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Dhanushkumar T, Selvam PK, M E S, Vasudevan K, C GPD, Zayed H, Kamaraj B. Rational design of a multivalent vaccine targeting arthropod-borne viruses using reverse vaccinology strategies. Int J Biol Macromol 2024; 258:128753. [PMID: 38104690 DOI: 10.1016/j.ijbiomac.2023.128753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 11/17/2023] [Accepted: 12/09/2023] [Indexed: 12/19/2023]
Abstract
Viruses transmitted by arthropods, such as Dengue, Zika, and Chikungunya, represent substantial worldwide health threats, particularly in countries like India. The lack of approved vaccines and effective antiviral therapies calls for developing innovative strategies to tackle these arboviruses. In this study, we employed immunoinformatics methodologies, incorporating reverse vaccinology, to design a multivalent vaccine targeting the predominant arboviruses. Epitopes of B and T cells were recognized within the non-structural proteins of Dengue, Zika, and Chikungunya viruses. The predicted epitopes were enhanced with adjuvants β-defensin and RS-09 to boost the vaccine's immunogenicity. Sixteen distinct vaccine candidates were constructed, each incorporating epitopes from all three viruses. FUVAC-11 emerged as the most promising vaccine candidate through molecular docking and molecular dynamics simulations, demonstrating favorable binding interactions and stability. Its effectiveness was further evaluated using computational immunological studies confirming strong immune responses. The in silico cloning performed using the pET-28a(+) plasmid facilitates the future experimental implementation of this vaccine candidate, paving the way for potential advancements in combating these significant arboviral threats. However, further in vitro and in vivo studies are warranted to confirm the results obtained in this computational study, which highlights the effectiveness of immunoinformatics and reverse vaccinology in creating vaccines against major Arboviruses, offering a promising model for developing vaccines for other vector-borne diseases and enhancing global health security.
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Affiliation(s)
- T Dhanushkumar
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru 560064, India
| | - Prasanna Kumar Selvam
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru 560064, India
| | - Santhosh M E
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru 560064, India
| | - Karthick Vasudevan
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru 560064, India.
| | - George Priya Doss C
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of BioSciences and Technology, Vellore Institute of Technology (VIT), Vellore, India.
| | - Hatem Zayed
- Department of Biomedical Sciences College of Health Sciences, QU Health, Qatar University, Doha, Qatar
| | - Balu Kamaraj
- Department of Dental Education, College of Dentistry, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
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Haasnoot AMJ, Kuiper JJ, de Boer JH. Predicting uveitis in juvenile idiopathic arthritis: from biomarkers to clinical practice. Expert Rev Clin Immunol 2019; 15:657-666. [DOI: 10.1080/1744666x.2019.1593139] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Anne-Mieke J.W. Haasnoot
- Department of Ophthalmology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Jonas J.W. Kuiper
- Department of Ophthalmology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Joke H. de Boer
- Department of Ophthalmology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
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Segawa H, Kukita Y, Kato K. HLA genotyping by next-generation sequencing of complementary DNA. BMC Genomics 2017; 18:914. [PMID: 29179676 PMCID: PMC5704545 DOI: 10.1186/s12864-017-4300-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 11/13/2017] [Indexed: 12/23/2022] Open
Abstract
Background Genotyping of the human leucocyte antigen (HLA) is indispensable for various medical treatments. However, unambiguous genotyping is technically challenging due to high polymorphism of the corresponding genomic region. Next-generation sequencing is changing the landscape of genotyping. In addition to high throughput of data, its additional advantage is that DNA templates are derived from single molecules, which is a strong merit for the phasing problem. Although most currently developed technologies use genomic DNA, use of cDNA could enable genotyping with reduced costs in data production and analysis. We thus developed an HLA genotyping system based on next-generation sequencing of cDNA. Methods Each HLA gene was divided into 3 or 4 target regions subjected to PCR amplification and subsequent sequencing with Ion Torrent PGM. The sequence data were then subjected to an automated analysis. The principle of the analysis was to construct candidate sequences generated from all possible combinations of variable bases and arrange them in decreasing order of the number of reads. Upon collecting candidate sequences from all target regions, 2 haplotypes were usually assigned. Cases not assigned 2 haplotypes were forwarded to 4 additional processes: selection of candidate sequences applying more stringent criteria, removal of artificial haplotypes, selection of candidate sequences with a relaxed threshold for sequence matching, and countermeasure for incomplete sequences in the HLA database. Results The genotyping system was evaluated using 30 samples; the overall accuracy was 97.0% at the field 3 level and 98.3% at the G group level. With one sample, genotyping of DPB1 was not completed due to short read size. We then developed a method for complete sequencing of individual molecules of the DPB1 gene, using the molecular barcode technology. Conclusion The performance of the automatic genotyping system was comparable to that of systems developed in previous studies. Thus, next-generation sequencing of cDNA is a viable option for HLA genotyping. Electronic supplementary material The online version of this article (10.1186/s12864-017-4300-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hidenobu Segawa
- Department of Molecular and Medical Genetics, Research Institute, Osaka Medical Center for Cancer and Cardiovascular Diseases, 1-3-3 Nakamichi, Higashinari-ku, Osaka, 537-8511, Japan
| | - Yoji Kukita
- Department of Molecular and Medical Genetics, Research Institute, Osaka Medical Center for Cancer and Cardiovascular Diseases, 1-3-3 Nakamichi, Higashinari-ku, Osaka, 537-8511, Japan
| | - Kikuya Kato
- Laboratory of Medical Genomics, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0101, Japan.
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Albrecht V, Zweiniger C, Surendranath V, Lang K, Schöfl G, Dahl A, Winkler S, Lange V, Böhme I, Schmidt AH. Dual redundant sequencing strategy: Full-length gene characterisation of 1056 novel and confirmatory HLA alleles. HLA 2017; 90:79-87. [PMID: 28547825 PMCID: PMC6084308 DOI: 10.1111/tan.13057] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 04/19/2017] [Accepted: 05/01/2017] [Indexed: 01/26/2023]
Abstract
The high‐throughput department of DKMS Life Science Lab encounters novel human leukocyte antigen (HLA) alleles on a daily basis. To characterise these alleles, we have developed a system to sequence the whole gene from 5′‐ to 3′‐UTR for the HLA loci A, B, C, DQB1 and DPB1 for submission to the European Molecular Biology Laboratory – European Nucleotide Archive (EMBL‐ENA) and the IPD‐IMGT/HLA Database. Our workflow is based on a dual redundant sequencing strategy. Using shotgun sequencing on an Illumina MiSeq instrument and single molecule real‐time (SMRT) sequencing on a PacBio RS II instrument, we are able to achieve highly accurate HLA full‐length consensus sequences. Remaining conflicts are resolved using the R package DR2S (Dual Redundant Reference Sequencing). Given the relatively high throughput of this strategy, we have developed the semi‐automated web service TypeLoader, to aid in the submission of sequences to the EMBL‐ENA and the IPD‐IMGT/HLA Database. In the IPD‐IMGT/HLA Database release 3.24.0 (April 2016; prior to the submission of the sequences described here), only 5.2% of all known HLA alleles have been fully characterised together with intronic and UTR sequences. So far, we have applied our strategy to characterise and submit 1056 HLA alleles, thereby more than doubling the number of fully characterised alleles. Given the increasing application of next generation sequencing (NGS) for full gene characterisation in clinical practice, extending the HLA database concomitantly is highly desirable. Therefore, we propose this dual redundant sequencing strategy as a workflow for submission of novel full‐length alleles and characterisation of sequences that are as yet incomplete. This would help to mitigate the predominance of partially known alleles in the database.
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Affiliation(s)
| | | | | | - K Lang
- DKMS Life Science Lab, Dresden, Germany
| | - G Schöfl
- DKMS Life Science Lab, Dresden, Germany
| | - A Dahl
- Deep Sequencing Group, CRTD - Center for Regenerative Therapies Dresden, Dresden, Germany
| | - S Winkler
- DNA Sequencing, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - V Lange
- DKMS Life Science Lab, Dresden, Germany
| | - I Böhme
- DKMS Life Science Lab, Dresden, Germany
| | - A H Schmidt
- DKMS Life Science Lab, Dresden, Germany.,DKMS, Tübingen, Germany
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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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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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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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Abstract
The invention of the Polymerase Chain Reaction (PCR) has revolutionized molecular biology enabling gene isolation and characterization in hours rather than days. Scientists working in transplant diagnostics have proven to be pioneers in adapting this molecular technique to the clinical needs of histocompatibility testing. This chapter describes a number of novel genotyping technologies which have been used to address the challenges posed by genetic diversity seen in the extensive polymorphism in HLA genes. These novel approaches include single-stranded and duplex conformational analyses, real-time PCR, microarray hybridization, RNA-based sequencing, and the present day Next Generation Sequencing. The chapter concludes with a brief look at a possible next, Next Generation Sequencing system.
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Chang CJ, Chen PL, Yang WS, Chao KM. A fault-tolerant method for HLA typing with PacBio data. BMC Bioinformatics 2014; 15:296. [PMID: 25183223 PMCID: PMC4161847 DOI: 10.1186/1471-2105-15-296] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 08/26/2014] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Human leukocyte antigen (HLA) genes are critical genes involved in important biomedical aspects, including organ transplantation, autoimmune diseases and infectious diseases. The gene family contains the most polymorphic genes in humans and the difference between two alleles is only a single base pair substitution in many cases. The next generation sequencing (NGS) technologies could be used for high throughput HLA typing but in silico methods are still needed to correctly assign the alleles of a sample. Computer scientists have developed such methods for various NGS platforms, such as Illumina, Roche 454 and Ion Torrent, based on the characteristics of the reads they generate. However, the method for PacBio reads was less addressed, probably owing to its high error rates. The PacBio system has the longest read length among available NGS platforms, and therefore is the only platform capable of having exon 2 and exon 3 of HLA genes on the same read to unequivocally solve the ambiguity problem caused by the "phasing" issue. RESULTS We proposed a new method BayesTyping1 to assign HLA alleles for PacBio circular consensus sequencing reads using Bayes' theorem. The method was applied to simulated data of the three loci HLA-A, HLA-B and HLA-DRB1. The experimental results showed its capability to tolerate the disturbance of sequencing errors and external noise reads. CONCLUSIONS The BayesTyping1 method could overcome the problems of HLA typing using PacBio reads, which mostly arise from sequencing errors of PacBio reads and the divergence of HLA genes, to some extent.
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Affiliation(s)
- Chia-Jung Chang
- />Department of Computer Science and Information Engineering, National Taiwan University, No.1, Sec.4, Roosevelt Road, Taipei, 10617 Taiwan
| | - Pei-Lung Chen
- />Departments of Medical Genetics and Internal Medicine, National Taiwan University Hospital, No. 8, Chung Shan S. Road, Taipei, 10041 Taiwan
- />Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, No. 1, Sec. 1, Jen Ai Road, Taipei, 10051 Taiwan
- />Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, No.1, Sec.4, Roosevelt Road, Taipei, 10617 Taiwan
- />Graduate Institute of Medical Genomics and Proteomics, National Taiwan University, No.1, Sec.4, Roosevelt Road, Taipei, 10617 Taiwan
| | - Wei-Shiung Yang
- />Departments of Medical Genetics and Internal Medicine, National Taiwan University Hospital, No. 8, Chung Shan S. Road, Taipei, 10041 Taiwan
- />Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, No. 1, Sec. 1, Jen Ai Road, Taipei, 10051 Taiwan
- />Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, No.1, Sec.4, Roosevelt Road, Taipei, 10617 Taiwan
| | - Kun-Mao Chao
- />Department of Computer Science and Information Engineering, National Taiwan University, No.1, Sec.4, Roosevelt Road, Taipei, 10617 Taiwan
- />Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, No.1, Sec.4, Roosevelt Road, Taipei, 10617 Taiwan
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Roberts T, Tumer G, Gebel HM, Bray RA. Solid-phase assays for the detection of alloantibody against human leukocyte antigens: Panacea or Pandora? Int J Immunogenet 2014; 41:362-9. [DOI: 10.1111/iji.12138] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 05/30/2014] [Accepted: 06/12/2014] [Indexed: 12/01/2022]
Affiliation(s)
- T. Roberts
- Department of Pathology; Emory University; Atlanta GA USA
| | - G. Tumer
- Department of Pathology; Emory University; Atlanta GA USA
| | - H. M. Gebel
- Department of Pathology; Emory University; Atlanta GA USA
| | - R. A. Bray
- Department of Pathology; Emory University; Atlanta GA USA
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11
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Status report from ‘double agent HLA’: Health and disease. Mol Immunol 2013; 55:2-7. [DOI: 10.1016/j.molimm.2012.08.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Revised: 07/31/2012] [Accepted: 08/07/2012] [Indexed: 11/19/2022]
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12
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Kim HJ, Pourmand N. HLA typing from RNA-seq data using hierarchical read weighting [corrected]. PLoS One 2013; 8:e67885. [PMID: 23840783 PMCID: PMC3696101 DOI: 10.1371/journal.pone.0067885] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Accepted: 05/23/2013] [Indexed: 11/18/2022] Open
Abstract
Correctly matching the HLA haplotypes of donor and recipient is essential to the success of allogenic hematopoietic stem cell transplantation. Current HLA typing methods rely on targeted testing of recognized antigens or sequences. Despite advances in Next Generation Sequencing, general high throughput transcriptome sequencing is currently underutilized for HLA haplotyping due to the central difficulty in aligning sequences within this highly variable region. Here we present the method, HLAforest, that can accurately predict HLA haplotype by hierarchically weighting reads and using an iterative, greedy, top down pruning technique. HLAforest correctly predicts >99% of allele group level (2 digit) haplotypes and 93% of peptide-level (4 digit) haplotypes of the most diverse HLA genes in simulations with read lengths and error rates modeling currently available sequencing technology. The method is very robust to sequencing error and can predict 99% of allele-group level haplotypes with substitution rates as high as 8.8%. When applied to data generated from a trio of cell lines, HLAforest corroborated PCR-based HLA haplotyping methods and accurately predicted 16/18 (89%) major class I genes for a daughter-father-mother trio at the peptide level. Major class II genes were predicted with 100% concordance between the daughter-father-mother trio. In fifty HapMap samples with paired end reads just 37 nucleotides long, HLAforest predicted 96.5% of allele group level HLA haplotypes correctly and 83% of peptide level haplotypes correctly. In sixteen RNAseq samples with limited coverage across HLA genes, HLAforest predicted 97.7% of allele group level haplotypes and 85% of peptide level haplotypes correctly.
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Affiliation(s)
- Hyunsung John Kim
- Biomolecular Engineering Department, Baskin School of Engineering, University of California, Santa Cruz, Santa Cruz, California, United States of America
- * E-mail: (HJK); (NP)
| | - Nader Pourmand
- Biomolecular Engineering Department, Baskin School of Engineering, University of California, Santa Cruz, Santa Cruz, California, United States of America
- * E-mail: (HJK); (NP)
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CD4 T-cell memory responses to viral infections of humans show pronounced immunodominance independent of duration or viral persistence. J Virol 2012; 87:2617-27. [PMID: 23255792 DOI: 10.1128/jvi.03047-12] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Little is known concerning immunodominance within the CD4 T-cell response to viral infections and its persistence into long-term memory. We tested CD4 T-cell reactivity against each viral protein in persons immunized with vaccinia virus (VV), either recently or more than 40 years ago, as a model self-limited viral infection. Similar tests were done with persons with herpes simplex virus 1 (HSV-1) infection as a model chronic infection. We used an indirect method capable of counting the CD4 T cells in blood reactive with each individual viral protein. Each person had a clear CD4 T-cell dominance hierarchy. The top four open reading frames accounted for about 40% of CD4 virus-specific T cells. Early and long-term memory CD4 T-cell responses to vaccinia virus were mathematically indistinguishable for antigen breadth and immunodominance. Despite the chronic intermittent presence of HSV-1 antigen, the CD4 T-cell dominance and diversity patterns for HSV-1 were identical to those observed for vaccinia virus. The immunodominant CD4 T-cell antigens included both long proteins abundantly present in virions and shorter, nonstructural proteins. Limited epitope level and direct ex vivo data were also consistent with pronounced CD4 T-cell immunodominance. We conclude that human memory CD4 T-cell responses show a pattern of pronounced immunodominance for both chronic and self-limited viral infections and that this pattern can persist over several decades in the absence of antigen.
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Dunn PPJ. Human leucocyte antigen typing: techniques and technology, a critical appraisal. Int J Immunogenet 2012; 38:463-73. [PMID: 22059555 DOI: 10.1111/j.1744-313x.2011.01040.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Methods for the identification of Human Leukocyte Antigens (HLA) have changed significantly since this group of polymorphic proteins were first characterized by serological reagents in the 1960s and 1970s. The invention and development of the Polymerase Chain Reaction (PCR) has been key in the progress of methods for HLA genotyping. As the complexity of HLA polymorphism has unravelled so it has exposed the weaknesses in techniques such as PCR - Restriction Fragment Length Polymorphism (RFLP) and Reference Strand Mediated Conformation Analysis (RSCA), which are no longer in use today. Methods which have been considered routine laboratory tools in recent years, such as Sequence-Specific Primer - PCR and Sequencing Based Typing (SBT) are now also threatened with extinction, not only because of the depth of HLA variation but also because of the rapid development of Next Generation Sequencing and technologies which will follow this. This review describes the merits and disadvantages of current technologies available to HLA Typing laboratories, future trends and the problems posed by new alleles.
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Affiliation(s)
- P P J Dunn
- Tissue Typing Laboratory, New Zealand Blood Service, Auckland, New Zealand.
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