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Lai SK, Luo AC, Chiu IH, Chuang HW, Chou TH, Hung TK, Hsu JS, Chen CY, Yang WS, Yang YC, Chen PL. A novel framework for human leukocyte antigen (HLA) genotyping using probe capture-based targeted next-generation sequencing and computational analysis. Comput Struct Biotechnol J 2024; 23:1562-1571. [PMID: 38650588 PMCID: PMC11035020 DOI: 10.1016/j.csbj.2024.03.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 03/20/2024] [Accepted: 03/31/2024] [Indexed: 04/25/2024] Open
Abstract
Human leukocyte antigen (HLA) genes play pivotal roles in numerous immunological applications. Given the immense number of polymorphisms, achieving accurate high-throughput HLA typing remains challenging. This study aimed to harness the human pan-genome reference consortium (HPRC) resources as a potential benchmark for HLA reference materials. We meticulously annotated specific four field-resolution alleles for 11 HLA genes (HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, -DRB1, -DRB3, -DRB4 and -DRB5) from 44 high-quality HPRC personal genome assemblies. For sequencing, we crafted HLA-specific probes and conducted capture-based targeted sequencing of the genomic DNA of the HPRC cohort, ensuring focused and comprehensive coverage of the HLA region of interest. We used publicly available short-read whole-genome sequencing (WGS) data from identical samples to offer a comparative perspective. To decipher the vast amount of sequencing data, we employed seven distinct software tools: OptiType, HLA-VBseq, HISAT genotype, SpecHLA, T1K, QzType, and DRAGEN. Each tool offers unique capabilities and algorithms for HLA genotyping, allowing comprehensive analysis and validation of the results. We then compared these results with benchmarks derived from personal genome assemblies. Our findings present a comprehensive four-field-resolution HLA allele annotation for 44 HPRC samples. Significantly, our innovative targeted next-generation sequencing (NGS) approach for HLA genes showed superior accuracy compared with conventional short-read WGS. An integrated analysis involving QzType, T1K, and DRAGEN was developed, achieving 100% accuracy for all 11 HLA genes. In conclusion, our study highlighted the combination of targeted short-read sequencing and astute computational analysis as a robust approach for HLA genotyping. Furthermore, the HPRC cohort has emerged as a valuable assembly-based reference in this realm.
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Affiliation(s)
- Sheng-Kai Lai
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, Taiwan
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Allen Chilun Luo
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - I-Hsuan Chiu
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Hui-Wen Chuang
- Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ting-Hsuan Chou
- Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Tsung-Kai Hung
- Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Jacob Shujui Hsu
- Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chien-Yu Chen
- Department of Biomechatronics Engineering, National Taiwan University, Taipei, Taiwan
| | - Wei-Shiung Yang
- Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
- Division of Endocrinology and Metabolism, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Ya-Chien Yang
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Pei-Lung Chen
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, Taiwan
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
- Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
- Division of Endocrinology and Metabolism, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
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2
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Yao H, Wang K, Lu S, Cao F, Dai P. Development of an ARMS multiplex real-time PCR assay for the detection of HLA-B*13:01 genotype by detecting highly specific SNPs. Pharmacogenet Genomics 2024; 34:53-59. [PMID: 38050734 DOI: 10.1097/fpc.0000000000000517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/06/2023]
Abstract
OBJECTIVES HLA-B*13:01 was strongly associated with Dapsone Hypersensitivity Syndrome (DHS). This study aimed to develop and validate a rapid and economical method for HLA-B*13:01 genotyping. METHODS Two tubes multiplex real-time PCR detection system comprising amplification refractory mutation system primers and TaqMan probes was established for HLA-B*13:01 genotyping. Sequence-based typing was applied to validate the accuracy of the assay. RESULTS The accuracy of the assay was 100% for HLA-B*13:01 genotyping. The detection limit of the new method was 0.025 ng DNA. The positive rate of HLA-B*13:01 in the Bouyei (20%, n = 50) populations was significantly higher than that in the Uighur population (4%, n = 100), Han (4.5%, n = 200), and Tibetan (1%, n = 100) ( P < 0.05). CONCLUSION The proposed method is rapid and reliable for HLA-B*13:01 screening in a clinical setting.
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Affiliation(s)
- Hao Yao
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University of Xi'an
| | - Kaixuan Wang
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University of Xi'an
| | - Sihai Lu
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University of Xi'an
| | - Fang Cao
- Department of Clinical Pharmacy, Shaanxi Provincial Cancer Hospital, Shaanxi Province, China
| | - Penggao Dai
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University of Xi'an
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3
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Wang F, Li W, Wang X, Luo X, Dai P. A single-tube multiplex real-time PCR for HLA-B*38:02 genotype by detecting highly specific SNPs. Pharmacogenomics 2023; 24:5-14. [PMID: 36661044 DOI: 10.2217/pgs-2022-0132] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Purpose: HLA-B*38:02 is closely related to carbimazole/methimazole-induced agranulocytosis. This study aimed to develop and validate a rapid and economical method for HLA-B*38:02 genotyping. Methods: A single-tube multiplex real-time PCR detection system comprising amplification refractory mutation system primers and TaqMan probes was established for HLA-B*38:02 genotyping. Sequence-based typing was applied to validate the accuracy of the assay. Results: The accuracy of the assay was 100% for HLA-B*38:02 genotyping. The detection limit of the new method was 0.05 ng DNA. The positive rate of HLA-B*38:02 in the Han (8%, n = 100), Bouyei (17.8%, n = 90) and Tibetan (12.7%, n = 110) populations was significantly higher than that in the Uighur population (1%, n = 100) (p < 0.05). Conclusion: The proposed method is rapid and reliable for HLA-B*38:02 screening in a clinical setting.
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Affiliation(s)
- Fei Wang
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University of Xi'an, Shaanxi Province, 710069, China
| | - Wenqi Li
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University of Xi'an, Shaanxi Province, 710069, China
| | - Xuan Wang
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University of Xi'an, Shaanxi Province, 710069, China
| | - Xiang Luo
- Department of Respiratory, Tongchuan People's Hospital Tongchuan, Shaanxi Province, People's Republic of China
| | - Penggao 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
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4
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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.
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5
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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: 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
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.
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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
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Yang J, Liu H, Pan W, Song M, Lu Y, Wang-Ngai Chow F, Hang-Mei Leung P, Deng Y, Hori M, He N, Li S. Recent Advances of Human Leukocyte Antigen (HLA) Typing Technology Based on High-Throughput Sequencing. J Biomed Nanotechnol 2022; 18:617-639. [PMID: 35715925 DOI: 10.1166/jbn.2022.3280] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The major histocompatibility complex (MHC) in humans is a genetic region consisting of cell surface proteins located on the short arm of chromosome 6. This is also known as the human leukocyte antigen (HLA) region. The HLA region consists of genes that exhibit complex genetic polymorphisms, and are extensively involved in immune responses. Each individual has a unique set of HLAs. Donor-recipient HLA allele matching is an important factor for organ transplantation. Therefore, an established rapid and accurate HLA typing technology is instrumental to preventing graft-verses-host disease (GVHD) in organ recipients. As of recent, high-throughput sequencing has allowed for an increase read length and higher accuracy and throughput, thus achieving complete and high-resolution full-length typing. With more advanced nanotechnology used in high-throughput sequencing, HLA typing is more widely used in third-generation single-molecule sequencing. This review article summarizes some of the most widely used sequencing typing platforms and evaluates the latest developments in HLA typing kits and their clinical applications.
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Affiliation(s)
- Jin Yang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, Hunan, China
| | - Hongna Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, Hunan, China
| | - Wenjing Pan
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, Hunan, China
| | - Mengru Song
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, Hunan, China
| | - Yutong Lu
- School of Electrical and Information Engineering, Hunan University, Changsha 410012, Hunan, China
| | - Franklin Wang-Ngai Chow
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Polly Hang-Mei Leung
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Yan Deng
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, Hunan, China
| | - Masahi Hori
- 2-16-5 Edagawa, Koto-Ku, Tokyo, 135-0051, Japan
| | - Nongyue He
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, Hunan, China
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, Hunan, China
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Gededzha MP, Mampeule N, Gandini A, Mayne ES. SARS-CoV-2 Host Immunogenetic Biomarkers. Methods Mol Biol 2022; 2511:133-147. [PMID: 35838957 DOI: 10.1007/978-1-0716-2395-4_10] [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] [Indexed: 06/15/2023]
Abstract
SARS-CoV-2 causes generally mild symptoms, with approximately 10-20% of cases progressing to severe disease. The pathophysiologic mechanisms by which SARS-CoV-2 causes severe disease are largely unknown. Data have indicated the involvement of different immunogenetic markers such as HLA, T, and B cells, to be associated with disease outcome. This has led to interest in these genes as potential biomarkers of SARS-CoV-2 susceptibility and for predicting prognosis and response to vaccines and other therapeutic strategies. In this chapter, we discussed outline protocols for characterizing these potential biomarkers and methods for identifying SARS-CoV-2 biomarkers using the Luminex® 100/200 technology and next-generation sequencing.
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Affiliation(s)
- Maemu P Gededzha
- Department of Immunology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
- National Health Laboratory Services, Johannesburg, South Africa.
| | - Nakampe Mampeule
- Department of Immunology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- National Health Laboratory Services, Johannesburg, South Africa
| | - Anastasia Gandini
- Department of Immunology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- National Health Laboratory Services, Johannesburg, South Africa
| | - Elizabeth S Mayne
- Department of Immunology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- National Health Laboratory Services, Johannesburg, South Africa
- Division of Immunology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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8
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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.
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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.
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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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10
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Frick R, Høydahl LS, Petersen J, du Pré MF, Kumari S, Berntsen G, Dewan AE, Jeliazkov JR, Gunnarsen KS, Frigstad T, Vik ES, Llerena C, Lundin KEA, Yaqub S, Jahnsen J, Gray JJ, Rossjohn J, Sollid LM, Sandlie I, Løset GÅ. A high-affinity human TCR-like antibody detects celiac disease gluten peptide-MHC complexes and inhibits T cell activation. Sci Immunol 2021; 6:6/62/eabg4925. [PMID: 34417258 DOI: 10.1126/sciimmunol.abg4925] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 07/22/2021] [Indexed: 12/12/2022]
Abstract
Antibodies specific for peptides bound to human leukocyte antigen (HLA) molecules are valuable tools for studies of antigen presentation and may have therapeutic potential. Here, we generated human T cell receptor (TCR)-like antibodies toward the immunodominant signature gluten epitope DQ2.5-glia-α2 in celiac disease (CeD). Phage display selection combined with secondary targeted engineering was used to obtain highly specific antibodies with picomolar affinity. The crystal structure of a Fab fragment of the lead antibody 3.C11 in complex with HLA-DQ2.5:DQ2.5-glia-α2 revealed a binding geometry and interaction mode highly similar to prototypic TCRs specific for the same complex. Assessment of CeD biopsy material confirmed disease specificity and reinforced the notion that abundant plasma cells present antigen in the inflamed CeD gut. Furthermore, 3.C11 specifically inhibited activation and proliferation of gluten-specific CD4+ T cells in vitro and in HLA-DQ2.5 humanized mice, suggesting a potential for targeted intervention without compromising systemic immunity.
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Affiliation(s)
- Rahel Frick
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway.,Centre for Immune Regulation and Department of Biosciences, University of Oslo, Oslo, Norway
| | - Lene S Høydahl
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway.,Centre for Immune Regulation and Department of Biosciences, University of Oslo, Oslo, Norway.,KG Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
| | - Jan Petersen
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.,Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
| | - M Fleur du Pré
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway.,KG Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
| | | | | | - Alisa E Dewan
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway.,KG Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
| | | | - Kristin S Gunnarsen
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway.,Centre for Immune Regulation and Department of Biosciences, University of Oslo, Oslo, Norway
| | | | | | - Carmen Llerena
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Knut E A Lundin
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway.,KG Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway.,Department of Gastroenterology, Oslo University Hospital-Rikshospitalet, Oslo, Norway
| | - Sheraz Yaqub
- Department of Gastrointestinal Surgery, Oslo University Hospital-Rikshospitalet, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Jørgen Jahnsen
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway
| | - Jeffrey J Gray
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, USA.,Department of Chemical and Biomolecular Engineering and Institute of NanoBioTechnology, Johns Hopkins University, Baltimore, MD, USA.,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Jamie Rossjohn
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.,Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia.,Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - Ludvig M Sollid
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway.,KG Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
| | - Inger Sandlie
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway.,Centre for Immune Regulation and Department of Biosciences, University of Oslo, Oslo, Norway
| | - Geir Åge Løset
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway. .,Centre for Immune Regulation and Department of Biosciences, University of Oslo, Oslo, Norway.,Nextera AS, Oslo, Norway
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11
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Baek IC, Choi EJ, Shin DH, Kim HJ, Choi H, Kim TG. Allele and haplotype frequencies of human leukocyte antigen-A, -B, -C, -DRB1, -DRB3/4/5, -DQA1, -DQB1, -DPA1, and -DPB1 by next generation sequencing-based typing in Koreans in South Korea. PLoS One 2021; 16:e0253619. [PMID: 34153078 PMCID: PMC8216545 DOI: 10.1371/journal.pone.0253619] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 06/08/2021] [Indexed: 11/18/2022] Open
Abstract
Allele frequencies and haplotype frequencies of HLA-A, -B, -C, -DRB1, -DRB3/4/5, -DQA1, -DQB1, -DPA1, and -DPB1 have been rarely reported in South Koreans using unambiguous, phase-resolved next generation DNA sequencing. In this study, HLA typing of 11 loci in 173 healthy South Koreans were performed using next generation DNA sequencing with long-range PCR, TruSight® HLA v2 kit, Illumina MiSeqDx platform system, and Assign™ for TruSight™ HLA software. Haplotype frequencies were calculated using the PyPop software. Direct counting methods were used to investigate the association with DRB1 for samples with only one copy of a particular secondary DRB locus. We compared these allele types with the ambiguous allele combinations of the IPD-IMGT/HLA database. We identified 20, 40, 26, 31, 19, 16, 4, and 16 alleles of HLA-A, HLA-B, HLA-C, HLA-DRB1, HLA-DQA1, HLA-DQB1, HLA-DPA1, and HLA-DPB1, respectively. The number of HLA-DRB3/4/5 alleles was 4, 5, and 3, respectively. The haplotype frequencies of most common haplotypes were as follows: A*33:03:01-B*44:03:01-C*14:03-DRB1*13:02:01-DQB1*06:04:01-DPB1*04:01:01 (2.89%), A*33:03:01-B*44:03:01-C*14:03 (4.91%), DRB1*08:03:02-DQA1*01:03:01-DQB1*06:01:01-DPA1*02:02:02-DPB1*05:01:01 (5.41%), DRB1*04:05:01-DRB4*01:03:01 (12.72%), DQA1*01:03:01-DQB1*06:01:01 (13.01%), and DPA1*02:02:02-DPB1*05:01:01 (30.83%). In samples with only one copy of a specific secondary DRB locus, we examined its association with DRB1. We, thus, resolved 10 allele ambiguities in HLA-B, -C (each exon 2+3), -DRB1, -DQB1, -DQA1, and -DPB1 (each exon 2) of the IPD-IMGT/HLA database. Korean population was geographically close to Japanese and Han Chinese populations in the genetic distances by multidimensional scaling (MDS) plots. The information obtained by HLA typing of the 11 extended loci by next generation sequencing may be useful for more exact diagnostic tests on various transplantations and the genetic population relationship studies in South Koreans.
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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
| | - Dong-Hwan Shin
- 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
- * E-mail:
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12
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Kong D, Lee N, Dela Cruz ID, Dames C, Maruthamuthu S, Golden T, Rajalingam R. Concurrent typing of over 4000 samples by long-range PCR amplicon-based NGS and rSSO revealed the need to verify NGS typing for HLA allelic dropouts. Hum Immunol 2021; 82:581-587. [PMID: 33980471 DOI: 10.1016/j.humimm.2021.04.008] [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: 02/02/2021] [Revised: 04/16/2021] [Accepted: 04/28/2021] [Indexed: 10/21/2022]
Abstract
Hematopoietic stem cell transplantation (HSCT) from HLA-matched donors significantly decreases the risks of graft-rejection and graft-versus-host disease. Long-range PCR- amplicon-based next-generation sequencing (NGS) is increasingly used as a standalone method in clinical laboratories to determine HLA compatibility for HSCT and solid-organ transplantation. We hypothesized that an allelic dropout is a frequent event in the long-range PCR amplicon-based NGS HLA typing method. To test the hypothesis, we typed 4,006 samples concurrently using a commercially available long-range PCR amplicon-based NGS-typing and short exon-specific amplicon-based reverse sequence-specific oligonucleotide (rSSO) methods. The concordance between the NGS and rSSO typing results was 100% at HLA-A, -B, -C, -DRB1, -DRB3, -DRB5, -DQA1, DPA1 loci. However, 4.5% of the samples (179/4006) showed allelic-dropouts at one of the other three loci: HLA-DRB4 (3.9%), HLA-DPB1 (0.4%), and HLA-DQB1*(0.15%). The allelic-dropouts are not associated with specific haplotypes, and some dropouts can be reagent lot-specific. Although DRB1-DRB3/4/5-DQB1 linkages help to diagnose these allelic-dropouts in some cases, the rSSO typing was crucial to identify the dropouts in DQB1 and DPB1 loci. These results uncover the critical limitations of using long-range PCR amplicon-based NGS as a standalone method in clinical histocompatibility laboratories and advocate the need for strategies to diagnose and resolve allelic-dropouts.
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Affiliation(s)
- Denice Kong
- Immunogenetics and Transplantation Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Nancy Lee
- Immunogenetics and Transplantation Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Imma Donna Dela Cruz
- Immunogenetics and Transplantation Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Charlyn Dames
- Immunogenetics and Transplantation Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Stalinraja Maruthamuthu
- Immunogenetics and Transplantation Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Todd Golden
- Immunogenetics and Transplantation Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Raja Rajalingam
- Immunogenetics and Transplantation Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA, USA.
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13
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McCowin SE, Moreau GB, Haque R, Noble JA, McDevitt SL, Donowitz JR, Alam MM, Kirkpatrick BD, Petri WA, Marie C. HLA class I and II associations with common enteric pathogens in the first year of life. EBioMedicine 2021; 67:103346. [PMID: 33910121 PMCID: PMC8093888 DOI: 10.1016/j.ebiom.2021.103346] [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: 02/04/2021] [Revised: 03/24/2021] [Accepted: 03/31/2021] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND genetic susceptibility to infection is mediated by numerous host factors, including the highly diverse, classical human leukocyte antigen (HLA) genes, which are critical genetic determinants of immunity. We systematically evaluated the effect of HLA alleles and haplotypes on susceptibility to 12 common enteric infections in children during the first year of life in an urban slum of Dhaka, Bangladesh. METHODS a birth cohort of 601 Bangladeshi infants was prospectively monitored for diarrhoeal disease. Each diarrhoeal stool sample was analyzed for enteric pathogens by multiplex TaqMan Array Card (TAC). High resolution genotyping of HLA class I (A and B) and II (DRB1, DQA1, and DQB1) genes was performed by next-generation sequencing. We compared the frequency of HLA alleles and haplotypes between infected and uninfected children. FINDINGS we identified six individual allele associations and one five-locus haplotype association. One allele was associated with protection: A*24:02 - EAEC. Five alleles were associated with increased risk: A*24:17 - typical EPEC, B*15:01 - astrovirus, B*38:02 - astrovirus, B*38:02 - Cryptosporidium and DQA1*01:01 - Cryptosporidium. A single five-locus haplotype was associated with protection: A*11:01~B*15:02~DRB1*12:02~DQA1*06:01~DQB1*03:01- adenovirus 40/41. INTERPRETATION our findings suggest a role for HLA in susceptibility to early enteric infection for five pathogens. Understanding the genetic contribution of HLA in susceptibility has important implications in vaccine design and understanding regional differences in incidence of enteric infection. FUNDING this research was supported by the National Institute of Health (NIH) and the Bill and Melinda Gates Foundation.
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Affiliation(s)
- Sayo E. McCowin
- Department of Medicine, Infectious Diseases and International Health, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - G. Brett Moreau
- International Centre for Diarrhoeal Diseases and Research, Dhaka, Bangladesh
| | - Rashidul Haque
- International Centre for Diarrhoeal Diseases and Research, Dhaka, Bangladesh
| | - Janelle A. Noble
- Department of Paediatrics, UCSF School of Medicine, San Francisco, CA, USA
| | - Shana L. McDevitt
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Jeffrey R. Donowitz
- Children's Hospital of Richmond at Virginia Commonwealth University, Richmond, VA, USA
| | - Md Masud Alam
- Department of Medicine, Infectious Diseases and International Health, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Beth D. Kirkpatrick
- Department of Microbiology and Molecular Genetics, University of Vermont College of Medicine, Burlington, VT, USA
| | - William A. Petri
- Department of Medicine, Infectious Diseases and International Health, University of Virginia School of Medicine, Charlottesville, VA, USA.,Department of Pathology, University of Virginia School of Medicine, Charlottesville, VA, USA.,Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Chelsea Marie
- Department of Medicine, Infectious Diseases and International Health, University of Virginia School of Medicine, Charlottesville, VA, USA.,Corresponding author.
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14
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Hu T, Chitnis N, Monos D, Dinh A. Next-generation sequencing technologies: An overview. Hum Immunol 2021; 82:801-811. [PMID: 33745759 DOI: 10.1016/j.humimm.2021.02.012] [Citation(s) in RCA: 193] [Impact Index Per Article: 64.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/18/2021] [Accepted: 02/23/2021] [Indexed: 12/14/2022]
Abstract
Since the days of Sanger sequencing, next-generation sequencing technologies have significantly evolved to provide increased data output, efficiencies, and applications. These next generations of technologies can be categorized based on read length. This review provides an overview of these technologies as two paradigms: short-read, or "second-generation," technologies, and long-read, or "third-generation," technologies. Herein, short-read sequencing approaches are represented by the most prevalent technologies, Illumina and Ion Torrent, and long-read sequencing approaches are represented by Pacific Biosciences and Oxford Nanopore technologies. All technologies are reviewed along with reported advantages and disadvantages. Until recently, short-read sequencing was thought to provide high accuracy limited by read-length, while long-read technologies afforded much longer read-lengths at the expense of accuracy. Emerging developments for third-generation technologies hold promise for the next wave of sequencing evolution, with the co-existence of longer read lengths and high accuracy.
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Affiliation(s)
- Taishan Hu
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Nilesh Chitnis
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, United States; Department of Surgery, Baylor College of Medicine, Houston, TX, United States
| | - Dimitri Monos
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, United States; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.
| | - Anh Dinh
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, United States; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.
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15
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New challenges, new opportunities: Next generation sequencing and its place in the advancement of HLA typing. Hum Immunol 2021; 82:478-487. [PMID: 33551127 DOI: 10.1016/j.humimm.2021.01.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 12/29/2020] [Accepted: 01/18/2021] [Indexed: 02/07/2023]
Abstract
The Human Leukocyte Antigen (HLA) system has a critical role in immunorecognition, transplantation, and disease association. Early typing techniques provided the foundation for genotyping methods that revealed HLA as one of the most complex, polymorphic regions of the human genome. Next Generation Sequencing (NGS), the latest molecular technology introduced in clinical tissue typing laboratories, has demonstrated advantages over other established methods. NGS offers high-resolution sequencing of entire genes in time frames and price points considered unthinkable just a few years ago, contributing a wealth of data informing histocompatibility assessment and standards of clinical care. Although the NGS platforms share a high-throughput massively parallel processing model, differing chemistries provide specific strengths and weaknesses. Research-oriented Third Generation Sequencing and related advances in bioengineering continue to broaden the future of NGS in clinical settings. These diverse applications have demanded equally innovative strategies for data management and computational bioinformatics to support and analyze the unprecedented volume and complexity of data generated by NGS. We discuss some of the challenges and opportunities associated with NGS technologies, providing a comprehensive picture of the historical developments that paved the way for the NGS revolution, its current state and future possibilities for HLA typing.
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16
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Baek IC, Choi EJ, Shin DH, Kim HJ, Choi H, Kim TG. Distributions of HLA-A, -B, and -DRB1 alleles typed by amplicon-based next generation sequencing in Korean volunteer donors for unrelated hematopoietic stem cell transplantation. HLA 2021; 97:112-126. [PMID: 33179442 DOI: 10.1111/tan.14134] [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: 04/24/2020] [Revised: 09/23/2020] [Accepted: 11/04/2020] [Indexed: 01/20/2023]
Abstract
HLA genes play a pivotal role for successful hematopoietic stem cell transplantation (HSCT). There is an increasing need for sophisticated screening of donor HLA genotypes for unrelated HSCT. Next generation sequencing (NGS) has emerged as an alternative for classical Sanger sequence for HLA typing. In this study, HLA-A, -B, and -DRB1 alleles were genotyped at the allelic (6-digit) level using MiSeqDx in 26,202 volunteers from the Korean Network for Organ Sharing. Exon 2 and 3 of HLA-A and -B and exon 2 of HLA-DRB1 were amplified by polymerase chain reaction (PCR) and each allele was determined by matching the targeted exons and the reference sequence consisting of the IPD-IMGT/HLA Database. Seventy alleles of HLA-A, 102 alleles of HLA-B, and 69 alleles of HLA-DRB1 were identified. According to common and well-documented catalogs, 34 alleles in HLA-A, 61 in HLA-B, and 45 in HLA-DRB1 locus were common alleles, and 12, 14, and 11 kinds, were well-documented alleles, respectively. Thirteen novel alleles including 3 alleles in HLA-A, 8 alleles in HLA-B, and 2 alleles in HLA-DRB1 loci were found. Ten haplotypes with a frequency of more than 1.0% accounted for 22.4% of the total haplotype frequencies. Cis/trans ambiguities of HLA-A and -B loci by combination of exons 2 and 3 were analyzed to be 0.17% of 3 and 3.95% of 22 genotypes, respectively. This information on rare and novel alleles found by accurate HLA typing with NGS may be helpful for unrelated HSCT among Koreans.
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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
| | - Dong-Hwan Shin
- 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
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17
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Ingrassia F, Pecoraro A, Blando M, Bruno F, Lo Brutto A, Mistretta S, Bavetta R, Cappuzzo V. Identification of a single nucleotide deletion in the novel HLA-DQB1*06:379N allele, detected by Polymerase Chain Reaction-Sequence Based Typing but not by Next Generation Sequencing. HLA 2020; 96:709-713. [PMID: 33006267 DOI: 10.1111/tan.14083] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/09/2020] [Accepted: 09/28/2020] [Indexed: 12/17/2022]
Abstract
In this report we describe the characterization of a novel null HLA-DQB1 allele, detected by polymerase chain reaction-sequence-based typing but not by next-generation sequencing (NGS). The new allele, HLA-DQB1*06:379N, was discovered in an Italian patient with acute myeloid leukemia and also in one of her healthy siblings. The new allele is largely homologous to DQB1*06:02:01:01 with a T deletion in exon 2, in codon 11, which causes a frameshift and the formation of an unusual and premature TGA STOP in codon 27. This case report underlines the importance of not removing Sanger method sequencing from routine use for high-resolution HLA typing, but to maintain it together with NGS technology.
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Affiliation(s)
- Francesco Ingrassia
- Laboratorio Regionale di Tipizzazione Tessutale ed Immunologia dei Trapianti, U.O.C. Medicina Trasfusionale e dei Trapianti-A.O.R. Villa Sofia-Cervello, Palermo, Italy
| | - Alice Pecoraro
- Laboratorio Regionale di Tipizzazione Tessutale ed Immunologia dei Trapianti, U.O.C. Medicina Trasfusionale e dei Trapianti-A.O.R. Villa Sofia-Cervello, Palermo, Italy
| | - Maria Blando
- Laboratorio Regionale di Tipizzazione Tessutale ed Immunologia dei Trapianti, U.O.C. Medicina Trasfusionale e dei Trapianti-A.O.R. Villa Sofia-Cervello, Palermo, Italy
| | - Floriana Bruno
- Laboratorio Regionale di Tipizzazione Tessutale ed Immunologia dei Trapianti, U.O.C. Medicina Trasfusionale e dei Trapianti-A.O.R. Villa Sofia-Cervello, Palermo, Italy
| | - Angela Lo Brutto
- Laboratorio Regionale di Tipizzazione Tessutale ed Immunologia dei Trapianti, U.O.C. Medicina Trasfusionale e dei Trapianti-A.O.R. Villa Sofia-Cervello, Palermo, Italy
| | - Serena Mistretta
- Laboratorio Regionale di Tipizzazione Tessutale ed Immunologia dei Trapianti, U.O.C. Medicina Trasfusionale e dei Trapianti-A.O.R. Villa Sofia-Cervello, Palermo, Italy
| | - Rosalba Bavetta
- Laboratorio Regionale di Tipizzazione Tessutale ed Immunologia dei Trapianti, U.O.C. Medicina Trasfusionale e dei Trapianti-A.O.R. Villa Sofia-Cervello, Palermo, Italy
| | - Valentina Cappuzzo
- Laboratorio Regionale di Tipizzazione Tessutale ed Immunologia dei Trapianti, U.O.C. Medicina Trasfusionale e dei Trapianti-A.O.R. Villa Sofia-Cervello, Palermo, Italy
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18
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Geretz A, Cofer L, Ehrenberg PK, Currier JR, Yoon IK, Alera MTP, Jarman R, Rothman AL, Thomas R. Next-generation sequencing of 11 HLA loci in a large dengue vaccine cohort from the Philippines. Hum Immunol 2020; 81:437-444. [PMID: 32654962 DOI: 10.1016/j.humimm.2020.06.010] [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] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 05/27/2020] [Accepted: 06/17/2020] [Indexed: 01/25/2023]
Abstract
HLA genotyping by next-generation sequencing (NGS) has evolved with significant advancements in the last decade. Here we describe full-length HLA genotyping of 11 loci in 612 individuals comprising a dengue vaccine cohort from Cebu province in the Philippines. The multi-locus individual tagging NGS (MIT-NGS) method that we developed initially for genotyping 4-6 loci in one MiSeq run was expanded to 11 loci including HLA-A, B, C, DPA1, DPB1, DQA1, DQB1, DRB1, and DRB3/4/5. This change did not affect the overall coverage or depth of the sequencing reads. HLA alleles with frequencies greater than 10% were A*11:01:01, A*24:02:01, A*24:07:01, A*34:01:01, B*38:02:01, B*15:35, B*35:05:01, C*07:02:01, C*04:01:01, DPA1*02:02:02, DPB1*05:01:01, DPB1*01:01:01, DQA1*01:02:01, DQA1*06:01:01, DQB1*05:02:01, DQB1*03:01:01, DRB1*15:02:01, DRB1*12:02:01, DRB3*03:01:03, DRB4*01:03:01, and DRB5*01:01:01. Improvements in sequencing library preparation provide uniform and even coverage across all exons and introns. This has led to a marked reduction in allele imbalance and dropout. Furthermore, including more loci, such as DRB3/4/5, decreases cross-mapping and incorrect allele assignment at the DRB1 locus. The increased number of loci sequenced for each sample does not reduce the number of samples that can be multiplexed on a single MiSeq run and is therefore more cost-efficient. We believe that such improvements will help HLA genotyping by NGS to gain momentum over other conventional methods by increasing confidence in the calls.
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Affiliation(s)
- Aviva Geretz
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Lauryn Cofer
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Philip K Ehrenberg
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Jeffrey R Currier
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - In-Kyu Yoon
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Maria T P Alera
- Philippines-AFRIMS Virology Research Unit, Cebu City, Philippines
| | - Richard Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Alan L Rothman
- Institute for Immunology and Informatics and Department of Cell and Molecular Biology, University of Rhode Island, Providence, RI, USA
| | - Rasmi Thomas
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA.
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19
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Mosbruger TL, Dinou A, Duke JL, Ferriola D, Mehler H, Pagkrati I, Damianos G, Mbunwe E, Sarmady M, Lyratzakis I, Tishkoff SA, Dinh A, Monos DS. Utilizing nanopore sequencing technology for the rapid and comprehensive characterization of eleven HLA loci; addressing the need for deceased donor expedited HLA typing. Hum Immunol 2020; 81:413-422. [PMID: 32595056 PMCID: PMC7870017 DOI: 10.1016/j.humimm.2020.06.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/03/2020] [Accepted: 06/03/2020] [Indexed: 12/12/2022]
Abstract
The comprehensive characterization of human leukocyte antigen (HLA) genomic sequences remains a challenging problem. Despite the significant advantages of next-generation sequencing (NGS) in the field of Immunogenetics, there has yet to be a single solution for unambiguous, accurate, simple, cost-effective, and timely genotyping necessary for all clinical applications. This report demonstrates the benefits of nanopore sequencing introduced by Oxford Nanopore Technologies (ONT) for HLA genotyping. Samples (n = 120) previously characterized at high-resolution three-field (HR-3F) for 11 loci were assessed using ONT sequencing paired to a single-plex PCR protocol (Holotype) and to two multiplex protocols OmniType (Omixon) and NGSgo®-MX6-1 (GenDx). The results demonstrate the potential of nanopore sequencing for delivering accurate HR-3F typing with a simple, rapid, and cost-effective protocol. The protocol is applicable to time-sensitive applications, such as deceased donor typings, enabling better assessments of compatibility and epitope analysis. The technology also allows significantly shorter turnaround time for multiple samples at a lower cost. Overall, the nanopore technology appears to offer a significant advancement over current next-generation sequencing platforms as a single solution for all HLA genotyping needs.
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Affiliation(s)
- Timothy L Mosbruger
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Amalia Dinou
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jamie L Duke
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Deborah Ferriola
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Hilary Mehler
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Ioanna Pagkrati
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Georgios Damianos
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Eric Mbunwe
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Mahdi Sarmady
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ioannis Lyratzakis
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Sarah A Tishkoff
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Anh Dinh
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Dimitri S Monos
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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20
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Moyer AM, Dukek B, Duellman P, Schneider B, Wakefield L, Skierka JM, Avula R, Bhagwate AV, Kalari KR, Kreuter JD, Goetz MP, Boughey JC, Black JL, Gandhi MJ. Concordance between predicted HLA type using next generation sequencing data generated for non-HLA purposes and clinical HLA type. Hum Immunol 2020; 81:423-429. [PMID: 32546429 DOI: 10.1016/j.humimm.2020.06.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 05/15/2020] [Accepted: 06/03/2020] [Indexed: 12/13/2022]
Abstract
We explored the feasibility of obtaining accurate HLA type using pre-existing NGS data not generated for HLA purposes. 83 exomes and 500 targeted NGS pharmacogenomic panels were analyzed using Omixon HLA Explore, OptiType, and/or HLA-Genotyper software. Results were compared against clinical HLA genotyping. 765 (94.2%) Omixon and 769 (94.7%) HLA-Genotyper of 812 germline allele calls across class I/II loci and 402 (99.5%) of 404 OptiType class I calls were concordant to the second field (i.e. HLA-A*02:01). An additional 19 (2.3%) Omixon, 39 (4.8%) HLA-Genotyper, and 2 (0.5%) OptiType allele calls were first field concordant (i.e. HLA-A*02). Using Omixon, four alleles (0.4%) were discordant and 24 (3.0%) failed to call, while 4 alleles (0.4%) were discordant using HLA-Genotyper. Tumor exomes were also evaluated and were 85.4%, 91.6%, and 100% concordant (Omixon and HLA-Genotyper with 96 alleles tested, and Optitype with 48 class I alleles, respectively). The 15 exomes and 500 pharmacogenomic panels were 100% concordant for each pharmacogenomic allele tested. This work has broad implications spanning future clinical care (pharmacogenomics, tumor response to immunotherapy, autoimmunity, etc.) and research applications.
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Affiliation(s)
- Ann M Moyer
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Brian Dukek
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Patti Duellman
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Brittany Schneider
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Laurie Wakefield
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Jennifer M Skierka
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Rajeswari Avula
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Aditya V Bhagwate
- Department of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, United States
| | - Krishna R Kalari
- Department of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, United States
| | - Justin D Kreuter
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Matthew P Goetz
- Department of Medical Oncology, Mayo Clinic, Rochester, MN, United States
| | - Judy C Boughey
- Department of Surgery, Mayo Clinic, Rochester, MN, United States
| | - John L Black
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Manish J Gandhi
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States.
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21
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Vianna R, Secco D, Hanhoerderster L, Motta J, Cardoso J, Porto LC. An
NGS
‐based
HLA
haplotype analysis and population comparison between two cities in Rio de Janeiro, Brazil. HLA 2020; 96:268-276. [DOI: 10.1111/tan.13940] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 04/10/2020] [Accepted: 05/15/2020] [Indexed: 02/02/2023]
Affiliation(s)
- Romulo Vianna
- Histocompatibility and Cryopreservation LaboratoryRio de Janeiro State University Rio de Janeiro Brazil
| | - Danielle Secco
- Histocompatibility and Cryopreservation LaboratoryRio de Janeiro State University Rio de Janeiro Brazil
| | - Leonardo Hanhoerderster
- Histocompatibility and Cryopreservation LaboratoryRio de Janeiro State University Rio de Janeiro Brazil
| | - Juliana Motta
- Histocompatibility and Cryopreservation LaboratoryRio de Janeiro State University Rio de Janeiro Brazil
| | - Juliana Cardoso
- Histocompatibility and Cryopreservation LaboratoryRio de Janeiro State University Rio de Janeiro Brazil
| | - Luís Cristóvão Porto
- Histocompatibility and Cryopreservation LaboratoryRio de Janeiro State University Rio de Janeiro Brazil
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22
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Do MD, Le LGH, Nguyen VT, Dang TN, Nguyen NH, Vu HA, Mai TP. High-Resolution HLA Typing of HLA-A, -B, -C, -DRB1, and -DQB1 in Kinh Vietnamese by Using Next-Generation Sequencing. Front Genet 2020; 11:383. [PMID: 32425978 PMCID: PMC7204072 DOI: 10.3389/fgene.2020.00383] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 03/27/2020] [Indexed: 12/19/2022] Open
Abstract
Human leukocyte antigen (HLA) genotyping displays the particular characteristics of HLA alleles and haplotype frequencies in each population. Although it is considered the current gold standard for HLA typing, high-resolution sequence-based HLA typing is currently unavailable in Kinh Vietnamese populations. In this study, high-resolution sequence-based HLA typing (3-field) was performed using an amplicon-based next-generation sequencing platform to identify the HLA-A, -B, -C, -DRB1, and -DQB1 alleles of 101 unrelated healthy Kinh Vietnamese individuals from southern Vietnam. A total of 28 HLA-A, 41 HLA-B, 21 HLA-C, 26 HLA-DRB1, and 25 HLA-DQB1 alleles were identified. The most frequently occurring HLA alleles were A∗11:01:01, B∗15:02:01, C∗07:02:01, DRB1∗12:02:01, and DQB1∗03:01:01. Haplotype calculation showed that A∗29:01:01∼B∗07:05:01, DRB1∗12:02:01∼DQB1∗3:01:01, A∗29:01:01∼C∗15:05:02∼B∗07:05:01, A∗33:03:01∼B∗58:01:01∼DRB1∗03:01:01, and A∗29:01:01∼C∗15:05:02∼B∗07:05:01∼DRB1∗10:01:01∼DQB1∗05:01:01 were the most common haplotypes in the southern Kinh Vietnamese population. Allele distribution and haplotype analyses demonstrated that the Vietnamese population shares HLA features with South-East Asians but retains unique characteristics. Data from this study will be potentially applicable in medicine and anthropology.
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Affiliation(s)
- Minh Duc Do
- Center for Molecular Biomedicine, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Linh Gia Hoang Le
- Center for Molecular Biomedicine, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Vinh The Nguyen
- Center for Molecular Biomedicine, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Tran Ngoc Dang
- Faculty of Public Health, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Nghia Hoai Nguyen
- Center for Molecular Biomedicine, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Hoang Anh Vu
- Center for Molecular Biomedicine, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Thao Phuong Mai
- Department of Physiology, Pathophysiology and Immunology, Faculty of Medicine, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
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23
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Isolation and characterization of new human carrier peptides from two important vaccine immunogens. Vaccine 2020; 38:2315-2325. [PMID: 32005537 DOI: 10.1016/j.vaccine.2020.01.065] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 01/15/2020] [Accepted: 01/21/2020] [Indexed: 02/01/2023]
Abstract
In the preparation of glycoconjugate vaccines in clinical practice, two highly immunogenic carrier proteins, CRM197 and tetanus toxoid (TT), are predominantly conjugated with the capsular polysaccharides (CPSs) of bacterial pathogens. In addition, TT has long been used as an effective vaccine to prevent tetanus. While these carrier proteins play an important role in immunogenicity and vaccine design alike, their defined human major histocompatibility complex class II (MHCII) T cell epitopes are inadequately characterized. In this current work, we use mass spectrometry to identify the peptides from these carrier proteins that are naturally processed and presented by human B cells via MHCII pathway. The MHCII-presented peptides are screened for their T cell stimulation using primary CD4+ T cells from four healthy adult donors. These combined methods reveal a subset of eleven CD4+ T cell epitopes that proliferate and stimulate human T cells with diverse MHCII allelic repertoire. Six of these peptides stand out as potential immunodominant epitopes by responding in three or more donors. Additionally, we provide evidence of these natural epitopes eliciting more significant T cell responses in donors than previously published TT peptides selected from T cell epitope screening. This study serves toward understanding carrier protein immune responses and thus enables the use of these peptides in developing novel knowledge-based vaccines to combat persisting problems in glycoconjugate vaccine design.
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24
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Kuffel A, Gray A, Nic Daeid N. Human Leukocyte Antigen alleles as an aid to STR in complex forensic DNA samples. Sci Justice 2019; 60:1-8. [PMID: 31924284 DOI: 10.1016/j.scijus.2019.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 09/09/2019] [Accepted: 09/15/2019] [Indexed: 10/25/2022]
Abstract
Human biological samples with multiple contributors remain one of the most challenging aspects of DNA typing within a forensic science context. With the increasing sensitivity of commercially available kits allowing detection of low template DNA, complex mixtures are now a standard component of forensic DNA evidence. Over the years, various methods and techniques have been developed to try to resolve the issue of mixed profiles. However, forensic DNA analysis has relied on the same markers to generate DNA profiles for the past 30 years causing considerable challenges in the deconvolution of complex mixed samples. The future of resolving complicated DNA mixtures may rely on utilising markers that have been previously applied to gene typing of non-forensic relevance. With Massively Parallel Sequencing (MPS), techniques becoming more popular and accessible even epigenetic markers have become a source of interest for forensic scientists. The aim of this review is to consider the potential of alleles from the Human Leukocyte Antigen (HLA) complex as effective forensic markers. While Massively Parallel Sequencing of HLA is routinely used in clinical laboratories in fields such as transplantation, pharmacology or population studies, there have not been any studies testing its suitability for forensic casework samples.
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Affiliation(s)
- Agnieszka Kuffel
- Leverhulme Research Centre for Forensic Science, Ewing Building, University of Dundee, Small's Lane, Dundee DD1 4HR, United Kingdom.
| | - Alexander Gray
- Leverhulme Research Centre for Forensic Science, Ewing Building, University of Dundee, Small's Lane, Dundee DD1 4HR, United Kingdom.
| | - Niamh Nic Daeid
- Leverhulme Research Centre for Forensic Science, Ewing Building, University of Dundee, Small's Lane, Dundee DD1 4HR, United Kingdom.
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25
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Glenn TC, Pierson TW, Bayona-Vásquez NJ, Kieran TJ, Hoffberg SL, Thomas IV JC, Lefever DE, Finger JW, Gao B, Bian X, Louha S, Kolli RT, Bentley KE, Rushmore J, Wong K, Shaw TI, Rothrock Jr MJ, McKee AM, Guo TL, Mauricio R, Molina M, Cummings BS, Lash LH, Lu K, Gilbert GS, Hubbell SP, Faircloth BC. Adapterama II: universal amplicon sequencing on Illumina platforms (TaggiMatrix). PeerJ 2019; 7:e7786. [PMID: 31616589 PMCID: PMC6791344 DOI: 10.7717/peerj.7786] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 08/29/2019] [Indexed: 12/26/2022] Open
Abstract
Next-generation sequencing (NGS) of amplicons is used in a wide variety of contexts. In many cases, NGS amplicon sequencing remains overly expensive and inflexible, with library preparation strategies relying upon the fusion of locus-specific primers to full-length adapter sequences with a single identifying sequence or ligating adapters onto PCR products. In Adapterama I, we presented universal stubs and primers to produce thousands of unique index combinations and a modifiable system for incorporating them into Illumina libraries. Here, we describe multiple ways to use the Adapterama system and other approaches for amplicon sequencing on Illumina instruments. In the variant we use most frequently for large-scale projects, we fuse partial adapter sequences (TruSeq or Nextera) onto the 5' end of locus-specific PCR primers with variable-length tag sequences between the adapter and locus-specific sequences. These fusion primers can be used combinatorially to amplify samples within a 96-well plate (8 forward primers + 12 reverse primers yield 8 × 12 = 96 combinations), and the resulting amplicons can be pooled. The initial PCR products then serve as template for a second round of PCR with dual-indexed iTru or iNext primers (also used combinatorially) to make full-length libraries. The resulting quadruple-indexed amplicons have diversity at most base positions and can be pooled with any standard Illumina library for sequencing. The number of sequencing reads from the amplicon pools can be adjusted, facilitating deep sequencing when required or reducing sequencing costs per sample to an economically trivial amount when deep coverage is not needed. We demonstrate the utility and versatility of our approaches with results from six projects using different implementations of our protocols. Thus, we show that these methods facilitate amplicon library construction for Illumina instruments at reduced cost with increased flexibility. A simple web page to design fusion primers compatible with iTru primers is available at: http://baddna.uga.edu/tools-taggi.html. A fast and easy to use program to demultiplex amplicon pools with internal indexes is available at: https://github.com/lefeverde/Mr_Demuxy.
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Affiliation(s)
- Travis C. Glenn
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
- Department of Genetics, University of Georgia, Athens, GA, United States of America
- Interdisciplinary Toxicology Program, University of Georgia, Athens, GA, United States of America
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States of America
| | - Todd W. Pierson
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
- Current affiliation: Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, United States of America
| | - Natalia J. Bayona-Vásquez
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States of America
| | - Troy J. Kieran
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
| | - Sandra L. Hoffberg
- Department of Genetics, University of Georgia, Athens, GA, United States of America
- Current affiliation: Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY, United States of America
| | - Jesse C. Thomas IV
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
- Current affiliation: Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Daniel E. Lefever
- Department of Veterinary Biosciences and Diagnostic Imaging, University of Georgia, Athens, GA, United States of America
- Current affiliation: Integrative Systems Biology and Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA, United States of America
| | - John W. Finger
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
- Interdisciplinary Toxicology Program, University of Georgia, Athens, GA, United States of America
- Current affiliation: Department of Biological Sciences, Auburn University, Auburn, AL, United States of America
| | - Bei Gao
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
- Current affiliation: Department of Medicine, University of California, San Diego, CA, United States of America
| | - Xiaoming Bian
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
- Current affiliation: Complex Carbohydrate Research Center and Department of Microbiology, University of Georgia, Athens, GA, United States of America
| | - Swarnali Louha
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States of America
| | - Ramya T. Kolli
- Interdisciplinary Toxicology Program, University of Georgia, Athens, GA, United States of America
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA, United States of America
- Current affiliation: Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, United States of America
| | - Kerin E. Bentley
- Department of Genetics, University of Georgia, Athens, GA, United States of America
- Current affiliation: LeafWorks Inc., Sebastopol, CA, United States of America
| | - Julie Rushmore
- School of Ecology & College of Veterinary Medicine, University of Georgia, Athens, GA, United States of America
- Current affiliation: Epicenter for Disease Dynamics, One Health Institute, School of Veterinary Medicine, University of California, Davis, CA, United States of America
| | - Kelvin Wong
- US Environmental Protection Agency, Athens, GA, United States of America
- Current affiliation: California Water Service, 1720 N First St, San Jose, CA, United States of America
| | - Timothy I. Shaw
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States of America
- US Environmental Protection Agency, Athens, GA, United States of America
- Current affiliation: Department of Computational Biology, St. Jude Childrens Research Hospital, Memphis, TN, United States of America
| | | | - Anna M. McKee
- South Atlantic Water Science Center, U.S. Geological Survey, Norcross, GA, United States of America
| | - Tai L. Guo
- Department of Veterinary Biosciences and Diagnostic Imaging, University of Georgia, Athens, GA, United States of America
| | - Rodney Mauricio
- Department of Genetics, University of Georgia, Athens, GA, United States of America
| | - Marirosa Molina
- US Environmental Protection Agency, Athens, GA, United States of America
- Current affiliation: National Exposure Research Laboratory, US Environmental Protection Agency, Research Triangle Park, NC, United States of America
| | - Brian S. Cummings
- Interdisciplinary Toxicology Program, University of Georgia, Athens, GA, United States of America
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA, United States of America
| | - Lawrence H. Lash
- Department of Pharmacology, Wayne State University, Detroit, MI, United States of America
| | - Kun Lu
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
- Current affiliation: Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, NC, United States of America
| | - Gregory S. Gilbert
- Environmental Studies Department, University of California, Santa Cruz, Santa Cruz, CA, United States of America
| | - Stephen P. Hubbell
- Smithsonian Tropical Research Institute, Balboa, Ancon, Panama
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States of America
| | - Brant C. Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA, United States of America
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26
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Klasberg S, Surendranath V, Lange V, Schöfl G. Bioinformatics Strategies, Challenges, and Opportunities for Next Generation Sequencing-Based HLA Genotyping. Transfus Med Hemother 2019; 46:312-325. [PMID: 31832057 PMCID: PMC6876610 DOI: 10.1159/000502487] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 07/30/2019] [Indexed: 12/16/2022] Open
Abstract
The advent of next generation sequencing (NGS) has altered the face of genotyping the human leukocyte antigen (HLA) system in clinical, stem cell donor registry, and research contexts. NGS has led to a dramatically increased sequencing throughput at high accuracy, while being more time and cost efficient than precursor technologies. This has led to a broader and deeper profiling of the key genes in the human immunogenetic make-up. The rapid evolution of sequencing technologies is evidenced by the development of varied short-read sequencing platforms with differing read lengths and sequencing capacities to long-read sequencing platforms capable of profiling full genes without fragmentation. Concomitantly, there has been development of a diverse set of computational analyses and software tools developed to deal with the various strengths and limitations of the sequencing data generated by the different sequencing platforms. This review surveys the different modalities involved in generating NGS HLA profiling sequence data. It systematically describes various computational approaches that have been developed to achieve HLA genotyping to different degrees of resolution. At each stage, this review enumerates the drawbacks and advantages of each of the platforms and analysis approaches, thus providing a comprehensive picture of the current state of HLA genotyping technologies.
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27
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Nakamura T, Shirouzu T, Nakata K, Yoshimura N, Ushigome H. The Role of Major Histocompatibility Complex in Organ Transplantation- Donor Specific Anti-Major Histocompatibility Complex Antibodies Analysis Goes to the Next Stage. Int J Mol Sci 2019; 20:ijms20184544. [PMID: 31540289 PMCID: PMC6769817 DOI: 10.3390/ijms20184544] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 09/04/2019] [Accepted: 09/11/2019] [Indexed: 02/06/2023] Open
Abstract
Organ transplantation has progressed with the comprehension of the major histocompatibility complex (MHC). It is true that the outcome of organ transplantation largely relies on how well rejection is managed. It is no exaggeration to say that to be well acquainted with MHC is a shortcut to control rejection. In human beings, MHC is generally recognized as human leukocyte antigens (HLA). Under the current circumstances, the number of alleles is still increasing, but the function is not completely understood. Their roles in organ transplantation are of vital importance, because mismatches of HLA alleles possibly evoke both cellular and antibody-mediated rejection. Even though the control of cellular rejection has improved by recent advances of immunosuppressants, there is no doubt that antibody-mediated rejection (AMR), which is strongly correlated with donor-specific anti-HLA antibodies (DSA), brings a poor outcome. Thus, to diagnose and treat AMR correctly is a clear proposition. In this review, we would like to focus on the detection of intra-graft DSA as a recent trend. Overall, here we will review the current knowledge regarding MHC, especially with intra-graft DSA, and future perspectives: HLA epitope matching; eplet risk stratification; predicted indirectly recognizable HLA epitopes etc. in the context of organ transplantation.
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Affiliation(s)
- Tsukasa Nakamura
- Department of Organ Transplantation and General Surgery, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan.
| | - Takayuki Shirouzu
- Molecular Diagnositcs Division, Wakunaga Pharmaceutical Co., Led. 4-5-36 Miyahara, Yodogawa-ku, Osaka 532-0003, Japan.
| | - Katsuya Nakata
- Molecular Diagnositcs Division, Wakunaga Pharmaceutical Co., Led. 4-5-36 Miyahara, Yodogawa-ku, Osaka 532-0003, Japan.
| | - Norio Yoshimura
- Department of Organ Transplantation and General Surgery, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan.
| | - Hidetaka Ushigome
- Department of Organ Transplantation and General Surgery, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan.
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28
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Wang Y, Zhang T, Zhang L, Pei Y, Zhao L, Li Y, Liu L, Wang H. Development of a rapid and reliable single-tube multiplex real-time PCR method for HLA-A*24:02 genotyping. Pharmacogenomics 2019; 20:803-812. [PMID: 31368852 DOI: 10.2217/pgs-2019-0052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Aim: HLA-A*24:02 is significantly associated with cutaneous adverse drug reactions caused by aromatic antiepileptic drugs. Here, we aimed to establish a fast and reliable detection method for HLA-A*24:02 genotyping. Methods: A single-tube multiplex quantitative real-time polymerase chain reaction (qPCR) assay for HLA-A*24:02 genotyping was established by combining allele-specific primers with TaqMan probes. Results: A 100% concordance was observed between qPCR and SBT result in 106 Han subjects. The detection limit of the new method was 0.05 ng DNA. The positive rate of HLA-A*24:02 in Tibetans (55.6%, n = 81) was significantly higher than those in Han (34%, n = 106), Uighur (27.5%, n = 102), Bouyei (25.9%, n = 116) and Miao populations (26.5%, n = 113). Conclusion: The newly established qPCR assay was reliable for HLA-A*24:02 screening in clinical applications.
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Affiliation(s)
- Yanxia Wang
- School of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, PR China.,National Engineering Research Center for Miniaturized Detection Systems, Xi'an 710069, PR China
| | - Tingting Zhang
- School of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, PR China.,National Engineering Research Center for Miniaturized Detection Systems, Xi'an 710069, PR China
| | - Lirong Zhang
- School of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, PR China.,National Engineering Research Center for Miniaturized Detection Systems, Xi'an 710069, PR China
| | - Yanrui Pei
- School of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, PR China.,National Engineering Research Center for Miniaturized Detection Systems, Xi'an 710069, PR China
| | - Lili Zhao
- School of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, PR China.,National Engineering Research Center for Miniaturized Detection Systems, Xi'an 710069, PR China
| | - Yanwei Li
- School of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, PR China.,National Engineering Research Center for Miniaturized Detection Systems, Xi'an 710069, PR China
| | - Lin Liu
- School of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, PR China
| | - Huijuan Wang
- School of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, PR China.,National Engineering Research Center for Miniaturized Detection Systems, Xi'an 710069, PR China
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29
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Seshasubramanian V, Venugopal M, D S Kannan A, Naganathan C, Manisekar NK, Kumar YN, Narayan S, Periathiruvadi S. Application of high-throughput next-generation sequencing for HLA typing of DNA extracted from postprocessing cord blood units. HLA 2019; 94:141-146. [PMID: 31056847 DOI: 10.1111/tan.13565] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 04/24/2019] [Accepted: 05/02/2019] [Indexed: 01/05/2023]
Abstract
Cord blood has become an acceptable source of hematopoietic stem cells for transplantation. HLA plays a major role in hematopoietic stem cell transplantation (HSCT). Typing of cord blood samples for HLA alleles has been performed based on the serological and molecular methods. However, with the advent of next-generation sequencing technology, HLA typing becomes more accurate and unambiguous (upto intron level). Contamination of cord blood cells with erythropoietic cells poses a challenge in DNA extraction and downstream application. In the present study, DNA extracted from buffy coat of cord blood samples was typed for HLA-A, -B, -C, DRB1, and DQB1 alleles by Illumina miniseq and the sequences were aligned, phased, and mapped by MIA FORA software algorithms. Most frequent alleles found were HLA A*01:01:01 (17%), A*24:02:01 (15.1%), A*11:01:01 (13.6%), B*40:06:01 (10.7%), C*06:02:01 (17.7%), C*04:01:01 (14.2%), C*15:02:01 (11.4%), C*07:02:01 (10.7%), DRB1*07:01:01 (15.9%), DRB1*10:01:01 (10.2%), DQB1*06:01:01 (17.4%), DQB1*05:01:01 (12.4%), and DQB1*05:03:01 (10.4%). One null allele (A*24:11N), two novel alleles in B loci and three rare alleles (B*40:06:04, B*51:01:05, and C*01:44) were also identified in the present study. This study shows that high-throughput, unambiguous (third-field resolution) HLA typing can be performed on cord blood samples. In order to preserve the precious sample for future use, minimal amount of cord blood samples (postprocessing) could be used for HLA typing purpose.
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Goeury T, Creary LE, Brunet L, Galan M, Pasquier M, Kervaire B, Langaney A, Tiercy JM, Fernández-Viña MA, Nunes JM, Sanchez-Mazas A. Deciphering the fine nucleotide diversity of full HLA class I and class II genes in a well-documented population from sub-Saharan Africa. HLA 2019; 91:36-51. [PMID: 29160618 PMCID: PMC5767763 DOI: 10.1111/tan.13180] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 11/01/2017] [Accepted: 11/15/2017] [Indexed: 01/06/2023]
Abstract
With the aim to understand how next‐generation sequencing (NGS) improves both our assessment of genetic variation within populations and our knowledge on HLA molecular evolution, we sequenced and analysed 8 HLA loci in a well‐documented population from sub‐Saharan Africa (Mandenka). The results of full‐gene NGS‐MiSeq sequencing compared with those obtained by traditional typing techniques or limited sequencing strategies showed that segregating sites located outside exon 2 are crucial to describe not only class I but also class II population diversity. A comprehensive analysis of exons 2, 3, 4 and 5 nucleotide diversity at the 8 HLA loci revealed remarkable differences among these gene regions, notably a greater variation concentrated in the antigen recognition sites of class I exons 3 and some class II exons 2, likely associated with their peptide‐presentation function, a lower diversity of HLA‐C exon 3, possibly related to its role as a KIR ligand, and a peculiar molecular diversity of HLA‐A exon 2, revealing demographic signals. Based on full‐length HLA sequences, we also propose that the most frequent DRB1 allele in the studied population, DRB1*13:04, emerged from an allelic conversion involving 3 potential alleles as donors and DRB1*11:02:01 as recipient. Finally, our analysis revealed a high occurrence of the DRB1*13:04‐DQA1*05:05:01‐DQB1*03:19 haplotype, possibly resulting from a selective sweep due to protection to Onchorcerca volvulus, a prevalent pathogen in West Africa. This study unveils highly relevant information on the molecular evolution of HLA genes in relation to their immune function, calling for similar analyses in other populations living in contrasting environments.
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Affiliation(s)
- T Goeury
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland
| | - L E Creary
- Department of Pathology, Stanford University School of Medicine, Palo Alto, California
| | - L Brunet
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland.,Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility (UIT/LNRH), Geneva University Hospital, Geneva, Switzerland
| | - M Galan
- INRA, UMR 1062 CBGP, avenue du Campus Agropolis, Montferrier sur Lez, France
| | - M Pasquier
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland
| | - B Kervaire
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland.,Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility (UIT/LNRH), Geneva University Hospital, Geneva, Switzerland
| | - A Langaney
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland
| | - J-M Tiercy
- Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland.,Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility (UIT/LNRH), Geneva University Hospital, Geneva, Switzerland
| | - M A Fernández-Viña
- Department of Pathology, Stanford University School of Medicine, Palo Alto, California
| | - J M Nunes
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland
| | - A Sanchez-Mazas
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland
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High-Resolution Full-Length HLA Typing Method Using Third Generation (Pac-Bio SMRT) Sequencing Technology. Methods Mol Biol 2019; 1802:135-153. [PMID: 29858806 DOI: 10.1007/978-1-4939-8546-3_9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The human HLA genes are among the most polymorphic genes in the human genome. Therefore, it is very difficult to find two unrelated individuals with identical HLA molecules. As a result, HLA Class I and Class II genes are routinely sequenced or serotyped for organ transplantation, autoimmune disease-association studies, drug hypersensitivity research, and other applications. However, these methods were able to give two or four digit data, which was not sufficient enough to understand the completeness of haplotypes of HLA genes. To overcome these limitations, we here described end-to-end workflow for sequencing of HLA class I and class II genes using third generation sequencing, SMRT technology. This method produces fully-phased, unambiguous, allele-level information on the PacBio System.
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Fawwad A, Govender D, Ahmedani MY, Basit A, Lane JA, Mack SJ, Atkinson MA, Henry Wasserfall C, Ogle GD, Noble JA. Clinical features, biochemistry and HLA-DRB1 status in youth-onset type 1 diabetes in Pakistan. Diabetes Res Clin Pract 2019; 149:9-17. [PMID: 30710658 PMCID: PMC6456725 DOI: 10.1016/j.diabres.2019.01.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 12/10/2018] [Accepted: 01/15/2019] [Indexed: 01/17/2023]
Abstract
Published information on diabetes in Pakistani youth is limited. We aimed to investigate the demographic, clinical, and biochemical features, and HLA-DRB1 alleles in new cases of diabetes affecting children and adolescents <22 years of age. The study was conducted at Baqai Institute of Diabetology and Endocrinology in Karachi from June 2013-December 2015. One hundred subjects aged <22 years at diagnosis were enrolled. Demographic characteristics, clinical information, biochemical parameters (blood glucose, HbA1c, C-peptide, glutamic acid decarboxylase 65 (GAD65) and islet antigen 2 (IA-2) autoantibodies) were measured. DNA from 100 subjects and 200 controls was extracted and genotyped for HLA-DRB1 using high-resolution genotyping technology. Ninety-nine subjects were clinically diagnosed as type 1 diabetes (T1D) and one as type 2 diabetes (T2D). Of the 99 with T1D, 57 (57.6%) were males and 42 (42.4%) females, with mean age at diagnosis 11.0 ± 5.2 years (range 1.6-21.7 years) and peaks at six and fifteen years. Fifty-seven subjects were assessed within one month of diagnosis and all within eleven months. For the subjects diagnosed as T1D, mean C-peptide was 0.63 ± 0.51 nmol/L (1.91 ± 1.53 ng/mL), with 16 (16.2%) IA2 positive, 53 (53.5%) GAD-65 positive, and 10 (10.1%) positive for both autoantibodies. In T1D patients, the allele DRB1*03:01 demonstrated highly significant T1D association (p < 10-16), with no apparent risk conferred by DRB1*04:xx alleles. CONCLUSIONS: Heterogeneous forms of T1D appear more common in children and youth in Pakistan than in European populations. Individual understanding of such cases could enable improved management strategies and healthier outcomes.
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Affiliation(s)
- Asher Fawwad
- Biochemistry Department, Baqai Medical University, Gadap, Karachi, Pakistan; Baqai Institute of Diabetology and Endocrinology, Nazimabad, Karachi, Pakistan.
| | - Denira Govender
- Life for a Child, Glebe, NSW 2037, Australia; Sydney Medical School, University of Sydney, NSW 2006, Australia.
| | | | - Abdul Basit
- Baqai Institute of Diabetology and Endocrinology, Nazimabad, Karachi, Pakistan.
| | - Julie Ann Lane
- Children's Hospital Oakland Research Institute, Oakland, CA 94609, USA.
| | - Steven John Mack
- Children's Hospital Oakland Research Institute, Oakland, CA 94609, USA.
| | - Mark Alvin Atkinson
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, Diabetes Institute, University of Florida, Gainesville, FL 32610, USA; Department of Pediatrics, College of Medicine, Diabetes Institute, University of Florida, Gainesville, FL 32610, USA.
| | - Clive Henry Wasserfall
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, Diabetes Institute, University of Florida, Gainesville, FL 32610, USA.
| | - Graham David Ogle
- Life for a Child, Glebe, NSW 2037, Australia; Diabetes NSW, Sydney, Australia.
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"Worldwide Network for Blood & Marrow Transplantation (WBMT) special article, challenges facing emerging alternate donor registries". Bone Marrow Transplant 2019; 54:1179-1188. [PMID: 30778127 PMCID: PMC6760540 DOI: 10.1038/s41409-019-0476-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 01/16/2019] [Accepted: 01/17/2019] [Indexed: 12/20/2022]
Abstract
Hematopoietic cell transplantation (HCT) activity is increasing at an unprecedented pace with > 50,000 allogeneic transplants occurring annually worldwide. Establishing a functional HCT donor registry can be very challenging with respect to ethnicities, financial, technical, and geopolitical issues. Extensive planning steps are essential to overcome the expected challenges while establishing the registry, and to maintain its functionality. A few strategies can help move past those challenges and push the development of such registries forward. Authorities involved in HCT donor registry establishment will have to balance the advantages and costs of such a project and accommodate the emerging alternatives such as cord blood or related haploidentical transplants. Miscalculations and incomplete understanding of the various aspects of the process can have tremendous impact on the optimization of a HCT donor registry especially in developing countries. Herein we present some challenges in establishing such a registry and present potential solutions.
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Profaizer T, Kumánovics A. Human Leukocyte Antigen Typing by Next-Generation Sequencing. Clin Lab Med 2018; 38:565-578. [DOI: 10.1016/j.cll.2018.07.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Feng X, Li W, Song J, Liu X, Gu Y, Yan C, Wu H, Xi J, Zhou S, Zhao C. HLA typing using next-generation sequencing for Chinese juvenile- and adult-onset myasthenia gravis patients. J Clin Neurosci 2018; 59:179-184. [PMID: 30595166 DOI: 10.1016/j.jocn.2018.10.077] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 09/27/2018] [Accepted: 10/14/2018] [Indexed: 11/15/2022]
Abstract
To compare HLA typing between juvenile- and adult-onset myasthenia gravis (MG), we enrolled 101 children (age ≤12 years) and 168 adults (age ≥20 years) with MG. We excluded patients with histories of thymoma, thyroid disease, or other autoimmune disease. We selected 41 seronegative juvenile-onset patients with ocular symptoms only, and 41 seropositive adult-onset patients with generalized symptoms. We used next-generation sequencing for typing and analysis of HLA genes (Loci: A, B, C, DPA1, DPB1, DQA1, DQB1 and DRB1). Haplotypes HLA-A∗02:07:01-B∗46:01:01-C∗01:02:01-DQA1∗01:01:01-DQB1∗03:03:02-DRB1∗09:01:02, HLA-A∗11:01:01, HLA-A∗24:02:01, and HLA-DPA1∗02:02:02 were found to be related to juvenile-onset MG and HLA-A∗01:01:01, HLA-A∗02:03:01, HLA-C∗03:04:01, and HLA-DQB1∗06:02:01 to adult-onset MG. Therefore, our findings suggested that HLA typing might determine the heterogeneity between AChR-Ab negative juvenile-onset and AChR-Ab positive adult-onset Chinese MG patients.
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Affiliation(s)
- Xuelin Feng
- Department of Neurology, Huashan Hospital, Shanghai Medical College, Fudan University, China
| | - Wenhui Li
- Department of Neurology, Children's Hospital of Fudan University, Shanghai, China
| | - Jie Song
- Department of Neurology, Huashan Hospital, Shanghai Medical College, Fudan University, China
| | - Xiaoni Liu
- Institute of Neurology, Fudan University, Shanghai, China
| | - Yuehua Gu
- Institute of Neurology, Fudan University, Shanghai, China
| | - Chong Yan
- Department of Neurology, Huashan Hospital, Shanghai Medical College, Fudan University, China
| | - Hui Wu
- Department of Neurology, Jing'an District Centre Hospital of Shanghai, China
| | - Jianying Xi
- Department of Neurology, Huashan Hospital, Shanghai Medical College, Fudan University, China
| | - Shuizhen Zhou
- Department of Neurology, Children's Hospital of Fudan University, Shanghai, China.
| | - Chongbo Zhao
- Department of Neurology, Huashan Hospital, Shanghai Medical College, Fudan University, China; Department of Neurology, Jing'an District Centre Hospital of Shanghai, China.
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Revisiting the potential power of human leukocyte antigen (HLA) genes on relationship testing by massively parallel sequencing-based HLA typing in an extended family. J Hum Genet 2018; 64:29-38. [PMID: 30348993 DOI: 10.1038/s10038-018-0521-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 09/27/2018] [Accepted: 10/01/2018] [Indexed: 11/08/2022]
Abstract
The human leukocyte antigen (HLA) genes are the most polymorphic genes in the human genome and have great power in forensic applications, especially in relationship testing and personal identification. However, the extreme polymorphism of HLA has made unambiguous genotyping of these genes very challenging and resulted in the limited application in relationship testing. Fortunately, massively parallel sequencing (MPS) technology offers the promise of unambiguous and high-throughput HLA typing. In this study, 11 HLA genes were typed in one extended family residing in North China and encompassing six generations. Phase-resolved genotypes for HLA genes were generated and HLA haplotype structure was defined. The paternity/kinship index, or in other words, likelihood ratio (LR) was calculated. A total of 88 alleles were identified, of which eight alleles were newly discovered. The inheritance of HLA alleles followed Mendelian law. With the discovery of new HLA alleles and three recombination events, a total of eleven new HLA haplotypes were identified in this population. LR distribution showed that, when HLA alleles were applied, the Log10LR for a single locus could reach very high and the median average Log10LRs of HLA genes were much higher than that of short tandem repeat loci. The result showed that high-throughput HLA genotyping could be achieved rapidly by MPS, and the contribution of HLA genes on system performance could be high, which may be applied as a supplement in forensic genetics studies. This study was also valuable in demonstrating the genetic mechanisms governing the generation of polymorphisms of the HLA genes.
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37
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Ahmadov GA, Govender D, Atkinson MA, Sultanova RA, Eubova AA, Wasserfall CH, Mack SJ, Lane JA, Noble JA, Ogle GD. Epidemiology of childhood-onset type 1 diabetes in Azerbaijan: Incidence, clinical features, biochemistry, and HLA-DRB1 status. Diabetes Res Clin Pract 2018; 144:252-259. [PMID: 30218742 PMCID: PMC6384092 DOI: 10.1016/j.diabres.2018.09.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 09/10/2018] [Indexed: 01/27/2023]
Abstract
AIMS Determine the incidence and typology of diabetes in children in Azerbaijan. METHODS Clinical features, C-peptide, autoantibodies (glutamic acid decarboxylase 65 (GAD65) and islet antigen 2 (IA-2)), and HLA-DRB1 status were studied in 106 subjects <18 years of age who were recently diagnosed. 104 cases were consecutive. Incidence was determined for Baku and Absheron regions, where ascertainment is estimated to be essentially 100%. RESULTS 104 of the 106 (98%) were diagnosed with type 1 diabetes, one with type 2 diabetes and one with atypical diabetes. Type 1 diabetes incidence in Baku City and Absheron was 7.05 per 100,000 population <15 years per year. Peak age of onset was 10 years. There was a slight male preponderance (male:female 1.17:1), and no temporal association with seasons. Almost all type 1 diabetes subjects presented with classic symptoms including a high incidence (58%) of diabetic ketoacidosis. 86% presented with low C-peptide values (<0.13 nmol/L, <0.40 ng/mL) and 74% were positive for at least one type 1 diabetes-related autoantibody. CONCLUSIONS Azerbaijan has a moderate type 1 diabetes incidence and clinical, biochemical and genetic features similar to that in European populations.
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Affiliation(s)
- Gunduz Ahmad Ahmadov
- Endocrine Centre, Binagadi, Baku City, Azerbaijan; 6th Children's Hospital, Baku City, Azerbaijan; Azerbaijan Medical University, Baku City, Azerbaijan
| | - Denira Govender
- International Diabetes Federation Life for a Child Program, Glebe, NSW 2037, Australia; Sydney Medical School, University of Sydney, Sydney 2006, Australia
| | - Mark Alvin Atkinson
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, Diabetes Institute, University of Florida, Gainesville, FL 32610, USA; Department of Pediatrics, College of Medicine, Diabetes Institute, University of Florida, Gainesville, FL 32610, USA
| | | | | | - Clive Henry Wasserfall
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, Diabetes Institute, University of Florida, Gainesville, FL 32610, USA
| | - Steven John Mack
- Children's Hospital Oakland Research Institute, Oakland, CA 94609, USA
| | - Julie Ann Lane
- Children's Hospital Oakland Research Institute, Oakland, CA 94609, USA
| | | | - Graham David Ogle
- International Diabetes Federation Life for a Child Program, Glebe, NSW 2037, Australia; Diabetes NSW, Glebe 2037, NSW, Australia.
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Geretz A, Ehrenberg PK, Bouckenooghe A, Fernández Viña MA, Michael NL, Chansinghakule D, Limkittikul K, Thomas R. Full-length next-generation sequencing of HLA class I and II genes in a cohort from Thailand. Hum Immunol 2018; 79:773-780. [PMID: 30243890 DOI: 10.1016/j.humimm.2018.09.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 08/17/2018] [Accepted: 09/18/2018] [Indexed: 01/02/2023]
Abstract
The human leukocyte antigen (HLA) genes are highly variable and are known to play an important role in disease outcomes, including infectious diseases. Prior knowledge of HLA polymorphisms in a population usually forms the basis for an effective case-control study design. As a prelude to future disease association analyses, we report HLA class I and II diversity in 334 unrelated donors from a Dengue vaccine efficacy trial conducted in Thailand. Long-range PCR amplification of six HLA loci was performed on DNA extracted from saliva samples. HLA-A, -B, -C, -DPB1, -DQB1 and -DRB1 were genotyped using a next-generation sequencing method presented at the 17th International HLA and Immunogenetics Workshop. In total, we identified 201 HLA alleles, including 35 HLA-A, 57 HLA-B, 28 HLA-C, 24 HLA-DPB1, 21 HLA-DQB1 and 36 HLA-DRB1 alleles. Very common HLA alleles with frequencies greater than 10 percent were A∗11:01:01, A∗33:03:01, A∗24:02:01, B∗46:01:01, C∗07:02:01, C∗01:02:01, C∗08:01:01, DPB1∗05:01:01, DPB1∗13:01:01, DPB1∗04:01:01, DPB1∗02:01:02, DQB1∗03:01:01, DQB1∗05:02:01, DQB1∗03:03:02, DRB1∗12:02:01, DRB1∗09:01:02, and DRB1∗15:02:01. A novel HLA allele, B∗15:450, had a non-synonymous substitution and occurred in more than one donor. Population-based full-length NGS HLA typing is more conclusive and provides a sound foundation for exploring disease association in a given population.
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Affiliation(s)
- Aviva Geretz
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Philip K Ehrenberg
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | | | | | - Nelson L Michael
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | | | - Kriengsak Limkittikul
- Department of Tropical Pediatrics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Rasmi Thomas
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA.
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Youngs D, Warner P, Gallagher M, Gimferrer I. New DQA1 allele specific antibody against epitope 2D (an exon 1 encoded amino acid). Considerations for alleles under the same P-group designation. Transpl Immunol 2018; 51:32-39. [PMID: 30153474 DOI: 10.1016/j.trim.2018.08.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 08/23/2018] [Accepted: 08/24/2018] [Indexed: 10/28/2022]
Abstract
The majority of polymorphisms of the Human Leukocyte Antigen (HLA) proteins are clustered at the peptide binding domain (PBD), defined as the area coded by exon 2 and 3 for class I and exon 2 for class II. HLA alleles with the same amino acid (AA) sequence at the PBD are considered functionally equivalent and can be grouped under the same P-group designation. Here we present a case of a kidney recipient, typed as DQA1*01:04, 01:05 and DQB1*05:01P, 05:03, who developed antibodies against all DQ antigens on our Luminex Single Antigen (LSA) panel. Our LSA panel does not include DQA1*01:05 or 01:04, but both alleles belong to the DQA1*01:01P group and beads carrying DQA1*01:01 tested positive. Mature protein sequence alignment demonstrated a single AA mismatch between DQA1*01:04/01:05 and DQA1*01:01 located at position 2 (G vs D), which is encoded by exon 1. Luminex assay by another manufacturer which include a bead carrying patient's own DQA1* type and crossmatch studies with surrogate donors confirmed the presence of an antibody against mismatched epitope 2D. This case illustrates that alleles included in the same P-group may have polymorphisms able to trigger immunological responses and brings attention to the fact that some mature HLA proteins express AA encoded by exon 1, which is structurally part of the PBD.
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Ton KNT, Cree SL, Gronert-Sum SJ, Merriman TR, Stamp LK, Kennedy MA. Multiplexed Nanopore Sequencing of HLA-B Locus in Māori and Pacific Island Samples. Front Genet 2018; 9:152. [PMID: 29760718 PMCID: PMC5936980 DOI: 10.3389/fgene.2018.00152] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 04/12/2018] [Indexed: 11/13/2022] Open
Abstract
The human leukocyte antigen (HLA) system encodes the human major histocompatibility complex (MHC). HLA-B is the most polymorphic gene in the MHC class I region and many HLA-B alleles have been associated with adverse drug reactions (ADRs) and disease susceptibility. The frequency of such HLA-B alleles varies by ethnicity, and therefore it is important to understand the prevalence of such alleles in different population groups. Research into HLA involvement in ADRs would be facilitated by improved methods for genotyping key HLA-B alleles. Here, we describe an approach to HLA-B typing using next generation sequencing (NGS) on the MinION™ nanopore sequencer, combined with data analysis with the SeqNext-HLA software package. The nanopore sequencer offers the advantages of long-read capability and single molecule reads, which can facilitate effective haplotyping. We developed this method using reference samples as well as individuals of New Zealand Māori or Pacific Island descent, because HLA-B diversity in these populations is not well understood. We demonstrate here that nanopore sequencing of barcoded, pooled, 943 bp polymerase chain reaction (PCR) amplicons of 49 DNA samples generated ample read depth for all samples. HLA-B alleles were assigned to all samples at high-resolution with very little ambiguity. Our method is a scaleable and efficient approach for genotyping HLA-B and potentially any other HLA locus. Finally, we report our findings on HLA-B genotypes of this cohort, which adds to our understanding of HLA-B allele frequencies among Māori and Pacific Island people.
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Affiliation(s)
- Kim N T Ton
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Simone L Cree
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | | | - Tony R Merriman
- Biochemistry Department, University of Otago, Dunedin, New Zealand
| | - Lisa K Stamp
- Department of Medicine, University of Otago, Christchurch, New Zealand
| | - Martin A Kennedy
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
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Construction of full-length Japanese reference panel of class I HLA genes with single-molecule, real-time sequencing. THE PHARMACOGENOMICS JOURNAL 2018; 19:136-146. [PMID: 29352165 PMCID: PMC6462828 DOI: 10.1038/s41397-017-0010-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 10/11/2017] [Accepted: 11/06/2017] [Indexed: 12/30/2022]
Abstract
Human leukocyte antigen (HLA) is a gene complex known for its exceptional diversity across populations, importance in organ and blood stem cell transplantation, and associations of specific alleles with various diseases. We constructed a Japanese reference panel of class I HLA genes (ToMMo HLA panel), comprising a distinct set of HLA-A, HLA-B, HLA-C, and HLA-H alleles, by single-molecule, real-time (SMRT) sequencing of 208 individuals included in the 1070 whole-genome Japanese reference panel (1KJPN). For high-quality allele reconstruction, we developed a novel pipeline, Primer-Separation Assembly and Refinement Pipeline (PSARP), in which the SMRT sequencing and additional short-read data were used. The panel consisted of 139 alleles, which were all extended from known IPD-IMGT/HLA sequences, contained 40 with novel variants, and captured more than 96.5% of allelic diversity in 1KJPN. These newly available sequences would be important resources for research and clinical applications including high-resolution HLA typing, genetic association studies, and analyzes of cis-regulatory elements.
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43
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Mack SJ, Udell J, Cohen F, Osoegawa K, Hawbecker SK, Noonan DA, Ladner MB, Goodridge D, Trachtenberg EA, Oksenberg JR, Erlich HA. High resolution HLA analysis reveals independent class I haplotypes and amino-acid motifs protective for multiple sclerosis. Genes Immun 2018; 20:308-326. [PMID: 29307888 PMCID: PMC6035897 DOI: 10.1038/s41435-017-0006-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 07/31/2017] [Accepted: 08/11/2017] [Indexed: 11/24/2022]
Abstract
We investigated association between HLA class I and class II alleles and haplotypes, and KIR loci and their HLA class I ligands, with multiple sclerosis (MS) in 412 European-American MS patients and 419 ethnically-matched controls, using next generation sequencing. The DRB1*15:01~DQB1*06:02 haplotype was highly predisposing (odds ratio (OR) = 3.98; 95% confidence interval (CI) = 3−5.31; p-value (p) = 2.22E−16), as was DRB1*03:01~DQB1*02:01 (OR = 1.63; CI = 1.19–2.24; p = 1.41E−03). Hardy-Weinberg (HW) analysis in MS patients revealed a significant DRB1*03:01~DQB1*02:01 homozyote excess (15 observed, 8.6 expected; p = 0.016). The OR for this genotype (5.27; CI = 1.47–28.52; p = 0.0036) suggests a recessive MS risk model. Controls displayed no HW deviations. The C*03:04~B*40:01 haplotype (OR = 0.27; CI = 0.14–0.51; p = 6.76E−06) was highly protective for MS, especially in haplotypes with A*02:01 (OR = 0.15; CI = 0.04–0.45; p = 6.51E−05). By itself, A*02:01 is moderately protective, (OR = 0.69; CI = 0.54–0.87; p = 1.46E−03), and haplotypes of A*02:01 with the HLA-B Thr80 Bw4 variant (Bw4T) more so (OR = 0.53; CI = 0.35–0.78; p = 7.55E−04). Protective associations with the Bw4 KIR ligand resulted from linkage disequilibrium (LD) with DRB1*15:01, but the Bw4T variant was protective (OR = 0.64; CI = 0.49–0.82; p = 3.37E−04) independent of LD with DRB1*15:01. The Bw4I variant was not associated with MS. Overall, we find specific class I HLA polymorphisms to be protective for MS, independent of the strong predisposition conferred by DRB1*15:01.
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Affiliation(s)
- Steven J Mack
- Center for Genetics, Children's Hospital Oakland Research Institute, Oakland, CA, USA.
| | - Julia Udell
- University of Minnesota Twin Cities, Minneapolis, MN, USA
| | - Franziska Cohen
- Center for Genetics, Children's Hospital Oakland Research Institute, Oakland, CA, USA
| | - Kazutoyo Osoegawa
- Histocompatibility, Immunogenetics & Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA
| | - Sharon K Hawbecker
- Center for Genetics, Children's Hospital Oakland Research Institute, Oakland, CA, USA
| | - David A Noonan
- Center for Genetics, Children's Hospital Oakland Research Institute, Oakland, CA, USA
| | - Martha B Ladner
- Center for Genetics, Children's Hospital Oakland Research Institute, Oakland, CA, USA
| | | | | | - Jorge R Oksenberg
- Department of Neurology, University of California, San Francisco, CA, USA
| | - Henry A Erlich
- Center for Genetics, Children's Hospital Oakland Research Institute, Oakland, CA, USA
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Yin Y, Lan J, Zhang Q. Application of High-Throughput Next-Generation Sequencing for HLA Typing on Buccal Extracted DNA. Methods Mol Biol 2018; 1802:101-113. [PMID: 29858804 DOI: 10.1007/978-1-4939-8546-3_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Next-generation sequencing (NGS) is increasingly recognized for its ability to deliver high-resolution and high-throughput HLA genotyping. As a result, there is active interest in applying NGS technologies to perform high volume bone marrow donor recruitment typing. Currently, buccal-based DNA specimens are considered a noninvasive and cost-effective method for registry typing. Here, we describe the feasibility of using long-range PCR and clonal sequencing by Illumina MiSeq to deliver unambiguous HLA typing on buccal-based donor recruitment samples.
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Affiliation(s)
- Yuxin Yin
- Department of Pathology & Laboratory Medicine, UCLA Immunogenetics Center, Los Angeles, CA, USA
| | - James Lan
- Nephrology and Kidney Transplantation, University of British Columbia, Vancouver General Hospital, Vancouver, BC, Canada
| | - Qiuheng Zhang
- Department of Pathology & Laboratory Medicine, UCLA Immunogenetics Center, Los Angeles, CA, USA.
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45
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Ehrenberg PK, Geretz A, Sindhu RK, Vayntrub T, Fernández Viña MA, Apps R, Michael NL, Thomas R. High‐throughput next‐generation sequencing to genotype six classical
HLA
loci from 96 donors in a single
MiSeq
run. HLA 2017; 90:284-291. [DOI: 10.1111/tan.13133] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 08/15/2017] [Accepted: 08/21/2017] [Indexed: 01/05/2023]
Affiliation(s)
- P. K. Ehrenberg
- U.S. Military HIV Research Program Walter Reed Army Institute of Research Silver Spring Maryland
| | - A. Geretz
- U.S. Military HIV Research Program Walter Reed Army Institute of Research Silver Spring Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine Bethesda Maryland
| | - R. K. Sindhu
- U.S. Military HIV Research Program Walter Reed Army Institute of Research Silver Spring Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine Bethesda Maryland
| | - T. Vayntrub
- Stanford Blood Center Stanford University School of Medicine Palo Alto California
| | - M. A. Fernández Viña
- Department of Pathology Stanford University School of Medicine Palo Alto California
| | - R. Apps
- Department of Microbiology, Immunology and Tropical Medicine George Washington University Washington DC
| | - N. L. Michael
- U.S. Military HIV Research Program Walter Reed Army Institute of Research Silver Spring Maryland
| | - R. Thomas
- U.S. Military HIV Research Program Walter Reed Army Institute of Research Silver Spring Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine Bethesda Maryland
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46
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47
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Hapl-o-Mat: open-source software for HLA haplotype frequency estimation from ambiguous and heterogeneous data. BMC Bioinformatics 2017; 18:284. [PMID: 28558647 PMCID: PMC5450239 DOI: 10.1186/s12859-017-1692-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 05/18/2017] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Knowledge of HLA haplotypes is helpful in many settings as disease association studies, population genetics, or hematopoietic stem cell transplantation. Regarding the recruitment of unrelated hematopoietic stem cell donors, HLA haplotype frequencies of specific populations are used to optimize both donor searches for individual patients and strategic donor registry planning. However, the estimation of haplotype frequencies from HLA genotyping data is challenged by the large amount of genotype data, the complex HLA nomenclature, and the heterogeneous and ambiguous nature of typing records. RESULTS To meet these challenges, we have developed the open-source software Hapl-o-Mat. It estimates haplotype frequencies from population data including an arbitrary number of loci using an expectation-maximization algorithm. Its key features are the processing of different HLA typing resolutions within a given population sample and the handling of ambiguities recorded via multiple allele codes or genotype list strings. Implemented in C++, Hapl-o-Mat facilitates efficient haplotype frequency estimation from large amounts of genotype data. We demonstrate its accuracy and performance on the basis of artificial and real genotype data. CONCLUSIONS Hapl-o-Mat is a versatile and efficient software for HLA haplotype frequency estimation. Its capability of processing various forms of HLA genotype data allows for a straightforward haplotype frequency estimation from typing records usually found in stem cell donor registries.
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48
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Profaizer T, Lázár-Molnár E, Pole A, Delgado JC, Kumánovics A. HLA genotyping using the Illumina HLA TruSight next-generation sequencing kits: A comparison. Int J Immunogenet 2017; 44:164-168. [DOI: 10.1111/iji.12322] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 03/21/2017] [Accepted: 04/20/2017] [Indexed: 12/25/2022]
Affiliation(s)
- T. Profaizer
- Department of Pathology; ARUP Institute for Clinical and Experimental Pathology; University of Utah School of Medicine; Salt Lake City UT USA
| | - E. Lázár-Molnár
- Department of Pathology; ARUP Institute for Clinical and Experimental Pathology; University of Utah School of Medicine; Salt Lake City UT USA
- Histocompatibility & Immunogenetics Lab oratory; University of Utah Healthcare; Salt Lake City UT USA
| | - A. Pole
- Histocompatibility & Immunogenetics Lab oratory; University of Utah Healthcare; Salt Lake City UT USA
| | - J. C. Delgado
- Department of Pathology; ARUP Institute for Clinical and Experimental Pathology; University of Utah School of Medicine; Salt Lake City UT USA
- Histocompatibility & Immunogenetics Lab oratory; University of Utah Healthcare; Salt Lake City UT USA
| | - A. Kumánovics
- Department of Pathology; ARUP Institute for Clinical and Experimental Pathology; University of Utah School of Medicine; Salt Lake City UT USA
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49
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Schöfl G, Lang K, Quenzel P, Böhme I, Sauter J, Hofmann JA, Pingel J, Schmidt AH, Lange V. 2.7 million samples genotyped for HLA by next generation sequencing: lessons learned. BMC Genomics 2017; 18:161. [PMID: 28196473 PMCID: PMC5309984 DOI: 10.1186/s12864-017-3575-z] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 02/09/2017] [Indexed: 11/10/2022] Open
Abstract
Background At the DKMS Life Science Lab, Next Generation Sequencing (NGS) has been used for ultra-high-volume high-resolution genotyping of HLA loci for the last three and a half years. Here, we report on our experiences in genotyping the HLA, CCR5, ABO, RHD and KIR genes using a direct amplicon sequencing approach on Illumina MiSeq and HiSeq 2500 instruments. Results Between January 2013 and June 2016, 2,714,110 samples largely from German, Polish and UK-based potential stem cell donors have been processed. 98.9% of all alleles for the targeted HLA loci (HLA-A, -B, -C, -DRB1, -DQB1 and -DPB1) were typed at high resolution or better. Initially a simple three-step workflow based on nanofluidic chips in conjunction with 4-primer amplicon tagging was used. Over time, we found that this setup results in PCR artefacts such as primer dimers and PCR-mediated recombination, which may necessitate repeat typing. Split workflows for low- and high-DNA-concentration samples helped alleviate these problems and reduced average per-locus repeat rates from 3.1 to 1.3%. Further optimisations of the workflow included the use of phosphorothioate oligos to reduce primer degradation and primer dimer formation, and employing statistical models to predict read yield from initial template DNA concentration to avoid intermediate quantification of PCR products. Finally, despite the populations typed at DKMS Life Science Lab being relatively homogenous genetically, an analysis of 1.4 million donors processed between January 2015 and May 2016 led to the discovery of 1,919 distinct novel HLA alleles. Conclusions Amplicon-based NGS HLA genotyping workflows have become the workhorse in high-volume tissue typing of registry donors. The optimisation of workflow practices over multiple years has led to insights and solutions that improve the efficiency and robustness of short amplicon based genotyping workflows. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3575-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gerhard Schöfl
- DKMS Life Science Lab, Blasewitzerstr. 43, 01307, Dresden, Germany.
| | - Kathrin Lang
- DKMS Life Science Lab, Blasewitzerstr. 43, 01307, Dresden, Germany
| | - Philipp Quenzel
- DKMS Life Science Lab, Blasewitzerstr. 43, 01307, Dresden, Germany
| | - Irina Böhme
- DKMS Life Science Lab, Blasewitzerstr. 43, 01307, Dresden, Germany
| | | | | | | | - Alexander H Schmidt
- DKMS Life Science Lab, Blasewitzerstr. 43, 01307, Dresden, Germany.,DKMS, Kressbach 1, 72072, Tübingen, Germany
| | - Vinzenz Lange
- DKMS Life Science Lab, Blasewitzerstr. 43, 01307, Dresden, Germany
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50
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Comparison of exome-based HLA class I genotyping tools: identification of platform-specific genotyping errors. J Hum Genet 2016; 62:397-405. [PMID: 27881843 PMCID: PMC5334549 DOI: 10.1038/jhg.2016.141] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 09/26/2016] [Accepted: 10/14/2016] [Indexed: 12/15/2022]
Abstract
Accurate human leukocyte antigen (HLA) genotyping is critical in studies involving the immune system. Several algorithms to estimate HLA genotypes from whole-exome data were developed. We compared the accuracy of seven algorithms, including Optitype, Polysolver and PHLAT, as well as investigated patterns and possible causes of miscalls using 12 clinical samples and 961 individuals from the 1000 Genomes Project. Optitype showed the highest accuracy of 97.2% for HLA class I alleles at the second field resolution, followed by 94.0% in Polysolver and 85.6% in PHLAT. In Optitype, 34 (21.1%) of 161 miscalls were across different serological types, and common miscalls were HLA-A*26:01 to HLA-A*25:01, HLA-B*45:01 to HLA-B*44:15 and HLA-C*08:02 to HLA-C*05:01 with error rates of 4.1%, 10.0% and 4.1%, respectively. In Polysolver, 193 (55.9%) of 345 miscalls occurred across different serological alleles, and a specific pattern of genotyping error from HLA-A*25:01 to HLA-A*26:01 was observed in 93.3% of HLA-A*25:01 carriers, due to dropping of HLA-A*25:01 sequence reads during the extraction process of HLA reads. In PHLAT, 147 (59.8%) of 246 miscalls in HLA-A were due to erroneous assignment of multiple alleles to either HLA-A*01:22 or HLA-A*01:81. These results suggest that careful considerations needed to be taken when using exome-based HLA class I genotyping data and applying these results in clinical settings.
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