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Geo JA, Ameen R, Al Shemmari S, Thomas J. Advancements in HLA Typing Techniques and Their Impact on Transplantation Medicine. Med Princ Pract 2024; 33:215-231. [PMID: 38442703 PMCID: PMC11175610 DOI: 10.1159/000538176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 02/28/2024] [Indexed: 03/07/2024] Open
Abstract
HLA typing serves as a standard practice in hematopoietic stem cell transplantation to ensure compatibility between donors and recipients, preventing the occurrence of allograft rejection and graft-versus-host disease. Conventional laboratory methods that have been widely employed in the past few years, including sequence-specific primer PCR and sequencing-based typing (SBT), currently face the risk of becoming obsolete. This risk stems not only from the extensive diversity within HLA genes but also from the rapid advancement of next-generation sequencing and third-generation sequencing technologies. Third-generation sequencing systems like single-molecule real-time (SMRT) sequencing and Oxford Nanopore (ONT) sequencing have the capability to analyze long-read sequences that span entire intronic-exonic regions of HLA genes, effectively addressing challenges related to HLA ambiguity and the phasing of multiple short-read fragments. The growing dominance of these advanced sequencers in HLA typing is expected to solidify further through ongoing refinements, cost reduction, and error rate minimization. This review focuses on hematopoietic stem cell transplantation (HSCT) and explores prospective advancements and application of HLA DNA typing techniques. It explores how the adoption of third-generation sequencing technologies can revolutionize the field by offering improved accuracy, reduced ambiguity, and enhanced assessment of compatibility in HSCT. Embracing these cutting-edge technologies is essential to advancing the success rates and outcomes of hematopoietic stem cell transplantation. This review underscores the importance of staying at the forefront of HLA typing techniques to ensure the best possible outcomes for patients undergoing HSCT.
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Affiliation(s)
- Jeethu Anu Geo
- Medical Laboratory Sciences Department, Health Sciences Center, Kuwait University, Kuwait City, Kuwait
- Department of Biotechnology, Karunya Institute of Technology and Sciences, Coimbatore, India
| | - Reem Ameen
- Medical Laboratory Sciences Department, Health Sciences Center, Kuwait University, Kuwait City, Kuwait
| | - Salem Al Shemmari
- Department of Medicine, Health Sciences Center, Kuwait University, Kuwait City, Kuwait
| | - Jibu Thomas
- Department of Biotechnology, Karunya Institute of Technology and Sciences, Coimbatore, India
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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: 18] [Impact Index Per Article: 6.0] [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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Yi J, Chen L, Xiao Y, Zhao Z, Su X. Investigations of sequencing data and sample type on HLA class Ia typing with different computational tools. Brief Bioinform 2020; 22:5871189. [PMID: 32662817 PMCID: PMC8138914 DOI: 10.1093/bib/bbaa143] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 06/09/2020] [Indexed: 12/16/2022] Open
Abstract
Human leukocyte antigen (HLA) can encode the human major histocompatibility complex (MHC) proteins and play a key role in adaptive and innate immunity. Emerging clinical evidences suggest that the presentation of tumor neoantigens and neoantigen-specific T cell response associated with MHC class I molecules are of key importance to activate the adaptive immune systemin cancer immunotherapy. Therefore, accurate HLA typing is very essential for the clinical application of immunotherapy. In this study, we conducted performance evaluations of 4 widely used HLA typing tools (OptiType, Phlat, Polysolver and seq2hla) for predicting HLA class Ia genes from WES and RNA-seq data of 28 cancer patients. HLA genotyping data using PCR-SBT method was firstly obtained as the golden standard and was subsequently compared with HLA typing data by using NGS techniques. For both WES data and RNA-seq data, OptiType showed the highest accuracy for HLA-Ia typing than the other 3 programs at 2-digit and 4-digit resolution. Additionally, HLA typing accuracy from WES data was higher than from RNA-seq data (99.11% for WES data versus 96.42% for RNA-seq data). The accuracy of HLA-Ia typing by OptiType can reach 100% with the average depth of HLA gene regions >20x. Besides, the accuracy of 2-digit and 4-digit HLA-Ia typing based on control samples was higher than tumor tissues. In conclusion, OptiType by using WES data from control samples with the high average depth (>20x) of HLA gene regions can present a probably superior performance for HLA-Ia typing, enabling its application in cancer immunotherapy.
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Affiliation(s)
- Jian Yi
- Cancer Translational Research Institute, YuceBio Technology Co., Ltd., Shenzhen, China
| | - Longyun Chen
- Cancer Translational Research Institute, YuceBio Technology Co., Ltd., Shenzhen, China
| | - Yajie Xiao
- Cancer Translational Research Institute, YuceBio Technology Co., Ltd., Shenzhen, China
| | - Zhikun Zhao
- Cancer Translational Research Institute, YuceBio Technology Co., Ltd., Shenzhen, China
| | - Xiaofan Su
- Yucebio Cancer Translational Research Institute and Chief Medical Officer for Yucebio Technology Co
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Madden K, Chabot-Richards D. HLA testing in the molecular diagnostic laboratory. Virchows Arch 2018; 474:139-147. [PMID: 30515565 DOI: 10.1007/s00428-018-2501-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 11/27/2018] [Indexed: 02/06/2023]
Abstract
The human leukocyte antigen (HLA) system is a highly polymorphic family of genes involved in immunity and responsible for identifying self versus non-self. HLA typing is essential for solid organ and bone marrow transplantation as well as in non-transplant settings such as disease association and pharmacogenomics. Typing of HLA genes differs from most molecular testing as, rather than evaluating differences from an accepted "wild-type" gene, it must distinguish between thousands of similar, but distinct alleles. This article will describe the HLA system and nomenclature. We will then discuss clinical uses of HLA typing including solid organ transplantation, hematopoietic stem cell transplantation, evaluation of platelet refractory patients, disease association, and pharmacogenetics. Finally, we describe common molecular methods of HLA typing.
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Affiliation(s)
- Kathleen Madden
- Department of Pathology, University of New Mexico, MSC08 4640, Reginald Heber Fitz Hall, Room 335, 1 University of New Mexico, 87131, Albuquerque, NM, Mexico
| | - Devon Chabot-Richards
- Department of Pathology, University of New Mexico, MSC08 4640, Reginald Heber Fitz Hall, Room 335, 1 University of New Mexico, 87131, Albuquerque, NM, Mexico.
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5
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Unambiguous high resolution genotyping of human leukocyte antigens. J Immunol Methods 2017; 445:10-14. [PMID: 28238798 DOI: 10.1016/j.jim.2017.02.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Indexed: 11/22/2022]
Abstract
We have developed a high resolution sequencing based typing method for genotyping Human Leukocyte Antigens (HLA) over a period of twenty years. The methods are based upon the separation of HLA alleles per locus at the initial amplification to simplify the analysis post-sequencing. The increasing discovery of polymorphism in HLA, manifested in new alleles, has necessitated the continuing development of this method. Here we present methods for the high resolution Sequence Based Typing of HLA-A, B, C (class I) and HLA-DQB1 and DRB1 (class II). The purpose of this article is to provide a valuable resource of methods and primers for other laboratories engaged in HLA typing.
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Lunz J, Hinsdale L, King C, Pastush R, Buenvenida M, Harmon M. The coordination of allocation: Logistics of kidney organ allocation to highly sensitized patients. Hum Immunol 2016; 78:16-18. [PMID: 27743878 DOI: 10.1016/j.humimm.2016.10.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 09/24/2016] [Accepted: 10/11/2016] [Indexed: 11/26/2022]
Abstract
Since implementation, the new UNOS OPTN kidney allocation system (KAS) has drastically expanded the pool of available kidneys to candidates that may have previously waited extended periods for an organ offer. This is particularly true for highly sensitized patients. The changes to the KAS have had ramifications throughout the transplant process, including for organ procurement organizations (OPO) and local transplant hospital call centers. Here, we will examine the impact of the new KAS on the organ donation process and highlight the necessary interactions between the OPO and transplant centers to best match donor kidneys and highly sensitized recipients.
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Affiliation(s)
- John Lunz
- Gift of Hope Organ and Tissue Donor Network, Itasca, IL, United States.
| | - Lisa Hinsdale
- Gift of Hope Organ and Tissue Donor Network, Itasca, IL, United States
| | - Casey King
- Emory Transplant Center Organ Placement Program, Atlanta, GA, United States
| | - Robin Pastush
- Emory Transplant Center Organ Placement Program, Atlanta, GA, United States
| | | | - Michael Harmon
- Gift of Hope Organ and Tissue Donor Network, Itasca, IL, United States
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Picascia A, Grimaldi V, Napoli C. From HLA typing to anti-HLA antibody detection and beyond: The road ahead. Transplant Rev (Orlando) 2016; 30:187-94. [DOI: 10.1016/j.trre.2016.07.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Revised: 07/07/2016] [Accepted: 07/22/2016] [Indexed: 01/27/2023]
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Diversity in exon 5 of HLA-C∗04:01:01G is significant in anthropological studies. Hum Immunol 2016; 77:426-8. [DOI: 10.1016/j.humimm.2016.03.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 03/15/2016] [Accepted: 03/23/2016] [Indexed: 11/21/2022]
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9
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Lamb G, Choi KL, Selwyn C, Wheeler A, Hammond L, Morgan J, Dunn PPJ. Identification of seven novel HLA class I alleles in New Zealand. Int J Immunogenet 2015. [DOI: 10.1111/iji.12221] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- G. Lamb
- Tissue Typing Laboratory; New Zealand Blood Service; Auckland New Zealand
| | - K.-L. Choi
- Tissue Typing Laboratory; New Zealand Blood Service; Auckland New Zealand
| | - C. Selwyn
- Tissue Typing Laboratory; New Zealand Blood Service; Auckland New Zealand
| | - A. Wheeler
- Tissue Typing Laboratory; New Zealand Blood Service; Auckland New Zealand
| | - L. Hammond
- Tissue Typing Laboratory; New Zealand Blood Service; Auckland New Zealand
| | - J. Morgan
- Tissue Typing Laboratory; New Zealand Blood Service; Auckland New Zealand
| | - P. P. J. Dunn
- Tissue Typing Laboratory; New Zealand Blood Service; Auckland New Zealand
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