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Baek IC, Choi EJ, Kim HJ, Choi H, Kim TG. Distributions of 11-loci HLA alleles typed by amplicon-based next-generation sequencing in South Koreans. HLA 2023; 101:613-622. [PMID: 36720674 DOI: 10.1111/tan.14981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 12/11/2022] [Accepted: 01/27/2023] [Indexed: 02/02/2023]
Abstract
The range of HLA typing for successful hematopoietic stem cell transplantation (HSCT) is gradually expanding with the next-generation sequencing (NGS)-based improvement in its quality. However, it is influenced by the allocation of finances and laboratory conditions. HLA-A, -B, -C, -DRB1/3/4/5, -DQA1, -DQB1, -DPA1, and -DPB1 alleles were genotyped at the 3-field level by amplicon-based NGS using MiSeqDx system and compared to our previous study employing long-range PCR and NGS using TruSight HLA v2 kit, in healthy donors from South Korea. Exon 2, exons 2/3, exons 2/3/4 or 5 of 11-loci were amplified by multiplex PCR. The sequence reads of over 53 depth counts were consistently obtained in each sample exon, depending on the target exon determined to match the reference sequence contained in the IPD-IMGT/HLA Database. HLA alleles were investigated by combinations of the determined exons. A total of 18 alleles with a frequency over 10% were found at the 11 HLA loci. Three ambiguities of HLA-A, -C, and -DRB1 were resolved. We observed a total of 26 HLA-A ~ C ~ B and 6 HLA-DRB1 ~ DQA1 ~ DQB1 ~ DPA1 ~ DPB1 haplotypes having significant linkage disequilibrium between alleles at all neighboring HLA loci. This result was compatible with the previous one, using TruSight HLA v2 kit. Advantages are simple and short progress time because one plate is used for each PCR step in one PCR machine and 11-loci HLA typing is possible even if only eight samples. These data suggested that expanded 11-loci HLA typing data by amplicon-based NGS might help perform HSCT.
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Affiliation(s)
- In-Cheol Baek
- Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Eun-Jeong Choi
- Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Hyoung-Jae Kim
- Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Haeyoun Choi
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Tai-Gyu Kim
- Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, South Korea.,Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, South Korea
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Crocchiolo R, Rombolà G. Human Leucocyte Antigen System and Selection of Unrelated Hematopoietic Stem Cell Donors: Impact of Patient-Donor (Mis)matching and New Challenges with the Current Technologies. J Clin Med 2023; 12:jcm12020646. [PMID: 36675576 PMCID: PMC9862309 DOI: 10.3390/jcm12020646] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 01/15/2023] Open
Abstract
The selection of hematopoietic stem cell donors for allogeneic transplantation (allo-HSCT) is mainly driven by human leucocyte antigen (HLA) matching between patient and donor, with HLA-identical matched siblings being the preferred choice in most situations. Although other clinical and demographical variables matter, especially, donor age, which is unequivocally associated with better transplant outcomes, the histocompatibility criteria have a central role in the search for the best donor, particularly in the setting of unrelated allo-HSCT where HLA disparities between patient and donor are frequent. The present review is focused on the role of HLA incompatibilities on patient outcome according to the most recent literature, in an attempt to guide transplant physicians and search coordinators during the process of adult unrelated-donor selection. The technological progresses in HLA typing, i.e., with next-generation sequencing (NGS), now allow disclosing a growing number of HLA incompatibilities associated with a heterogeneous and sometimes unknown spectrum of clinical severity. Their immunogenic characteristics, i.e., their position inside or outside the antigen recognition domain (ARD), their permissiveness, their intronic or exonic nature and even the expected expression of the HLA loci where those mismatches occur, will be presented and discussed here, integrating the advances in the immunobiology of transplantation with survival and toxicity outcomes reported in the most relevant studies, within the perspective of improving donor selection in the current practice.
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Affiliation(s)
- Roberto Crocchiolo
- Servizio di Immunoematologia e Medicina Trasfusionale, ASST Grande Ospedale Metropolitano Niguarda, Piazza dell’Ospedale Maggiore, 3, 20162 Milano, Italy
- Correspondence: ; Tel.: +39-02-64443962
| | - Gianni Rombolà
- Laboratory of Immunogenetics and Transplant Immunology, Azienda Ospedaliero-Universitaria Careggi, 50134 Firenze, Italy
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Spencer Mangum D, Caywood E. A clinician’s guide to HLA matching in allogeneic hematopoietic stem cell transplant. Hum Immunol 2022; 83:687-694. [DOI: 10.1016/j.humimm.2022.03.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 02/14/2022] [Accepted: 03/02/2022] [Indexed: 12/26/2022]
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Turner TR, Hayward DR, Gymer AW, Barker DJ, Leen G, Cambridge CA, Macpherson HL, Georgiou X, Cooper MA, Lucas JAM, Nadeem D, Robinson J, Mayor NP, Marsh SGE. Widespread non‐coding polymorphism in
HLA
class
II
genes of International
HLA
and Immunogenetics Workshop cell lines. HLA 2022; 99:328-356. [DOI: 10.1111/tan.14571] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 12/01/2022]
Affiliation(s)
- Thomas R. Turner
- Anthony Nolan Research Institute, Royal Free Hospital London UK
- UCL Cancer Institute, Royal Free Campus London UK
| | | | - Arthur W. Gymer
- Anthony Nolan Research Institute, Royal Free Hospital London UK
| | | | - Gayle Leen
- Anthony Nolan Research Institute, Royal Free Hospital London UK
- UCL Cancer Institute, Royal Free Campus London UK
| | | | | | - Xenia Georgiou
- Anthony Nolan Research Institute, Royal Free Hospital London UK
| | | | | | - Daud Nadeem
- Anthony Nolan Research Institute, Royal Free Hospital London UK
| | - James Robinson
- Anthony Nolan Research Institute, Royal Free Hospital London UK
- UCL Cancer Institute, Royal Free Campus London UK
| | - Neema P. Mayor
- Anthony Nolan Research Institute, Royal Free Hospital London UK
- UCL Cancer Institute, Royal Free Campus London UK
| | - Steven G. E. Marsh
- Anthony Nolan Research Institute, Royal Free Hospital London UK
- UCL Cancer Institute, Royal Free Campus London UK
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Sarri CA, Giannoulis T, Moutou KA, Mamuris Z. HLA class II peptide-binding-region analysis reveals funneling of polymorphism in action. Immunol Lett 2021; 238:75-95. [PMID: 34329645 DOI: 10.1016/j.imlet.2021.07.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 07/05/2021] [Accepted: 07/17/2021] [Indexed: 01/24/2023]
Abstract
BACKGROUND HLA-class II proteins hold important roles in key physiological processes. The purpose of this study was to compile all class II alleles reported in human population and investigate patterns in pocket variants and their combinations, focusing on the peptide-binding region (PBR). METHODS For this purpose, all protein sequences of DPA1, DQA1, DPB1, DQB1 and DRB1 were selected and filtered, in order to have full PBR sequences. Proportional representation was used for pocket variants while population data were also used. RESULTS All pocket variants and PBR sequences were retrieved and analyzed based on the preference of amino acids and their properties in all pocket positions. The observed number of pocket variants combinations was much lower than the possible inferred, suggesting that PBR formation is under strict funneling. Also, although class II proteins are very polymorphic, in the majority of the reported alleles in all populations, a significantly less polymorphic pocket core was found. CONCLUSIONS Pocket variability of five HLA class II proteins was studied revealing favorable properties of each protein. The actual PBR sequences of HLA class II proteins appear to be governed by restrictions that lead to the establishment of only a fraction of the possible combinations and the polymorphism recorded is the result of intense funneling based on function.
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Affiliation(s)
- Constantina A Sarri
- Department of Biochemistry and Biotechnology, Laboratory of Genetics, Comparative and Evolutionary Biology, University of Thessaly, Viopolis, Mezourlo, 41500, Larisa, Greece
| | - Themistoklis Giannoulis
- Department of Biochemistry and Biotechnology, Laboratory of Genetics, Comparative and Evolutionary Biology, University of Thessaly, Viopolis, Mezourlo, 41500, Larisa, Greece; Department of Animal Science, University of Thessaly, Trikallon 224, 43100 Karditsa, Greece
| | - Katerina A Moutou
- Department of Biochemistry and Biotechnology, Laboratory of Genetics, Comparative and Evolutionary Biology, University of Thessaly, Viopolis, Mezourlo, 41500, Larisa, Greece
| | - Zissis Mamuris
- Department of Biochemistry and Biotechnology, Laboratory of Genetics, Comparative and Evolutionary Biology, University of Thessaly, Viopolis, Mezourlo, 41500, Larisa, Greece.
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Dehn J, Spellman S, Hurley CK, Shaw BE, Barker JN, Burns LJ, Confer DL, Eapen M, Fernandez-Vina M, Hartzman R, Maiers M, Marino SR, Mueller C, Perales MA, Rajalingam R, Pidala J. Selection of unrelated donors and cord blood units for hematopoietic cell transplantation: guidelines from the NMDP/CIBMTR. Blood 2019; 134:924-34. [PMID: 31292117 DOI: 10.1182/blood.2019001212] [Citation(s) in RCA: 162] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 06/24/2019] [Indexed: 01/01/2023] Open
Abstract
Allogeneic hematopoietic cell transplantation involves consideration of both donor and recipient characteristics to guide the selection of a suitable graft. Sufficient high-resolution donor-recipient HLA match is of primary importance in transplantation with adult unrelated donors, using conventional graft-versus-host disease prophylaxis. In cord blood transplantation, optimal unit selection requires consideration of unit quality, cell dose and HLA-match. In this summary, the National Marrow Donor Program (NMDP) and the Center for International Blood and Marrow Transplant Research, jointly with the NMDP Histocompatibility Advisory Group, provide evidence-based guidelines for optimal selection of unrelated donors and cord blood units.
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Hurley CK, Spellman S, Dehn J, Barker JN, Devine S, Fernandez-Vina M, Gautreaux M, Logan B, Maiers M, Mueller C, Perales MA, Yu N, Pidala J. Regarding "Recipients Receiving Better HLA-Matched Hematopoietic Cell Transplantation Grafts, Uncovered by a Novel HLA Typing Method, Have Superior Survival: A Retrospective Study". Biol Blood Marrow Transplant 2019; 25:e268-9. [PMID: 31145991 DOI: 10.1016/j.bbmt.2019.05.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 05/22/2019] [Indexed: 11/24/2022]
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8
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Hou L, Enriquez E, Persaud M, Steiner N, Oudshoorn M, Hurley CK. Next generation sequencing characterizes HLA diversity in a registry population from the Netherlands. HLA 2019; 93:474-483. [DOI: 10.1111/tan.13535] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 02/13/2019] [Accepted: 03/21/2019] [Indexed: 01/21/2023]
Affiliation(s)
- Lihua Hou
- CW Bill Young Marrow Donor Recruitment and Research Program, Departments of Pediatrics and Oncology Georgetown University Washington District of Columbia
| | - Elizabeth Enriquez
- CW Bill Young Marrow Donor Recruitment and Research Program, Departments of Pediatrics and Oncology Georgetown University Washington District of Columbia
| | - Misti Persaud
- CW Bill Young Marrow Donor Recruitment and Research Program, Departments of Pediatrics and Oncology Georgetown University Washington District of Columbia
| | - Noriko Steiner
- CW Bill Young Marrow Donor Recruitment and Research Program, Departments of Pediatrics and Oncology Georgetown University Washington District of Columbia
| | | | - Carolyn Katovich Hurley
- CW Bill Young Marrow Donor Recruitment and Research Program, Departments of Pediatrics and Oncology Georgetown University Washington District of Columbia
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Mayor NP, Hayhurst JD, Turner TR, Szydlo RM, Shaw BE, Bultitude WP, Sayno JR, Tavarozzi F, Latham K, Anthias C, Robinson J, Braund H, Danby R, Perry J, Wilson MC, Bloor AJ, McQuaker IG, MacKinnon S, Marks DI, Pagliuca A, Potter MN, Potter VT, Russell NH, Thomson KJ, Madrigal JA, Marsh SG. Recipients Receiving Better HLA-Matched Hematopoietic Cell Transplantation Grafts, Uncovered by a Novel HLA Typing Method, Have Superior Survival: A Retrospective Study. Biol Blood Marrow Transplant 2019; 25:443-450. [DOI: 10.1016/j.bbmt.2018.12.768] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 12/22/2018] [Indexed: 10/27/2022]
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10
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Hurley CK, Ng J. Continue to focus clinical decision-making on the antigen recognition domain for the present. Hum Immunol 2019; 80:79-84. [DOI: 10.1016/j.humimm.2018.04.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 04/10/2018] [Accepted: 04/15/2018] [Indexed: 02/04/2023]
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11
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Vazirabad I, Chhabra S, Nytes J, Mehra V, Narra RK, Szabo A, Jerkins JH, Dhakal B, Hari P, Anderson MW. Direct HLA Genetic Comparisons Identify Highly Matched Unrelated Donor-Recipient Pairs with Improved Transplantation Outcome. Biol Blood Marrow Transplant 2018; 25:921-931. [PMID: 30537549 DOI: 10.1016/j.bbmt.2018.12.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 12/03/2018] [Indexed: 12/01/2022]
Abstract
HLA matching by allele-level genotyping is largely based on genetic similarity between a few exons that encode the antigen recognition domain (ARD) of the HLA protein. Next-generation sequencing (NGS) can identify HLA genetic polymorphisms in non-ARD-encoding exons, introns, and untranslated regions, but the impact of these polymorphisms on hematopoietic cell transplantation (HCT) outcome is unclear. We performed NGS-based sequencing of 11 HLA loci on a well-characterized retrospective cohort of 166 unrelated donor-recipient HCT pairs. Genetic differences between HCT pairs were identified and visualized using a novel bioinformatics approach that directly compares phased full-length HLA sequences. Our approach was able to correctly classify HCT pairs without known HLA allele-level mismatches and also to identify a subset of HLA allele-matched HCT pairs with very few to no genetic differences in the sequenced HLA regions. This highly HLA genetically matched unrelated HCT group shows improved overall survival and reduced acute graft-versus-host disease compared with HCT pairs with HLA allele-level mismatches. These results suggest that direct genetic matching of HLA loci may offer an additional means of HCT donor selection beyond traditional HLA allele comparisons and suggests that genetic similarity as defined by HLA sequencing may have a novel role in unrelated HCT donor selection. Finally, our approach can enable larger cohort studies with adequate power to detect differences in other HCT outcomes based on genetic similarity within the HLA loci.
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Affiliation(s)
- Ibrahim Vazirabad
- Diagnostic Laboratories and Blood Research Institute, BloodCenter of Wisconsin, Milwaukee, Wisconsin
| | - Saurabh Chhabra
- Division of Hematology/Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - James Nytes
- Diagnostic Laboratories and Blood Research Institute, BloodCenter of Wisconsin, Milwaukee, Wisconsin
| | - Vatsal Mehra
- Diagnostic Laboratories and Blood Research Institute, BloodCenter of Wisconsin, Milwaukee, Wisconsin
| | - Ravi K Narra
- Division of Hematology/Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Aniko Szabo
- Division of Biostatistics, Institute for Health and Equity, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - James H Jerkins
- Division of Hematology/Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Binod Dhakal
- Division of Hematology/Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Parameswaran Hari
- Division of Hematology/Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Matthew W Anderson
- Diagnostic Laboratories and Blood Research Institute, BloodCenter of Wisconsin, Milwaukee, Wisconsin.
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Liu C, Xiao F, Hoisington-Lopez J, Lang K, Quenzel P, Duffy B, Mitra RD. Accurate Typing of Human Leukocyte Antigen Class I Genes by Oxford Nanopore Sequencing. J Mol Diagn 2018; 20:428-435. [PMID: 29625249 PMCID: PMC6039791 DOI: 10.1016/j.jmoldx.2018.02.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 01/13/2018] [Accepted: 02/13/2018] [Indexed: 11/18/2022] Open
Abstract
Oxford Nanopore Technologies' MinION has expanded the current DNA sequencing toolkit by delivering long read lengths and extreme portability. The MinION has the potential to enable expedited point-of-care human leukocyte antigen (HLA) typing, an assay routinely used to assess the immunologic compatibility between organ donors and recipients, but the platform's high error rate makes it challenging to type alleles with accuracy. We developed and validated accurate typing of HLA by Oxford nanopore (Athlon), a bioinformatic pipeline that i) maps nanopore reads to a database of known HLA alleles, ii) identifies candidate alleles with the highest read coverage at different resolution levels that are represented as branching nodes and leaves of a tree structure, iii) generates consensus sequences by remapping the reads to the candidate alleles, and iv) calls the final diploid genotype by blasting consensus sequences against the reference database. Using two independent data sets generated on the R9.4 flow cell chemistry, Athlon achieved a 100% accuracy in class I HLA typing at the two-field resolution.
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Affiliation(s)
- Chang Liu
- Department of Pathology and Immunology, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri.
| | - Fangzhou Xiao
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California
| | - Jessica Hoisington-Lopez
- Division of Laboratory and Genomic Medicine, and the Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri
| | | | | | - Brian Duffy
- HLA Laboratory, Barnes-Jewish Hospital, St. Louis, Missouri
| | - Robi D Mitra
- Division of Laboratory and Genomic Medicine, and the Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri.
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Hurley CK, Hou L, Lazaro A, Gerfen J, Enriquez E, Galarza P, Rodriguez Cardozo MB, Halagan M, Maiers M, Behm D, Ng J. Next generation sequencing characterizes the extent of HLA diversity in an Argentinian registry population. HLA 2018; 91:175-186. [DOI: 10.1111/tan.13210] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Revised: 12/22/2017] [Accepted: 01/09/2018] [Indexed: 01/11/2023]
Affiliation(s)
- C. K. Hurley
- CW Bill Young Marrow Donor Recruitment and Research Program, Departments of Oncology and Pediatrics Georgetown University Washington District of Columbia
| | - L. Hou
- CW Bill Young Marrow Donor Recruitment and Research Program, Departments of Oncology and Pediatrics Georgetown University Washington District of Columbia
| | - A. Lazaro
- CW Bill Young Marrow Donor Recruitment and Research Program, Departments of Oncology and Pediatrics Georgetown University Washington District of Columbia
| | - J. Gerfen
- CW Bill Young Marrow Donor Recruitment and Research Program, Departments of Oncology and Pediatrics Georgetown University Washington District of Columbia
| | - E. Enriquez
- CW Bill Young Marrow Donor Recruitment and Research Program, Departments of Oncology and Pediatrics Georgetown University Washington District of Columbia
| | - P. Galarza
- Directora Del Registro Nacional De Donantes De Celulas Progenitoras Hematopoyeticas Instituto Nacional Central Único Coordinador de Ablación e Implante (INCUCAI) Buenos Aires Argentina
| | - M. B. Rodriguez Cardozo
- Directora Del Registro Nacional De Donantes De Celulas Progenitoras Hematopoyeticas Instituto Nacional Central Único Coordinador de Ablación e Implante (INCUCAI) Buenos Aires Argentina
| | - M. Halagan
- Bioinformatics Research National Marrow Donor Program Minneapolis Minnesota
| | - M. Maiers
- Bioinformatics Research National Marrow Donor Program Minneapolis Minnesota
| | - D. Behm
- CW Bill Young Marrow Donor Recruitment and Research Program, Departments of Oncology and Pediatrics Georgetown University Washington District of Columbia
| | - J. Ng
- CW Bill Young Marrow Donor Recruitment and Research Program, Departments of Oncology and Pediatrics Georgetown University Washington District of Columbia
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Roelen D, de Vaal Y, Vierra-green C, Waldvogel S, Spellman S, Claas F, Oudshoorn M. HLA mismatches that are identical for the antigen recognition domain are less immunogenic. Bone Marrow Transplant 2018; 53:729-40. [DOI: 10.1038/s41409-018-0108-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 12/18/2017] [Accepted: 01/04/2018] [Indexed: 11/08/2022]
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15
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Louzoun Y, Alter I, Gragert L, Albrecht M, Maiers M. Modeling coverage gaps in haplotype frequencies via Bayesian inference to improve stem cell donor selection. Immunogenetics 2017; 70:279-292. [DOI: 10.1007/s00251-017-1040-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 10/23/2017] [Indexed: 11/24/2022]
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16
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Schäfer C, Schmidt AH, Sauter J. Hapl-o-Mat: open-source software for HLA haplotype frequency estimation from ambiguous and heterogeneous data. BMC Bioinformatics 2017; 18:284. [PMID: 28558647 DOI: 10.1186/s12859-017-1692-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 05/18/2017] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Knowledge of HLA haplotypes is helpful in many settings as disease association studies, population genetics, or hematopoietic stem cell transplantation. Regarding the recruitment of unrelated hematopoietic stem cell donors, HLA haplotype frequencies of specific populations are used to optimize both donor searches for individual patients and strategic donor registry planning. However, the estimation of haplotype frequencies from HLA genotyping data is challenged by the large amount of genotype data, the complex HLA nomenclature, and the heterogeneous and ambiguous nature of typing records. RESULTS To meet these challenges, we have developed the open-source software Hapl-o-Mat. It estimates haplotype frequencies from population data including an arbitrary number of loci using an expectation-maximization algorithm. Its key features are the processing of different HLA typing resolutions within a given population sample and the handling of ambiguities recorded via multiple allele codes or genotype list strings. Implemented in C++, Hapl-o-Mat facilitates efficient haplotype frequency estimation from large amounts of genotype data. We demonstrate its accuracy and performance on the basis of artificial and real genotype data. CONCLUSIONS Hapl-o-Mat is a versatile and efficient software for HLA haplotype frequency estimation. Its capability of processing various forms of HLA genotype data allows for a straightforward haplotype frequency estimation from typing records usually found in stem cell donor registries.
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Marsh SGE. Nomenclature for factors of the HLA system, update December 2016. Int J Immunogenet 2017; 44:86-92. [DOI: 10.1111/iji.12308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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