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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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2
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Sverchkova A, Burkholz S, Rubsamen R, Stratford R, Clancy T. Integrative HLA typing of tumor and adjacent normal tissue can reveal insights into the tumor immune response. BMC Med Genomics 2024; 17:37. [PMID: 38281021 PMCID: PMC10821267 DOI: 10.1186/s12920-024-01808-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 01/12/2024] [Indexed: 01/29/2024] Open
Abstract
BACKGROUND The HLA complex is the most polymorphic region of the human genome, and its improved characterization can help us understand the genetics of human disease as well as the interplay between cancer and the immune system. The main function of HLA genes is to recognize "non-self" antigens and to present them on the cell surface to T cells, which instigate an immune response toward infected or transformed cells. While sequence variation in the antigen-binding groove of HLA may modulate the repertoire of immunogenic antigens presented to T cells, alterations in HLA expression can significantly influence the immune response to pathogens and cancer. METHODS RNA sequencing was used here to accurately genotype the HLA region and quantify and compare the level of allele-specific HLA expression in tumors and patient-matched adjacent normal tissue. The computational approach utilized in the study types classical and non-classical Class I and Class II HLA alleles from RNA-seq while simultaneously quantifying allele-specific or personalized HLA expression. The strategy also uses RNA-seq data to infer immune cell infiltration into tumors and the corresponding immune cell composition of matched normal tissue, to reveal potential insights related to T cell and NK cell interactions with tumor HLA alleles. RESULTS The genotyping method outperforms existing RNA-seq-based HLA typing tools for Class II HLA genotyping. Further, we demonstrate its potential for studying tumor-immune interactions by applying the method to tumor samples from two different subtypes of breast cancer and their matched normal breast tissue controls. CONCLUSIONS The integrative RNA-seq-based HLA typing approach described in the study, coupled with HLA expression analysis, neoantigen prediction and immune cell infiltration, may help increase our understanding of the interplay between a patient's tumor and immune system; and provide further insights into the immune mechanisms that determine a positive or negative outcome following treatment with immunotherapy such as checkpoint blockade.
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Affiliation(s)
- Angelina Sverchkova
- NEC OncoImmunity, Oslo Cancer Cluster, Innovation Park, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Scott Burkholz
- Flow Pharma, Inc, Warrensville Heights, Galaxy Parkway, OH, 4829, USA
| | - Reid Rubsamen
- Flow Pharma, Inc, Warrensville Heights, Galaxy Parkway, OH, 4829, USA
- University Hospitals, Cleveland Medical Center, Cleveland, OH, USA
- Case Western Reserve School of Medicine, Cleveland, OH, USA
| | - Richard Stratford
- NEC OncoImmunity, Oslo Cancer Cluster, Innovation Park, Oslo, Norway
| | - Trevor Clancy
- NEC OncoImmunity, Oslo Cancer Cluster, Innovation Park, Oslo, Norway.
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Jung K, Kim JG, Shin S, Roh EY, Hong YJ, Song EY. Allele and haplotype frequencies of 11 HLA loci in Koreans by next-generation sequencing. HLA 2023; 101:602-612. [PMID: 36719349 DOI: 10.1111/tan.14980] [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: 01/03/2022] [Revised: 12/24/2022] [Accepted: 01/27/2023] [Indexed: 02/01/2023]
Abstract
Data on HLA genotype distribution, including DQA1 and DPA1, in the Korean population are limited. We aimed to investigate the allele and haplotype frequencies of 11 HLA loci in 339 Korean subjects using next-generation sequencing (NGS)-based HLA typing. A total of 339 samples from unrelated healthy subjects were genotyped for HLA-A, -B, -C, -DRB1, -DRB3, -DRB4, -DRB5, -DQB1, -DQA1, -DPB1, and -DPA1 using two different NGS-based HLA typing kits (166 tested using the NGSgo-MX11-3 kit [GenDx, Netherlands] and 173 by the AllType NGS 11 Loci Amplification kit [One Lambda, USA]). PyPop software was used to estimate allele and haplotype frequencies and linkage disequilibrium between the loci. Additionally, a principal component analysis was performed to compare the allele distribution of Koreans with that of other populations. A total of 214 HLA alleles (97 class I and 117 class II alleles) were assigned. The most frequent alleles for each locus were A*24:02:01 (24.78%), B*15:01:01 (10.18%), C*01:02:01 (18.44%), DRB1*04:05:01 (9.59%), DRB3*02:02:01 (13.72%), DRB4*01:03:01 (25.81%), DRB5*01:01:01 (9.0%), DQA1*01:02:01 (16.96%), DQB1*03:01:01 (14.31%), DPA1*01:03:01 (44.4%), and DPB1*05:01:01 (35.1%), respectively. The most frequent haplotypes were A*33:03:01-C*03:02:02-B*58:01:01 for HLA class I (5.01%) and DRB1*04:05:01-DQA1*03:03:01-DQB1*04:01:01-DPA1*02:02:02-DPB1*05:01:01 for HLA class II (6.23%). The total allelic ambiguities by NGS were estimated to be minimal and considerably decreased compared with those by Sanger sequencing. The Japanese population had the most similar allele distribution to Koreans, followed by the Chinese population. Frequency data of 11 HLA loci in Koreans can provide essential data for population genetics and disease association studies.
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Affiliation(s)
- Kiwook Jung
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Laboratory Medicine, Chungbuk National University Hospital, Cheongju, Republic of Korea
| | - Jisoo G Kim
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sue Shin
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Laboratory Medicine, Seoul National University Boramae Medical Center, Seoul, Republic of Korea
| | - Eun Youn Roh
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Laboratory Medicine, Seoul National University Boramae Medical Center, Seoul, Republic of Korea
| | - Yun Ji Hong
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Eun Young Song
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
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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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Brassica and Sinapis Seeds in Medieval Archaeological Sites: An Example of Multiproxy Analysis for Their Identification and Ethnobotanical Interpretation. PLANTS 2022; 11:plants11162100. [PMID: 36015403 PMCID: PMC9412621 DOI: 10.3390/plants11162100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/05/2022] [Accepted: 08/08/2022] [Indexed: 11/22/2022]
Abstract
The genus Brassica includes some of the most important vegetable and oil crops worldwide. Many Brassica seeds (which can show diagnostic characters useful for species identification) were recovered from two archaeological sites in northern Italy, dated from between the Middle Ages and the Renaissance. We tested the combined use of archaeobotanical keys, ancient DNA barcoding, and references to ancient herbarium specimens to address the issue of diagnostic uncertainty. An unequivocal conventional diagnosis was possible for much of the material recovered, with the samples dominated by five Brassica species and Sinapis. The analysis using ancient DNA was restricted to the seeds with a Brassica-type structure and deployed a variant of multiplexed tandem PCR. The quality of diagnosis strongly depended on the molecular locus used. Nevertheless, many seeds were diagnosed down to species level, in concordance with their morphological identification, using one primer set from the core barcode site (matK). The number of specimens found in the Renaissance herbaria was not high; Brassica nigra, which is of great ethnobotanical importance, was the most common taxon. Thus, the combined use of independent means of species identification is particularly important when studying the early use of closely related crops, such as Brassicaceae.
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Li Y, Nieuwenhuis LM, Keating BJ, Festen EA, de Meijer VE. The Impact of Donor and Recipient Genetic Variation on Outcomes After Solid Organ Transplantation: A Scoping Review and Future Perspectives. Transplantation 2022; 106:1548-1557. [PMID: 34974452 PMCID: PMC9311456 DOI: 10.1097/tp.0000000000004042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 11/16/2021] [Accepted: 11/25/2021] [Indexed: 11/25/2022]
Abstract
At the outset of solid organ transplantation, genetic variation between donors and recipients was recognized as a major player in mechanisms such as allograft tolerance and rejection. Genome-wide association studies have been very successful in identifying novel variant-trait associations, but have been difficult to perform in the field of solid organ transplantation due to complex covariates, era effects, and poor statistical power for detecting donor-recipient interactions. To overcome a lack of statistical power, consortia such as the International Genetics and Translational Research in Transplantation Network have been established. Studies have focused on the consequences of genetic dissimilarities between donors and recipients and have reported associations between polymorphisms in candidate genes or their regulatory regions with transplantation outcomes. However, knowledge on the exact influence of genetic variation is limited due to a lack of comprehensive characterization and harmonization of recipients' or donors' phenotypes and validation using an experimental approach. Causal research in genetics has evolved from agnostic discovery in genome-wide association studies to functional annotation and clarification of underlying molecular mechanisms in translational studies. In this overview, we summarize how the recent advances and progresses in the field of genetics and genomics have improved the understanding of outcomes after solid organ transplantation.
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Affiliation(s)
- Yanni Li
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Lianne M. Nieuwenhuis
- Department of Surgery, section of Hepatobiliary Surgery and Liver Transplantation, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Brendan J. Keating
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Eleonora A.M. Festen
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Vincent E. de Meijer
- Department of Surgery, section of Hepatobiliary Surgery and Liver Transplantation, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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Cornaby C, Montgomery MC, Liu C, Weimer ET. Unique Molecular Identifier-Based High-Resolution HLA Typing and Transcript Quantitation Using Long-Read Sequencing. Front Genet 2022; 13:901377. [PMID: 35879986 PMCID: PMC9308011 DOI: 10.3389/fgene.2022.901377] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 05/05/2022] [Indexed: 01/03/2023] Open
Abstract
HLA typing provides essential results for stem cell and solid organ transplants, as well as providing diagnostic benefits for various rheumatology, gastroenterology, neurology, and infectious diseases. It is becoming increasingly clear that understanding the expression of patient HLA transcripts can provide additional benefits for many of these same patient groups. Our study cohort was evaluated using a long-read RNA sequencing methodology to provide rapid HLA genotyping results and normalized HLA transcript expression. Our assay used NGSEngine to determine the HLA genotyping result and normalized mRNA transcript expression using Athlon2. The assay demonstrated an excellent concordance rate of 99.7%. Similar to previous studies, for the class I loci, patients demonstrated significantly lower expression of HLA-C than HLA-A and -B (Mann-Whitney U, p value = 0.0065 and p value = 0.0154, respectively). In general, the expression of class II transcripts was lower than that of class I transcripts. This study demonstrates a rapid high-resolution HLA typing assay using RNA-Seq that can provide accurate HLA genotyping and HLA allele-specific transcript expression in 7-8 h, a timeline short enough to perform the assay for deceased donors.
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Affiliation(s)
- Caleb Cornaby
- Molecular Immunology Laboratory, McLendon Clinical Laboratories, UNC Health, Chapel Hill, NC, United States
| | - Maureen C Montgomery
- Molecular Immunology Laboratory, McLendon Clinical Laboratories, UNC Health, Chapel Hill, NC, United States
| | - Chang Liu
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, School of Medicine, Washington University in St. Louis, St. Louis, MO, United States
| | - Eric T Weimer
- Molecular Immunology Laboratory, McLendon Clinical Laboratories, UNC Health, Chapel Hill, NC, United States.,Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, United States
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Lin G, Zhang K, Li J. A national proficiency scheme for human leucocyte antigen typing by next-generation sequencing. Clin Chim Acta 2022; 533:85-88. [PMID: 35738456 DOI: 10.1016/j.cca.2022.06.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 06/12/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUND Accurate human leucocyte antigen (HLA) typing is essential for solid organ transplantation (SOT) and hematopoietic stem cell transplantation (HSCT). Next-generation sequencing (NGS) is increasingly adopted by clinical laboratories performing HLA typing. To ensure reliable NGS-based HLA typing throughout China, a HLA-NGS proficiency testing (PT) scheme was set up. METHODS A panel of 10 DNA reference materials for 11 HLA loci were distributed to 24 participants. They were asked to submit NGS typing results for at least six loci including HLA-A, HLA-B, HLA-C, HLA-DRB1, HLA-DQB1, and HLA-DPB1. Information regarding individual laboratory's sample preparation method, NGS platform, and genotyping software was also collected. RESULTS Thirteen participants correctly identified HLA alleles in all samples. The total concordance rate for all HLA alleles typed was 99.2% (3390/3420). The overall discordance was 0.2% (3/1440) for Class I, and 1.4% (27/1980) for Class II loci. Further investigation of the typing mistakes pointed to poor sequencing coverage and wrong allele calls. The errors identified reflect the deficient aspect of NGS in HLA typing, which may have implications for quality improvement for relevant laboratories. CONCLUSIONS The results of this PT underscore the necessity of regular participation in external quality assessment for clinical laboratories that perform HLA-NGS typing.
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Affiliation(s)
- Guigao Lin
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/ National Center of Gerontology, PR China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China
| | - Kuo Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/ National Center of Gerontology, PR China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/ National Center of Gerontology, PR China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China.
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Shimizu M, Takahashi D, Suzuki S, Shigenari A, Ito S, Miyata S, Satake M, Matsuhashi M, Kulski JK, Murata M, Azuma F, Shiina T. A novel swab storage gel is superior to dry swab DNA collection, and enables long-range high resolution NGS HLA typing from buccal cell samples. HLA 2022; 99:590-606. [PMID: 35322605 DOI: 10.1111/tan.14611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 01/31/2022] [Accepted: 03/21/2022] [Indexed: 11/29/2022]
Abstract
HLA sequence-based DNA typing (SBT) by long-range PCR amplification (LR PCR) and next-generation sequencing (NGS) is a high-throughput DNA sequencing method (LR-NGS-SBT) for the efficient and sensitive detection of novel and null HLA alleles to the field-4 level of allelic resolution without phase ambiguity. However, the accuracy and reliability of the HLA typing results using buccal cells (BCs) and saliva as genetic source materials for the LR-NGS-SBT method are dependent largely on the quality of the extracted genomic DNA (gDNA) because a large degree of gDNA fragmentation can result in insufficient PCR amplification with the incorrect assignment of HLA alleles due to allele dropouts. In this study, we developed a new cost-efficient swab storage gel (SSG) for wet swab collection of BCs (BC-SSG) and evaluated its usefulness by performing different DNA analytical parameters including LR-NGS-SBT to compare the quality and quantity of gDNA extracted from BCs (in SSG or air dried), blood and saliva of 30 subjects. The BC-SSG samples after 5 days of storage revealed qualitative and quantitative DNA values equivalent to that of blood and/or saliva and better than swabs that were only air-dried (BC-nSSG). Moreover, all the gDNA extracted from blood, saliva and BC-SSG samples were HLA-typed successfully to an equivalent total of 408 alleles for each sample type. Therefore, the application of BC-SSG collection media for LR-NGS-SBT has benefits over BC dried samples (dry swabs) such as reducing retesting and the number of untestable BC samples due to insufficient DNA amplification. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Marie Shimizu
- Central Blood Institute, Japanese Red Cross Society, Tokyo, Japan
| | | | - Shingo Suzuki
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa, Japan
| | - Atsuko Shigenari
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa, Japan
| | - Sayaka Ito
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa, Japan
| | - Shigeki Miyata
- Central Blood Institute, Japanese Red Cross Society, Tokyo, Japan
| | - Masahiro Satake
- Central Blood Institute, Japanese Red Cross Society, Tokyo, Japan
| | - Mika Matsuhashi
- Kanto-Koshinetsu Block Blood Center, Japanese Red Cross Society, Tokyo, Japan
| | - Jerzy K Kulski
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa, Japan.,Discipline of Psychiatry, Medical School, The University of Western Australia, Crawley, WA, Australia
| | - Makoto Murata
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Aichi, Japan
| | - Fumihiro Azuma
- Blood Service Headquarters, Japanese Red Cross Society, Tokyo, Japan
| | - Takashi Shiina
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa, Japan
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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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11
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Next generation sequencing of human platelet antigens for routine clinical investigations and donor screening. Transfus Med Rev 2022; 36:87-96. [DOI: 10.1016/j.tmrv.2022.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/04/2022] [Accepted: 01/06/2022] [Indexed: 11/21/2022]
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12
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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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13
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Rosenbaum JN, Berry AB, Church AJ, Crooks K, Gagan JR, López-Terrada D, Pfeifer JD, Rennert H, Schrijver I, Snow AN, Wu D, Ewalt MD. A Curriculum for Genomic Education of Molecular Genetic Pathology Fellows: A Report of the Association for Molecular Pathology Training and Education Committee. J Mol Diagn 2021; 23:1218-1240. [PMID: 34245921 DOI: 10.1016/j.jmoldx.2021.07.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 06/16/2021] [Accepted: 07/01/2021] [Indexed: 12/19/2022] Open
Abstract
Molecular genetic pathology (MGP) is a subspecialty of pathology and medical genetics and genomics. Genomic testing, which we define as that which generates large data sets and interrogates large segments of the genome in a single assay, is increasingly recognized as essential for optimal patient care through precision medicine. The most common genomic testing technologies in clinical laboratories are next-generation sequencing and microarray. It is essential to train in these methods and to consider the data generated in the context of the diagnosis, medical history, and other clinical findings of individual patients. Accordingly, updating the MGP fellowship curriculum to include genomics is timely, important, and challenging. At the completion of training, an MGP fellow should be capable of independently interpreting and signing out results of a wide range of genomic assays and, given the appropriate context and institutional support, of developing and validating new assays in compliance with applicable regulations. The Genomics Task Force of the MGP Program Directors, a working group of the Association for Molecular Pathology Training and Education Committee, has developed a genomics curriculum framework and recommendations specific to the MGP fellowship. These recommendations are presented for consideration and implementation by MGP fellowship programs with the understanding that MGP programs exist in a diversity of clinical practice environments with a spectrum of available resources.
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Affiliation(s)
- Jason N Rosenbaum
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Anna B Berry
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Swedish Cancer Institute and Institute of Systems Biology, Seattle, Washington
| | - Alanna J Church
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Boston Children's Hospital, Boston, Massachusetts
| | - Kristy Crooks
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Jeffrey R Gagan
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Dolores López-Terrada
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Baylor College of Medicine, Houston, Texas
| | - John D Pfeifer
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Washington University School of Medicine, St. Louis, Missouri
| | - Hanna Rennert
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Iris Schrijver
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Anthony N Snow
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, University of Iowa Hospitals and Clinics, Iowa City, Iowa
| | - David Wu
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
| | - Mark D Ewalt
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
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14
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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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15
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Yu Y, Wang K, Fahira A, Yang Q, Sun R, Li Z, Wang Z, Shi Y. Systematic comparative study of computational methods for HLA typing from next-generation sequencing. HLA 2021; 97:481-492. [PMID: 33655664 DOI: 10.1111/tan.14244] [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: 11/24/2020] [Revised: 02/21/2021] [Accepted: 02/25/2021] [Indexed: 12/25/2022]
Abstract
The human leukocyte antigen (HLA) system plays an important role in hematopoietic stem cell transplantation (HSCT) and organ transplantations, immune disorders as well as oncological immunotherapy. However, HLA typing remains a challenging task due to the high level of polymorphism and homology among HLA genes. Based on the high-throughput next-generation sequencing data, new HLA typing algorithms and software tools were developed. But there is still a deficit of systematic comparative studies to assist in the selection of the optimal analytical approaches under different conditions. Here, we present a detailed comparison of eight software tools for HLA typing on different real datasets (whole-genome sequencing, whole-exome sequencing and transcriptomic sequencing data) and in-silico samples with different sequencing lengths, depths, and error rates. We figure out the algorithms with the best efficiency in different scenarios, and demonstrate the effect of different raw reads on analytical performances. Our results provide a comprehensive picture of specifications and performances of the eight existing HLA genotyping algorithms, which could assist researchers in selecting the most appropriate tool for specific raw datasets.
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Affiliation(s)
- Yuechun Yu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China
| | - Ke Wang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China
| | - Aamir Fahira
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China
| | - Qiangzhen Yang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China
| | - Renliang Sun
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China
| | - Zhiqiang Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China
| | - Zhuo Wang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China
| | - Yongyong Shi
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China
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16
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Yin Y, Butler C, Zhang Q. Challenges in the application of NGS in the clinical laboratory. Hum Immunol 2021; 82:812-819. [PMID: 33892986 DOI: 10.1016/j.humimm.2021.03.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/25/2021] [Accepted: 03/29/2021] [Indexed: 02/07/2023]
Abstract
Next-generation sequencing (NGS), also known as massively parallel sequencing, has revolutionized genomic research. The current advances in NGS technology make it possible to provide high resolution, high throughput HLA typing in clinical laboratories. The focus of this review is on the recent development and implementation of NGS in clinical laboratories. Here, we examine the critical role of NGS technologies in clinical immunology for HLA genotyping. Two major NGS platforms (Illumina and Ion Torrent) are characterized including NGS library preparation, data analysis, and validation. Challenges of NGS implementation in the clinical laboratory are also discussed, including sequencing error rate, bioinformatics, result interpretation, analytic sensitivity, as well as large data storage. This review aims to promote the broader applications of NGS technology in clinical laboratories and advocate for the novel applications of NGS to drive future research.
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Affiliation(s)
- Yuxin Yin
- UCLA Immunogenetics Center, Department of Pathology & Laboratory Medicine, Los Angeles, CA, USA
| | - Carrie Butler
- UCLA Immunogenetics Center, Department of Pathology & Laboratory Medicine, Los Angeles, CA, USA
| | - Qiuheng Zhang
- UCLA Immunogenetics Center, Department of Pathology & Laboratory Medicine, Los Angeles, CA, USA.
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17
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Liu P, Yao M, Gong Y, Song Y, Chen Y, Ye Y, Liu X, Li F, Dong H, Meng R, Chen H, Zheng A. Benchmarking the Human Leukocyte Antigen Typing Performance of Three Assays and Seven Next-Generation Sequencing-Based Algorithms. Front Immunol 2021; 12:652258. [PMID: 33868290 PMCID: PMC8045758 DOI: 10.3389/fimmu.2021.652258] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 03/03/2021] [Indexed: 11/13/2022] Open
Abstract
With the great progress made recently in next generation sequencing (NGS) technology, sequencing accuracy and throughput have increased, while the cost for data has decreased. Various human leukocyte antigen (HLA) typing algorithms and assays have been developed and have begun to be used in clinical practice. In this study, we compared the HLA typing performance of three HLA assays and seven NGS-based HLA algorithms and assessed the impact of sequencing depth and length on HLA typing accuracy based on 24 benchmarked samples. The algorithms HISAT-genotype and HLA-HD showed the highest accuracy at both the first field and the second field resolution, followed by HLAscan. Our internal capture-based HLA assay showed comparable performance with whole exome sequencing (WES). We found that the minimal depth was 100X for HISAT-genotype and HLA-HD to obtain more than 90% accuracy at the third field level. The top three algorithms were quite robust to the change of read length. Thus, we recommend using HISAT-genotype and HLA-HD for NGS-based HLA genotyping because of their higher accuracy and robustness to read length. We propose that a minimal sequence depth for obtaining more than 90% HLA typing accuracy at the third field level is 100X. Besides, targeting capture-based NGS HLA typing may be more suitable than WES in clinical practice due to its lower sequencing cost and higher HLA sequencing depth.
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Affiliation(s)
- Ping Liu
- Department of Oncology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Minya Yao
- The First Affiliated Hospital of Zhejiang University, School of Medicine, Hangzhou, China
| | - Yu Gong
- Department of Urology, Second Affiliated Hospital, Zhejiang University College of Medicine, Hangzhou, China
| | - Yunjie Song
- The Bioinformatics Department, 3DMed Inc., Shanghai, China
| | - Yanan Chen
- The Bioinformatics Department, 3DMed Inc., Shanghai, China
| | - Yizhou Ye
- The Bioinformatics Department, 3DMed Inc., Shanghai, China
| | - Xiao Liu
- The Bioinformatics Department, 3DMed Inc., Shanghai, China
| | - Fugen Li
- The Bioinformatics Department, 3DMed Inc., Shanghai, China
| | - Hua Dong
- The Bioinformatics Department, 3DMed Inc., Shanghai, China
| | - Rui Meng
- Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hao Chen
- The Bioinformatics Department, 3DMed Inc., Shanghai, China
| | - Aiwen Zheng
- Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China.,Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, Hangzhou, China
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18
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Liu C, Yang X, Duffy BF, Hoisington-Lopez J, Crosby M, Porche-Sorbet R, Saito K, Berry R, Swamidass V, Mitra RD. High-resolution HLA typing by long reads from the R10.3 Oxford nanopore flow cells. Hum Immunol 2021; 82:288-295. [PMID: 33612390 DOI: 10.1016/j.humimm.2021.02.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 02/08/2021] [Accepted: 02/08/2021] [Indexed: 01/12/2023]
Abstract
Nanopore sequencing has been investigated as a rapid and cost-efficient option for HLA typing in recent years. Despite the lower raw read accuracy, encouraging typing accuracy has been reported, and long reads from the platform offer additional benefits of the improved phasing of distant variants. The newly released R10.3 flow cells are expected to provide higher read-level accuracy than previous chemistries. We examined the performance of R10.3 flow cells on the MinION device in HLA typing after enrichment of target genes by multiplexed PCR. We also aimed to mimic a 1-day workflow with 8-24 samples per sequencing run. A diverse collection of 102 unique samples were typed for HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, -DRB1, -DRB3/4/5 loci. The concordance rates at 2-field and 3-field resolutions were 99.5% (1836 alleles) and 99.3% (1710 alleles). We also report important quality metrics from these sequencing runs. Continued research and independent validations are warranted to increase the robustness of nanopore-based HLA typing for broad clinical application.
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Affiliation(s)
- Chang Liu
- Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
| | - Xiao Yang
- GeneGenieDx, 160 E Tasman Dr Ste 109, San Jose, CA, USA
| | - Brian F Duffy
- HLA Laboratory, Barnes-Jewish Hospital, St. Louis, MO, USA
| | - Jessica Hoisington-Lopez
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - MariaLynn Crosby
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Rhonda Porche-Sorbet
- Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Rick Berry
- PlatformSTL, 4340 Duncan Ave. St. Louis, MO, USA
| | | | - Robi D Mitra
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
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19
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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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20
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Liu C. A long road/read to rapid high-resolution HLA typing: The nanopore perspective. Hum Immunol 2020; 82:488-495. [PMID: 32386782 DOI: 10.1016/j.humimm.2020.04.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/24/2020] [Accepted: 04/29/2020] [Indexed: 01/18/2023]
Abstract
Next-generation sequencing (NGS) has been widely adopted for clinical HLA typing and advanced immunogenetics researches. Current methodologies still face challenges in resolving cis-trans ambiguity involving distant variant positions, and the turnaround time is affected by testing volume and batching. Nanopore sequencing may become a promising addition to the existing options for HLA typing. The technology delivered by the MinION sequencer of Oxford Nanopore Technologies (ONT) can record the ionic current changes during the translocation of DNA/RNA strands through transmembrane pores and translate the signals to sequence reads. It features simple and flexible library preparations, long sequencing reads, portable and affordable sequencing devices, and rapid, real-time sequencing. However, the error rate of the sequencing reads is high and remains a hurdle for its broad application. This review article will provide a brief overview of this technology and then focus on the opportunities and challenges of using nanopore sequencing for high-resolution HLA typing and immunogenetics research.
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Affiliation(s)
- Chang Liu
- Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63105, United States.
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21
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Liu C, Duffy BF, Weimer ET, Montgomery MC, Jennemann JE, Hill R, Phelan D, Lay L, Parikh BA. Performance of a multiplexed amplicon-based next-generation sequencing assay for HLA typing. PLoS One 2020; 15:e0232050. [PMID: 32324777 PMCID: PMC7179861 DOI: 10.1371/journal.pone.0232050] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 04/06/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Next-generation sequencing (NGS) has enabled efficient high-resolution typing of human leukocyte antigen (HLA) genes with minimal ambiguity. Most commercially available assays amplify individual or subgroup of HLA genes by long-range PCR followed by library preparation and sequencing. The AllType assay simplifies the workflow by amplifying 11 transplant-relevant HLA genes in one PCR reaction. Here, we report the performance of this unique workflow evaluated using 218 genetically diverse samples. METHODS Five whole genes (HLA-A/B/C/DQA1/DPA1) and six near-whole genes (HLA-DRB1/DRB345/DQB1/DPB1; excluding exon 1 and part of intron 1) were amplified in a multiplexed, long-range PCR. Manual library preparation was performed per manufacturer's protocol, followed by template preparation and chip loading on the Ion Chef, and sequencing on the Ion S5 sequencer. Pre-specified rules for quality control and repeat testing were followed; technologists were blinded to the reference results. The concordance between AllType and reference results was determined at 2-field resolution. We also describe the ranges of input DNA and library concentrations, read number per sample and per locus, and key health metrics in relation to typing results. RESULTS The concordance rates were 98.6%, 99.8% and 99.9% at the sample (n = 218), genotype (n = 1688), and allele (n = 3376) levels, respectively. Three genotypes were discordant, all of which shared the same G group typing results with the reference. Most ambiguous genotypes (116 out of 144, 80.6%) were due to the lack of exon 1 and intron 1 coverage for HLA-DRB1/DRB345/DQB1/DPB1 genes. A broad range of input DNA concentrations and library concentrations were tolerated. Per sample read numbers were adequate for accurate genotyping. Per locus read numbers showed some inter-lot variations, and a trend toward improved inter-locus balance was observed with later lots of reagents. CONCLUSION The AllType assay on the Ion Chef/Ion S5 platform offers a robust and efficient workflow for clinical HLA typing at the 2-field resolution. The multiplex PCR strategy simplifies the laboratory procedure without compromising the typing accuracy.
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Affiliation(s)
- Chang Liu
- Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Brian F. Duffy
- HLA Laboratory, Barnes-Jewish Hospital, St. Louis, Missouri, United States of America
| | - Eric T. Weimer
- Department of Pathology & Laboratory Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, United States of America
- Molecular Immunology Laboratory, McLendon Clinical Laboratories, UNC Hospitals, Chapel Hill, North Carolina, United States of America
| | - Maureen C. Montgomery
- Molecular Immunology Laboratory, McLendon Clinical Laboratories, UNC Hospitals, Chapel Hill, North Carolina, United States of America
| | - Jo-Ellen Jennemann
- HLA Laboratory, Barnes-Jewish Hospital, St. Louis, Missouri, United States of America
| | - Rachel Hill
- HLA Laboratory, Barnes-Jewish Hospital, St. Louis, Missouri, United States of America
| | - Donna Phelan
- HLA Laboratory, Barnes-Jewish Hospital, St. Louis, Missouri, United States of America
| | - Lindsay Lay
- HLA Laboratory, Barnes-Jewish Hospital, St. Louis, Missouri, United States of America
| | - Bijal A. Parikh
- Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri, United States of America
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22
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Tang C, He Z, Liu H, Xu Y, Huang H, Yang G, Xiao Z, Li S, Liu H, Deng Y, Chen Z, Chen H, He N. Application of magnetic nanoparticles in nucleic acid detection. J Nanobiotechnology 2020; 18:62. [PMID: 32316985 PMCID: PMC7171821 DOI: 10.1186/s12951-020-00613-6] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/25/2020] [Indexed: 12/16/2022] Open
Abstract
Nucleic acid is the main material for storing, copying, and transmitting genetic information. Gene sequencing is of great significance in DNA damage research, gene therapy, mutation analysis, bacterial infection, drug development, and clinical diagnosis. Gene detection has a wide range of applications, such as environmental, biomedical, pharmaceutical, agriculture and forensic medicine to name a few. Compared with Sanger sequencing, high-throughput sequencing technology has the advantages of larger output, high resolution, and low cost which greatly promotes the application of sequencing technology in life science research. Magnetic nanoparticles, as an important part of nanomaterials, have been widely used in various applications because of their good dispersion, high surface area, low cost, easy separation in buffer systems and signal detection. Based on the above, the application of magnetic nanoparticles in nucleic acid detection was reviewed.
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Affiliation(s)
- Congli Tang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Ziyu He
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Hongmei Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Yuyue Xu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Hao Huang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Gaojian Yang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Ziqi Xiao
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Hongna Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Yan Deng
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, 210096 China
| | - Zhu Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Hui Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Nongyue He
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, 210096 China
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23
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Fabreti-Oliveira RA, Oliveira CKF, Vale EMG, Nascimento E. Next-generation sequencing of HLA: validation and identification of new polymorphisms in a Brazilian population. HLA 2020; 96:13-23. [PMID: 32222028 DOI: 10.1111/tan.13880] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 02/27/2020] [Accepted: 03/22/2020] [Indexed: 01/09/2023]
Abstract
BACKGROUND Next-generation sequencing (NGS) is the most modern sequencing technique that has revolutionized HLA typing, providing high-resolution results with low ambiguity rates. This study aimed to show the experiences and challenges of an HLA laboratory in the validation process of the NGS methodology for HLA typing and show the use of this method for the study of HLA genetic diversity. METHODS We used 115 samples that comprised a comprehensive testing panel for validation of the NGS methodology using the AllType kit (One Lambda, Canoga Park, California) on the Ion Torrent S5 NGS platform. All quality metrics were analyzed. During validation, two new HLA sequences were identified and named by the HLA Nomenclature Committee. RESULTS A total of 1380 alleles from the HLA-A, -B, -C, -DRB1, -DQB1, and -DPB1 loci were examined by NGS. This validation panel provided a wide range of HLA sequence variations, including non-CWD HLA alleles, new variants, and homozygous alleles. The concordance rate with Sanger sequencing-based typing was 100.0% for HLA-A, -B, -C, -DRB1, -DQB1, and 99.93% for HLA-DPB1. The newly identified HLA alleles were HLA-B*14:69N and HLA-DQB1*02:145. CONCLUSION We have successfully validated NGS HLA typing despite numerous challenges, contributing to the identification of novel alleles that impact on HLA matching and antibody evaluation in organ and tissue transplantation.
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Affiliation(s)
- Raquel A Fabreti-Oliveira
- Faculty of Medical Sciences, Belo Horizonte, Brazil.,IMUNOLAB-Histocompatibility Laboratory, Belo Horizonte, Brazil
| | | | - Eliane M G Vale
- Faculty of Medical Sciences, Belo Horizonte, Brazil.,IMUNOLAB-Histocompatibility Laboratory, Belo Horizonte, Brazil
| | - Evaldo Nascimento
- Faculty of Medical Sciences, Belo Horizonte, Brazil.,IMUNOLAB-Histocompatibility Laboratory, Belo Horizonte, Brazil
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24
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A new set of reagents and related software used for NGS based classical and non-classical HLA typing showing evidence for a greater HLA haplotype diversity. Hum Immunol 2020; 81:202-205. [PMID: 32122686 DOI: 10.1016/j.humimm.2020.02.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 02/01/2020] [Accepted: 02/12/2020] [Indexed: 01/28/2023]
Abstract
To evaluate the HLA typing performance of a new Long-Range PCR NGS set of reagents and its dedicated software, a panel of 41 reference homozygous cell lines from the International Histocompatibility Working Group (IHWG) and a panel of 376 volunteer bone marrow donors were analyzed for classical and non-classical HLA class I and class II genes. All results, except HLA-DPB1, were obtained without any ambiguities at the 3rd field level. Based on the high resolution performance of the reagents, a number of new alleles have been described not only for classical but also for non-classical HLA class I genes, leading to a more accurate haplotype definition. Linkage disequilibrium between HLA-A and HLA-G genes has been defined at 4th field level of resolution. Moreover, for the first time, HLA-DQA2 and DQB2 polymorphisms and their linkage disequilibrium with DQB1 were described.
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25
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Smith CC, Bixby LM, Miller KL, Selitsky SR, Bortone DS, Hoadley KA, Vincent BG, Serody JS. Using RNA Sequencing to Characterize the Tumor Microenvironment. Methods Mol Biol 2020; 2055:245-272. [PMID: 31502156 DOI: 10.1007/978-1-4939-9773-2_12] [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] [Indexed: 12/20/2022]
Abstract
RNA sequencing (RNA-seq) is an integral tool in immunogenomics, allowing for interrogation of the transcriptome of a tumor and its microenvironment. Analytical methods to deconstruct the genomics data can then be applied to infer gene expression patterns associated with the presence of various immunocyte populations. High quality RNA-seq is possible from formalin-fixed, paraffin-embedded (FFPE), fresh-frozen, and fresh tissue, with a wide variety of sequencing library preparation methods, sequencing platforms, and downstream bioinformatics analyses currently available. Selection of an appropriate library preparation method is largely determined by tissue type, quality of RNA, and quantity of RNA. Downstream of sequencing, many analyses can be applied to the data, including differential gene expression analysis, immune gene signature analysis, gene pathway analysis, T/B-cell receptor inference, HLA inference, and viral transcript quantification. In this chapter, we will describe our workflow for RNA-seq from bulk tissue to evaluable data, including extraction of RNA, library preparation methods, sequencing of libraries, alignment and quality assurance of data, and initial downstream analyses of RNA-seq data to extract relevant immunogenomics features. Systems biology methods that draw additional insights by integrating these features are covered further in Chapters 28 - 30 .
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Affiliation(s)
- C C Smith
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - L M Bixby
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - K L Miller
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - S R Selitsky
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - D S Bortone
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - K A Hoadley
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - B G Vincent
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Division of Hematology/Oncology, Department of Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - J S Serody
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, USA. .,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. .,Division of Hematology/Oncology, Department of Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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26
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Using Nanopore Whole-Transcriptome Sequencing for Human Leukocyte Antigen Genotyping and Correlating Donor Human Leukocyte Antigen Expression with Flow Cytometric Crossmatch Results. J Mol Diagn 2020; 22:101-110. [DOI: 10.1016/j.jmoldx.2019.09.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 08/27/2019] [Accepted: 09/11/2019] [Indexed: 01/07/2023] Open
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27
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Cargou M, Ralazamahaleo M, Blouin L, Top I, Elsermans V, Andreani M, Guidicelli G, Visentin J. Evaluation of the AllType kit for HLA typing using the Ion Torrent S5 XL platform. HLA 2019; 95:30-39. [DOI: 10.1111/tan.13708] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 09/04/2019] [Accepted: 09/20/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Marine Cargou
- CHU de Bordeaux, Laboratoire d'Immunologie et Immunogénétique Hôpital Pellegrin Bordeaux France
- Immuno ConcEpT Bordeaux France
- Université de Bordeaux Bordeaux France
| | - Mamy Ralazamahaleo
- CHU de Bordeaux, Laboratoire d'Immunologie et Immunogénétique Hôpital Pellegrin Bordeaux France
| | - Laura Blouin
- CHU de Bordeaux, Laboratoire d'Immunologie et Immunogénétique Hôpital Pellegrin Bordeaux France
| | - Isabelle Top
- CHRU de Lille, Institut d'Immunologie‐HLA Lille France
| | | | - Marco Andreani
- Laboratorio d'Immunogenetica dei Trapianti IRCCS Ospedale Pediatrico Bambino Gesù Roma Italy
| | - Gwendaline Guidicelli
- CHU de Bordeaux, Laboratoire d'Immunologie et Immunogénétique Hôpital Pellegrin Bordeaux France
| | - Jonathan Visentin
- CHU de Bordeaux, Laboratoire d'Immunologie et Immunogénétique Hôpital Pellegrin Bordeaux France
- Immuno ConcEpT Bordeaux France
- Université de Bordeaux Bordeaux France
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28
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Hayashi S, Moriyama T, Yamaguchi R, Mizuno S, Komura M, Miyano S, Nakagawa H, Imoto S. ALPHLARD-NT: Bayesian Method for Human Leukocyte Antigen Genotyping and Mutation Calling through Simultaneous Analysis of Normal and Tumor Whole-Genome Sequence Data. J Comput Biol 2019; 26:923-937. [PMID: 30942618 PMCID: PMC6748403 DOI: 10.1089/cmb.2018.0224] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Human leukocyte antigen (HLA) genes provide useful information on the relationship between cancer and the immune system. Despite the ease of obtaining these data through next-generation sequencing methods, interpretation of these relationships remains challenging owing to the complexity of HLA genes. To resolve this issue, we developed a Bayesian method, ALPHLARD-NT, to identify HLA germline and somatic mutations as well as HLA genotypes from whole-exome sequencing (WES) and whole-genome sequencing (WGS) data. ALPHLARD-NT showed 99.2% accuracy for WGS-based HLA genotyping and detected five HLA somatic mutations in 25 colon cancer cases. In addition, ALPHLARD-NT identified 88 HLA somatic mutations, including recurrent mutations and a novel HLA-B type, from WES data of 343 colon adenocarcinoma cases. These results demonstrate the potential of ALPHLARD-NT for conducting an accurate analysis of HLA genes even from low-coverage data sets. This method can become an essential tool for comprehensive analyses of HLA genes from WES and WGS data, helping to advance understanding of immune regulation in cancer as well as providing guidance for novel immunotherapy strategies.
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Affiliation(s)
- Shuto Hayashi
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Takuya Moriyama
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Rui Yamaguchi
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Shinichi Mizuno
- Department of Health Sciences, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Mitsuhiro Komura
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Satoru Miyano
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | | | - Seiya Imoto
- Health Intelligence Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
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29
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Point-counterpoint series: Confirmation of homozygous HLA alleles: Is it a necessity? Hum Immunol 2019; 80:151-156. [DOI: 10.1016/j.humimm.2019.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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30
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Raghavan M, Yarzabek B, Zaitouna AJ, Krishnakumar S, Ramon DS. Strategies for the measurements of expression levels and half-lives of HLA class I allotypes. Hum Immunol 2019; 80:221-227. [PMID: 30735755 DOI: 10.1016/j.humimm.2019.02.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 12/05/2018] [Accepted: 02/01/2019] [Indexed: 12/12/2022]
Abstract
HLA class I molecules are highly polymorphic cell surface proteins that trigger immune responses by CD8+ T cells and natural killer (NK) cells. Most humans express six different HLA class I proteins encoded by the HLA-A, HLA-B and HLA-C genes. HLA class I molecules bind to peptide antigens and present these antigens to T cell receptors (TCR) of CD8+ T cells. HLA class I expression levels also regulate NK cell activation. The presence of individual HLA class I genes is linked to many different disease, transplantation and therapy outcomes. An understanding of HLA class I expression and stability patterns is fundamentally important towards a better understanding of the associations of HLA class I genes with disease and treatment outcomes, and towards HLA class I targeting for vaccine development. Quantitative flow cytometry allows for assessments of variations in expression levels of HLA class I molecules in cells from a single blood donor over time, as well as averaged measurements across donors for the same allotype. Since all HLA class I molecules are structurally-related, cellular measurements of the HLA class I expression levels and stabilities of individual variants in human cells require careful choices of donors and antibodies, which are discussed here.
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Affiliation(s)
- Malini Raghavan
- Department of Microbiology and Immunology, Michigan Medicine, 1150 W. Medical Center Drive, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Brogan Yarzabek
- Department of Microbiology and Immunology, Michigan Medicine, 1150 W. Medical Center Drive, University of Michigan, Ann Arbor, MI 48109, USA
| | - Anita J Zaitouna
- Department of Microbiology and Immunology, Michigan Medicine, 1150 W. Medical Center Drive, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sujatha Krishnakumar
- Sirona Genomics, Immucor Inc, Suite A, 1916 Old Middlefield Way Mountain View, CA 94043, USA
| | - Daniel S Ramon
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 5777 E. Mayo Blvd, Phoenix, AZ 85054, USA
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31
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Pérez-Sánchez N, Jurado-Escobar R, Doña I, Soriano-Gomis V, Moreno-Aguilar C, Bartra J, Isidoro-García M, Torres MJ, Cornejo-García JA. Pharmacogenomics as a Tool for Management of Drug Hypersensitivity Reactions. CURRENT TREATMENT OPTIONS IN ALLERGY 2019. [DOI: 10.1007/s40521-019-0199-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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32
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Montgomery MC, Berka J, Weimer ET. Suitability of dried DNA for long-range PCR amplification and HLA typing by next-generation sequencing. Hum Immunol 2018; 80:135-139. [PMID: 30529364 DOI: 10.1016/j.humimm.2018.12.002] [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: 08/06/2018] [Revised: 12/03/2018] [Accepted: 12/03/2018] [Indexed: 12/17/2022]
Abstract
Storage and stable shipment of genomic DNA are of great concern to laboratories that may need to perform testing off archived samples. There are some dry-state storage methods that are available that have the potential to provide a way to store samples at room temperature for long periods of time as well as offer a means to ship DNA to other facilities without the same safety concerns that come with shipping liquid samples. The recovered DNA should be of sufficient integrity such that downstream applications can be performed without concern of the sample quality. This work describes sample properties between two methods of DNA storage, dried (room temperature) and traditional (-80 °C). DNA was evaluated for purity, fragment length, and the ability to generate HLA typing using next-generation sequencing.
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Affiliation(s)
- Maureen C Montgomery
- UNC Hospitals, Molecular Immunology Laboratory, Chapel Hill, NC 27514, United States
| | - Jordan Berka
- UNC-Chapel Hill School of Medicine, Department of Pathology & Laboratory Medicine, Chapel Hill, NC 27514, United States
| | - Eric T Weimer
- UNC Hospitals, Molecular Immunology Laboratory, Chapel Hill, NC 27514, United States; UNC-Chapel Hill School of Medicine, Department of Pathology & Laboratory Medicine, Chapel Hill, NC 27514, United States.
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33
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Allen ES, Yang B, Garrett J, Ball ED, Maiers M, Morris GP. Improved accuracy of clinical HLA genotyping by next-generation DNA sequencing affects unrelated donor search results for hematopoietic stem cell transplantation. Hum Immunol 2018; 79:848-854. [DOI: 10.1016/j.humimm.2018.10.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 09/10/2018] [Accepted: 10/10/2018] [Indexed: 11/24/2022]
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34
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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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35
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Hayashi S, Yamaguchi R, Mizuno S, Komura M, Miyano S, Nakagawa H, Imoto S. ALPHLARD: a Bayesian method for analyzing HLA genes from whole genome sequence data. BMC Genomics 2018; 19:790. [PMID: 30384854 PMCID: PMC6211482 DOI: 10.1186/s12864-018-5169-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 10/15/2018] [Indexed: 12/22/2022] Open
Abstract
Background Although human leukocyte antigen (HLA) genotyping based on amplicon, whole exome sequence (WES), and RNA sequence data has been achieved in recent years, accurate genotyping from whole genome sequence (WGS) data remains a challenge due to the low depth. Furthermore, there is no method to identify the sequences of unknown HLA types not registered in HLA databases. Results We developed a Bayesian model, called ALPHLARD, that collects reads potentially generated from HLA genes and accurately determines a pair of HLA types for each of HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, and -DRB1 genes at 3rd field resolution. Furthermore, ALPHLARD can detect rare germline variants not stored in HLA databases and call somatic mutations from paired normal and tumor sequence data. We illustrate the capability of ALPHLARD using 253 WES data and 25 WGS data from Illumina platforms. By comparing the results of HLA genotyping from SBT and amplicon sequencing methods, ALPHLARD achieved 98.8% for WES data and 98.5% for WGS data at 2nd field resolution. We also detected three somatic point mutations and one case of loss of heterozygosity in the HLA genes from the WGS data. Conclusions ALPHLARD showed good performance for HLA genotyping even from low-coverage data. It also has a potential to detect rare germline variants and somatic mutations in HLA genes. It would help to fill in the current gaps in HLA reference databases and unveil the immunological significance of somatic mutations identified in HLA genes. Electronic supplementary material The online version of this article (10.1186/s12864-018-5169-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shuto Hayashi
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Rui Yamaguchi
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Shinichi Mizuno
- Center for Advanced Medical Innovation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Mitsuhiro Komura
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Satoru Miyano
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Hidewaki Nakagawa
- RIKEN Center for Integrative Medical Sciences, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Seiya Imoto
- Health Intelligence Center, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan.
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36
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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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The Importance of New Generation Sequencing (NGS) HLA Typing in Renal Transplantation—Preliminary Report. Transplant Proc 2018; 50:1605-1615. [DOI: 10.1016/j.transproceed.2018.05.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 04/14/2018] [Accepted: 05/07/2018] [Indexed: 01/03/2023]
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38
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Fabreti-Oliveira R, Lasmar M, Oliveira C, Vale E, Nascimento E. Genetic Mechanisms Involved in the Generation of HLA Alleles in Brazilians: Description and Comparison of HLA Alleles. Transplant Proc 2018; 50:835-840. [DOI: 10.1016/j.transproceed.2018.02.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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39
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Abstract
The HLA region is the most polymorphic genes in the human genome and is associated with an increasing number of disease states. Historically, HLA typing methodology has been governed by phenotypic determination. This practice has evolved into the use of molecular methods such as real-time PCR, sequence-specific oligonucleotides, and sequencing-based methods. Numerous studies have identified HLA matching as a key determinate to improve patient outcomes from transplantation. Solid-organ transplants focus on HLA-DRB1 in renal organ allocation while hematopoietic cell transplants focus on HLA-A, -B, -C, -DRB1 matching. The role of HLA typing in the future will be driven by HLA expression, understanding of HLA haplotypes, and rapid HLA typing.
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Affiliation(s)
- Claire H Edgerly
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Eric T Weimer
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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40
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Abstract
Inferring HLA types from genome-wide sequencing data has gained growing attention with the development of new cost-efficient sequencing technologies and the increasing need to integrate HLA types with transcriptomic or other genomic information for insights into immune-mediated diseases, vaccination, and cancer immunotherapy. PHLAT is a computational tool designed for high-resolution (4-digit) typing of the major class I and class II HLA genes using RNAseq or exome sequencing data as input. We illustrate here how PHLAT can be installed, configured, and executed. This document also provides guidance for how to read and interpret the output results. Finally, the best practices of using PHLAT are also discussed.
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41
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Montgomery MC, Petraroia R, Weimer ET. Buccal swab genomic DNA fragmentation predicts likelihood of successful HLA genotyping by next-generation sequencing. Hum Immunol 2017; 78:634-641. [DOI: 10.1016/j.humimm.2017.08.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 08/07/2017] [Accepted: 08/08/2017] [Indexed: 10/19/2022]
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42
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Gandhi MJ, Ferriola D, Lind C, Duke JL, Huynh A, Papazoglou A, Mackiewicz K, Christiansen M, Dong W, Hsu S, Thomas D, Schneider B, Pierce E, Kearns J, Kamoun M, Monos D, Askar M. Assessing a single targeted next generation sequencing for human leukocyte antigen typing protocol for interoperability, as performed by users with variable experience. Hum Immunol 2017; 78:642-648. [DOI: 10.1016/j.humimm.2017.07.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 06/30/2017] [Accepted: 07/17/2017] [Indexed: 11/17/2022]
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43
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Buchkovich ML, Brown CC, Robasky K, Chai S, Westfall S, Vincent BG, Weimer ET, Powers JG. HLAProfiler utilizes k-mer profiles to improve HLA calling accuracy for rare and common alleles in RNA-seq data. Genome Med 2017; 9:86. [PMID: 28954626 PMCID: PMC5618726 DOI: 10.1186/s13073-017-0473-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 09/11/2017] [Indexed: 11/30/2022] Open
Abstract
Background The human leukocyte antigen (HLA) system is a genomic region involved in regulating the human immune system by encoding cell membrane major histocompatibility complex (MHC) proteins that are responsible for self-recognition. Understanding the variation in this region provides important insights into autoimmune disorders, disease susceptibility, oncological immunotherapy, regenerative medicine, transplant rejection, and toxicogenomics. Traditional approaches to HLA typing are low throughput, target only a few genes, are labor intensive and costly, or require specialized protocols. RNA sequencing promises a relatively inexpensive, high-throughput solution for HLA calling across all genes, with the bonus of complete transcriptome information and widespread availability of historical data. Existing tools have been limited in their ability to accurately and comprehensively call HLA genes from RNA-seq data. Results We created HLAProfiler (https://github.com/ExpressionAnalysis/HLAProfiler), a k-mer profile-based method for HLA calling in RNA-seq data which can identify rare and common HLA alleles with > 99% accuracy at two-field precision in both biological and simulated data. For 68% of novel alleles not present in the reference database, HLAProfiler can correctly identify the two-field precision or exact coding sequence, a significant advance over existing algorithms. Conclusions HLAProfiler allows for accurate HLA calls in RNA-seq data, reliably expanding the utility of these data in HLA-related research and enabling advances across a broad range of disciplines. Additionally, by using the observed data to identify potential novel alleles and update partial alleles, HLAProfiler will facilitate further improvements to the existing database of reference HLA alleles. HLAProfiler is available at https://expressionanalysis.github.io/HLAProfiler/. Electronic supplementary material The online version of this article (doi:10.1186/s13073-017-0473-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Martin L Buchkovich
- Translational Genomics Department, Q2 Solutions
- EA Genomics, a Quintiles Quest Joint Venture, Morrisville, NC, 27560, USA.
| | - Chad C Brown
- Translational Genomics Department, Q2 Solutions
- EA Genomics, a Quintiles Quest Joint Venture, Morrisville, NC, 27560, USA
| | - Kimberly Robasky
- Translational Genomics Department, Q2 Solutions
- EA Genomics, a Quintiles Quest Joint Venture, Morrisville, NC, 27560, USA
| | - Shengjie Chai
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Sharon Westfall
- Translational Genomics Department, Q2 Solutions
- EA Genomics, a Quintiles Quest Joint Venture, Morrisville, NC, 27560, USA
| | - Benjamin G Vincent
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.,Division of Hematology/Oncology, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Eric T Weimer
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Jason G Powers
- Translational Genomics Department, Q2 Solutions
- EA Genomics, a Quintiles Quest Joint Venture, Morrisville, NC, 27560, USA
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44
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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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Alizadeh M, Walencik A, Frassati C, Moskovtchenko P, Lafarge X, Verite F, Semana G. Evidence for a higher resolution of HLA genotyping by a new NGS-based approach. Transfus Clin Biol 2017. [DOI: 10.1016/j.tracli.2017.05.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Yohe S, Thyagarajan B. Review of Clinical Next-Generation Sequencing. Arch Pathol Lab Med 2017; 141:1544-1557. [PMID: 28782984 DOI: 10.5858/arpa.2016-0501-ra] [Citation(s) in RCA: 203] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT - Next-generation sequencing (NGS) is a technology being used by many laboratories to test for inherited disorders and tumor mutations. This technology is new for many practicing pathologists, who may not be familiar with the uses, methodology, and limitations of NGS. OBJECTIVE - To familiarize pathologists with several aspects of NGS, including current and expanding uses; methodology including wet bench aspects, bioinformatics, and interpretation; validation and proficiency; limitations; and issues related to the integration of NGS data into patient care. DATA SOURCES - The review is based on peer-reviewed literature and personal experience using NGS in a clinical setting at a major academic center. CONCLUSIONS - The clinical applications of NGS will increase as the technology, bioinformatics, and resources evolve to address the limitations and improve quality of results. The challenge for clinical laboratories is to ensure testing is clinically relevant, cost-effective, and can be integrated into clinical care.
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Affiliation(s)
- Sophia Yohe
- From the Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis
| | - Bharat Thyagarajan
- From the Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis
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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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Abstract
Ever since the discovery of the major histocompatibility complex, scientific and clinical understanding in the field of transplantation has been advanced through genetic and genomic studies. Candidate-gene approaches and recent genome-wide association studies (GWAS) have enabled a deeper understanding of the complex interplay of the donor-recipient interactions that lead to transplant tolerance or rejection. Genetic analysis in transplantation, when linked to demographic and clinical outcomes, has the potential to drive personalized medicine by enabling individualized risk stratification and immunosuppression through the identification of variants associated with immune-mediated complications, post-transplant disease or alterations in drug-metabolizing genes.
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Affiliation(s)
- Joshua Y C Yang
- Division of Transplant Surgery, University of California San Francisco, 513 Parnassus Avenue, San Francisco, California 94143, USA
| | - Minnie M Sarwal
- Division of Transplant Surgery, University of California San Francisco, 513 Parnassus Avenue, San Francisco, California 94143, USA
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Gandhi MJ, Ferriola D, Huang Y, Duke JL, Monos D. Targeted Next-Generation Sequencing for Human Leukocyte Antigen Typing in a Clinical Laboratory: Metrics of Relevance and Considerations for Its Successful Implementation. Arch Pathol Lab Med 2017; 141:806-812. [PMID: 28234015 DOI: 10.5858/arpa.2016-0537-ra] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT - Numerous feasibility studies to type human leukocyte antigens (HLAs) by next-generation sequencing (NGS) have led to the development of vendor-supported kits for HLA typing by NGS. Some clinical laboratories have introduced HLA-NGS, and many are investigating the introduction. Standards from accrediting agencies form the regulatory framework for introducing this test into clinical laboratories. OBJECTIVES - To provide an assessment of metrics and considerations relevant to the successful implementation of clinical HLA-NGS typing, and to provide as a reference a validated HLA-NGS protocol used clinically since December 2013 at the Children's Hospital of Philadelphia (Philadelphia, Pennsylvania). DATA SOURCES - The HLA-NGS has been performed on 2532 samples. The initial 1046 and all homozygous samples were also typed by an alternate method. The HLA-NGS demonstrated 99.7% concordance with the alternate method. Ambiguous results were most common at the DPB1 locus because of a lack of phasing between exons 2 and 3 or the unsequenced exon 1 (533 of 2954 alleles; 18.04%) and the DRB1 locus because of not sequencing exon 1 (75 of 3972 alleles; 1.89%). No ambiguities were detected among the other loci. Except for 2 false homozygous samples, all homozygous samples (1891) demonstrated concordance with the alternate method. The article is organized to address the critical elements in the preanalytic, analytic, and postanalytic phases of introducing this assay into the clinical laboratory. CONCLUSIONS - The results demonstrate that HLA typing by NGS is a highly accurate, reproducible, efficient method that provides more-complete sequencing information for the length of the HLA gene and can be the single methodology for HLA typing in clinical immunogenetics laboratories.
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Affiliation(s)
| | | | | | | | - Dimitri Monos
- From the Division of Transfusion Medicine, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota (Dr Gandhi); the Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania (Ms Ferriola and Drs Huang, Duke, and Monos); and the Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia (Dr Monos)
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