1
|
Arhire AI, Ioacara S, Papuc T, Chiper MS, Dutescu IM, Moise A, Badea IR, Florea S, Vlad A, Fica S. Association of HLA Haplotypes with Autoimmune Pathogenesis in Newly Diagnosed Type 1 Romanian Diabetic Children: A Pilot, Single-Center Cross-Sectional Study. Life (Basel) 2024; 14:781. [PMID: 38929763 PMCID: PMC11205248 DOI: 10.3390/life14060781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 06/16/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND The increasing incidence of autoimmune diseases in type 1 diabetes mellitus (T1DM) patients highlights the influence of human leukocyte antigen (HLA) haplotypes on their development. This study aims to determine genetic predisposition to autoimmune diseases in T1DM patients, including thyroid disease and celiac diseases, and explore its correlation with vitamin D deficiency. METHODS A cross-sectional study involving thirty-six T1DM children was conducted. Typing was performed for the HLA A, B, C, DP, DR, and DQ loci. Regression analysis linked DR-DQ haplotypes to T1DM and the associated conditions. RESULTS The most frequent predisposing alleles and haplotypes were HLA-DR3 (70.27%), DQ2 (70.27%), DR3-DQ2 (70.27%), DQB1*02:01 (70.27%), A02 (54.05%), whereas the most prevalent protecting allele was DPB1*04:01 (52.63%). Positive correlations were observed between positive anti-thyroid peroxidase antibodies and the absence of protective alleles (DPB1*04:02, p = 0.036; DPB1*04:01, p = 0.002). Associations were found between the absence of DPB1*04:01 and anti-thyroglobulin antibodies (p = 0.03). HLA allele DPB1*03:01 was linked with vitamin D deficiency (p = 0.021). Positive anti-transglutaminase antibodies correlated with C03:03 (p = 0.026) and DRB1*04:01-DQA1*03-DQB1*03:01 (p < 0.0001) and the lack of DQA1*01:03-DQB1*06:03-DRB1*13:01 (p < 0.0001). CONCLUSIONS The predisposing T1DM haplotypes were associated with the presence of anti-transglutaminase and anti-thyroid antibodies, indicating a genetic predisposition to autoimmune diseases.
Collapse
Affiliation(s)
- Amalia Ioana Arhire
- General Medicine Faculty, “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania; (A.I.A.); (A.V.); (S.F.)
- Department of Pediatric Endocrinology and Diabetes, Elias Emergency University Hospital, 011461 Bucharest, Romania; (T.P.); (M.S.C.)
| | - Sorin Ioacara
- General Medicine Faculty, “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania; (A.I.A.); (A.V.); (S.F.)
- Department of Pediatric Endocrinology and Diabetes, Elias Emergency University Hospital, 011461 Bucharest, Romania; (T.P.); (M.S.C.)
| | - Teodora Papuc
- Department of Pediatric Endocrinology and Diabetes, Elias Emergency University Hospital, 011461 Bucharest, Romania; (T.P.); (M.S.C.)
| | - Miruna Sânziana Chiper
- Department of Pediatric Endocrinology and Diabetes, Elias Emergency University Hospital, 011461 Bucharest, Romania; (T.P.); (M.S.C.)
| | - Irina Monica Dutescu
- HLA Laboratory, “C.T. Nicolau” National Institute of Blood Transfusion, 011154 Bucharest, Romania; (I.M.D.); (A.M.); (I.R.B.)
| | - Ana Moise
- HLA Laboratory, “C.T. Nicolau” National Institute of Blood Transfusion, 011154 Bucharest, Romania; (I.M.D.); (A.M.); (I.R.B.)
| | - Ioana Roxana Badea
- HLA Laboratory, “C.T. Nicolau” National Institute of Blood Transfusion, 011154 Bucharest, Romania; (I.M.D.); (A.M.); (I.R.B.)
| | - Suzana Florea
- Immunology Laboratory, Elias Emergency University Hospital, 011461 Bucharest, Romania;
| | - Adelina Vlad
- General Medicine Faculty, “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania; (A.I.A.); (A.V.); (S.F.)
| | - Simona Fica
- General Medicine Faculty, “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania; (A.I.A.); (A.V.); (S.F.)
- Department of Pediatric Endocrinology and Diabetes, Elias Emergency University Hospital, 011461 Bucharest, Romania; (T.P.); (M.S.C.)
| |
Collapse
|
2
|
Stasiak M, Stasiak B, Zawadzka-Starczewska K, Lewiński A. Significance of HLA in Graves' disease and Graves' orbitopathy in Asian and Caucasian populations - a systematic review. Front Immunol 2023; 14:1256922. [PMID: 37841270 PMCID: PMC10568027 DOI: 10.3389/fimmu.2023.1256922] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 09/04/2023] [Indexed: 10/17/2023] Open
Abstract
Introduction Graves' disease (GD) and Graves' orbitopathy (GO) development were suspected to be HLA-related in both Asian and Caucasian populations. However, most studies were performed with application of serological methods or low resolution genetic typing, which led to inconsistent results even among the same population. The present review is intended to summarize the state-of-art knowledge on the HLA significance in GD and GO in Asians and Caucasians, as well as to find the most significant alleles for each of the populations. Methods PubMed was searched for relevant articles using the following search terms: HLA plus thyroid-associated ophthalmopathy or Graves' disease or Graves' orbitopathy or thyroid eye disease or thyroid-associated orbitopathy. Results In Asian population GD was found to be associated mostly with B*46:01, DPB1*05:01, DRB1*08:02/03, DRB1*16:02, DRB1*14:03, DRB1*04:05, DQB1*05:02 and DQB1*03:03, while DRB1*07:01, DRB1*01:01, DRB1*13:02, DRB1*12:02 are potentially protective. HLA-B*38:02, DRB1*16:02, DQA1*01:02, DQB1*05:02 can be considered associated with increased risk of GO in Asians, while HLA-B*54:01 may play protective role. In Caucasians, C*07:01, DQA1*05:01, DRB1*03, DQB1*02:01 are associated with GD risk while DRB1*07:01, DQA1*02:01 may be protective. Significance of HLA in the course of GD and novel aspects of HLA amino acid variants and potential HLA-based treatment modalities were also discussed.
Collapse
Affiliation(s)
- Magdalena Stasiak
- Department of Endocrinology and Metabolic Diseases, Polish Mother’s Memorial Hospital—Research Institute, Lodz, Poland
| | - Bartłomiej Stasiak
- Institute of Information Technology, Lodz University of Technology, Lodz, Poland
| | | | - Andrzej Lewiński
- Department of Endocrinology and Metabolic Diseases, Polish Mother’s Memorial Hospital—Research Institute, Lodz, Poland
- Department of Endocrinology and Metabolic Diseases, Medical University of Lodz, Lodz, Poland
| |
Collapse
|
3
|
Li J, Xiao Z, Wang D, Jia L, Nie S, Zeng X, Hu W. The screening, identification, design and clinical application of tumor-specific neoantigens for TCR-T cells. Mol Cancer 2023; 22:141. [PMID: 37649123 PMCID: PMC10466891 DOI: 10.1186/s12943-023-01844-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 08/16/2023] [Indexed: 09/01/2023] Open
Abstract
Recent advances in neoantigen research have accelerated the development of tumor immunotherapies, including adoptive cell therapies (ACTs), cancer vaccines and antibody-based therapies, particularly for solid tumors. With the development of next-generation sequencing and bioinformatics technology, the rapid identification and prediction of tumor-specific antigens (TSAs) has become possible. Compared with tumor-associated antigens (TAAs), highly immunogenic TSAs provide new targets for personalized tumor immunotherapy and can be used as prospective indicators for predicting tumor patient survival, prognosis, and immune checkpoint blockade response. Here, the identification and characterization of neoantigens and the clinical application of neoantigen-based TCR-T immunotherapy strategies are summarized, and the current status, inherent challenges, and clinical translational potential of these strategies are discussed.
Collapse
Affiliation(s)
- Jiangping Li
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, People's Republic of China.
| | - Zhiwen Xiao
- Department of Otolaryngology Head and Neck Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, People's Republic of China
| | - Donghui Wang
- Department of Radiation Oncology, The Third Affiliated Hospital Sun Yat-Sen University, Guangzhou, 510630, People's Republic of China
| | - Lei Jia
- International Health Medicine Innovation Center, Shenzhen University, Shenzhen, 518060, People's Republic of China
| | - Shihong Nie
- Department of Radiation Oncology, West China Hospital, Sichuan University, Cancer Center, Chengdu, 610041, People's Republic of China
| | - Xingda Zeng
- Department of Parasitology of Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Wei Hu
- Division of Vascular Surgery, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072, People's Republic of China
| |
Collapse
|
4
|
Dong L, He Y, Li Y, Zhang W, Zhu F. Identification of the novel HLA-DQA1*01:04:04 allele by next-generation sequencing. HLA 2023; 102:252-254. [PMID: 37068776 DOI: 10.1111/tan.15065] [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: 03/30/2023] [Accepted: 04/03/2023] [Indexed: 04/19/2023]
Abstract
HLA-DQA1*01:04:04 differs from HLA-DQA1*01:04:01:01 by a single nucleotide substitution at position 225 C > T.
Collapse
Affiliation(s)
- Lina Dong
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, China
- HLA Typing Laboratory, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, China
| | - Yizhen He
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, China
- HLA Typing Laboratory, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, China
| | - Ying Li
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, China
- HLA Typing Laboratory, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, China
| | - Wei Zhang
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, China
- HLA Typing Laboratory, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, China
| | - Faming Zhu
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, China
- HLA Typing Laboratory, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, China
| |
Collapse
|
5
|
Vasoya D, Tzelos T, Benedictus L, Karagianni AE, Pirie S, Marr C, Oddsdóttir C, Fintl C, Connelley T. High-Resolution Genotyping of Expressed Equine MHC Reveals a Highly Complex MHC Structure. Genes (Basel) 2023; 14:1422. [PMID: 37510326 PMCID: PMC10379315 DOI: 10.3390/genes14071422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/29/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023] Open
Abstract
The Major Histocompatibility Complex (MHC) genes play a key role in a number of biological processes, most notably in immunological responses. The MHCI and MHCII genes incorporate a complex set of highly polymorphic and polygenic series of genes, which, due to the technical limitations of previously available technologies, have only been partially characterized in non-model but economically important species such as the horse. The advent of high-throughput sequencing platforms has provided new opportunities to develop methods to generate high-resolution sequencing data on a large scale and apply them to the analysis of complex gene sets such as the MHC. In this study, we developed and applied a MiSeq-based approach for the combined analysis of the expressed MHCI and MHCII repertoires in cohorts of Thoroughbred, Icelandic, and Norwegian Fjord Horses. The approach enabled us to generate comprehensive MHCI/II data for all of the individuals (n = 168) included in the study, identifying 152 and 117 novel MHCI and MHCII sequences, respectively. There was limited overlap in MHCI and MHCII haplotypes between the Thoroughbred and the Icelandic/Norwegian Fjord horses, showcasing the variation in MHC repertoire between genetically divergent breeds, and it can be inferred that there is much more MHC diversity in the global horse population. This study provided novel insights into the structure of the expressed equine MHC repertoire and highlighted unique features of the MHC in horses.
Collapse
Affiliation(s)
- Deepali Vasoya
- The Roslin Institute, The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Roslin EH25 9RG, UK
| | - Thomas Tzelos
- The Roslin Institute, The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Roslin EH25 9RG, UK
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik EH26 0PZ, UK
| | - Lindert Benedictus
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, The Netherlands
| | - Anna Eleonora Karagianni
- The Roslin Institute, The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Roslin EH25 9RG, UK
| | - Scott Pirie
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Roslin EH25 9RG, UK
| | - Celia Marr
- Rossdales Equine Hospital, Cotton End Road, Exning, Newmarket CD8 7NN, UK
| | - Charlotta Oddsdóttir
- The Institute for Experimental Pathology at Keldur, University of Iceland Keldnavegur 3, 112 Reykjavík, Iceland
| | - Constanze Fintl
- Department of Companion Animal Clinical Sciences, Faculty of Veterinary Medicine and Biosciences, Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
| | - Timothy Connelley
- The Roslin Institute, The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Roslin EH25 9RG, UK
| |
Collapse
|
6
|
Baek IC, Choi EJ, Kim HJ, Choi H, Kim TG. Distributions of 11-loci HLA alleles typed by amplicon-based next-generation sequencing in South Koreans. HLA 2023; 101:613-622. [PMID: 36720674 DOI: 10.1111/tan.14981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 12/11/2022] [Accepted: 01/27/2023] [Indexed: 02/02/2023]
Abstract
The range of HLA typing for successful hematopoietic stem cell transplantation (HSCT) is gradually expanding with the next-generation sequencing (NGS)-based improvement in its quality. However, it is influenced by the allocation of finances and laboratory conditions. HLA-A, -B, -C, -DRB1/3/4/5, -DQA1, -DQB1, -DPA1, and -DPB1 alleles were genotyped at the 3-field level by amplicon-based NGS using MiSeqDx system and compared to our previous study employing long-range PCR and NGS using TruSight HLA v2 kit, in healthy donors from South Korea. Exon 2, exons 2/3, exons 2/3/4 or 5 of 11-loci were amplified by multiplex PCR. The sequence reads of over 53 depth counts were consistently obtained in each sample exon, depending on the target exon determined to match the reference sequence contained in the IPD-IMGT/HLA Database. HLA alleles were investigated by combinations of the determined exons. A total of 18 alleles with a frequency over 10% were found at the 11 HLA loci. Three ambiguities of HLA-A, -C, and -DRB1 were resolved. We observed a total of 26 HLA-A ~ C ~ B and 6 HLA-DRB1 ~ DQA1 ~ DQB1 ~ DPA1 ~ DPB1 haplotypes having significant linkage disequilibrium between alleles at all neighboring HLA loci. This result was compatible with the previous one, using TruSight HLA v2 kit. Advantages are simple and short progress time because one plate is used for each PCR step in one PCR machine and 11-loci HLA typing is possible even if only eight samples. These data suggested that expanded 11-loci HLA typing data by amplicon-based NGS might help perform HSCT.
Collapse
Affiliation(s)
- In-Cheol Baek
- Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Eun-Jeong Choi
- Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Hyoung-Jae Kim
- Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Haeyoun Choi
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Tai-Gyu Kim
- Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, South Korea.,Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| |
Collapse
|
7
|
Wang K, Sun Z, Zhu F, Xu Y, Zhou F. Development of a high-resolution mass-spectrometry-based method and software for human leukocyte antigen typing. Front Immunol 2023; 14:1188381. [PMID: 37187759 PMCID: PMC10175642 DOI: 10.3389/fimmu.2023.1188381] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 04/12/2023] [Indexed: 05/17/2023] Open
Abstract
Introduction The human leukocyte antigen (HLA) system plays a critical role in the human immune system and is strongly associated with immune recognition and rejection in organ transplantation. HLA typing method has been extensively studied to increase the success rates of clinical organ transplantation. However, while polymerase chain reaction sequence-based typing (PCR-SBT) remains the gold standard, cis/trans ambiguity and nucleotide sequencing signal overlay during heterozygous typing present a problem. The high cost and low processing speed of Next Generation Sequencing (NGS) also render this approach inadequate for HLA typing. Methods and materials To address these limitations of the current HLA typing methods, we developed a novel typing technology based on nucleic acid mass spectrometry (MS) of HLA. Our method takes advantage of the high-resolution mass analysis function of MS and HLAMSTTs (HLA MS Typing Tags, some short fragment PCR amplification target products) with precise primer combinations. Results We correctly typed HLA by measuring the molecular weights of HLAMSTTs with single nucleotide polymorphisms (SNPs). In addition, we developed a supporting HLA MS typing software to design PCR primers, construct the MS database, and select the best-matching HLA typing results. With this new method, we typed 16 HLA-DQA1 samples, including 6 homozygotes and 10 heterozygotes. The MS typing results were validated by PCR-SBT. Discussion The MS HLA typing method is rapid, efficient, accurate, and readily applicable to typing of homozygous and heterozygous samples.
Collapse
Affiliation(s)
- Kun Wang
- Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Zetao Sun
- Institute of Transfusion Medicine, Shenzhen Blood Center, Shenzhen, Guangdong, China
| | - Fei Zhu
- Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yunping Xu
- Institute of Transfusion Medicine, Shenzhen Blood Center, Shenzhen, Guangdong, China
- *Correspondence: Yunping Xu, ; Feng Zhou,
| | - Feng Zhou
- Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion, Minister of Education, and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- *Correspondence: Yunping Xu, ; Feng Zhou,
| |
Collapse
|
8
|
Cornaby C, Weimer ET. HLA Typing by Next-Generation Sequencing: Lessons Learned and Future Applications. Clin Lab Med 2022; 42:603-612. [PMID: 36368785 DOI: 10.1016/j.cll.2022.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Caleb Cornaby
- McLendon Clinical Laboratories, UNC Hospitals, 101 Manning Drive, Chapel Hill, NC 27514, USA
| | - Eric T Weimer
- McLendon Clinical Laboratories, UNC Hospitals, 101 Manning Drive, Chapel Hill, NC 27514, USA; Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27514, USA.
| |
Collapse
|
9
|
Xi P, Wang H, Zhong Z, Liu S, Tang J, Guo C, Dai P. rs144012689 is a highly specific representative marker of HLA-B*15:02 in the Chinese population. Pharmacogenomics 2022; 23:835-845. [PMID: 36169168 DOI: 10.2217/pgs-2022-0075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Objective: To develop an accurate and rapid real-time PCR technique for HLA-B*15:02 genotyping and investigate HLA-B*15:02 allele frequency in four ethnic populations in China. Materials & methods: Based on the highly specific representative markers, a real-time PCR assay was developed for HLA-B*15:02 genotyping, and HLA-B*15:02 allele frequencies were screened in four ethnic populations of China. Sequence-based typing was used to validate the accuracy of the assay. Results: The sensitivity and specificity of the assay were 100%, and the detection limit was 0.2 ng. The frequency of HLA-B*15:02 alleles distributed in the Bouyei population was significantly higher than in the Han group (p < 0.01). Neither the Tibetan nor the Uyghur population carried the HLA-B*15:02 haplotype. Conclusion: The authors developed an accurate HLA-B*15:02 genotyping method for evaluating the risk of adverse drug reactions induced by carbamazepine in various ethnic populations in China.
Collapse
Affiliation(s)
- Pei Xi
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University of Xi'an, Shaanxi Province, 710069, China.,Shaanxi Lifegen Co.,Ltd, Building 1, Collaborative Innovation Port, Fengdong New City, Xixian New Area, Xi'an, Shaanxi Province, 712000, China
| | - Hao Wang
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University of Xi'an, Shaanxi Province, 710069, China
| | - Zihua Zhong
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University of Xi'an, Shaanxi Province, 710069, China
| | - Shihui Liu
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University of Xi'an, Shaanxi Province, 710069, China
| | - Jiaxuan Tang
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University of Xi'an, Shaanxi Province, 710069, China
| | - Chunli Guo
- Pulmonary and Critical Care Medicine, Tongchuan People's Hospital, Tongchuan, Shaanxi Province, People's Republic of China
| | - Penggai Dai
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University of Xi'an, Shaanxi Province, 710069, China.,Shaanxi Lifegen Co.,Ltd, Building 1, Collaborative Innovation Port, Fengdong New City, Xixian New Area, Xi'an, Shaanxi Province, 712000, China
| |
Collapse
|
10
|
Simakova T, Suvorova A, Krivonosova K, Abramova A, Loginova M, Paramonov I. NovAT tool-Reliable novel HLA alleles identification from next-generation sequencing data. HLA 2021; 99:3-11. [PMID: 34791827 DOI: 10.1111/tan.14491] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 11/03/2021] [Accepted: 11/09/2021] [Indexed: 12/19/2022]
Abstract
HLA molecules are expressed in almost all nucleated cells of the body. These molecules are extremely variable and responsible for tissue specificity recognition. Precise HLA typing is crucial for tissue and organ transplantation. Usually, HLA-typing NGS methods are based on the assignment of reads to a certain previously reported HLA allele presented in the IPD-IMGT/HLA Database. But there is a limited number of tools able to identify novel alleles that have not yet been reported and thus absent in the database. Such alleles carry mismatches distinguishing them from all known alleles in the database. Therefore, manual evaluation of the identified HLA alleles in the genome browser is a compulsory step in the analysis, and one that is labor intensive and time consuming. We present the development and validation of a freely available web-application for the identification of novel HLA alleles in the most relevant HLA class I and II genes from NGS data. The tool can also be used for automated data quality assessment. The software was validated by analyzing 330 alleles. The results are concordant with orthogonal methods.
Collapse
Affiliation(s)
| | - Arina Suvorova
- R&D Department, Parseq Lab Co. Ltd., St. Petersburg, Russia
| | | | - Anna Abramova
- R&D Department, Parseq Lab Co. Ltd., St. Petersburg, Russia
| | - Maria Loginova
- Federal State Budget Research Institution, Kirov Hematology and Blood Transfusion Research Institute under the Federal Medicine and Biology Agency, Kirov, Russia
| | - Igor Paramonov
- Federal State Budget Research Institution, Kirov Hematology and Blood Transfusion Research Institute under the Federal Medicine and Biology Agency, Kirov, Russia
| |
Collapse
|
11
|
Lee M, Seo JH, Song S, Song IH, Kim SY, Kim YA, Gong G, Kim JE, Lee HJ. A New Human Leukocyte Antigen Typing Algorithm Combined With Currently Available Genotyping Tools Based on Next-Generation Sequencing Data and Guidelines to Select the Most Likely Human Leukocyte Antigen Genotype. Front Immunol 2021; 12:688183. [PMID: 34659196 PMCID: PMC8517438 DOI: 10.3389/fimmu.2021.688183] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 09/15/2021] [Indexed: 12/25/2022] Open
Abstract
Background High-precision human leukocyte antigen (HLA) genotyping is crucial for anti-cancer immunotherapy, but existing tools predicting HLA genotypes using next-generation sequencing (NGS) data are insufficiently accurate. Materials and Methods We compared availability, accuracy, correction score, and complementary ratio of eight HLA genotyping tools (OptiType, HLA-HD, PHLAT, seq2HLA, arcasHLA, HLAscan, HLA*LA, and Kourami) using 1,005 cases from the 1000 Genomes Project data. We created a new HLA-genotyping algorithm combining tools based on the precision and the accuracy of tools’ combinations. Then, we assessed the new algorithm’s performance in 39 in-house samples with normal whole-exome sequencing (WES) data and polymerase chain reaction–sequencing-based typing (PCR-SBT) results. Results Regardless of the type of tool, the calls presented by more than six tools concordantly showed high accuracy and precision. The accuracy of the group with at least six concordant calls was 100% (97/97) in HLA-A, 98.2% (112/114) in HLA-B, 97.3% (142/146) in HLA-C. The precision of the group with at least six concordant calls was over 98% in HLA-ABC. We additionally calculated the accuracy of the combination tools considering the complementary ratio of each tool and the accuracy of each tool, and the accuracy was over 98% in all groups with six or more concordant calls. We created a new algorithm that matches the above results. It was to select the HLA type if more than six out of eight tools presented a matched type. Otherwise, determine the HLA type experimentally through PCR-SBT. When we applied the new algorithm to 39 in-house cases, there were more than six matching calls in all HLA-A, B, and C, and the accuracy of these concordant calls was 100%. Conclusions HLA genotyping accuracy using NGS data could be increased by combining the current HLA genotyping tools. This new algorithm could also be useful for preliminary screening to decide whether to perform an additional PCR-based experimental method instead of using tools with NGS data.
Collapse
Affiliation(s)
- Miseon Lee
- Department of Hospital Pathology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Jeong-Han Seo
- Department of Biomedical Sciences, Asan Medical Institute of Convergence Science and Technology, University of Ulsan College of Medicine, Asan Medical Center, Seoul, South Korea.,NeogenTC Corp, Seoul, South Korea
| | | | - In Hye Song
- Department of Hospital Pathology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Su Yeon Kim
- University of Ulsan College of Medicine, Seoul, South Korea
| | | | - Gyungyub Gong
- Department of Pathology, University of Ulsan College of Medicine, Asan Medical Center, Seoul, South Korea
| | - Jeong Eun Kim
- Department of Oncology, University of Ulsan College of Medicine, Asan Medical Center, Seoul, South Korea
| | - Hee Jin Lee
- Department of Biomedical Sciences, Asan Medical Institute of Convergence Science and Technology, University of Ulsan College of Medicine, Asan Medical Center, Seoul, South Korea.,NeogenTC Corp, Seoul, South Korea.,Department of Pathology, University of Ulsan College of Medicine, Asan Medical Center, Seoul, South Korea
| |
Collapse
|
12
|
Cornaby C, Schmitz JL, Weimer ET. Next-generation sequencing and clinical histocompatibility testing. Hum Immunol 2021; 82:829-837. [PMID: 34521569 DOI: 10.1016/j.humimm.2021.08.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/12/2021] [Accepted: 08/16/2021] [Indexed: 11/28/2022]
Abstract
Histocompatibility testing is essential for donor identification and risk assessment in solid organ and hematopoietic stem cell transplant. Additionally, it is useful for identifying donor specific alleles for monitoring donor specific antibodies in post-transplant patients. Next-generation sequence (NGS) based human leukocyte antigen (HLA) typing has improved many aspects of histocompatibility testing in hematopoietic stem cell and solid organ transplant. HLA disease association testing and research has also benefited from the advent of NGS technologies. In this review we discuss the current impact and future applications of NGS typing on clinical histocompatibility testing for transplant and non-transplant purposes.
Collapse
Affiliation(s)
- Caleb Cornaby
- McLendon Clinical Laboratories, UNC Health, Chapel Hill, NC, USA
| | - John L Schmitz
- McLendon Clinical Laboratories, UNC Health, Chapel Hill, NC, USA; Department of Pathology & Laboratory Medicine, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Eric T Weimer
- McLendon Clinical Laboratories, UNC Health, Chapel Hill, NC, USA; Department of Pathology & Laboratory Medicine, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
| |
Collapse
|
13
|
Jekarl DW, Lee GD, Yoo JB, Kim JR, Yu H, Yoo J, Lim J, Kim M, Kim Y. HLA-A, -B, -C, -DRB1 allele and haplotype frequencies of the Korean population and performance characteristics of HLA typing by next-generation sequencing. HLA 2021; 97:188-197. [PMID: 33314756 DOI: 10.1111/tan.14167] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/06/2020] [Accepted: 12/07/2020] [Indexed: 01/10/2023]
Abstract
INTRODUCTION Human leukocyte antigen (HLA) identification at the allelic level is important for haematopoietic stem cell transplantation (HSCT). Next-generation sequencing (NGS) resolves ambiguous alleles by determining the phase of the polymorphisms. The aim of this study was to validate the software for HLA-SBT (sequence-based typing), assess Korean allele frequency, and characterise the performance of NGS-HLA typing. METHODS From the 2009 to 2016 registry, 1293 unrelated healthy donors with a complete dataset of previously characterised HLA-A, -B, -C, and -DRB1 loci were selected and assessed for frequency, haplotype inference, and relative linkage disequilibrium. For performance characteristics of NGS-HLA, alleles included in 1293 cases and ambiguous or alleles assigned as new by SBT-HLA software, or unassigned alleles were included. A total of 91 and 41 quality control samples resulted in 1056 alleles (132 samples × 4 loci × 2 diploid) for analysis. The GenDx NGSgo kit was used for NGS-HLA typing using the Illumina MiSeq platform. RESULTS A panel of 132 samples covered 231 alleles, including 53 HLA-A, 80 HLA-B, 43 HLA-C, and 55 HLA-DRB1 by HLA-SBT typing. Comparison of SBT-HLA and NGS-HLA typing showed 99.7% (1053/1056) concordance and discrepant cases were resolved by manual evaluation. Typing by NGS resulted in 67 HLA-A, 112 HLA-B, 71 HLA-C, and 72 HLA-DRB1 alleles. A total of 132 ambiguous, 4 new, and 1 unassigned alleles by HLA-SBT were resolved by NGS-HLA typing. CONCLUSIONS NGS-HLA typing provided robust and conclusive results without ambiguities, and its implementation could support HSCT in clinical settings.
Collapse
Affiliation(s)
- Dong Wook Jekarl
- Department of Laboratory Medicine, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea.,Department of Laboratory Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea Seoul, Republic of Korea
| | - Gun Dong Lee
- Department of Laboratory Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea Seoul, Republic of Korea
| | - Jae Bin Yoo
- Department of Laboratory Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea Seoul, Republic of Korea
| | - Jung Rok Kim
- Department of Laboratory Medicine, Eunpyeong St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea
| | - Haein Yu
- Department of Laboratory Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea Seoul, Republic of Korea
| | - Jaeeun Yoo
- Department of Laboratory Medicine, College of Medicine, Incheon St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jihyang Lim
- Department of Laboratory Medicine, College of Medicine, Eunpyeong St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea
| | - Myungshin Kim
- Department of Laboratory Medicine, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea.,Department of Laboratory Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea Seoul, Republic of Korea.,Catholic Genetic Laboratory Center, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea
| | - Yonggoo Kim
- Department of Laboratory Medicine, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea.,Department of Laboratory Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea Seoul, Republic of Korea.,Catholic Genetic Laboratory Center, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea
| |
Collapse
|
14
|
Profaizer T, Pole A, Monds C, Delgado JC, Lázár-Molnár E. Clinical utility of next generation sequencing based HLA typing for disease association and pharmacogenetic testing. Hum Immunol 2020; 81:354-360. [PMID: 32499099 DOI: 10.1016/j.humimm.2020.05.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 04/22/2020] [Accepted: 05/02/2020] [Indexed: 12/17/2022]
Abstract
HLA associations have been linked to many diseases and are important for risk assessment of drug hypersensitivity reactions. The increasing number of HLA alleles discovered generated a list of ambiguities that cannot be resolved with the current clinical assays, which commonly include sequence-specific oligonucleotide probe (SSOP) genotyping, and real-time PCR with melting curve analysis. HLA typing by next-generation sequencing (NGS) has recently been adopted by clinical laboratories for transplantation testing, as it provides unambiguous and cost-effective HLA typing. The goal of this study was to evaluate the feasibility of using NGS-based HLA-B and DQ genotyping for clinical HLA disease association testing, and provide direct comparison with the currently used clinical tests, including SSOP genotyping, and real-time PCR with melting curve analysis. While the real-time PCR method is easy and inexpensive to perform, ambiguities are rapidly increasing as more and more HLA alleles are discovered. SSOP genotyping identifies the alleles present but limitations include ambiguities and underreporting less common alleles. Our data show that HLA typing by NGS is superior to the existing clinical methods for identifying HLA alleles associated with disease or drug hypersensitivity, and offers a viable approach for high volume clinical diagnostic laboratories.
Collapse
Affiliation(s)
- Tracie Profaizer
- ARUP Institute for Clinical and Experimental Pathology, United States.
| | - Ann Pole
- Histocompatibility & Immunogenetics Laboratory, University of Utah Health, Salt Lake City, UT 84108, United States.
| | - Cassandra Monds
- ARUP Institute for Clinical and Experimental Pathology, United States.
| | - Julio C Delgado
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84108, United States.
| | - Eszter Lázár-Molnár
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84108, United States.
| |
Collapse
|
15
|
Jawdat D, Mohammadi M, Haneef L, Alaskar AS, Hajeer AH. Novel HLA-C*06:284 allele, identified by next-generation sequencing in a Saudi individual. HLA 2020; 96:224-225. [PMID: 32301271 DOI: 10.1111/tan.13906] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 03/12/2020] [Accepted: 03/12/2020] [Indexed: 11/27/2022]
Abstract
HLA-C*06:284 differs from HLA-C*06:02:01:02 by two single nucleotide substitutions in codon 24 (Ser > Thr).
Collapse
Affiliation(s)
- Dunia Jawdat
- Saudi Stem Cell Donor Registry, 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
| | - Mahammad Mohammadi
- Saudi Stem Cell Donor Registry, 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
| | - Loay Haneef
- Saudi Stem Cell Donor Registry, 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
| | - Ahmed S Alaskar
- Division of Adult Hematology & HSCT, Department of Oncology, 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
| | - Ali H 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
| |
Collapse
|
16
|
Alanazi H, Alqasem A, Aloufi F, Macpherson HL, Hajeer AH. The novel HLA-DQB1*06:358 allele, identified by Next-Generation Sequencing in a Saudi individual. HLA 2019; 95:157-158. [PMID: 31664784 DOI: 10.1111/tan.13737] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 10/25/2019] [Indexed: 11/26/2022]
Abstract
HLA-DQB1*06:358 differs from HLA-DQB1*06:09:01:01 by two single nucleotide substitutions: 2949 C>T and 3001 A>T.
Collapse
Affiliation(s)
- Hanan Alanazi
- HLA Typing Lab, Department of Pathology and Laboratory Medicine, KSAU-HS, MNGHA, Riyadh, Saudi Arabia
| | - Afnan Alqasem
- HLA Typing Lab, Department of Pathology and Laboratory Medicine, KSAU-HS, MNGHA, Riyadh, Saudi Arabia
| | - Faisal Aloufi
- HLA Typing Lab, Department of Pathology and Laboratory Medicine, KSAU-HS, MNGHA, Riyadh, Saudi Arabia
| | | | - Ali H Hajeer
- HLA Typing Lab, Department of Pathology and Laboratory Medicine, KSAU-HS, MNGHA, Riyadh, Saudi Arabia
| |
Collapse
|
17
|
Alblaihed A, Alburaq M, AlSebaiheen F, Alshubaili A, Hajeer AH. A novel HLA-C null allele, HLA-C*12:299N, identified by next-generation sequencing in a Saudi individual. HLA 2019; 94:457-458. [PMID: 31397064 DOI: 10.1111/tan.13661] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 08/05/2019] [Accepted: 08/06/2019] [Indexed: 10/26/2022]
Abstract
A single nucleotide deletion in HLA-C*12:03:01:01 results in a novel null allele, HLA-C*12:299N.
Collapse
Affiliation(s)
- Asma Alblaihed
- HLA Typing Lab, Department of Pathology and Laboratory Medicine, King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), MNGHA, Riyadh, Saudi Arabia
| | - Mohammed Alburaq
- HLA Typing Lab, Department of Pathology and Laboratory Medicine, King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), MNGHA, Riyadh, Saudi Arabia
| | - Farrah AlSebaiheen
- HLA Typing Lab, Department of Pathology and Laboratory Medicine, King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), MNGHA, Riyadh, Saudi Arabia
| | - Abdullah Alshubaili
- HLA Typing Lab, Department of Pathology and Laboratory Medicine, King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), MNGHA, Riyadh, Saudi Arabia
| | - Ali H Hajeer
- HLA Typing Lab, Department of Pathology and Laboratory Medicine, King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), MNGHA, Riyadh, Saudi Arabia
| |
Collapse
|
18
|
Alqasem A, Alanazi H, Aloufi F, Alanazi A, Hajeer AH. A novel HLA‐B allele,
HLA‐B*44:03:01:19
, identified by next‐generation sequencing in a Saudi individual. HLA 2019; 94:381-382. [DOI: 10.1111/tan.13618] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 06/17/2019] [Accepted: 06/17/2019] [Indexed: 12/01/2022]
Affiliation(s)
- Afnan Alqasem
- HLA Typing Lab, Department of Pathology and Laboratory MedicineKSAU‐HS, MNGHA Riyadh Saudi Arabia
| | - Hanan Alanazi
- HLA Typing Lab, Department of Pathology and Laboratory MedicineKSAU‐HS, MNGHA Riyadh Saudi Arabia
| | - Faisal Aloufi
- HLA Typing Lab, Department of Pathology and Laboratory MedicineKSAU‐HS, MNGHA Riyadh Saudi Arabia
| | - Aisha Alanazi
- HLA Typing Lab, Department of Pathology and Laboratory MedicineKSAU‐HS, MNGHA Riyadh Saudi Arabia
| | - Ali H. Hajeer
- HLA Typing Lab, Department of Pathology and Laboratory MedicineKSAU‐HS, MNGHA Riyadh Saudi Arabia
| |
Collapse
|
19
|
Alburaq M, AlSebaiheen F, Alblaihed A, Alshubaili A, Hajeer AH. A novel HLA-B allele, HLA-B*08:242, identified by next-generation sequencing in a Saudi individual. HLA 2019; 94:375-376. [PMID: 31218830 DOI: 10.1111/tan.13617] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 06/17/2019] [Accepted: 06/17/2019] [Indexed: 11/30/2022]
Abstract
HLA-B*08:242 differs from HLA-B*08:01:01:01 in codons 33 and 36 of exon 2.
Collapse
Affiliation(s)
- Mohammed Alburaq
- HLA Typing Lab, Department of Pathology and Laboratory Medicine, KSAU-HS, MNGHA, Riyadh, Saudi Arabia
| | - Farrah AlSebaiheen
- HLA Typing Lab, Department of Pathology and Laboratory Medicine, KSAU-HS, MNGHA, Riyadh, Saudi Arabia
| | - Asma Alblaihed
- HLA Typing Lab, Department of Pathology and Laboratory Medicine, KSAU-HS, MNGHA, Riyadh, Saudi Arabia
| | - Abdullah Alshubaili
- HLA Typing Lab, Department of Pathology and Laboratory Medicine, KSAU-HS, MNGHA, Riyadh, Saudi Arabia
| | - Ali H Hajeer
- HLA Typing Lab, Department of Pathology and Laboratory Medicine, KSAU-HS, MNGHA, Riyadh, Saudi Arabia
| |
Collapse
|
20
|
Alanazi A, Alburaq M, Alblaihed A, AlSebaiheen F, Alshubaili A. Identification of the novel
HLA‐B*37:87
allele in a Saudi individual. HLA 2019; 94:158-159. [DOI: 10.1111/tan.13556] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 04/19/2019] [Indexed: 12/23/2022]
Affiliation(s)
- Aisha Alanazi
- HLA Typing LabDepartment of Pathology and Laboratory Medicine, KSAU‐HS, MNGHA Riyadh Saudi Arabia
| | - Mohammed Alburaq
- HLA Typing LabDepartment of Pathology and Laboratory Medicine, KSAU‐HS, MNGHA Riyadh Saudi Arabia
| | - Asma Alblaihed
- HLA Typing LabDepartment of Pathology and Laboratory Medicine, KSAU‐HS, MNGHA Riyadh Saudi Arabia
| | - Farrah AlSebaiheen
- HLA Typing LabDepartment of Pathology and Laboratory Medicine, KSAU‐HS, MNGHA Riyadh Saudi Arabia
| | - Abdullah Alshubaili
- HLA Typing LabDepartment of Pathology and Laboratory Medicine, KSAU‐HS, MNGHA Riyadh Saudi Arabia
| |
Collapse
|
21
|
Wang W, Wang F, You X, He J, Zhu F. Identification of the novel HLA-C*12:220 allele in a Chinese individual. HLA 2019; 94:80-81. [PMID: 30953389 DOI: 10.1111/tan.13548] [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: 04/03/2019] [Revised: 04/03/2019] [Accepted: 04/04/2019] [Indexed: 12/12/2022]
Abstract
The new allele HLA-C*12:220 differs from HLA-C*12:03:01:01 by one nucleotide substitution in exon 7.
Collapse
Affiliation(s)
- Wei Wang
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, Zhejiang Province, China.,HLA Typing Laboratory, Key Laboratory of Blood Safety Research, Hangzhou, Zhejiang Province, China
| | - Fang Wang
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, Zhejiang Province, China.,HLA Typing Laboratory, Key Laboratory of Blood Safety Research, Hangzhou, Zhejiang Province, China
| | - Xuan You
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, Zhejiang Province, China.,HLA Typing Laboratory, Key Laboratory of Blood Safety Research, Hangzhou, Zhejiang Province, China
| | - Ji He
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, Zhejiang Province, China.,HLA Typing Laboratory, Key Laboratory of Blood Safety Research, Hangzhou, Zhejiang Province, China
| | - Faming Zhu
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, Zhejiang Province, China.,HLA Typing Laboratory, Key Laboratory of Blood Safety Research, Hangzhou, Zhejiang Province, China
| |
Collapse
|
22
|
Aloufi F, Gattan M, Alanazi H, Alqasem A, Hajeer AH. Identification of the novel
HLA‐DRB5*02:21
allele in a Saudi individual. HLA 2019; 93:507-508. [DOI: 10.1111/tan.13507] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 02/21/2019] [Accepted: 02/21/2019] [Indexed: 10/27/2022]
Affiliation(s)
- Faisal Aloufi
- HLA Typing Lab, Department of Pathology and Laboratory MedicineKSAU‐HS, MNGHA Riyadh Saudi Arabia
| | - Manal Gattan
- HLA Typing Lab, Department of Pathology and Laboratory MedicineKSAU‐HS, MNGHA Riyadh Saudi Arabia
| | - Hanan Alanazi
- HLA Typing Lab, Department of Pathology and Laboratory MedicineKSAU‐HS, MNGHA Riyadh Saudi Arabia
| | - Afnan Alqasem
- HLA Typing Lab, Department of Pathology and Laboratory MedicineKSAU‐HS, MNGHA Riyadh Saudi Arabia
| | - Ali H. Hajeer
- HLA Typing Lab, Department of Pathology and Laboratory MedicineKSAU‐HS, MNGHA Riyadh Saudi Arabia
| |
Collapse
|
23
|
He Y, Wang W, You X, He J, Faming Z. Characterization of the novel HLA-C*08:159 allele by next-generation sequencing. HLA 2019; 93:502-503. [PMID: 30790477 DOI: 10.1111/tan.13500] [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: 02/12/2019] [Revised: 02/18/2019] [Accepted: 02/19/2019] [Indexed: 12/28/2022]
Abstract
HLA-C*08:159 differs from HLA-C*08:02:01:01 by one nucleotide substitution at codon 219 in exon 4.
Collapse
Affiliation(s)
- Yanmin He
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, China.,HLA Typing Laboratory, Key Laboratory of Blood Safety Research, Hangzhou, China
| | - Wei Wang
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, China.,HLA Typing Laboratory, Key Laboratory of Blood Safety Research, Hangzhou, China
| | - Xuan You
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, China.,HLA Typing Laboratory, Key Laboratory of Blood Safety Research, Hangzhou, China
| | - Ji He
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, China.,HLA Typing Laboratory, Key Laboratory of Blood Safety Research, Hangzhou, China
| | - Zhu Faming
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, China.,HLA Typing Laboratory, Key Laboratory of Blood Safety Research, Hangzhou, China
| |
Collapse
|
24
|
Gattan M, Aloufi F, Alanazi H, Alqasem A, Hajeer AH. Identification of the novel HLA-A*30:02:01:04 allele in a Saudi individual. HLA 2018; 93:103-104. [PMID: 30471209 DOI: 10.1111/tan.13433] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 11/21/2018] [Accepted: 11/21/2018] [Indexed: 11/28/2022]
Abstract
HLA-A*30:02:01:04 differs from HLA-A*30:02:01:01 by a single nucleotide substitution (G ➔ C) at position 3222.
Collapse
Affiliation(s)
- Manal Gattan
- HLA Typing Lab, Department of Pathology and Laboratory Medicine, King Saud bin Abdulaziz University for Health Sciences, MNGHA, Riyadh, Saudi Arabia
| | - Faisal Aloufi
- HLA Typing Lab, Department of Pathology and Laboratory Medicine, King Saud bin Abdulaziz University for Health Sciences, MNGHA, Riyadh, Saudi Arabia
| | - Hanan Alanazi
- HLA Typing Lab, Department of Pathology and Laboratory Medicine, King Saud bin Abdulaziz University for Health Sciences, MNGHA, Riyadh, Saudi Arabia
| | - Afnan Alqasem
- HLA Typing Lab, Department of Pathology and Laboratory Medicine, King Saud bin Abdulaziz University for Health Sciences, MNGHA, Riyadh, Saudi Arabia
| | - Ali H Hajeer
- HLA Typing Lab, Department of Pathology and Laboratory Medicine, King Saud bin Abdulaziz University for Health Sciences, MNGHA, Riyadh, Saudi Arabia
| |
Collapse
|