of the UAE Arabs were compared to those previously reported for 70 other world populations, and a strong genetic similarity was detected between the UAE Arabs and the Saudi Arabians from the west with evidence of a limited gene flow between the UAE Arabs and Pakistani across the Gulf from the east, and the UAE Arabs and Omani from the south of the Gulf Peninsula.
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Affiliation(s)
- Jerzy K Kulski
- School of Psychiatry and Clinical Neurosciences, The University of Western Australia, Crawley, Western Australia, Australia
| | - Habiba S AlSafar
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.,Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Aurelie Mawart
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Andreas Henschel
- Department of Electrical Engineering and Computer Science, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Guan K Tay
- School of Psychiatry and Clinical Neurosciences, The University of Western Australia, Crawley, Western Australia, Australia.,Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.,Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
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18
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Kishore A, Petrek M. Next-Generation Sequencing Based HLA Typing: Deciphering Immunogenetic Aspects of Sarcoidosis. Front Genet 2018; 9:503. [PMID: 30410504 PMCID: PMC6210504 DOI: 10.3389/fgene.2018.00503] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 10/05/2018] [Indexed: 12/31/2022] Open
Abstract
Unraveling of the HLA-related immunogenetic basis of several immune disorders is complex due to the extensive HLA polymorphism and strong linkage-disequilibrium between HLA loci. A lack of in phase sequence information, a relative deficiency of high resolution genotyping including non-coding regions and ambiguous haplotype assignment make it difficult to compare findings across association studies and to attribute a causal role to specific HLA alleles/haplotypes in disease susceptibility and modification of disease phenotypes. Earlier, historical antibody and DNA-based methods of HLA typing, primarily of low resolution at antigen/alellic group levels, yielded "indicative" findings which were partially improved by high-resolution DNA-based typing. Only recently, next-generation sequencing (NGS) approaches based on deep-sequencing of the complete HLA genes combined with bioinformatics tools began to provide the access to complete information at an allelic level. Analyzing HLA with NGS approaches, therefore, promises to provide further insight in the etiopathogenesis of several immune disorders in which HLA associations have been implicated. These range from coeliac disease and rheumatological conditions to even more complex disorders, such as type-1 diabetes, systemic lupus erythematosus and sarcoidosis. A systemic disease of unknown etiology, sarcoidosis has previously been associated with numerous HLA variants and also other gene polymorphisms, often in linkage with the HLA region. To date, the biological significance of these associations has only partially been defined. Therefore, more precise assignments of HLA alleles/haplotypes using NGS approaches could help to elucidate the exact role of HLA variation in the multifaceted etiopathogenesis of sarcoidosis, including epigenetic mechanisms. NGS-based HLA analyses may be also relevant for defining variable clinical phenotypes and for predicting the disease course or the response to current/plausible novel therapies.
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Affiliation(s)
- Amit Kishore
- Department of Pathological Physiology, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czechia
| | - Martin Petrek
- Department of Pathological Physiology, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czechia
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19
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Hajjej A, Almawi WY, Arnaiz-Villena A, Hattab L, Hmida S. The genetic heterogeneity of Arab populations as inferred from HLA genes. PLoS One 2018. [PMID: 29522542 PMCID: PMC5844529 DOI: 10.1371/journal.pone.0192269] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
This is the first genetic anthropology study on Arabs in MENA (Middle East and North Africa) region. The present meta-analysis included 100 populations from 36 Arab and non-Arab communities, comprising 16,006 individuals, and evaluates the genetic profile of Arabs using HLA class I (A, B) and class II (DRB1, DQB1) genes. A total of 56 Arab populations comprising 10,283 individuals were selected from several databases, and were compared with 44 Mediterranean, Asian, and sub-Saharan populations. The most frequent alleles in Arabs are A*01, A*02, B*35, B*51, DRB1*03:01, DRB1*07:01, DQB1*02:01, and DQB1*03:01, while DRB1*03:01-DQB1*02:01 and DRB1*07:01-DQB1*02:02 are the most frequent class II haplotypes. Dendrograms, correspondence analyses, genetic distances, and haplotype analysis indicate that Arabs could be stratified into four groups. The first consists of North Africans (Algerians, Tunisians, Moroccans, and Libyans), and the first Arabian Peninsula cluster (Saudis, Kuwaitis, and Yemenis), who appear to be related to Western Mediterraneans, including Iberians; this might be explained for a massive migration into these areas when Sahara underwent a relatively rapid desiccation, starting about 10,000 years BC. The second includes Levantine Arabs (Palestinians, Jordanians, Lebanese, and Syrians), along with Iraqi and Egyptians, who are related to Eastern Mediterraneans. The third comprises Sudanese and Comorians, who tend to cluster with Sub-Saharans. The fourth comprises the second Arabian Peninsula cluster, made up of Omanis, Emiratis, and Bahrainis. It is noteworthy that the two large minorities (Berbers and Kurds) are indigenous (autochthonous), and are not genetically different from "host" and neighboring populations. In conclusion, this study confirmed high genetic heterogeneity among present-day Arabs, and especially those of the Arabian Peninsula.
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Affiliation(s)
- Abdelhafidh Hajjej
- Department of Immunogenetics, National Blood Transfusion Center, Tunis, Tunisia
- * E-mail:
| | - Wassim Y. Almawi
- Department of Medicine, Harvard Medical School, Boston, MA, United States of America
| | - Antonio Arnaiz-Villena
- Department of Immunology, University Complutense, School of Medicine, Madrid Regional Blood Center, Madrid, Spain
| | - Lasmar Hattab
- Department of Medical Analysis, Hospital of Gabes (Ghannouch), Gabes, Tunisia
| | - Slama Hmida
- Department of Immunogenetics, National Blood Transfusion Center, Tunis, Tunisia
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Al Jumah M, Kojan S, Al Shehri AM, Al Balwi M, Al Abdulkarim I, Masuadi EM, Alhaidan Y, Alabdulrahman A, Fakhoury HM, Hajeer AH. HLA class II polymorphism in Saudi patients with multiple sclerosis. HLA 2017; 91:17-22. [PMID: 29131543 DOI: 10.1111/tan.13173] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 10/18/2017] [Accepted: 11/07/2017] [Indexed: 01/23/2023]
Abstract
Several studies have investigated the association of different HLA antigens with multiple sclerosis (MS). However, only few studies have considered the association of high-resolution HLA type and MS with none yet from Saudi Arabia. The aim of this study was to investigate the association of HLA class II alleles with MS in the Saudi population. We used next-generation sequencing to investigate HLA association with MS. This study was conducted at King Abdulaziz Medical City in Riyadh, Saudi Arabia. We found that several HLA-DRB1 and DQB1 alleles were associated with MS. These alleles included HLA-DRB1*15:01 (odds ratio [OR]: 3.01; 95%, confidence interval [CI]: 1.68-5.54; P = .0001), HLA-DQB1*02:01 (OR: 1.76; 95% CI: 1.20-2.58; P = .0022), HLA-DQB1*06:02 (OR: 3.52; 95% CI: 1.87-6.86; P < .0001), and HLA-DQB1*06:03 (OR: 2.42; 95% CI: 1.16-5.25; P = 0.01). Interestingly, HLA-DRB1*15:01 was associated with increased risk of previous relapses. In addition, HLA-DRB1*15:01 and HLA-DQB1*06:02 were found to be associated with lower vitamin D levels. This study provides insights on the association of different HLA alleles with clinical characteristics and outcome of MS among Saudis. These insights can have future implications for the clinical management of MS based on the patient genetic profile.
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Affiliation(s)
- M Al Jumah
- Department of Neurology, King Abdulaziz Medical City, National Guard Hospital, Riyadh, Saudi Arabia.,Population Genetics, King Abdullah International Medical Research Centre, Riyadh, Saudi Arabia
| | - S Kojan
- Department of Neurology, King Abdulaziz Medical City, National Guard Hospital, Riyadh, Saudi Arabia
| | - A M Al Shehri
- Department of Neurology, King Abdulaziz Medical City, National Guard Hospital, Riyadh, Saudi Arabia
| | - M Al Balwi
- Population Genetics, King Abdullah International Medical Research Centre, Riyadh, Saudi Arabia
| | - I Al Abdulkarim
- Population Genetics, King Abdullah International Medical Research Centre, Riyadh, Saudi Arabia
| | - E M Masuadi
- Research Unit, Department of Medical Education, College of Medicine, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Y Alhaidan
- Population Genetics, King Abdullah International Medical Research Centre, Riyadh, Saudi Arabia
| | - A Alabdulrahman
- Population Genetics, King Abdullah International Medical Research Centre, Riyadh, Saudi Arabia
| | - H M Fakhoury
- Department of Biochemistry and Molecular Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - A H Hajeer
- College of Medicine, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
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21
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Alrogy A, Dirar A, Alrogy W, Fakhoury H, Hajeer A. Association of human leukocyte antigen DRB1 with anti-cyclic citrullinated peptide autoantibodies in Saudi patients with rheumatoid arthritis. Ann Saudi Med 2017; 37:38-41. [PMID: 28151455 PMCID: PMC6148974 DOI: 10.5144/0256-4947.2017.38] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND The genetic association between human leukocyte antigen (HLA)-DRB1 alleles and the risk of development of autoantibodies has been investigated, but there are few studies from the Gulf region. OBJECTIVES To investigate the association between the HLA-DRB1 shared epitope and the risk for development of autoantibodies in rheumatoid arthritis (RA) patients in a Saudi population. DESIGN Analytical cross-sectional study. SETTING Tertiary care hospital in Riyadh, Saudi Arabia. PATIENTS AND METHODS We enrolled consecutive Saudi RA patients attending the rheumatology clinic between January and April 2015. Previously published data on HLA typing on unmatched healthy controls were used for comparison. HLA typing was performed using sequence-specific oligonucleotide probes (SSOP). Rheumatoid factor (RF), anti-cyclic citrullinated peptide (anti-CCP) antibodies, and antinuclear antibodies (ANA) were also measured. Logistic regression analysis was used to study the autoantibodies as possible explanatory variables for the presence of the HLA-DRB1 shared epitope. MAIN OUTCOME MEASURE(S) The association between the presence of the shared epitope and the risk of developing anti-CCP antibodies, ANA, and RF. RESULTS In 76 patients with RA, carrying the shared epitope was associated with a significantly higher risk of having RA [OR=2.65, 95% CI (1.42-4.94), P=.0009]. However, only HLA-DRB1*04:05 was significantly as.sociated with RA [OR=3.73, 95% CI (1.61-8.96), Pc=.016]. In the logistic regression analysis, only anti-CCP was significantly associated with the shared epitope [OR=14.51, 95% CI (1.53-137.49), P=.02]. CONCLUSIONS Our analysis indicates that the presence of the HLA-DRB1 shared epitope is strongly associated with the development of anti-CCP antibodies in Saudi patients with RA. LIMITATIONS A larger sample size is needed to confirm our finding.
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Affiliation(s)
| | | | | | | | - Ali Hajeer
- Prof. Ali Hajeer, King Saud bin Abdulaziz University for Health Sciences,, Immunology, National Guard Health Affairs,, Riyadh, 11426, Saudi Arabia, T: 966-11-4294047, F: 966-11-2520130, , ORCID: orcid.org/0000-0003-2727-9964
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Hajeer AH, Balkhy H, Johani S, Yousef MZ, Arabi Y. Association of human leukocyte antigen class II alleles with severe Middle East respiratory syndrome-coronavirus infection. Ann Thorac Med 2016; 11:211-3. [PMID: 27512511 PMCID: PMC4966224 DOI: 10.4103/1817-1737.185756] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND: Middle East Respiratory Syndrome (MERS) is a disease of the lower respiratory tract and is characterized by high mortality. It is caused by a beta coronavirus (CoV) referred to as MERS-CoV. Majority of MERS-CoV cases have been reported from Saudi Arabia. AIM: We investigated the human leukocyte antigen (HLA) Class II alleles in patients with severe MERS who were admitted in our Intensive Care Unit. METHODS: A total of 23 Saudi patients with severe MERS-CoV infection were typed for HLA class II, results were compared with those of 161 healthy controls. RESULTS: Two HLA class II alleles were associated with the disease; HLA-DRB1*11:01 and DQB1*02:02, but not with the disease outcome. CONCLUSIONS: Our results suggest that the HLA-DRB1*11:01 and DQB1*02:02 may be associated with susceptibility to MERS.
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Affiliation(s)
- Ali H Hajeer
- Department of Basic Medical Sciences, King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Riyadh, Saudi Arabia; Department of Pathology and Laboratory, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Hanan Balkhy
- Department of Infection Prevention and Control, King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Riyadh, Saudi Arabia; King Abdullah International Medical Research Center, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Sameera Johani
- Department of Pathology and Laboratory, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Mohammed Z Yousef
- Department of Basic Medical Sciences, King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Yaseen Arabi
- King Abdullah International Medical Research Center, King Abdulaziz Medical City, Riyadh, Saudi Arabia; Department of Intensive Care, King Abdulaziz Medical City, Riyadh, Saudi Arabia
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The impact of next-generation sequencing technologies on HLA research. J Hum Genet 2015; 60:665-73. [PMID: 26311539 PMCID: PMC4660052 DOI: 10.1038/jhg.2015.102] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 06/10/2015] [Accepted: 07/21/2015] [Indexed: 01/11/2023]
Abstract
In the past decade, the development of next-generation sequencing (NGS) has paved the way for whole-genome analysis in individuals. Research on the human leukocyte antigen (HLA), an extensively studied molecule involved in immunity, has benefitted from NGS technologies. The HLA region, a 3.6-Mb segment of the human genome at 6p21, has been associated with more than 100 different diseases, primarily autoimmune diseases. Recently, the HLA region has received much attention because severe adverse effects of various drugs are associated with particular HLA alleles. Owing to the complex nature of the HLA genes, classical direct sequencing methods cannot comprehensively elucidate the genomic makeup of HLA genes. Thus far, several high-throughput HLA-typing methods using NGS have been developed. In HLA research, NGS facilitates complete HLA sequencing and is expected to improve our understanding of the mechanisms through which HLA genes are modulated, including transcription, regulation of gene expression and epigenetics. Most importantly, NGS may also permit the analysis of HLA-omics. In this review, we summarize the impact of NGS on HLA research, with a focus on the potential for clinical applications.
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Fakhoury HA, Jawdat D, Alaskar AS, Al Jumah M, Cereb N, Hajeer AH. Three new HLA-C alleles (HLA-C*14:02:13, HLA-C*15:72 and HLA-C*15:74) in Saudi bone marrow donors. Int J Immunogenet 2015; 42:359-60. [PMID: 26239392 DOI: 10.1111/iji.12218] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 04/01/2015] [Accepted: 06/23/2015] [Indexed: 11/28/2022]
Abstract
Three new HLA-C alleles were identified by sequence-based typing method (SBT) in donors for the Saudi Bone Marrow Donor Registry (SBMDR). HLA-C*14:02:13 differs from HLA-C*14:02:01 by a silent G to A substitution at nucleotide position 400 in exon 2, where lysine at position 66 remains unchanged. HLA-C*15:72 differs from HLA-C*15:22 by a nonsynonymous C to A substitution at nucleotide position 796 in exon 3, resulting in an amino acid change from phenylalanine to leucine at position 116. HLA-C*15:74 differs from HLA-C*15:08 by a nonsynonymous C to T substitution at nucleotide position 914 in exon 3, resulting in an amino acid change from arginine to tryptophan at position 156.
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Affiliation(s)
- H A Fakhoury
- Department of Basic Sciences, College of Science and Health Professions, King Saud bin Abdulaziz University for Health Sciences, National Guard Health Affairs, Riyadh, Saudi Arabia
| | - D Jawdat
- King Abdullah International Medical Research Center, National Guard Health Affairs, Riyadh, Saudi Arabia
| | - A S Alaskar
- King Abdullah International Medical Research Center, National Guard Health Affairs, Riyadh, Saudi Arabia
| | - M Al Jumah
- King Abdullah International Medical Research Center, National Guard Health Affairs, Riyadh, Saudi Arabia
| | - N Cereb
- Histogenetics, Ossining, NY, USA
| | - A H Hajeer
- Department of Basic Medical Sciences, College of Medicine, King Saud bin Abdulaziz University for Health Sciences, National Guard Health Affairs, Riyadh, Saudi Arabia.,Saudi Stem Cell Donor Registry, King Abdullah International Medical Research Center, National Guard Health Affairs, Riyadh, Saudi Arabia
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Fakhoury HA, Alaskar AS, Hajeer AH. A novel HLA-DQ allele,HLA-DQB1*05:48, found in the Saudi Stem Cells Donor Registry. ACTA ACUST UNITED AC 2015. [DOI: 10.1111/tan.12628] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- H. A. Fakhoury
- Department of Basic Sciences, College of Science and Health Professions, King Saud bin Abdulaziz University for Health Sciences; National Guard Health Affairs; Riyadh Saudi Arabia
| | - A. S. Alaskar
- King Abdullah International Medical Research Center; National Guard Health Affairs; Riyadh Saudi Arabia
| | - A. H. Hajeer
- Department of Basic Medical Sciences, College of Medicine, King Saud bin Abdulaziz University for Health Sciences; National Guard Health Affairs; Riyadh Saudi Arabia
- Saudi Stem Cell Donor Registry, King Abdullah International Medical Research Center; National Guard Health Affairs; Riyadh Saudi Arabia
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26
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Jawdat D, Qurashi SA, Sayyari AA, Hajeer AH. Screening panel-reactive antibody negative, single-antigen positive: a case report. Prog Transplant 2014; 24:341-3. [PMID: 25488556 DOI: 10.7182/pit2014161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Sensitized patients remain a challenge for successful transplant. Virtual crossmatch is used to determine the presence or absence of donor-specific antibodies. A 60-year-old woman with a negative screening for panel-reactive antibodies (PRA) received an A*11, A*68 type kidney with a negative anti-human globulin/complement-dependent cytotoxicity (AHG-CDC) crossmatch. Her transplant course was complicated by delayed graft function, and she required hemodialysis. On day 8 after receiving the transplant, she had a kidney biopsy that showed features of antibody-mediated rejection/severe acute tubular necrosis, which was treated by plasmapheresis for 5 sessions and intravenous immunoglobulin (2 g/kg). Her serum level of creatinine decreased from 6.7 to 3.6 mg/dL (600-320 μmol/L). Panel-reactive antibody by Luminex was repeated and again was negative. Single-antigen detection was tried next. Surprisingly, A*11:02 came up positive with a mean fluorescence intensity of 9500. High-resolution donor HLA type was A*68:01 and A*11:01. A*11:02 is not part of the screening Luminex PRA whereas the 11:01 allele is. Serologically, HLA-A11 has 2 defined splits, A11.1 and A11.2, which encode A*11:01 and A*11:02, respectively. In this case, the A*11:02 antibody does not seem to be responsible for the increasing creatinine level. However, if the donor had been A*11:02, a humeral rejection would have occurred and been missed by a virtual crossmatch. Thus virtual crossmatch may not work at all times. Screening for PRA by single antigens is suggested even in PRA-negative cases, if only virtual crossmatch is to be used.
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Affiliation(s)
- Dunia Jawdat
- King Abdullah International Medical Research Center, Riyadh, Saudi Arabia King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | | | | | - Ali H Hajeer
- King Abdulaziz Medical City, Riyadh, Saudi Arabia King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
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Sanchez-Mazas A, Meyer D. The relevance of HLA sequencing in population genetics studies. J Immunol Res 2014; 2014:971818. [PMID: 25126587 PMCID: PMC4122113 DOI: 10.1155/2014/971818] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 06/20/2014] [Indexed: 11/18/2022] Open
Abstract
Next generation sequencing (NGS) is currently being adapted by different biotechnological platforms to the standard typing method for HLA polymorphism, the huge diversity of which makes this initiative particularly challenging. Boosting the molecular characterization of the HLA genes through efficient, rapid, and low-cost technologies is expected to amplify the success of tissue transplantation by enabling us to find donor-recipient matching for rare phenotypes. But the application of NGS technologies to the molecular mapping of the MHC region also anticipates essential changes in population genetic studies. Huge amounts of HLA sequence data will be available in the next years for different populations, with the potential to change our understanding of HLA variation in humans. In this review, we first explain how HLA sequencing allows a better assessment of the HLA diversity in human populations, taking also into account the methodological difficulties it introduces at the statistical level; secondly, we show how analyzing HLA sequence variation may improve our comprehension of population genetic relationships by facilitating the identification of demographic events that marked human evolution; finally, we discuss the interest of both HLA and genome-wide sequencing and genotyping in detecting functionally significant SNPs in the MHC region, the latter having also contributed to the makeup of the HLA molecular diversity observed today.
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Affiliation(s)
- Alicia Sanchez-Mazas
- Department of Genetics and Evolution—Anthropology Unit, University of Geneva and Institute of Genetics and Genomics of Geneva (IGE3), 12 Rue Gustave-Revilliod, 1211 Geneva 4, Switzerland
| | - Diogo Meyer
- Department of Genetics and Evolutionary Biology, University of São Paulo, Rua do Matão 277, São Paulo, SP 05508-090, Brazil
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Fakhoury HA, Jawdat D, Alaskar AS, Al Jumah M, Cereb N, Hajeer AH. Two novel alleles HLA-A*02:433 and HLA-A*02:434 identified in Saudi bone marrow donors using sequence-based typing. Int J Immunogenet 2014; 41:338-9. [PMID: 24919814 DOI: 10.1111/iji.12131] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2014] [Revised: 04/28/2014] [Accepted: 04/29/2014] [Indexed: 11/28/2022]
Abstract
In this report, we present two novel HLA-A alleles: HLA-A*02:433 and HLA-A*02:434. These alleles were identified by sequence-based typing method (SBT), in two donors for the Saudi Bone Marrow Donor Registry (SBMDR). Allele A*02:433 is identical to A*02:05:01G except for a G to A substitution at nucleotide position 449 in exon 2. This substitution results in glycine to serine substitution at position 83. Whereas, allele A*02:434 is identical to A*02:01:01G except for a C to A substitution at nucleotide position 245 in exon 2, which results in phenylalanine to threonine substitution at position 15. The generation of both alleles appears to be the result of nucleotide point mutation involving 02:01:01 and 02:05:01.
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Affiliation(s)
- H A Fakhoury
- Department of Basic Sciences, College of Science and Health Professions, King Saud bin Abdulaziz University for Health Sciences, National Guard Health Affairs, Riyadh, Saudi Arabia
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Fakhoury HA, Cereb N, Jawdat D, Al Jumah M, Alaskar AS, Hajeer AH. Two novel alleles HLA-DRB1*11:150 and HLA-DRB1*14:145 identified in Saudi individuals. Int J Immunogenet 2014; 41:340-1. [DOI: 10.1111/iji.12133] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 04/28/2014] [Accepted: 05/04/2014] [Indexed: 11/30/2022]
Affiliation(s)
- H. A. Fakhoury
- Department of Basic Sciences; College of Science and Health Professions; King Saud bin Abdulaziz University for Health Sciences; National Guard Health Affairs; Riyadh Saudi Arabia
| | | | - D. Jawdat
- King Abdullah International Medical Research Center; National Guard Health Affairs; Riyadh Saudi Arabia
| | - M. Al Jumah
- King Abdullah International Medical Research Center; National Guard Health Affairs; Riyadh Saudi Arabia
| | - A. S. Alaskar
- King Abdullah International Medical Research Center; National Guard Health Affairs; Riyadh Saudi Arabia
| | - A. H. Hajeer
- Department of Basic Medical Sciences; College of Medicine; King Saud bin Abdulaziz University for Health Sciences; National Guard Health Affairs; Riyadh Saudi Arabia
- Saudi Stem Cell Donor Registry; King Abdullah International Medical Research Center; National Guard Health Affairs; Riyadh Saudi Arabia
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