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Sharma D, Egidio C, Grskovic M, Viña MAF, Zhang BM. Chimerism Monitoring with Highly Sensitive and Precise Next-Generation Sequencing Assay in Patients Post-Allogeneic Hematopoietic Stem Cell Transplantation. Biol Blood Marrow Transplant 2020. [DOI: 10.1016/j.bbmt.2019.12.412] [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: 11/30/2022]
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Thorstenson YR, Creary LE, Huang H, Rozot V, Nguyen TT, Babrzadeh F, Kancharla S, Fukushima M, Kuehn R, Wang C, Li M, Krishnakumar S, Mindrinos M, Fernandez Viña MA, Scriba TJ, Davis MM. Allelic resolution NGS HLA typing of Class I and Class II loci and haplotypes in Cape Town, South Africa. Hum Immunol 2018; 79:839-847. [PMID: 30240896 DOI: 10.1016/j.humimm.2018.09.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [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: 05/01/2017] [Revised: 07/23/2018] [Accepted: 09/17/2018] [Indexed: 11/18/2022]
Abstract
The development of next-generation sequencing (NGS) methods for HLA genotyping has already had an impact on the scope and precision of HLA research. In this study, allelic resolution HLA typing was obtained for 402 individuals from Cape Town, South Africa. The data were produced by high-throughput NGS sequencing as part of a study of T-cell responses to Mycobacterium tuberculosis in collaboration with the University of Cape Town and Stanford University. All samples were genotyped for 11 HLA loci, namely HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, -DRB1, -DRB3, -DRB4, and -DRB5. NGS HLA typing of samples from Cape Town inhabitants revealed a unique cohort, including unusual haplotypes, and 22 novel alleles not previously reported in the IPD-IMGT/HLA Database. Eight novel alleles were in Class I loci and 14 were in Class II. There were 62 different alleles of HLA-A, 72 of HLA-B, and 47 of HLA-C. Alleles A∗23:17, A∗43:01, A∗29:11, A∗68:27:01, A∗01:23, B∗14:01:01, B∗15:10:01, B∗39:10:01, B∗45:07, B∗82:02:01 and C∗08:04:01 were notably more frequent in Cape Town compared to other populations reported in the literature. Class II loci had 21 different alleles of DPA1, 46 of DPB1, 27 of DQA1, 26 of DQB1, 41 of DRB1, 5 of DRB3, 4 of DRB4 and 6 of DRB5. The Cape Town cohort exhibited high degrees of HLA diversity and relatively high heterozygosity at most loci. Genetic distances between Cape Town and five other sub-Saharan African populations were also calculated and compared to European Americans.
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Affiliation(s)
| | - Lisa E Creary
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Huang Huang
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Virginie Rozot
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | | | | | | | | | - Raquel Kuehn
- Immucor, Sirona Genomics, Mountain View, CA, USA
| | - Chunlin Wang
- Immucor, Sirona Genomics, Mountain View, CA, USA
| | - Ming Li
- Immucor, Sirona Genomics, Mountain View, CA, USA
| | | | | | | | - Thomas J Scriba
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Mark M Davis
- Stanford University and Howard Hughes Medical Institute, Stanford, CA
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Sengsayadeth S, Wang T, Lee SJ, Haagenson MD, Spellman S, Fernandez Viña MA, Muller CR, Verneris MR, Savani BN, Jagasia M. Cytotoxic T-lymphocyte antigen-4 single nucleotide polymorphisms are not associated with outcomes after unrelated donor transplantation: a center for international blood and marrow transplant research analysis. Biol Blood Marrow Transplant 2014; 20:900-3. [PMID: 24631737 DOI: 10.1016/j.bbmt.2014.03.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [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: 01/20/2014] [Accepted: 03/07/2014] [Indexed: 10/25/2022]
Abstract
Cytotoxic T-lymphocyte antigen-4 (CTLA-4) plays an essential role in T cell homeostasis by restraining immune responses. AG and GG genotypes of donor CTLA-4 SNP rs4553808 in patients after unrelated donor hematopoietic stem cell transplantations (HSCT) have been shown to be an independent predictor of inferior relapse-free survival (RFS) and overall survival (OS) compared with those with the AA genotype, in single-center studies. We tested the hypothesis that SNP rs4553808 is associated with RFS, OS, nonrelapse mortality (NRM) and the cumulative incidence of acute graft-versus-host disease (GVHD) and chronic GVHD in adults with acute myeloid leukemia and advanced myelodysplastic syndrome undergoing a first 8/8 or 7/8 HLA-matched unrelated donor HSCT. Multivariable analysis adjusting for relevant donor and recipient characteristics showed no significant association between SNP rs4553808 and OS, RFS, NRM, and incidence of acute and chronic GVHD. An exploratory analysis of other CTLA-4 SNPs, as well as studying the interaction with antithymocyte globulin, also demonstrated no significant associations. Our results indicate that CTLA-4 SNPs are not associated with HSCT outcomes.
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Affiliation(s)
- Salyka Sengsayadeth
- Section of Hematology and Stem Cell Transplantation, Vanderbilt-Ingram Cancer Center, Nashville, Tennessee.
| | - Tao Wang
- Division of Biostatistics, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Stephanie J Lee
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Center for International Blood & Marrow Transplant Research, National Marrow Donor Program, Minneapolis, Minnesota
| | - Michael D Haagenson
- Center for International Blood & Marrow Transplant Research, National Marrow Donor Program, Minneapolis, Minnesota
| | - Stephen Spellman
- Center for International Blood & Marrow Transplant Research, National Marrow Donor Program, Minneapolis, Minnesota
| | | | | | - Michael R Verneris
- Blood and Marrow Transplant Program, Department of Medicine, University of Minnesota, Minneapolis, Minnesota
| | - Bipin N Savani
- Section of Hematology and Stem Cell Transplantation, Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
| | - Madan Jagasia
- Section of Hematology and Stem Cell Transplantation, Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
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Pidala J, Lee SJ, Spellman SR, Wang H, Ahn KW, Aljurf MD, Askar M, Dehn J, Fernandez Viña MA, Gratwohl A, Gupta V, Hanna R, Hurley CK, Inamoto Y, Kassim AA, Nishihori T, Oudshoorn M, Petersdorf EW, Prasad VK, Saber W, Schultz KR, Wood WA, Storek J, Woolfrey AE, Anasetti C. HLA-Mismatch Is Associated with Worse Outcomes after Myeloablative Conditioning and Unrelated Donor Hematopoietic Cell Transplantation: A Cibmtr Analysis. Biol Blood Marrow Transplant 2014. [DOI: 10.1016/j.bbmt.2013.12.008] [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: 10/25/2022]
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