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Schmidt AH, Sauter J, Schetelig J, Neujahr E, Pingel J. Providing hematopoietic stem cell products from unrelated donors to the world: DKMS donor centers and DKMS Registry. Best Pract Res Clin Haematol 2024; 37:101541. [PMID: 38490766 DOI: 10.1016/j.beha.2024.101541] [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: 02/15/2024] [Revised: 02/27/2024] [Accepted: 02/29/2024] [Indexed: 03/17/2024]
Abstract
Allogeneic hematopoietic stem cell (HSC) transplantation is a curative therapy for many severe blood diseases. As many patients have no suitable family donor, large unrelated donor registries and donor centers have been established in many countries, along with an international system for the provision of unrelated donor HSC products. As an essential part of this system, DKMS operates donor centers in 7 countries with a total of 12.2 million donors and over 114,000 donations so far, and a multinational donor registry. In 2022, DKMS donors contributed 57.5% of all cross-border donations worldwide. In this review, we describe the international system for the provision of unrelated donor HSC products as well as tasks and responsibilities of donor registries and donor centers. We also discuss relevant aspects of DKMS donor centers, namely donor file composition, matching and donation probabilities and actual donations, and the unique multinational approach of the DKMS Registry.
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Affiliation(s)
- Alexander H Schmidt
- DKMS Group, Tübingen, Germany; DKMS Clinical Trials Unit, Dresden, Germany; DKMS Registry, Tübingen, Germany.
| | | | - Johannes Schetelig
- DKMS Clinical Trials Unit, Dresden, Germany; University Hospital Carl Gustav Carus, Dresden, Germany
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2
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Heinemann FM, Baumgart C, Binder C, Börger V, Fischer JC, Heinold A, Jiménez Klingberg C, Lenz V, Riebschläger S, Zeiler T, Horn PA, Kordelas L. Recruiting refugees and migrants as potential hematopoietic stem cell donors to serve patients of comparable ethnicities with rare human leucocyte antigen patterns - The BluStar.NRW project in North Western Germany. Transpl Immunol 2024; 82:101985. [PMID: 38184211 DOI: 10.1016/j.trim.2024.101985] [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: 09/15/2023] [Revised: 12/12/2023] [Accepted: 01/02/2024] [Indexed: 01/08/2024]
Abstract
Currently, approximately 19 million people with a migration background live in Germany. The majority of those descend from regions where the population has a genetically different distribution of HLA antigens when compared to the HLA frequencies usually found in North Western Europe. In case of severe haematological disorders of these individuals, allogeneic stem cell transplantation may be the treatment of choice. However, finding appropriate histocompatible hematopoietic stem cell donors continues to be a major challenge. If no matching sibling donors are available, there are only few suitable donors with a similar genetic background available in international blood stem cell donor registries. The "BluStar.NRW" project aimed to recruit new blood and hematopoietic stem cell donors with a migration background and to noticeably increase the number of suitable donors for patients within this group. Since December 2017, a total number of 9100 blood and stem cell donors with a migration background were recruited and typed for this project. HLA typing for HLA-A, -B, -C, -DRB1, -DQB1, and -DPB1 was performed by Next Generation Sequencing. We assessed the proportion of rare alleles according to HLA frequency tables, as defined by a frequency of <1:1000. The rare HLA allele frequencies according to HLA frequency tables of the BluStar.NRW cohort were compared with a matched control donor cohort: Rare HLA-A, -B, -C, -DRB1 and -DQB1 alleles occurred three times more frequent than in the control group, but rare HLA-DPB1 alleles occurred more frequently in the control cohort. This difference was highly significant for all HLA alleles (p < 0.0001 for HLA-A, -B, -C, -DRB1, -DPB1; p = 0.0002 for HLA-DQB1). In addition, the distribution of rare alleles differed between the two groups. To date, 29 work-ups were initiated, 12 PBSC, one BM and three DLI were collected so far out of the BluStar.NRW cohort. The apheresis probability is twofold higher (0.18% vs. 0.07%) compared to the control group which clearly shows a serious medical need. However, 13 work-ups were cancelled in the BluStar.NRW donor cohort which represents an almost twice as higher cancellation rate (45% vs. 25%). This single registry analysis with a large sample cohort clearly indicates that hematopoietic stem cell donors with a migration background represent an adequate donor pool to serve patients of comparable ethnicity.
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Affiliation(s)
- F M Heinemann
- Institute for Transfusion Medicine, University Hospital, University Medicine Essen, Germany.
| | - C Baumgart
- Institute for Transfusion Medicine, University Hospital, University Medicine Essen, Germany
| | - C Binder
- Westdeutsche SpenderZentrale WSZE, Ratingen, Germany
| | - V Börger
- Institute for Transfusion Medicine, University Hospital, University Medicine Essen, Germany
| | - J C Fischer
- Institute for Transplantation Diagnostics and Cell Therapeutics, University Hospital Düsseldorf, Düsseldorf, Germany
| | - A Heinold
- Institute for Transfusion Medicine, University Hospital, University Medicine Essen, Germany
| | - C Jiménez Klingberg
- German Red Cross Blood Service West, Hagen, Breitscheid, Münster and Bad-Salzuflen, Germany
| | - V Lenz
- Institute for Transfusion Medicine, University Hospital, University Medicine Essen, Germany
| | - S Riebschläger
- Institute for Transfusion Medicine, University Hospital, University Medicine Essen, Germany
| | - T Zeiler
- German Red Cross Blood Service West, Hagen, Breitscheid, Münster and Bad-Salzuflen, Germany
| | - P A Horn
- Institute for Transfusion Medicine, University Hospital, University Medicine Essen, Germany
| | - L Kordelas
- Westdeutsche SpenderZentrale WSZE, Ratingen, Germany; Clinic for Hematology and Stem Cell Transplantation, University Medicine Essen, Essen, Germany
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Barriga F, Solloch UV, Giani A, Palma J, Wietstruck A, Sarmiento M, Carvallo C, Mosso C, Ramirez P, Sanchez M, Rojas N, Alfaro J, Saldaña S, Ende K, Flaig D, Pattillo I, Schmidt AH. 5 years DKMS Chile: approach, results and impact of the first unrelated stem cell donor center in Chile. Front Med (Lausanne) 2023; 10:1236506. [PMID: 37901400 PMCID: PMC10601464 DOI: 10.3389/fmed.2023.1236506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 09/29/2023] [Indexed: 10/31/2023] Open
Abstract
Introduction Allogeneic hematopoietic stem cell transplantation (allo-HSCT) is performed worldwide to treat blood cancer and other life-threatening blood disorders. As successful transplantation requires an HLA-compatible donor, unrelated donor centers and registries have been established worldwide to identify donors for patients without a family match. Ethnic minorities are underrepresented in large donor registries. Matching probabilities are higher when donors and patients share the same ethnic background, making it desirable to increase the diversity of the global donor pool by recruiting donors in new regions. Here, we report the establishment and the first 5 years of operation of the first unrelated stem cell donor center in Chile, a high-income country in South America with a population of over 19 million. Methods We used online and in-person donor recruitment practices through patient appeals and donor drives in companies, universities, the armed forces, and public services. After confirmatory typing donors were subjected to medical work-up and cleared for donation. Results We recruited almost 170,000 donors in 5 years. There were 1,488 requests received for confirmatory typing and donor availability checks, of which 333 resulted in medical work-up, leading to 194 stem cell collections. Products were shipped to Chile (48.5%) and abroad. Even when the COVID-19 pandemic challenged our activities, the number of donors recruited and shipped stem cell products remained steady. In Chile there was an almost 8-fold increase in unrelated donor transplantation activity from 16 procedures in 2016-2018 to 124 procedures in 2019-2021, mainly for pediatric patients following the center's establishment. We estimate that 49.6% of Chilean patients would find at least one matched unrelated donor in the global DKMS donor pool. Discussion Establishing a DKMS donor center in Chile has significantly increased donor availability for Chilean patients and contributed to an increase of unrelated donor stem cell transplant activity.
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Affiliation(s)
| | | | - Anette Giani
- Fundación de Beneficencia Pública DKMS, Santiago, Chile
| | - Julia Palma
- Hospital Alta Complejidad Luis Calvo Mackenna, Santiago, Chile
| | | | - Mauricio Sarmiento
- Departamento de Hematologia Oncologia, Red de Salud UC Christus, Santiago, Chile
| | | | | | - Pablo Ramirez
- Clinica Las Condes, Santiago, Chile
- Clinica Dávila, Santiago, Chile
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A Single-Center Experience on HLA Typing with 11 Loci Next Generation Sequencing in Korean Patients with Hematologic Disease. Diagnostics (Basel) 2022; 12:diagnostics12051074. [PMID: 35626230 PMCID: PMC9139519 DOI: 10.3390/diagnostics12051074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/23/2022] [Accepted: 04/23/2022] [Indexed: 11/17/2022] Open
Abstract
The human leukocyte antigen (HLA) system comprises the most polymorphic genes of the human genome and is famous for its potential pathological roles. To accurately type HLA genes and find HLA-matched donors, which are critical for effective hematopoietic transplantation, HLA typing using next-generation sequencing (NGS) was implemented. We aimed to share the experience of HLA typing using NGS in patients with hematologic malignancies and evaluate its association with hematologic diseases. Data from 211 Korean, non-familial patients diagnosed with a hematologic disease were reviewed, and NGS was performed for 11 HLA loci. Three-field HLA typing with G code was successfully achieved for all loci and the known linkage between HLA-DRB3/4/5 and HLA-DRB1 was fully matched. Therefore, NGS-based HLA typing enables a detailed, high-resolution analysis of the HLA system that can help with the selection of suitable donors. Notably, HLA-DRB1*08:02:01G was significantly associated with myelodysplastic syndrome. Although this result confirms the tendency of some alleles to be associated with hematological disorders, this may not be the case in hematologic malignancies. Nonetheless, NGS-based HLA typing data for HLA-DP, HLA-DQ, and HLA-DRB3/4/5 are still warranted for a better understanding of the corresponding locus.
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Douillard V, Castelli EC, Mack SJ, Hollenbach JA, Gourraud PA, Vince N, Limou S. Approaching Genetics Through the MHC Lens: Tools and Methods for HLA Research. Front Genet 2021; 12:774916. [PMID: 34925459 PMCID: PMC8677840 DOI: 10.3389/fgene.2021.774916] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/08/2021] [Indexed: 01/11/2023] Open
Abstract
The current SARS-CoV-2 pandemic era launched an immediate and broad response of the research community with studies both about the virus and host genetics. Research in genetics investigated HLA association with COVID-19 based on in silico, population, and individual data. However, they were conducted with variable scale and success; convincing results were mostly obtained with broader whole-genome association studies. Here, we propose a technical review of HLA analysis, including basic HLA knowledge as well as available tools and advice. We notably describe recent algorithms to infer and call HLA genotypes from GWAS SNPs and NGS data, respectively, which opens the possibility to investigate HLA from large datasets without a specific initial focus on this region. We thus hope this overview will empower geneticists who were unfamiliar with HLA to run MHC-focused analyses following the footsteps of the Covid-19|HLA & Immunogenetics Consortium.
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Affiliation(s)
- Venceslas Douillard
- Centre de Recherche en Transplantation et Immunologie, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, Université de Nantes, Nantes, France
| | | | - Steven J. Mack
- Division of Allergy, Immunology and Bone Marrow Transplantation, Department of Pediatrics, School of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Jill A. Hollenbach
- Department of Neurology, University of California, San Francisco, San Francisco, CA, United States
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, United States
| | - Pierre-Antoine Gourraud
- Centre de Recherche en Transplantation et Immunologie, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, Université de Nantes, Nantes, France
| | - Nicolas Vince
- Centre de Recherche en Transplantation et Immunologie, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, Université de Nantes, Nantes, France
| | - Sophie Limou
- Centre de Recherche en Transplantation et Immunologie, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, Université de Nantes, Nantes, France
- Ecole Centrale de Nantes, Department of Computer Sciences and Mathematics in Biology, Nantes, France
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Solloch UV, Schmidt AH, Sauter J. Graphical user interface for the haplotype frequency estimation software Hapl-o-Mat. Hum Immunol 2021; 83:107-112. [PMID: 34799151 DOI: 10.1016/j.humimm.2021.11.002] [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: 06/14/2021] [Revised: 10/07/2021] [Accepted: 11/04/2021] [Indexed: 12/01/2022]
Abstract
Population-specific human leukocyte antigen (HLA) haplotype frequencies are an essential basis of advanced algorithms for donor selection in unrelated hematopoietic stem cell transplantation. In 2016, we introduced Hapl-o-Mat, a versatile tool for haplotype frequency estimation based on an expectation-maximization algorithm (https://github.com/DKMS/hapl-o-Mat). Hapl-o-Mat is specifically tailored to the analysis of HLA genes and able to cope with the heterogeneous genotyping data usually found in donor registries. To make Hapl-o-Mat accessible to a wider range of users, we designed a graphical user interface module that considerably facilitates the interaction with the application (https://github.com/DKMS/hapl-o-Mat_GUI). We further provide a precompiled version of Hapl-o-Mat that can be used on Windows personal computers without dependency on additional software libraries (https://github.com/DKMS/hapl-o-Mat_WinBin). We are confident that these new, user-oriented features will encourage more researchers to apply Hapl-o-Mat to their data, thereby increasing knowledge and public availability of population-specific HLA haplotype frequencies.
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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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8
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Mayor NP, Wang T, Lee SJ, Kuxhausen M, Vierra-Green C, Barker DJ, Auletta J, Bhatt VR, Gadalla SM, Gragert L, Inamoto Y, Morris GP, Paczesny S, Reshef R, Ringdén O, Shaw BE, Shaw P, Spellman SR, Marsh SGE. Impact of Previously Unrecognized HLA Mismatches Using Ultrahigh Resolution Typing in Unrelated Donor Hematopoietic Cell Transplantation. J Clin Oncol 2021; 39:2397-2409. [PMID: 33835855 PMCID: PMC8280068 DOI: 10.1200/jco.20.03643] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/08/2021] [Accepted: 03/02/2021] [Indexed: 12/13/2022] Open
Abstract
PURPOSE Ultrahigh resolution (UHR) HLA matching is reported to result in better outcomes following unrelated donor hematopoietic cell transplantation, improving survival and reducing post-transplant complications. However, most studies included relatively small numbers of patients. Here we report the findings from a large, multicenter validation study. METHODS UHR HLA typing was available on 5,140 conventionally 10 out of 10 HLA-matched patients with malignant disease transplanted between 2008 and 2017. RESULTS After UHR HLA typing, 82% of pairs remained 10 out of 10 UHR-matched; 12.3% of patients were 12 out of 12 UHR HLA-matched. Compared with 12 out of 12 UHR-matched patients, probabilities of grade 2-4 acute graft-versus-host disease (aGVHD) were significantly increased with UHR mismatches (overall P = .0019) and in those patients who were HLA-DPB1 T-cell epitope permissively mismatched or nonpermissively mismatched (overall P = .0011). In the T-cell-depleted subset, the degree of UHR HLA mismatch was only associated with increased transplant-related mortality (TRM) (overall P = .0068). In the T-cell-replete subset, UHR HLA matching was associated with a lower probability of aGVHD (overall P = .0020); 12 out of 12 UHR matching was associated with reduced TRM risk when compared with HLA-DPB1 T-cell epitope permissively mismatched patients, whereas nonpermissive mismatching resulted in a greater risk (overall P = .0003). CONCLUSION This study did not confirm that UHR 12 out of 12 HLA matching increases the probability of overall survival but does demonstrate that aGVHD risk, and in certain settings TRM, is lowest in UHR HLA-matched pairs and thus warrants consideration when multiple 10 out of 10 HLA-matched donors of equivalent age are available.
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Affiliation(s)
- Neema P. Mayor
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK
- UCL Cancer Institute, University College London, London, UK
| | - Tao Wang
- Division of Biostatistics, Medical College of Wisconsin, Milwaukee, WI
- Center for International Blood and Marrow Transplant Research, Medical College of Wisconsin, Milwaukee, WI
| | - Stephanie J. Lee
- Center for International Blood and Marrow Transplant Research, National Marrow Donor Program/Be The Match, Minneapolis, MN
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Michelle Kuxhausen
- Center for International Blood and Marrow Transplant Research, National Marrow Donor Program/Be The Match, Minneapolis, MN
| | - Cynthia Vierra-Green
- Center for International Blood and Marrow Transplant Research, National Marrow Donor Program/Be The Match, Minneapolis, MN
| | | | - Jeffrey Auletta
- Blood and Marrow Transplant Program and Host Defense Program, Nationwide Children's Hospital, Columbus, OH
| | - Vijaya R. Bhatt
- Division of Hematology-Oncology, University of Nebraska Medical Center, Omaha, NE
| | - Shahinaz M. Gadalla
- Division of Cancer Epidemiology and Genetics, NIH-NCI Clinical Genetics Branch, Rockville, MD
| | - Loren Gragert
- Tulane Cancer Center, Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA
| | - Yoshihiro Inamoto
- Department of Hematopoietic Stem Cell Transplantation, National Cancer Center Hospital, Tokyo, Japan
| | - Gerald P. Morris
- Department of Pathology, University of California San Diego, San Diego, CA
| | - Sophie Paczesny
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC
| | - Ran Reshef
- Division of Hematology/Oncology and Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY
| | - Olle Ringdén
- Department of Clinical Sciences, Intervention and Technology, Translational Cell Therapy Research Group, Karolinska Institute, Stockholm, Sweden
| | - Bronwen E. Shaw
- Center for International Blood and Marrow Transplant Research, Medical College of Wisconsin, Milwaukee, WI
| | - Peter Shaw
- Department of Child and Adolescent Health, Cancer Centre for Children, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Stephen R. Spellman
- Center for International Blood and Marrow Transplant Research, National Marrow Donor Program/Be The Match, Minneapolis, MN
| | - Steven G. E. Marsh
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK
- UCL Cancer Institute, University College London, London, UK
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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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10
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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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11
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Mengling T, Rall G, Bernas SN, Astreou N, Bochert S, Boelk T, Buk D, Burkard K, Endert D, Gnant K, Hildebrand S, Köksaldi H, Petit I, Sauter J, Seitz S, Stolze J, Weber K, Weber M, Lange V, Pingel J, Platz A, Schäfer T, Schetelig J, Wienand E, Geist S, Neujahr E, Schmidt AH. Stem cell donor registry activities during the COVID-19 pandemic: a field report by DKMS. Bone Marrow Transplant 2020; 56:798-806. [PMID: 33219340 PMCID: PMC7677905 DOI: 10.1038/s41409-020-01138-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 09/18/2020] [Accepted: 11/03/2020] [Indexed: 11/09/2022]
Abstract
The COVID-19 pandemic has serious implications also for patients with other diseases. Here, we describe the effects of the pandemic on unrelated hematopoietic stem cell donation and transplantation from the perspective of DKMS, a large international donor registry. Especially, we cover the development of PBSC and bone marrow collection figures, donor management including Health and Availability Check (HAC), transport and cryopreservation of stem cell products, donor recruitment and business continuity measures. The total number of stem cell products provided declined by around 15% during the crisis with a particularly strong decrease in bone marrow products. We modified donor management processes to ensure donor and product safety. HAC instead of confirmatory typing was helpful especially in countries with strict lockdowns. New transport modes were developed so that stem cell products could be safely delivered despite COVID-19-related travel restrictions. Cryopreservation of stem cell products became the new temporary standard during the pandemic to minimize risks related to transport logistics and donor availability. However, many products from unrelated donors will never be transfused. DKMS discontinued public offline donor recruitment, leading to a 40% decline in new donors during the crisis. Most DKMS employees worked from home to ensure business continuity during the crisis.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Julia Pingel
- DKMS, Tübingen, Germany.,DKMS Registry, Tübingen, Germany
| | - Alexander Platz
- DKMS Life Science Lab, Dresden, Germany.,DKMS Stem Cell Bank, Dresden, Germany
| | - Thomas Schäfer
- DKMS Life Science Lab, Dresden, Germany.,DKMS Stem Cell Bank, Dresden, Germany
| | - Johannes Schetelig
- DKMS, Clinical Trials Unit, Dresden, Germany.,Medizinische Klinik I, University Hospital Carl Gustav Carus, Dresden, Germany
| | | | | | - Elke Neujahr
- DKMS, Tübingen, Germany.,DKMS Life Science Lab, Dresden, Germany.,DKMS Registry, Tübingen, Germany.,DKMS Stem Cell Bank, Dresden, Germany.,DKMS, Clinical Trials Unit, Dresden, Germany
| | - Alexander H Schmidt
- DKMS, Tübingen, Germany.,DKMS Life Science Lab, Dresden, Germany.,DKMS Registry, Tübingen, Germany.,DKMS Stem Cell Bank, Dresden, Germany.,DKMS, Clinical Trials Unit, Dresden, Germany
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NGS and HLA: The long road ahead. Hum Immunol 2020; 81:280-284. [PMID: 32192758 DOI: 10.1016/j.humimm.2020.03.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 03/04/2020] [Accepted: 03/06/2020] [Indexed: 01/29/2023]
Abstract
This manuscript is a continuation of this laboratory's journey to identifying novel HLA alleles while performing routine clinical HLA laboratory testing. Since our last paper, we have identified an additional 28 novel HLA alleles that are identified and described herein. One novel allele was found in two unrelated patients that were HLA typed for different reasons at two different times, suggesting that novel alleles may be much more frequent than previously expected. If the rate of identification is hindered by bioinformatics challenges, there is a great potential for our patients to suffer needlessly from incomplete information in either diagnostics or unrecognized incompatibilities with potential donors.
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Schmidt AH, Sauter J, Baier DM, Daiss J, Keller A, Klussmeier A, Mengling T, Rall G, Riethmüller T, Schöfl G, Solloch UV, Torosian T, Means D, Kelly H, Jagannathan L, Paul P, Giani AS, Hildebrand S, Schumacher S, Markert J, Füssel M, Hofmann JA, Schäfer T, Pingel J, Lange V, Schetelig J. Immunogenetics in stem cell donor registry work: The DKMS example (Part 1). Int J Immunogenet 2020; 47:13-23. [PMID: 31903698 PMCID: PMC7003907 DOI: 10.1111/iji.12471] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 12/06/2019] [Accepted: 12/06/2019] [Indexed: 01/27/2023]
Abstract
Currently, stem cell donor registries include more than 35 million potential donors worldwide to provide HLA-matched stem cell products for patients in need of an unrelated donor transplant. DKMS is a leading stem cell donor registry with more than 9 million donors from Germany, Poland, the United States, the United Kingdom, India and Chile. DKMS donors have donated hematopoietic stem cells more than 80,000 times. Many aspects of donor registry work are closely related to topics from immunogenetics or population genetics. In this two-part review article, we describe, analyse and discuss these areas of donor registry work by using the example of DKMS. Part 1 of the review gives a general overview on DKMS and includes typical donor registry activities with special focus on the HLA system: high-throughput HLA typing of potential stem cell donors, HLA haplotype frequencies and resulting matching probabilities, and donor file optimization with regard to HLA diversity.
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Affiliation(s)
- Alexander H. Schmidt
- DKMSTübingenGermany
- DKMS Life Science LabDresdenGermany
- DKMSClinical Trials UnitDresdenGermany
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Latha Jagannathan
- DKMS BMST Foundation IndiaBangaloreIndia
- Bangalore Medical Services TrustBangaloreIndia
| | | | | | | | | | | | | | | | | | | | | | - Johannes Schetelig
- DKMSClinical Trials UnitDresdenGermany
- University Hospital Carl Gustav CarusMedizinische Klinik IDresdenGermany
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Klasberg S, Surendranath V, Lange V, Schöfl G. Bioinformatics Strategies, Challenges, and Opportunities for Next Generation Sequencing-Based HLA Genotyping. Transfus Med Hemother 2019; 46:312-325. [PMID: 31832057 PMCID: PMC6876610 DOI: 10.1159/000502487] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 07/30/2019] [Indexed: 12/16/2022] Open
Abstract
The advent of next generation sequencing (NGS) has altered the face of genotyping the human leukocyte antigen (HLA) system in clinical, stem cell donor registry, and research contexts. NGS has led to a dramatically increased sequencing throughput at high accuracy, while being more time and cost efficient than precursor technologies. This has led to a broader and deeper profiling of the key genes in the human immunogenetic make-up. The rapid evolution of sequencing technologies is evidenced by the development of varied short-read sequencing platforms with differing read lengths and sequencing capacities to long-read sequencing platforms capable of profiling full genes without fragmentation. Concomitantly, there has been development of a diverse set of computational analyses and software tools developed to deal with the various strengths and limitations of the sequencing data generated by the different sequencing platforms. This review surveys the different modalities involved in generating NGS HLA profiling sequence data. It systematically describes various computational approaches that have been developed to achieve HLA genotyping to different degrees of resolution. At each stage, this review enumerates the drawbacks and advantages of each of the platforms and analysis approaches, thus providing a comprehensive picture of the current state of HLA genotyping technologies.
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