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Madbouly A, Bolon YT. Race, ethnicity, ancestry, and aspects that impact HLA data and matching for transplant. Front Genet 2024; 15:1375352. [PMID: 38560292 PMCID: PMC10978785 DOI: 10.3389/fgene.2024.1375352] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 02/29/2024] [Indexed: 04/04/2024] Open
Abstract
Race, ethnicity, and ancestry are terms that are often misinterpreted and/or used interchangeably. There is lack of consensus in the scientific literature on the definition of these terms and insufficient guidelines on the proper classification, collection, and application of this data in the scientific community. However, defining groups for human populations is crucial for multiple healthcare applications and clinical research. Some examples impacted by population classification include HLA matching for stem-cell or solid organ transplant, identifying disease associations and/or adverse drug reactions, defining social determinants of health, understanding diverse representation in research studies, and identifying potential biases. This article describes aspects of race, ethnicity and ancestry information that impact the stem-cell or solid organ transplantation field with particular focus on HLA data collected from donors and recipients by donor registries or transplant centers.
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Affiliation(s)
- Abeer Madbouly
- Center for International Blood and Marrow Transplant Research (CIBMTR), Minneapolis, MN, United States
| | - Yung-Tsi Bolon
- Center for International Blood and Marrow Transplant Research (CIBMTR), Minneapolis, MN, United States
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Israeli S, Gragert L, Madbouly A, Bashyal P, Schneider J, Maiers M, Louzoun Y. Combined imputation of HLA genotype and self-identified race leads to better donor-recipient matching. Hum Immunol 2023; 84:110721. [PMID: 37867095 PMCID: PMC10842039 DOI: 10.1016/j.humimm.2023.110721] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 09/05/2023] [Accepted: 10/14/2023] [Indexed: 10/24/2023]
Abstract
Allogeneic Hematopoietic Cell Transplantation (HCT) is a curative therapy for hematologic disorders and often requires human leukocyte antigen (HLA)-matched donors. Donor registries have recruited donors utilizing evolving technologies of HLA genotyping methods. This necessitates in-silico ambiguity resolution and statistical imputation based on haplotype frequencies estimated from donor data stratified by self-identified race and ethnicity (SIRE). However, SIRE has limited genetic validity and presents a challenge for individuals with unknown or mixed SIRE. We present MR-GRIMM "Multi-Race Graph IMputation and Matching" that simultaneously imputes the race/ethnic category and HLA genotype using a SIRE based prior. Additionally, we propose a novel method to impute HLA typing inconsistent with current haplotype frequencies. The performance of MR-GRIMM was validated using a dataset of 170,000 donor-recipient pairs. MR-GRIMM has an average 20 % lower matching error (1-AUC) than single-race imputation. The recall metric (sensitivity) of the race/ethnic category imputation from HLA was measured by comparing the imputed donor race with the donor-provided SIRE. Accuracies of 0.74 and 0.55 were obtained for the prediction of 5 broad and 21 detailed US population groups respectively. The operational implementation of this algorithm in a registry search could help improve match predictions and access to HLA-matched donors.
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Affiliation(s)
- Sapir Israeli
- Department of Mathematics, Bar-Ilan University, Ramat Gan, Israel
| | - Loren Gragert
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA, United States
| | - Abeer Madbouly
- National Marrow Donor Program/Be The Match, Minneapolis, MN, United States; Center for International Blood and Marrow Transplant Research, Minneapolis, MN, United States
| | - Pradeep Bashyal
- National Marrow Donor Program/Be The Match, Minneapolis, MN, United States; Center for International Blood and Marrow Transplant Research, Minneapolis, MN, United States
| | - Joel Schneider
- National Marrow Donor Program/Be The Match, Minneapolis, MN, United States
| | - Martin Maiers
- National Marrow Donor Program/Be The Match, Minneapolis, MN, United States; Center for International Blood and Marrow Transplant Research, Minneapolis, MN, United States
| | - Yoram Louzoun
- Department of Mathematics, Bar-Ilan University, Ramat Gan, Israel.
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Sajulga R, Madbouly A, Fingerson S, Gragert L, Bashyal P, Bolon YT, Maiers M. Predicting HLA-DPB1 permissive probabilities through a DPB1 prediction service towards the optimization of HCT donor selection. Hum Immunol 2021; 82:903-911. [PMID: 34362573 DOI: 10.1016/j.humimm.2021.06.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/26/2021] [Accepted: 06/25/2021] [Indexed: 12/01/2022]
Abstract
Despite its demonstrated importance in hematopoietic cell transplantation, the HLA-DPB1 locus is only typed in one in five unrelated donors in the United States. Addressing this issue, we developed a DPB1 Prediction Service that leverages seven-locus haplotype frequencies (HLA-A ∼ C ∼ B ∼ DRB3/4/5 ∼ DRB1 ∼ DQB1 ∼ DPB1) to extend the imputation of six-locus HLA typing (HLA-A ∼ C ∼ B ∼ DRB3/4/5 ∼ DRB1 ∼ DQB1) to the HLA-DPB1 locus, including the novel prediction of HLA-DPB1 TCE groups to calculate donor-recipient TCE permissive match probabilities. Simulations of current-day patient searches reveal the service can fill in missing gaps for another four in five donors that appears on lists. To validate its performance, samples of 206,328 registered donors and 5,218 donor-recipient pairs with known high-resolution HLA-DPB1 typing were used for predicted-versus-observed comparisons. These comparisons demonstrated that the predictions were correct for 11.9-19.7% of HLA-DPB1 genotypes, 64.9-70.0% of TCE groups, and 61.0% of permissive match categories. Although HLA-DPB1 match predictions must be confirmed by additional typing, knowledge of TCE match probabilities facilitates rapid and improved identification of best donor options, especially for populations of color. Thus, we developed the TCE Prediction Tool user interface for a pilot program with several transplant centers to preview the accuracy and utility of this prediction framework, which provides valuable upfront optimization of donor selection.
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Affiliation(s)
- Ray Sajulga
- National Marrow Donor Program/Be The Match®, Minneapolis, MN 55401, USA; Center for International Blood and Marrow Transplant Research, Minneapolis, MN 55401, USA.
| | - Abeer Madbouly
- National Marrow Donor Program/Be The Match®, Minneapolis, MN 55401, USA; Center for International Blood and Marrow Transplant Research, Minneapolis, MN 55401, USA
| | - Stephanie Fingerson
- National Marrow Donor Program/Be The Match®, Minneapolis, MN 55401, USA; Center for International Blood and Marrow Transplant Research, Minneapolis, MN 55401, USA
| | - Loren Gragert
- National Marrow Donor Program/Be The Match®, Minneapolis, MN 55401, USA; Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Pradeep Bashyal
- National Marrow Donor Program/Be The Match®, Minneapolis, MN 55401, USA; Center for International Blood and Marrow Transplant Research, Minneapolis, MN 55401, USA
| | - Yung-Tsi Bolon
- National Marrow Donor Program/Be The Match®, Minneapolis, MN 55401, USA; Center for International Blood and Marrow Transplant Research, Minneapolis, MN 55401, USA
| | - Martin Maiers
- National Marrow Donor Program/Be The Match®, Minneapolis, MN 55401, USA
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Simanovsky AL, Madbouly A, Halagan M, Maiers M, Louzoun Y. Single haplotype admixture models using large scale HLA genotype frequencies to reproduce human admixture. Immunogenetics 2019; 71:589-604. [PMID: 31741008 DOI: 10.1007/s00251-019-01144-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 04/17/2019] [Accepted: 10/19/2019] [Indexed: 12/20/2022]
Abstract
The human leukocyte antigen (HLA) is the most polymorphic region in humans. Anthropologists use HLA to trace populations' migration and evolution. However, recent admixture between populations can mask the ancestral haplotype frequency distribution. We present a statistical method based on high-resolution HLA haplotype frequencies to resolve population admixture using a non-negative matrix factorization formalism and validated using haplotype frequencies from 56 world populations. The result is a minimal set of source components (SCs) decoding roughly 90% of the total variance in the studied admixtures. These SCs agree with the geographical distribution, phylogenies, and recent admixture events of the studied groups. With the growing population of multi-ethnic individuals, or individuals that do not report race/ethnic information, the HLA matching process for stem-cell and solid organ transplants is becoming more challenging. The presented algorithm provides a framework that facilitates the breakdown of highly admixed populations into SCs, which can be used to better match the rapidly growing population of multi-ethnic individuals worldwide.
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Affiliation(s)
| | - Abeer Madbouly
- Bioinformatics Research, Center for International Blood and Marrow Transplant Research, Minneapolis, MN, USA
| | - Michael Halagan
- Bioinformatics Research, Center for International Blood and Marrow Transplant Research, Minneapolis, MN, USA
| | - Martin Maiers
- Bioinformatics Research, Center for International Blood and Marrow Transplant Research, Minneapolis, MN, USA
| | - Yoram Louzoun
- Department of Mathematics and Gonda brain research institute, Bar-Ilan University, 52900, Ramat-Gan, Israel.
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Sapir-Pichhadze R, Zhang X, Ferradji A, Madbouly A, Tinckam KJ, Gebel HM, Blum D, Marrari M, Kim SJ, Fingerson S, Bashyal P, Cardinal H, Foster BJ. Epitopes as characterized by antibody-verified eplet mismatches determine risk of kidney transplant loss. Kidney Int 2019; 97:778-785. [PMID: 32059998 DOI: 10.1016/j.kint.2019.10.028] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [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: 07/01/2019] [Revised: 09/26/2019] [Accepted: 10/17/2019] [Indexed: 01/01/2023]
Abstract
To optimize strategies that mitigate the risk of graft loss associated with HLA incompatibility, we evaluated whether sequence defined HLA targets (eplets) that result in donor-specific antibodies are associated with transplant outcomes. To define this, we fit multivariable Cox proportional hazard models in a cohort of 118 382 United States first kidney transplant recipients to assess risk of death-censored graft failure by increments of ten antibody-verified eplet mismatches. To verify robustness of our findings, we conducted sensitivity analysis in this United States cohort and assessed the role of antibody-verified eplet mismatches as autonomous predictors of transplant glomerulopathy in an independent Canadian cohort. Antibody-verified eplet mismatches were found to be independent predictors of death-censored graft failure with hazard ratios of 1.231 [95% confidence interval 1.195, 1. 268], 1.268 [1.231, 1.305] and 1.411 [1.331, 1.495] for Class I (HLA-A, B, and C), -DRB1 and -DQB1 loci, respectively. To address linkage disequilibrium between HLA-DRB1 and -DQB1, we fit models in a subcohort without HLA-DQB1 eplet mismatches and found hazard ratios for death-censored graft failure of 1.384 [1.293, 1.480] for each additional antibody-verified HLA-DRB1 eplet mismatch. In a subcohort without HLA-DRB1 mismatches, the hazard ratio was 1.384 [1.072, 1.791] for each additional HLA-DQB1 mismatch. In the Canadian cohort, antibody-verified eplet mismatches were independent predictors of transplant glomerulopathy with hazard ratios of 5.511 [1.442, 21.080] for HLA-DRB1 and 3.640 [1.574, 8.416] for -DRB1/3/4/5. Thus, donor-recipient matching for specific HLA eplets appears to be a feasible and clinically justifiable strategy to mitigate risk of graft loss.
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Affiliation(s)
- Ruth Sapir-Pichhadze
- Division of Nephrology, Royal Victoria Hospital, McGill University Health Centre, Montreal, Quebec, Canada; The Multi Organ Transplant Program, Royal Victoria Hospital, McGill University Health Centre, Montreal, Quebec, Canada; Centre for Outcomes Research and Evaluation (CORE), McGill University Health Centre, Montreal, Quebec, Canada; Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, Quebec, Canada.
| | - Xun Zhang
- Centre for Outcomes Research and Evaluation (CORE), McGill University Health Centre, Montreal, Quebec, Canada
| | - Abdelhakim Ferradji
- Research Institute, McGill University Health Centre, Montreal, Quebec, Canada
| | - Abeer Madbouly
- Bioinformatics Research, Center for International Blood and Marrow Transplant Research, Minneapolis, Minnesota, USA
| | - Kathryn J Tinckam
- Division of Nephrology, Toronto General Hospital, University Health Network, Toronto, Ontario, Canada; The Kidney Transplant Program, Toronto General Hospital, University Health Network, Toronto, Ontario, Canada; Division of Nephrology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada; Department of Laboratory Medicine, University of Toronto, Toronto, Ontario, Canada; Department of Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Howard M Gebel
- Department of Pathology, Emory University, Atlanta, Georgia, USA
| | - Daniel Blum
- Division of Nephrology, St Michael's Hospital, Toronto, Ontario, Canada
| | - Marilyn Marrari
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - S Joseph Kim
- Division of Nephrology, Toronto General Hospital, University Health Network, Toronto, Ontario, Canada; The Kidney Transplant Program, Toronto General Hospital, University Health Network, Toronto, Ontario, Canada; Division of Nephrology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada; Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Stephanie Fingerson
- Bioinformatics Research, Center for International Blood and Marrow Transplant Research, Minneapolis, Minnesota, USA
| | - Pradeep Bashyal
- Bioinformatics Research, Center for International Blood and Marrow Transplant Research, Minneapolis, Minnesota, USA
| | | | - Bethany J Foster
- Centre for Outcomes Research and Evaluation (CORE), McGill University Health Centre, Montreal, Quebec, Canada; Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, Quebec, Canada; Montreal Children's Hospital, McGill University Health Centre, Montreal, Quebec, Canada
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Bishara A, Halagan M, Brautbar C, Israel S, Maiers M, Madbouly A. High resolution HLA allele and haplotype frequencies for Arab donors in the Hadassah bone marrow donor registry. Hum Immunol 2019; 80:823-827. [DOI: 10.1016/j.humimm.2019.05.003] [Citation(s) in RCA: 2] [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: 12/30/2018] [Revised: 04/29/2019] [Accepted: 05/10/2019] [Indexed: 01/10/2023]
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Askar M, Madbouly A, Zhrebker L, Willis A, Kennedy S, Padros K, Rodriguez MB, Bach C, Spriewald B, Ameen R, Shemmari SA, Tarassi K, Tsirogianni A, Hamdy N, Mossallam G, Hönger G, Spinnler R, Fischer G, Fae I, Charlton R, Dunk A, Vayntrub TA, Halagan M, Osoegawa K, Fernández-Viña M. HLA Haplotypes In 250 Families: The Baylor Laboratory Results And A Perspective On A Core NGS Testing Model For The 17 th International HLA And Immunogenetics Workshop. Hum Immunol 2019; 80:897-905. [PMID: 31558329 DOI: 10.1016/j.humimm.2019.07.298] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 01/09/2019] [Revised: 07/24/2019] [Accepted: 07/25/2019] [Indexed: 01/05/2023]
Abstract
Since their inception, the International HLA & Immunogenetics Workshops (IHIW) served as a collaborative platform for exchange of specimens, reference materials, experiences and best practices. In this report we present a subset of the results of human leukocyte antigen (HLA) haplotypes in families tested by next generation sequencing (NGS) under the 17th IHIW. We characterized 961 haplotypes in 921 subjects belonging to 250 families from 8 countries (Argentina, Austria, Egypt, Jamaica, Germany, Greece, Kuwait, and Switzerland). These samples were tested in a single core laboratory in a high throughput fashion using 6 different reagents/software platforms. Families tested included patients evaluated clinically as transplant recipients (kidney and hematopoietic cell transplant) and their respective family members. We identified 486 HLA alleles at the following loci HLA-A, -B, -C, -DRB1, -DRB3, -DRB4, -DRB5, -DQA1, -DQB1, -DPA1, -DPB1 (77, 115, 68, 69, 10, 6, 4, 44, 31, 20 and 42 alleles, respectively). We also identified nine novel alleles with polymorphisms in coding regions. This approach of testing samples from multiple laboratories across the world in different stages of technology implementation in a single core laboratory may be useful for future international workshops. Although data presented may not be reflective of allele and haplotype frequencies in the countries to which the families belong, they represent an extensive collection of 3rd and 4th field resolution level 11-locus haplotype associations of 486 alleles identified in families from 8 countries.
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Affiliation(s)
- Medhat Askar
- Baylor University Medical Center, Dallas, TX, USA; Texas A&M Health Science Center College of Medicine, Bryan, TX, USA.
| | - Abeer Madbouly
- Bioinformatics Research, Center for International Blood and Marrow Transplant Research, Minneapolis, MN, USA
| | | | | | | | - Karin Padros
- Primer Centro Argentino de Immunogenetica (PRICAI), Fundacion Favaloro, CABA, Argentina
| | | | - Christian Bach
- Departments of Internal Medicine & Hematology and Oncology, Friedrich-Alexander-University Erlangen-Nürnberg, Germany
| | - Bernd Spriewald
- Departments of Internal Medicine & Hematology and Oncology, Friedrich-Alexander-University Erlangen-Nürnberg, Germany
| | - Reem Ameen
- Health Sciences Center, Kuwait University, Jabriya, Kuwait
| | | | | | | | - Nayera Hamdy
- National Cancer Institute, Cairo University, Cairo, Egypt
| | | | - Gideon Hönger
- Transplantation Immunology, Department of Biomedicine, University Hospital Basel, Basel, Switzerland; HLA-Diagnostics and Immunogenetics, Department of Laboratory Medicine, University Hospital Basel, Basel, Switzerland
| | - Regina Spinnler
- HLA-Diagnostics and Immunogenetics, Department of Laboratory Medicine, University Hospital Basel, Basel, Switzerland
| | | | - Ingrid Fae
- Medical University of Vienna, Vienna, Austria
| | - Ronald Charlton
- Caribbean Bone Marrow Registry, Plantation, FL, USA; Laboratory Consultants of Florida, Jacksonville, FL, USA
| | - Arthur Dunk
- Caribbean Bone Marrow Registry, Plantation, FL, USA
| | | | - Michael Halagan
- Bioinformatics Research, Center for International Blood and Marrow Transplant Research, Minneapolis, MN, USA
| | | | - Marcelo Fernández-Viña
- Stanford Blood Center, Palo Alto, CA, USA; Stanford University School of Medicine, Palo Alto, CA, USA
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Askar M, Sayer D, Wang T, Haagenson M, Spellman SR, Lee SJ, Madbouly A, Fleischhauer K, Hsu KC, Verneris MR, Thomas D, Zhang A, Sobecks RM, Majhail NS. Analysis of Single Nucleotide Polymorphisms in the Gamma Block of the Major Histocompatibility Complex in Association with Clinical Outcomes of Hematopoietic Cell Transplantation: A Center for International Blood and Marrow Transplant Research Study. Biol Blood Marrow Transplant 2018; 25:664-672. [PMID: 30537553 DOI: 10.1016/j.bbmt.2018.12.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 12/06/2018] [Indexed: 01/08/2023]
Abstract
HLA haplotype mismatches have been associated with an elevated risk of acute graft-versus-host disease (aGVHD) in patients undergoing HLA-matched unrelated donor (URD) hematopoietic cell transplantation (HCT). The gamma block (GB) is located in the central MHC region between beta and delta blocks (encoding HLA-B and -C and HLA-DQ and -DR antigens, respectively) and contains numerous inflammatory and immune regulatory genes, including Bf, C2, and C4 genes. A single-center study showed that mismatches in SNPs c.2918+98G, c.3316C, and c.4385C in the GB block (C4 SNPs) were associated with higher risk of grade III-IV aGVHD. We investigated the association of GB SNP (GBS) mismatches with outcomes after 10/10 and 9/10 URD HCT (n = 714). The primary outcome was acute GVHD. Overall survival, disease-free survival, transplantation-related mortality, relapse, chronic GVHD, and engraftment were also analyzed. DNA samples were GBS genotyped by identifying 338 SNPs across 20 kb using the Illumina NGS platform. The overall 100-day incidence of aGVHD grade II-IV and II-IV were 41% and 17%, respectively. The overall incidence of matching at all GBSs tested and at the C4 SNPs were 23% and 81%, respectively. Neither being matched across all GB SNPs tested (versus mismatched) nor having a higher number of GBS mismatches was associated with transplantation outcomes. There was no association between C4 SNP mismatches and outcomes except for an unexpected significant association between having 2 C4 SNP mismatches and a higher hazard ratio (HR) for relapse (association seen in 15 patients only; HR, 3.38, 95% confidence interval, 1.75 to 6.53; P = .0003). These data do not support the hypothesis that mismatching at GB is associated with outcomes after HCT.
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Affiliation(s)
- Medhat Askar
- Baylor University Medical Center, Transplant Immunology, Dallas, Texas
| | - David Sayer
- Illumina, Conexio Genomics, Fremantle, Australia
| | - Tao Wang
- Center for International Blood and Marrow Transplant Research, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Michael Haagenson
- Center for International Blood and Marrow Transplant Research, Minneapolis, Minnesota
| | - Stephen R Spellman
- Center for International Blood and Marrow Transplant Research, Minneapolis, Minnesota.
| | | | - Abeer Madbouly
- Center for International Blood and Marrow Transplant Research, Minneapolis, Minnesota
| | - Katharina Fleischhauer
- Institute for Experimental Cellular Therapy, Essen University Hospital Essen, Essen, Germany
| | | | - Michael R Verneris
- Children's Hospital Colorado, University of Colorado School of Medicine, Pediatrics-Heme/Onc and Bone Marrow Transplantation, Aurora, Colorado
| | - Dawn Thomas
- Cleveland Clinic Foundation, Cleveland, Hematology and Medical Oncology, Ohio
| | - Aiwen Zhang
- Cleveland Clinic Foundation, Cleveland, Hematology and Medical Oncology, Ohio
| | - Ronald M Sobecks
- Cleveland Clinic Foundation, Cleveland, Hematology and Medical Oncology, Ohio
| | - Navneet S Majhail
- Cleveland Clinic Foundation, Cleveland, Hematology and Medical Oncology, Ohio
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Valenzuela NM, Askar M, Heidt S, Jindra P, Madbouly A, Pinelli D, Jackson A, Hidalgo LG. Minimal data reporting standards for serological testing for histocompatibility. Hum Immunol 2018; 79:865-868. [DOI: 10.1016/j.humimm.2018.08.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 08/15/2018] [Indexed: 12/30/2022]
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10
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Narayan S, Maiers M, Halagan M, Sathishkannan A, Naganathan C, Madbouly A, Periathiruvadi S. Human leucocyte antigen (HLA)-A, -B, -C, -DRB1 and -DQB1 haplotype frequencies from 2491 cord blood units from Tamil speaking population from Tamil Nadu, India. Mol Biol Rep 2018; 45:2821-2829. [PMID: 30229475 DOI: 10.1007/s11033-018-4382-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [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: 07/30/2018] [Accepted: 09/12/2018] [Indexed: 10/28/2022]
Abstract
The Public Cord Blood Bank of Jeevan Stem Cell Foundation was established in 2008 to harvest cord blood units and make them available to treat multiple blood disorders through Hematopoietic Stem Cell Transplants. We studied Human Leucocyte Antigen (HLA)-A, -B, -C, -DRB1 and -DQB1 allele and haplotype diversity in a sample of 2491 unrelated cord-blood units from Jeevan's Public Cord Blood Bank (part of Be The Cure Registry) in the Tamil Nadu state in the Indian Peninsula.
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Affiliation(s)
- Saranya Narayan
- Jeevan Stem Cell Foundation, No. 22, Wheatcrofts Road, Nungambakkam, Chennai, 600034, India.
| | | | - Mike Halagan
- National Marrow Donor Program, Minneapolis, MN, USA
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Halagan M, Manor S, Shriki N, Yaniv I, Zisser B, Madbouly A, Maiers M, Stein J. East Meets West-Impact of Ethnicity on Donor Match Rates in the Ezer Mizion Bone Marrow Donor Registry. Biol Blood Marrow Transplant 2017; 23:1381-1386. [PMID: 28396163 DOI: 10.1016/j.bbmt.2017.04.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [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: 12/12/2016] [Accepted: 04/05/2017] [Indexed: 11/24/2022]
Abstract
HLA haplotype frequencies in a volunteer bone marrow donor registry should reflect the frequencies of potential transplant recipients served by that registry, a challenge in a country with diverse subethnicities of immigrants from Eastern and Western cultures, such as Israel. We evaluated the likelihood of finding suitable donors for hypothetical patients drawn from defined subethnicities in the Ezer Mizion Bone Marrow Donor Registry (EM BMDR) from donors both within and outside the registry now and during the coming decade. On average, bioinformatics modeling predicts that, given current donor recruitment trends, 6/6 high-resolution HLA match rates for Israelis, which currently stand at 40% to 55% for most subethnicities, will rise by up to 1% per year over the next decade. Subethnicities with historically lower rates of interethnic admixture are less likely to find matches outside of their designated group but will benefit from expansion of the registry, whereas ethnically directed drives will enhance matching rates for currently underrepresented subethnicities. Donor searches for the same cohort using a large extramural registry was of only slight benefit for most of the 19 EM BMDR subethnicities evaluated, confirming that local donor registries that reflect the ethnic diversity of the community being served are best equipped to serve the needs of their respective communities. Contemporary trends of an increasingly multiethnic admixture in Israel may impact the effect of ethnic profiling in assessing future match rates for EM BMDR.
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Affiliation(s)
- Michael Halagan
- Bioinformatics Research, National Marrow Donor Program, Minneapolis, Minnesota.
| | - Sigal Manor
- Ezer Mizion Bone Marrow Donor Registry, Petah-Tikva, Israel
| | - Nira Shriki
- Ezer Mizion Bone Marrow Donor Registry, Petah-Tikva, Israel
| | - Isaac Yaniv
- Ezer Mizion Bone Marrow Donor Registry, Petah-Tikva, Israel; Bone Marrow Transplant Unit, Schneider Children's Medical Center of Israel, Petah-Tikva, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Bracha Zisser
- Ezer Mizion Bone Marrow Donor Registry, Petah-Tikva, Israel
| | - Abeer Madbouly
- Bioinformatics Research, National Marrow Donor Program, Minneapolis, Minnesota
| | - Martin Maiers
- Bioinformatics Research, National Marrow Donor Program, Minneapolis, Minnesota
| | - Jerry Stein
- Bone Marrow Transplant Unit, Schneider Children's Medical Center of Israel, Petah-Tikva, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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Madbouly A, Wang T, Haagenson M, Paunic V, Vierra-Green C, Fleischhauer K, Hsu KC, Verneris MR, Majhail NS, Lee SJ, Spellman SR, Maiers M. Investigating the Association of Genetic Admixture and Donor/Recipient Genetic Disparity with Transplant Outcomes. Biol Blood Marrow Transplant 2017; 23:1029-1037. [PMID: 28263917 DOI: 10.1016/j.bbmt.2017.02.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [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: 12/14/2016] [Accepted: 02/27/2017] [Indexed: 12/16/2022]
Abstract
Disparities in survival after allogeneic hematopoietic cell transplantation have been reported for some race and ethnic groups, despite comparable HLA matching. Individuals' ethnic and race groups, as reported through self-identification, can change over time because of multiple sociological factors. We studied the effect of 2 measures of genetic similarity in 1378 recipients who underwent myeloablative first allogeneic hematopoietic cell transplantation between 1995 and 2011 and their unrelated 10 of 10 HLA-A, -B, -C, -DRB1, and-DQB1- matched donors. The studied factors were as follows (1) donor and recipient genetic ancestral admixture and (2) pairwise donor/recipient genetic distance. Increased African genetic admixture for either transplant recipients or donors was associated with increased risk of overall mortality (hazard ratio [HR], 2.26; P = .005 and HR, 3.09; P = .0002, respectively) and transplant-related mortality (HR, 3.3; P = .0003 and HR, 3.86; P = .0001, respectively) and decreased disease-free survival (HR, 1.9; P = .02 and HR, 2.46; P = .002 respectively). The observed effect, albeit statistically significant, was relevant to a small subset of the studied population and was notably correlated with self-reported African-American race. We were not able to control for other nongenetic factors, such as access to health care or other socioeconomic factors; however, the results suggest the influence of a genetic driver. Our findings confirm what has been previously reported for African-American recipients and show similar results for donors. No significant association was found with donor/recipient genetic distance.
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Affiliation(s)
- Abeer Madbouly
- National Marrow Donor Program/Be The Match, Minneapolis, Minnesota.
| | - Tao Wang
- Center for International Blood and Marrow Transplant Research, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Michael Haagenson
- Center for International Blood and Marrow Transplant Research, Minneapolis, Minnesota
| | - Vanja Paunic
- National Marrow Donor Program/Be The Match, Minneapolis, Minnesota
| | - Cynthia Vierra-Green
- Center for International Blood and Marrow Transplant Research, Minneapolis, Minnesota
| | | | | | | | | | - Stephanie J Lee
- Center for International Blood and Marrow Transplant Research, Medical College of Wisconsin, Milwaukee, Wisconsin; Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Stephen R Spellman
- Center for International Blood and Marrow Transplant Research, Minneapolis, Minnesota
| | - Martin Maiers
- National Marrow Donor Program/Be The Match, Minneapolis, Minnesota
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13
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Askar M, Sobecks R, Wang T, Haagenson M, Majhail N, Madbouly A, Thomas D, Zhang A, Fleischhauer K, Hsu K, Verneris M, Lee SJ, Spellman SR, Fernández-Viña M. MHC Class I Chain-Related Gene A (MICA) Donor-Recipient Mismatches and MICA-129 Polymorphism in Unrelated Donor Hematopoietic Cell Transplantations Has No Impact on Outcomes in Acute Lymphoblastic Leukemia, Acute Myeloid Leukemia, or Myelodysplastic Syndrome: A Center for International Blood and Marrow Transplant Research Study. Biol Blood Marrow Transplant 2016; 23:436-444. [PMID: 27987385 DOI: 10.1016/j.bbmt.2016.11.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [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: 08/02/2016] [Accepted: 11/24/2016] [Indexed: 11/26/2022]
Abstract
Single-center studies have previously reported associations of MHC Class I Chain-Related Gene A (MICA) polymorphisms and donor-recipient MICA mismatching with graft-versus-host disease (GVHD) after unrelated donor hematopoietic cell transplantation (HCT). In this study, we investigated the association of MICA polymorphism (MICA-129, MM versus MV versus VV) and MICA mismatches after HCT with 10/10 HLA-matched (n = 552) or 9/10 (n = 161) unrelated donors. Included were adult patients with a first unrelated bone marrow or peripheral blood HCT for acute lymphoblastic leukemia, acute myeloid leukemia, or myelodysplastic syndrome that were reported to the Center for International Blood and Marrow Transplant Research between 1999 and 2011. Our results showed that neither MICA mismatch nor MICA-129 polymorphism were associated with any transplantation outcome (P < .01), with the exception of a higher relapse in recipients of MICA-mismatched HLA 10/10 donors (hazard ratio [HR], 1.7; P = .003). There was a suggestion of association between MICA mismatches and a higher risk of acute GVHD grades II to IV (HR, 1.4; P = .013) There were no significant interactions between MICA mismatches and HLA matching (9/10 versus 10/10). In conclusion, the findings in this cohort did not confirm prior studies reporting that MICA polymorphism and MICA mismatches were associated with HCT outcomes.
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Affiliation(s)
- Medhat Askar
- Department of Pathology, Baylor University Medical Center, Dallas, Texas.
| | - Ronald Sobecks
- Blood and Marrow Transplant Program, Cleveland Clinic Foundation, Cleveland, Ohio
| | - Tao Wang
- Center for International Blood and Marrow Transplant Research, Milwaukee, Wisconsin
| | - Mike Haagenson
- Center for International Blood and Marrow Transplant Research, Minneapolis, Minnesota
| | - Navneet Majhail
- Blood and Marrow Transplant Program, Cleveland Clinic Foundation, Cleveland, Ohio
| | - Abeer Madbouly
- Center for International Blood and Marrow Transplant Research, Minneapolis, Minnesota
| | - Dawn Thomas
- Blood and Marrow Transplant Program, Cleveland Clinic Foundation, Cleveland, Ohio
| | - Aiwen Zhang
- Blood and Marrow Transplant Program, Cleveland Clinic Foundation, Cleveland, Ohio
| | | | - Katharine Hsu
- Division of Hematologic Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center-Adults, New York, New York
| | - Michael Verneris
- Division of Hematology, Oncology, and Transplantation, Department of Pediatrics, University of Minnesota Medical Center, Minneapolis, Minnesota
| | - Stephanie J Lee
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Stephen R Spellman
- Center for International Blood and Marrow Transplant Research, Minneapolis, Minnesota
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14
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Manor S, Halagan M, Shriki N, Yaniv I, Zisser B, Maiers M, Madbouly A, Stein J. High-resolution HLA A∼B∼DRB1 haplotype frequencies from the Ezer Mizion Bone Marrow Donor Registry in Israel. Hum Immunol 2016; 77:1114-1119. [PMID: 27650516 DOI: 10.1016/j.humimm.2016.09.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [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: 08/10/2016] [Revised: 09/15/2016] [Accepted: 09/16/2016] [Indexed: 11/17/2022]
Abstract
We have investigated HLA population alleles and haplotype frequencies for the ethnicities that comprise the contemporary population of Israel, using a large data set from the Ezer Mizion Bone Barrow Donor Registry. We genotyped 275,699 individuals at the HLA-A, -B and -DRB1 loci using HLA genotyping methods. HLA A∼B∼DRB1 haplotype frequencies were estimated from 19 sub-ethnic Jewish populations and other non-Jewish minorities using the maximum likelihood model, which accommodates typing ambiguities. We present overall and sub-ethnicity specific HLA diversity results of the registry, which will help guide a data-driven strategy for future registry expansion.
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Affiliation(s)
- Sigal Manor
- Ezer Mizion Bone Marrow Donor Registry, Petach Tikva, Israel.
| | - Michael Halagan
- Bioinformatics Research, National Marrow Donor Program, Minneapolis, MN, USA
| | - Nira Shriki
- Ezer Mizion Bone Marrow Donor Registry, Petach Tikva, Israel
| | - Isaac Yaniv
- Ezer Mizion Bone Marrow Donor Registry, Petach Tikva, Israel; Bone Marrow Transplant Unit, Schneider Children's Medical Center of Israel, Petach Tikva, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Bracha Zisser
- Ezer Mizion Bone Marrow Donor Registry, Petach Tikva, Israel
| | - Martin Maiers
- Bioinformatics Research, National Marrow Donor Program, Minneapolis, MN, USA
| | - Abeer Madbouly
- Bioinformatics Research, National Marrow Donor Program, Minneapolis, MN, USA
| | - Jerry Stein
- Bone Marrow Transplant Unit, Schneider Children's Medical Center of Israel, Petach Tikva, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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15
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Madbouly A, Gragert L, Freeman J, Leahy N, Gourraud PA, Hollenbach JA, Kamoun M, Fernandez-Vina M, Maiers M. Validation of statistical imputation of allele-level multilocus phased genotypes from ambiguous HLA assignments. ACTA ACUST UNITED AC 2014; 84:285-92. [DOI: 10.1111/tan.12390] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Revised: 03/28/2014] [Accepted: 05/12/2014] [Indexed: 11/29/2022]
Affiliation(s)
- A. Madbouly
- Bioinformatics Research; National Marrow Donor Program; Minneapolis MN USA
| | - L. Gragert
- Bioinformatics Research; National Marrow Donor Program; Minneapolis MN USA
| | - J. Freeman
- Bioinformatics Research; National Marrow Donor Program; Minneapolis MN USA
| | - N. Leahy
- Bioinformatics Research; National Marrow Donor Program; Minneapolis MN USA
| | - P.-A. Gourraud
- Department of Neurology; University of California San Francisco; San Francisco CA USA
| | | | - M. Kamoun
- Pathology and Laboratory Medicine; Hospital of the University of Pennsylvania; Philadelphia PA USA
| | - M. Fernandez-Vina
- Department of Pathology, School of Medicine; Stanford University; Stanford CA USA
| | - M. Maiers
- Bioinformatics Research; National Marrow Donor Program; Minneapolis MN USA
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16
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Bishara A, Brautbar C, Israel S, Halagan M, Madbouly A, Vina MF, Maiers M. 106-P. Hum Immunol 2013. [DOI: 10.1016/j.humimm.2013.08.181] [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: 10/26/2022]
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17
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Gragert L, Madbouly A, Freeman J, Maiers M. Six-locus high resolution HLA haplotype frequencies derived from mixed-resolution DNA typing for the entire US donor registry. Hum Immunol 2013; 74:1313-20. [DOI: 10.1016/j.humimm.2013.06.025] [Citation(s) in RCA: 275] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 06/06/2013] [Accepted: 06/14/2013] [Indexed: 11/24/2022]
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18
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Maiers M, Gragert L, Madbouly A, Steiner D, Marsh SGE, Gourraud PA, Oudshoorn M, van der Zanden H, Schmidt AH, Pingel J, Hofmann J, Müller C, Eberhard HP. 16(th) IHIW: global analysis of registry HLA haplotypes from 20 million individuals: report from the IHIW Registry Diversity Group. Int J Immunogenet 2012; 40:66-71. [PMID: 23280139 PMCID: PMC3561701 DOI: 10.1111/iji.12031] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2012] [Revised: 11/10/2012] [Accepted: 11/12/2012] [Indexed: 12/23/2022]
Abstract
This project has the goal to validate bioinformatics methods and tools for HLA haplotype frequency analysis specifically addressing unique issues of haematopoietic stem cell registry data sets. In addition to generating new methods and tools for the analysis of registry data sets, the intent is to produce a comprehensive analysis of HLA data from 20 million donors from the Bone Marrow Donors Worldwide (BMDW) database. This report summarizes the activity on this project as of the 16IHIW meeting in Liverpool.
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Affiliation(s)
- M Maiers
- Bioinformatics Research, National Marrow Donor Program (NMDP), Minneapolis, MN, USA.
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19
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Al-Awwami M, Aljurf M, Al-Humidan H, El-Solh H, Almeshari K, Al-Seraihy A, Ayas M, Aldawsari G, Al-Dayel F, Freeman J, Madbouly A, Maiers M, Gragert L. 85-P. Hum Immunol 2012. [DOI: 10.1016/j.humimm.2012.07.211] [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: 10/27/2022]
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20
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Milius B, Schneider J, Heuer M, Bashyal P, George M, Schneyman D, Pollack J, Madbouly A, Gragert L, Hollenbach J, Mack SJ, Bakker J, Bochtler W, Robinson J, Müller C, Marsh SG, Maiers M. 8-OR. Hum Immunol 2012. [DOI: 10.1016/j.humimm.2012.07.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Abstract
In hematopoietic stem cell transplantation, donor selection is based primarily on matching donor and patient HLA genes. These genes are highly polymorphic and their typing can result in exact allele assignment at each gene (the resolution at which patients and donors are matched), but it can also result in a set of ambiguous assignments, depending on the typing methodology used. To facilitate rapid identification of matched donors, registries employ statistical algorithms to infer HLA alleles from ambiguous genotypes. Linkage disequilibrium information encapsulated in haplotype frequencies is used to facilitate prediction of the most likely haplotype assignment. An HLA typing with less ambiguity produces fewer high-probability haplotypes and a more reliable prediction. We estimated ambiguity for several HLA typing methods across four continental populations using an information theory-based measure, Shannon's entropy. We used allele and haplotype frequencies to calculate entropy for different sets of 1,000 subjects with simulated HLA typing. Using allele frequencies we calculated an average entropy in Caucasians of 1.65 for serology, 1.06 for allele family level, 0.49 for a 2002-era SSO kit, and 0.076 for single-pass SBT. When using haplotype frequencies in entropy calculations, we found average entropies of 0.72 for serology, 0.73 for allele family level, 0.05 for SSO, and 0.002 for single-pass SBT. Application of haplotype frequencies further reduces HLA typing ambiguity. We also estimated expected confirmatory typing mismatch rates for simulated subjects. In a hypothetical registry with all donors typed using the same method, the entropy values based on haplotype frequencies correspond to confirmatory typing mismatch rates of 1.31% for SSO versus only 0.08% for SBT. Intermediate-resolution single-pass SBT contains the least ambiguity of the methods we evaluated and therefore the most certainty in allele prediction. The presented measure objectively evaluates HLA typing methods and can help define acceptable HLA typing for donor recruitment.
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Affiliation(s)
- Vanja Paunić
- Bioinformatics Research, National Marrow Donor Program, Minneapolis, Minnesota, United States of America
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Loren Gragert
- Bioinformatics Research, National Marrow Donor Program, Minneapolis, Minnesota, United States of America
- * E-mail:
| | - Abeer Madbouly
- Bioinformatics Research, National Marrow Donor Program, Minneapolis, Minnesota, United States of America
| | - John Freeman
- Bioinformatics Research, National Marrow Donor Program, Minneapolis, Minnesota, United States of America
| | - Martin Maiers
- Bioinformatics Research, National Marrow Donor Program, Minneapolis, Minnesota, United States of America
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22
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Hollenbach JA, Madbouly A, Gragert L, Vierra-Green C, Flesch S, Spellman S, Begovich A, Noreen H, Trachtenberg E, Williams T, Yu N, Shaw B, Fleischhauer K, Fernandez-Vina M, Maiers M. A combined DPA1~DPB1 amino acid epitope is the primary unit of selection on the HLA-DP heterodimer. Immunogenetics 2012; 64:559-69. [PMID: 22526601 PMCID: PMC3395342 DOI: 10.1007/s00251-012-0615-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Accepted: 03/18/2012] [Indexed: 01/05/2023]
Abstract
Here, we present results for DPA1 and DPB1 four-digit allele-level typing in a large (n = 5,944) sample of unrelated European American stem cell donors previously characterized for other class I and class II loci. Examination of genetic data for both chains of the DP heterodimer in the largest cohort to date, at the amino acid epitope, allele, genotype, and haplotype level, allows new insights into the functional units of selection and association for the DP heterodimer. The data in this study suggest that for the DPA1-DPB1 heterodimer, the unit of selection is the combined amino acid epitope contributed by both the DPA1 and DPB1 genes, rather than the allele, and that patterns of LD are driven primarily by dimer stability and conformation of the P1 pocket. This may help explain the differential pattern of allele frequency distribution observed for this locus relative to the other class II loci. These findings further support the notion that allele-level associations in disease and transplantation may not be the most important unit of analysis, and that they should be considered instead in the molecular context.
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