1
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Won DI. A novel analysis strategy for HLA typing using a sequence-specific oligonucleotide probe method. HLA 2017; 90:276-283. [PMID: 28796439 DOI: 10.1111/tan.13114] [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: 04/12/2017] [Revised: 07/01/2017] [Accepted: 08/04/2017] [Indexed: 12/01/2022]
Abstract
The technique of reverse sequence-specific oligonucleotide probes (SSOPs) is commonly used in human leukocyte antigen (HLA) typing. In the conventional method for data analysis (exact pattern matching, EPM), the larger is the number of mismatched probes, the longer the time for final typing assignment. A novel strategy, filtering and scoring (FnS), has been developed to easily assign the best-fit allele pair. In the FnS method, candidate alleles and allele pairs were filtered based on (1) subject's ethnicity, and (2) the measured partial reaction pattern with only definitely negative or positive probes. Then, the complete reaction pattern for all probes (CRPoAPs) were compared between the raw sample and expected residual allele pairs to obtain mismatch scores. To compare the FnS and EPM methods, each analysis time (minutes:seconds) for reverse SSOP HLA typing with intermediate resolution (n = 507) was measured. The analysis time with FnS method was shorter than that of the EPM method [00:21 (00:08-01:47) and 01:04 (00:15-23:45), respectively, P < .05]. In addition, the analysis time of the FnS method was relatively constant, regardless of the number of mismatched probes. The alternative approach of filtering based only on definite probes (neglecting ethnicity) took a long time for analysis. However, this approach did not compromise the accuracy. The FnS method showed improved accuracy and efficiency of HLA typing in a comprehensive and quantitative comparison between measured and expected CRPoAPs of candidate allele pairs. Therefore, this analysis strategy might be useful in a clinical setting.
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Affiliation(s)
- D I Won
- Department of Clinical Pathology, Kyungpook National University School of Medicine, Daegu, South Korea
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2
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Cereb N, Kim HR, Ryu J, Yang SY. Advances in DNA sequencing technologies for high resolution HLA typing. Hum Immunol 2015; 76:923-7. [PMID: 26423536 DOI: 10.1016/j.humimm.2015.09.015] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Revised: 09/24/2015] [Accepted: 09/24/2015] [Indexed: 01/12/2023]
Abstract
This communication describes our experience in large-scale G group-level high resolution HLA typing using three different DNA sequencing platforms - ABI 3730 xl, Illumina MiSeq and PacBio RS II. Recent advances in DNA sequencing technologies, so-called next generation sequencing (NGS), have brought breakthroughs in deciphering the genetic information in all living species at a large scale and at an affordable level. The NGS DNA indexing system allows sequencing multiple genes for large number of individuals in a single run. Our laboratory has adopted and used these technologies for HLA molecular testing services. We found that each sequencing technology has its own strengths and weaknesses, and their sequencing performances complement each other. HLA genes are highly complex and genotyping them is quite challenging. Using these three sequencing platforms, we were able to meet all requirements for G group-level high resolution and high volume HLA typing.
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Affiliation(s)
- Nezih Cereb
- Histogenetics, 300 Executive Blvd, Ossining, NY 10562, USA.
| | - Hwa Ran Kim
- Histogenetics, 300 Executive Blvd, Ossining, NY 10562, USA
| | - Jaejun Ryu
- Histogenetics, 300 Executive Blvd, Ossining, NY 10562, USA
| | - Soo Young Yang
- Histogenetics, 300 Executive Blvd, Ossining, NY 10562, USA
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3
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Pan Q, Fan S, Wang X, Zhao X, Pan M, Wang C, Shen J. The distribution of HLA-A, -B, and -DRB1 alleles and haplotypes in inhabitants of Guizhou Province of China. J Biomed Res 2013; 25:328-34. [PMID: 23554708 PMCID: PMC3596729 DOI: 10.1016/s1674-8301(11)60044-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Revised: 10/30/2010] [Accepted: 03/23/2011] [Indexed: 12/04/2022] Open
Abstract
The present study was aimed to analyze the frequencies of human leukocyte antigen (HLA)-A, -B, and -DRB1 alleles and A-B-DRB1, A-B, A-DRB1 and B-DRB1 haplotypes in inhabitants of Guizhou province, China. All samples were typed in the HLA-A,-B, and -DRB1 loci using the polymerase chain reaction-reverse sequence specific oligonucleotide probe (PCR-rSSOP) method and HLA polymorphisms were analyzed. A total of 18 HLA-A, 31 HLA-B, and 13 HLA-DRB1 alleles were found in the Guizhou population. The first two frequent alleles in the HLA-A, -B, and -DRB1 loci were A*11(30.72%) and A*02(30.65%), B*40(16.27%) and B*46(16.27%), and DRB1*09(15.91%) and DRB1*15(13.51%), respectively. The most common haplotype was A*02-B*46-DRB1*09(5.59%) in A-B-DRB1, A*02-B*46(11.73%) in A-B, B*46-DRB1*09(7.49%) in B-DRB1, and A*02-DRB1*09(8.08%) in A-DRB1. Some haplotypes with strong linkage disequilibrium (LD) were found not only in the common haplotypes, such as A*33-B*58, B*30-DRB1*07, and B*33-DRB1*03, but also in the rare haplotypes, such as A*01-B*37, B*37-DRB1*10, and A*01-DRB1*10. Guizhou inhabitants shared some characteristics of the Southern Chinese population but also had their own unique features. Overall, HLA polymorphism in Guizhou population was more consistent with that of Chengdu population than that of other populations in China.
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Affiliation(s)
- Qinqin Pan
- HLA Laboratory, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
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4
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Paunić V, Gragert L, Madbouly A, Freeman J, Maiers M. Measuring ambiguity in HLA typing methods. PLoS One 2012; 7:e43585. [PMID: 22952712 PMCID: PMC3430707 DOI: 10.1371/journal.pone.0043585] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Accepted: 07/26/2012] [Indexed: 11/18/2022] Open
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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5
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Ko DH, Chung HY, Lim YM, Han BY, Song EY, Park MH. [Discrepancies between human leukocyte antigen registry typing and confirmatory typing results of unrelated hematopoietic stem cell donors]. Korean J Lab Med 2010; 30:668-74. [PMID: 21157155 DOI: 10.3343/kjlm.2010.30.6.668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND In unrelated hematopoietic stem cell transplantation, the accuracy of HLA registry typing (RT) of donors is important for timely search and coordination of HLA-matched donors. We analyzed discrepancies between HLA RT and confirmatory typing (CT) results of stem cell donors in Korean and foreign registries. METHODS We analyzed the HLA typing results of 834 donors for whom CT was performed at Seoul National University Hospital between April 1997 and March 2010. For CT, DNA typing was used in majority of the cases and HLA-A and HLA-B serological typing was used in some early cases. The discrepancies between the typing results were analyzed at the serological/generic level. RESULTS The overall discrepancy rate (RT error rate) was 3.2%, and the rate was similar in the Korean and foreign registries. The discrepancy rates in the Korean and foreign registries were more than 10% in the 1997-2001 searches, but decreased to less than 3% in the 2002-2010 searches. Analysis of 19 cases of RT errors in the Korean registry revealed 3 cases of sample switchover errors and 16 cases of typing errors in one of the HLA-A, HLA-B, or HLA-DR loci. The RT error rate in Japan Marrow Donor Program was lower than those in other foreign registries. CONCLUSIONS The error rate of HLA RT results of unrelated stem cell donors in the Korean registry was similar to those in the foreign registries, and has decreased in the recent searches following the change in the typing method from serological to DNA typing.
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Affiliation(s)
- Dae-Hyun Ko
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea
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6
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Spellman S, Setterholm M, Maiers M, Noreen H, Oudshoorn M, Fernandez-Viña M, Petersdorf E, Bray R, Hartzman RJ, Ng J, Hurley CK. Advances in the selection of HLA-compatible donors: refinements in HLA typing and matching over the first 20 years of the National Marrow Donor Program Registry. Biol Blood Marrow Transplant 2008; 14:37-44. [PMID: 18721779 DOI: 10.1016/j.bbmt.2008.05.001] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2008] [Accepted: 05/01/2008] [Indexed: 10/21/2022]
Affiliation(s)
- Stephen Spellman
- National Marrow Donor Program, Minneapolis, Minnesota 55413, USA.
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7
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Estimation of HLA-A, -B, -DRB1 Haplotype Frequencies Using Mixed Resolution Data from a National Registry with Selective Retyping of Volunteers. Hum Immunol 2007; 68:950-8. [DOI: 10.1016/j.humimm.2007.10.009] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2005] [Revised: 09/16/2007] [Accepted: 10/05/2007] [Indexed: 11/21/2022]
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8
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Lin WL, Fincke JE, Sharer LR, Monos DS, Lu S, Gaughan J, Platsoucas CD, Oleszak EL. Oligoclonal T cells are infiltrating the brains of children with AIDS: sequence analysis reveals high proportions of identical beta-chain T-cell receptor transcripts. Clin Exp Immunol 2005; 141:338-56. [PMID: 15996199 PMCID: PMC1809433 DOI: 10.1111/j.1365-2249.2005.02845.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
We have recently described the presence of perivascular CD3+ CD45RO+ T cells infiltrating the brains of children with AIDS. To determine whether these infiltrates contain oligoclonal populations of T cells, we amplified by PCR beta-chain T-cell receptor (TCR) transcripts from autopsy brains of four paediatric patients with AIDS. The amplified transcripts were cloned and sequenced. Sequence analysis of the beta-chain TCR transcripts from all four patients revealed multiple identical copies of TCR beta-chain transcripts, suggesting the presence of oligoclonal populations of T-cells. These TCR transcripts were novel. The presence of oligoclonal populations of T cells in the brains of these four paediatric patients with AIDS suggests that these T cells have undergone antigen-driven proliferation and clonal expansion very likely in situ, in the brains of these AIDS patients, in response to viral or self-antigens. Although the specificity of the clonally expanded beta-chain TCR transcripts remains to be elucidated, none of the beta-chain TCR transcripts identified in this study were identical to those specific for HIV-1 antigens that are currently reported in the GENBANK/EMBL databases. Certain common CDR3 motifs were observed in brain-infiltrating T cells within and between certain patients. Large proportions (24 of 61; 39%) of beta-chain TCR clones from one patient (NP95-73) and 2 of 27 (7%) of another patient (NP95-184-O) exhibited substantial CDR3 homology to myelin basic protein (MBP)-specific TCR derived from normal donors or TCR expressed in the brain of patients with multiple sclerosis (MS) or with viral encephalitis. These two patients (NP95-73 and NP95-184-O) also shared HLA class II with the normal donors and the MS patients who expressed these homologous TCR. Pathologic examination at autopsy of the brains revealed the presence of myelin pallor only in patient NP95-73. T-cell clones identified in the brain of patients NP95-73 and NP95-184-O may recognize MBP or another CNS self antigen and this recognition may be restricted by either DRB1*15 or DQB1*0602 specificities.
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Affiliation(s)
- W L Lin
- Department of Microbiology and Immunology, Temple University School of Medicine, Philadelphia, PA 19140, USA
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9
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Bunin N, Aplenc R, Leahey A, Magira E, Grupp S, Pierson G, Monos D. Outcomes of transplantation with partial T-cell depletion of matched or mismatched unrelated or partially matched related donor bone marrow in children and adolescents with leukemias. Bone Marrow Transplant 2005; 35:151-8. [PMID: 15531896 DOI: 10.1038/sj.bmt.1704754] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Graft-versus-host disease (GVHD) remains a major barrier to successful hematopoietic stem cell transplant for patients who lack a matched related donor. Partial T-cell depletion (TCD) of the graft may decrease the risk of severe GVHD with unrelated donors (URD) and partially matched related donors (PMRD) while retaining an antileukemic effect. We analyzed our experience using URD and PMRD for pediatric patients with leukemias from 1990 to 2001. A subgroup of 'matched' URD donor pairs was retrospectively analyzed for high-resolution class I. Partial TCD was accomplished with monoclonal antibody T10B9 or OKT3 and complement. There were 76 URD (45% matched) and 28 PMRD recipients. Event-free survival (EFS) was 38.3%, and overall survival (OS) 45.1% at 3 years. On multivariate analysis, there was no difference in survival based upon marrow source, but nonrelapse mortality was higher with the use of PMRD. Relapse occurred in 6% of ALL patients, and 22.8% of AML/MDS patients. Grades III-IV GVHD was observed in only 6.7% of patients. Partial TCD allows use of matched or mismatched URD, or PMRD with little mortality from GVHD, durable engraftment, and no increase in relapse risk.
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Affiliation(s)
- N Bunin
- Division of Oncology, The Children's Hospital of Philadelphia, 34th and Civic Center Blvd., Philadelphia, PA 19104, USA.
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10
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Ringquist S, Alexander AM, Styche A, Pecoraro C, Rudert WA, Trucco M. HLA class II DRB high resolution genotyping by pyrosequencing: comparison of group specific PCR and pyrosequencing primers. Hum Immunol 2005; 65:163-74. [PMID: 14969771 DOI: 10.1016/j.humimm.2003.11.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2003] [Accepted: 11/21/2003] [Indexed: 11/24/2022]
Abstract
Sequencing of alleles of the highly polymorphic, multiple loci HLA-DRB gene family was performed by pyrosequencing using purified DNA from the 11(th) International Histocompatibility Workshop human lymphoblastiod cell lines as well as genomic DNA isolated from blood samples obtained from healthy adult volunteers. Genomic DNA was prepared from donors whose blood had been stored either frozen or as dried blood spots. Pyrosequence-based typing was optimized for identifying alleles of the HLA-DRB1, -3, -4, and -5 genes. The procedure should be applicable to other HLA loci including the class I genes HLA-A and -B that, along with HLA-DRB, are crucial for histocompatibility matching of tissue antigens during transplantation. Computer simulation of pyrosequencing data suggest that alleles of HLA-DRB1, -3, -4, and -5 were readily identifiable by pyrosequencing as were their heterozygous allelic combinations. Pyrosequencing primers were designed to specifically sequence HLA loci of interest even in a background of other amplified, closely related sequences such as alleles of the pseudogene HLA-DRB6, -7, -8, and -9. Polymorphic residues of HLA-DRB genes were identified within each pyrosequencing reaction, obtained by 50 to 70 nucleotide read lengths. Heterozygous allelic combinations of HLA genes were analyzed and compared successfully to genotyping of alleles by sequence-specific oligonucleotide probe hybridization as well as allele specific polymerase chain reaction protocols. Pyrosequence-based typing is compatible with genotyping of allelic combinations expected from heterozygous individuals, resulting in nucleotide resolution of the highly polymorphic HLA system. Using a single pyrosequence instrument, complete typing of HLA-DRB genes can be performed daily on hundreds of individuals for high resolution histocompatibility genotyping studies.
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Affiliation(s)
- Steven Ringquist
- Department of Pediatrics, Division of Immunogenetics, Rangos Research Center, Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
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11
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Bunin N, Aplenc R, Iannone R, Leahey A, Grupp S, Monos D, Pierson G. Unrelated donor bone marrow transplantation for children with severe aplastic anemia: minimal GVHD and durable engraftment with partial T cell depletion. Bone Marrow Transplant 2005; 35:369-73. [PMID: 15640818 DOI: 10.1038/sj.bmt.1704803] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Both increased graft rejection and increased graft vs host disease (GVHD) remain obstacles to success for unrelated donor (URD) BMT for patients with SAA. Partial T cell depletion (PTCD) may decrease the risk of severe GVHD, while still maintaining sufficient donor T lymphocytes to ensure engraftment. We report on 12 patients with SAA who underwent PTCD URD BMT. All patients had failed medical therapy or relapsed following initial responses, and were transfusion dependent. The median age was 6 years, and there were five males. Donors were matched for four patients, and mismatched for eight. All patients received total body irradiation with either Ara-C or thiotepa and cyclophosphamide. PTCD was accomplished using monoclonal antibody T10B9 or OKT3 and complement. All patients engrafted, with a median time of 18 days to ANC >500. Only one patient had greater than grade II acute GVHD; two patients had limited and one patient extensive chronic GVHD. Nine patients are alive and transfusion independent at a median months post BMT. Three patients died from infection or renal failure. This series suggests that an aggressive immunosuppressive conditioning regimen with PTCD results in successful engraftment and minimal GVHD in pediatric patients with SAA, even with HLA mismatched donors.
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Affiliation(s)
- N Bunin
- The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
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12
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Hurley CK, Fernandez Vina M, Setterholm M. Maximizing optimal hematopoietic stem cell donor selection from registries of unrelated adult volunteers. TISSUE ANTIGENS 2003; 61:415-24. [PMID: 12823765 DOI: 10.1034/j.1399-0039.2003.00096.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Today, more than 50 registries of HLA-typed potential adult hematopoietic stem cell donors have been established in 40 countries and include more than 7.5 million volunteers. HLA testing of new volunteers includes HLA-A, -B and often -DR typing at low to intermediate resolution. Searching patients are tested for these same loci, preferably at a higher level of resolution. Over 95,000 patient searches are received by registries annually resulting in approximately 4660 unrelated transplants. In 2001, nearly one-third of transplants involved a patient in one country receiving stem cells from a donor in another. The diversity of the HLA system complicates the search process, requiring sophisticated registry algorithms for matching, and expertise in allele and haplotype frequencies and associations to design search strategies. Within registries, HLA frequency data have been used to evaluate optimal registry size and composition.
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Affiliation(s)
- C K Hurley
- Department of Oncology, CW Bill Young Marrow Donor Recruitment and Research Program, Georgetown University Medical Center, 3970 Reservoir Road NW, Washington, DC 20057, USA.
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13
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Hurley CK. HLA diversity: detection and impact on unrelated hematopoietic stem cell donor characterization and selection. Int J Hematol 2002; 76 Suppl 2:152-4. [PMID: 12430917 DOI: 10.1007/bf03165107] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Matching of patient and unrelated donor for HLA molecules significantly decreases the probability of graft rejection, graft vs. host disease, and transplant-related mortality in hematopoietic stem cell transplantation. A significant challenge in the identification of matched donors is the diversity of the HLA system. Almost 1500 alleles have been identified at 12 HLA loci. Significant progress has been made in the application of DNA-based testing to identify this diversity in patients and unrelated volunteer donors; however, the resolution of registry testing remains limited by the need to test many donors inexpensively. Thus, the transplant center must predict which donor might be a match for their patient using incomplete typing information. Design of a typing strategy based on knowledge of allele and haplotype frequencies is critical to speed donor identification. A further challenge is to compare patient HLA assignments to the over 7.7 million volunteer donors on registries carrying both DNA and serologic assignments. The links between alleles and serologic specificities remain unclear in many cases and complicate the design of computer algorithms used to match patients and donors. Finally, since few patients will find donors who are allele matched for all HLA loci, studies are underway to understand which of the HLA loci are most critical to match and to define rules of permissive mismatching to achieve an acceptable outcome.
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14
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Gourley IS, Kearns J, McKeen M, Birkos S, Brown M, Kamoun M. HLA Class I typing of volunteers for a bone marrow registry: QC analysis by DNA-based methodology identifies serological typing discrepancies in the assignment of HLA-A and B antigens. TISSUE ANTIGENS 2002; 59:211-5. [PMID: 12074711 DOI: 10.1034/j.1399-0039.2002.590305.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Until recently, the majority of newly recruited volunteer donors were typed for HLA-A and -B by serology onto the National Marrow Donor Program Registry. Quality control of this serological typing performed by contracted laboratories was carried out by retesting approximately 1% of each laboratory's test volume utilizing DNA-based techniques (SSOP). The criteria used for selection included samples presumed to be homozygotes, samples with split antigen specificities and samples with antigens considered to be difficult to define. Out of 1983 samples analyzed, 156 HLA-A (3.9%) and 265 HLA-B (6.7%) locus discrepancies were identified. Review of these discrepancies by both the serological and QC laboratory revealed that the majority of discrepancies were due to errors in serological typing. Serological discrepancies were categorized as follows: blank antigens identified (36.8%) and misassignments (63.2%). Misassignments were defined as either the incorrect assignment of antigens within a group ("wrong split"), or a complete misassignment. Antigens reported as blanks most frequently belonged to the A19 and A28 groups and to the B70, 46 and 40 groups. The most frequent misassignments within groups were the A19 and A10 groups, and the B40 and B15 groups. Other HLA-A misassignments included A2 vs A28 or A2 vs A69, while other HLA-B misassignments included B35 and B70. This QC analysis showed that serological typing of class I antigens for the purposes of NMDP registry typing is prone to a significant error rate. Careful evaluation and selection of contracted laboratories by the NMDP suggests methodological limitations rather than poor performance as the main cause of these observations.
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Affiliation(s)
- I S Gourley
- Department of Pathology and Laboratory Medicine university of Pennsylvania, Philadelphia 19035, USA
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15
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Kapoor N. Hematopoietic stem cell transplantation: current status of old issues. J Clin Immunol 2001; 21:377-80. [PMID: 11811782 DOI: 10.1023/a:1013197825053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Since 1968 hematopoietic stem cell transplantation (HSCT) has progressed from an experimental to standard therapeutic procedure. There are many obstacles to the successful outcome of HSCT procedures. Some of these obstacles are lack of healthy histocompatible donors, graft versus host disease, graft rejection and infections. Many advances have been made to overcome these obstacles with significant success. However, these issues and associated problems continue to persist at different levels as the field evolves with expanding indications for HSCT, use of alternative sources for hematopoietic stem cells and alternative transplant procedures. Newer interventions have allowed us to overcome some of these obstacles.
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Affiliation(s)
- N Kapoor
- Department of Pediatrics, Keck School of Medicine, Childrens Hospital of Los Angeles, California 90027, USA
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16
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Anasetti C, Petersdorf EW, Martin PJ, Woolfrey A, Hansen JA. Trends in transplantation of hematopoietic stem cells from unrelated donors. Curr Opin Hematol 2001; 8:337-41. [PMID: 11604572 DOI: 10.1097/00062752-200111000-00004] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Transplants of hematopoietic stem cells from unrelated donors have become feasible for patients with a growing variety of hematologic disorders. The probability of finding a suitable donor has increased because of the expansion of the network of registries containing more than seven million HLA-typed donors worldwide. The selection of compatible donors has become more effective, thanks to the discovery of new HLA alleles and the development of precise and efficient HLA typing methods using DNA technology. Improved methods for transplantation may provide the opportunity to further decrease treatment-related toxicity and improve survival.
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Affiliation(s)
- C Anasetti
- Department of Medicine, Division of Oncology, University of Washington, Seattle, Washington, USA.
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17
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Gourley IS, Kearns J, Hou J, Wu J, Bassinger S, Montoya GD, McKeen M, Birkos S, Williams TM, Kamoun M. Novel HLA-B alleles identified in potential marrow donors: B*3917, B*1405 and B*3528. TISSUE ANTIGENS 2001; 58:201-4. [PMID: 11703832 DOI: 10.1034/j.1399-0039.2001.580312.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Sequence-specific oligonucleotide probe hybridization and sequence-specific primer polymerase chain reaction (PCR) typing of volunteer bone marrow donors suggested the presence of variants of known HLA-B alleles in five individuals. PCR products encompassing HLA-B locus exons 1 through 3 were prepared and subcloned. Three African-American individuals had a novel HLA-B*39 allele (B*3917), and another African-American was found to have a novel HLA-B*14 allele (B*1405). In a third individual of Hispanic origin, a novel HLA-B*35 allele (B*3528) was identified. These findings further illustrate the substantial genetic variation present at the HLA-B locus within human populations.
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Affiliation(s)
- I S Gourley
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19035, USA
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18
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Noreen HJ, Yu N, Setterholm M, Ohashi M, Baisch J, Endres R, Fernandez-Vina M, Heine U, Hsu S, Kamoun M, Mitsuishi Y, Monos D, Perlee L, Rodriguez-Marino S, Smith A, Yang SY, Shipp K, Hegland J, Hurley CK. Validation of DNA-based HLA-A and HLA-B testing of volunteers for a bone marrow registry through parallel testing with serology. TISSUE ANTIGENS 2001; 57:221-9. [PMID: 11285130 DOI: 10.1034/j.1399-0039.2001.057003221.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A total of 42,160 individuals were typed for HLA-A and HLA-B by both serology and PCR-based typing. The HLA assignments included all of the known serological equivalents. The majority of the individuals (99.9%) were from U.S. minority population groups. The serologic typing was performed between 1993 and 1997 at the time of recruitment for the National Bone Marrow Program (NMDP) registry. The polymerase chain reaction (PCR)-based typing was carried out in two phases. In phase I, DNA typing was performed by PCR using sequence-specific oligonucleotide probes (PCR-SSOP) or PCR using sequence-specific primers (PCR-SSP) without knowledge of the serologic assignments. Discrepancies were identified between the serologic and DNA assignments in 24% of the volunteers (8% of volunteers differed for only HLA-A assignments, 13% for HLA-B, and 3% for both HLA-A and -B) and a potential explanation was assigned each discrepant serology/DNA pair. In phase II, a random sampling scheme was used to select a statistically significant number of individuals for repeat DNA typing from each of these categories. The categories included antigens missed by serology, nonexpressed (null) alleles, PCR amplification failures, misassignment of antigens and nomenclature issues. Only a single individual was found to carry a null allele. DNA-based testing correctly typed nearly 99% of the donors at HLA-A, more than 98% at HLA-B, and more than 97% at both HLA-A and -B validating this methodology for registry typing.
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Affiliation(s)
- H J Noreen
- Fairview-University of Minnesota Medical Center, Histocompatibility Laboratory, Minneapolis, Minnesota 55455, USA.
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19
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Helmberg W, Hegland J, Hurley CK, Maiers M, Marsh SG, Müller C, Rozemuller EH. Going back to the roots: effective utilisation of HLA typing information for bone marrow registries requires full knowledge of the DNA sequences of the oligonucleotide reagents used in the testing. TISSUE ANTIGENS 2000; 56:99-102. [PMID: 10958364 DOI: 10.1034/j.1399-0039.2000.560115.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Information obtained by DNA-based HLA typing assays is more detailed and of higher quality than that obtained by conventional serological techniques. Nevertheless, it is common for data acquired in this way to be presented in the more familiar serological format. In many cases this representation can lead to significant loss of information, which may only become apparent at a later time, with the discovery of novel allele sequences. DNA-based typing methods, such as sequence-specific oligonucleotide probing (SSOP) or sequence-specific priming (SSP) generate fragmentary sequence data which is information rich. An alternative to assigning allele names to these fragments is to simply store the sequence data itself without interpretation. Bone marrow donor repositories can then be searched directly with sequence information, which though complex is more complete, rather than searching by derivative allele names.
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Affiliation(s)
- W Helmberg
- Department of Transfusionmedicine, University Hospital Graz, Austria.
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