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Barsakis K, Babrzadeh F, Chi A, Mallempati K, Pickle W, Mindrinos M, Fernández-Viña MA. Complete nucleotide sequence characterization of DRB5 alleles reveals a homogeneous allele group that is distinct from other DRB genes. Hum Immunol 2019; 80:437-448. [PMID: 30954494 PMCID: PMC6622178 DOI: 10.1016/j.humimm.2019.04.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 03/23/2019] [Accepted: 04/01/2019] [Indexed: 01/28/2023]
Abstract
Next Generation Sequencing allows for testing and typing of entire genes of the HLA region. A better and comprehensive sequence assessment can be achieved by the inclusion of full gene sequences of all the common alleles at a given locus. The common alleles of DRB5 are under-characterized with the full exon-intron sequence of two alleles available. In the present study the DRB5 genes from 18 subjects alleles were cloned and sequenced; haplotype analysis showed that 17 of them had a single copy of DRB5 and one consanguineous subject was homozygous at all HLA loci. Methodological approaches including robust and efficient long-range PCR amplification, molecular cloning, nucleotide sequencing and de novo sequence assembly were combined to characterize DRB5 alleles. DRB5 sequences covering from 5'UTR to the end of intron 5 were obtained for DRB5*01:01, 01:02 and 02:02; partial coverage including a segment spanning exon 2 to exon 6 was obtained for DRB5*01:03, 01:08N and 02:03. Phylogenetic analysis of the generated sequences showed that the DRB5 alleles group together and have distinctive differences with other DRB loci. Novel intron variants of DRB5*01:01:01, 01:02 and 02:02 were identified. The newly characterized DRB5 intron variants of each DRB5 allele were found in subjects harboring distinct associations with alleles of DRB1, B and/or ethnicity. The new information provided by this study provides reference sequences for HLA typing methodologies. Extending sequence coverage may lead to identify the disease susceptibility factors of DRB5 containing haplotypes while the unexpected intron variations may shed light on understanding of the evolution of the DRB region.
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Affiliation(s)
- Konstantinos Barsakis
- Stanford Blood Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA; Department of Biology, University of Crete, Heraklion, Crete 71003, Greece
| | - Farbod Babrzadeh
- Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Anjo Chi
- Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Kalyan Mallempati
- Stanford Blood Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - William Pickle
- Stanford Blood Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Michael Mindrinos
- Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
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Güleç D, Soyöz M, Koçyiğit AÖ, Pirim I, Ayna TK. Comparison of Single Antigen Bead-Based, Cell-Based, and Solid Phase-Based Crossmatch Methods. Transplant Proc 2019; 51:1016-1020. [PMID: 31101162 DOI: 10.1016/j.transproceed.2019.02.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 02/04/2019] [Indexed: 10/27/2022]
Abstract
AIM Antibody assessment during pretransplantation term is important to detect donor specific antibodies. These donor-specific antibodies are determined by various crossmatch methods (flow cytometric [FCXM], complement-dependent cytotoxic [CDCXM], and Luminex [LMXM]). Recently, single antigen bead (SAB) assays have been used for the assessment of hypersensitized patients. The aim of this study was to compare sensitivity and specificity of the 3 crossmatch methods in reference to the SAB method. METHOD In this study, 69 hypersensitized patients with high class I and/or class II panel reactive antibodies were tested using the flow cytometric SAB method. Serum samples were cross-matched by 3 crossmatch methods with the cells of a volunteer healthy individual, and the results were evaluated according to HLA and cross-reactive epitope groups (CREGs). RESULTS Sensitivity was found to be better with T FCXM (0.91) and class I LMXM (0.87). Specificity of peripheral blood lymphocyte CDCXM method (1.0) was found to be better than the other 2 methods (0.33 and 0.57, respectively). Sensitivity of class II LMXM (0.88) was found to be better than the others (0.42 for B CDCXM and 0.82 for B FCXM, respectively). The specificity of the B CDCXM, B FCXM, and class II LMXM was similar (0.44, 0.44, and 0.33, respectively). CREGs results were similar to HLA results. CONCLUSION Although CDCXM has high specificity for the detection of anti-HLA antibodies, it has low sensitivity. To increase sensitivity, FCXM or LMXM methods may be used with the CDCXM test. These results will be beneficial for laboratories and clinicians during graft survival and patient health assessment.
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Affiliation(s)
- D Güleç
- Tissue Typing Laboratory, Tepecik Education and Research Hospital, Izmir, Turkey.
| | - M Soyöz
- Tissue Typing Laboratory, Tepecik Education and Research Hospital, Izmir, Turkey; Medical Biology and Genetics Department, Faculty of Medicine, İzmir Katip Celebi University, Izmir, Turkey
| | - A Ö Koçyiğit
- Tissue Typing Laboratory, Tepecik Education and Research Hospital, Izmir, Turkey; Medical Biology and Genetics Department, Faculty of Medicine, İzmir Katip Celebi University, Izmir, Turkey
| | - I Pirim
- Tissue Typing Laboratory, Tepecik Education and Research Hospital, Izmir, Turkey; Medical Biology and Genetics Department, Faculty of Medicine, İzmir Katip Celebi University, Izmir, Turkey
| | - T K Ayna
- Tissue Typing Laboratory, Tepecik Education and Research Hospital, Izmir, Turkey; Medical Biology and Genetics Department, Faculty of Medicine, İzmir Katip Celebi University, Izmir, Turkey
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Mack SJ, Cano P, Hollenbach JA, He J, Hurley CK, Middleton D, Moraes ME, Pereira SE, Kempenich JH, Reed EF, Setterholm M, Smith AG, Tilanus MG, Torres M, Varney MD, Voorter CEM, Fischer GF, Fleischhauer K, Goodridge D, Klitz W, Little AM, Maiers M, Marsh SGE, Müller CR, Noreen H, Rozemuller EH, Sanchez-Mazas A, Senitzer D, Trachtenberg E, Fernandez-Vina M. Common and well-documented HLA alleles: 2012 update to the CWD catalogue. ACTA ACUST UNITED AC 2013; 81:194-203. [PMID: 23510415 DOI: 10.1111/tan.12093] [Citation(s) in RCA: 173] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 02/14/2013] [Accepted: 02/15/2013] [Indexed: 11/26/2022]
Abstract
We have updated the catalogue of common and well-documented (CWD) human leukocyte antigen (HLA) alleles to reflect current understanding of the prevalence of specific allele sequences. The original CWD catalogue designated 721 alleles at the HLA-A, -B, -C, -DRB1, -DRB3/4/5, -DQA1, -DQB1, and -DPB1 loci in IMGT (IMmunoGeneTics)/HLA Database release 2.15.0 as being CWD. The updated CWD catalogue designates 1122 alleles at the HLA-A, -B, -C, -DRB1, -DRB3/4/5, -DQA1, -DQB1, -DPA1 and -DPB1 loci as being CWD, and represents 14.3% of the HLA alleles in IMGT/HLA Database release 3.9.0. In particular, we identified 415 of these alleles as being 'common' (having known frequencies) and 707 as being 'well-documented' on the basis of ~140,000 sequence-based typing observations and available HLA haplotype data. Using these allele prevalence data, we have also assigned CWD status to specific G and P designations. We identified 147/151 G groups and 290/415 P groups as being CWD. The CWD catalogue will be updated on a regular basis moving forward, and will incorporate changes to the IMGT/HLA Database as well as empirical data from the histocompatibility and immunogenetics community. This version 2.0.0 of the CWD catalogue is available online at cwd.immunogenomics.org, and will be integrated into the Allele Frequencies Net Database, the IMGT/HLA Database and National Marrow Donor Program's bioinformatics web pages.
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Affiliation(s)
- S J Mack
- Center for Genetics, Children's Hospital Oakland Research Institute, Oakland, CA, USA.
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Cao Y, Schmitz JL, Yang J, Hogan SL, Bunch D, Hu Y, Jennette CE, Berg EA, Arnett FC, Jennette JC, Falk RJ, Preston GA. DRB1*15 allele is a risk factor for PR3-ANCA disease in African Americans. J Am Soc Nephrol 2011; 22:1161-7. [PMID: 21617122 DOI: 10.1681/asn.2010101058] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Anti-neutrophil cytoplasmic autoantibody (ANCA) disease rarely occurs in African Americans and risk factors for the disease in this population are unknown. Here, we genotyped MHC class II alleles and found that, among African Americans, those with proteinase 3-ANCA (PR3-ANCA) had 73.3-fold higher odds of having HLA-DRB1*15 alleles than community-based controls (OR 73.3; 95% CI 9.1 to 591). In addition, a disproportionate number of African American patients carried the DRB1*1501 allelic variant of Caucasian descent rather than the DRB1*1503 allelic variant of African descent. Among Caucasians, those with PR3-ANCA had 2.2-fold higher odds of carrying DRB1*1501 than controls (OR 2.2; 95% CI 1.2 to 4.0). A validation study supported by the Vasculitis Clinical Research Consortium confirmed the strong association between the DRB1*15 allele and PR3-ANCA disease, among African Americans. Furthermore, we found that DRB1*1501 protein binds with high affinity to amino acid sequences of sense-PR3, purportedly an antigenic epitope, and to the amino acid sequence complementary to this epitope in vitro. Peptides of sense-PR3 and complementary-PR3 also bound to TNF-α-induced surface expression of DRB1*1501 on peripheral neutrophils. Taken together, these data suggest HLA-DRB1*15 alleles contribute to the pathogenesis of PR3-ANCA disease.
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Affiliation(s)
- Yali Cao
- UNC Kidney Center, Department of Medicine, Division of Nephrology and Hypertension, Chapel Hill, NC 27599, USA
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Vaidya S, Partlow D, Susskind B, Noor M, Barnes T, Gugliuzza K. Prediction of crossmatch outcome of highly sensitized patients by single and/or multiple antigen bead luminex assay. Transplantation 2007; 82:1524-8. [PMID: 17164726 DOI: 10.1097/01.tp.0000246311.43634.0a] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND We used a solid-phase assay to identify human leukocyte antigen (HLA) Class I and II specificities in highly reactive sera, and applied this information to predict crossmatch outcome with greater than 90% accuracy. METHODS Sera from 20 highly sensitized end-stage renal disease patients reactive to 70-100% of HLA Class I and II antigen panel were analyzed by single and/or multiple antigen flow microparticle bead assay using Luminex platform (Luminex assay). These sera contained antibodies directed against high frequency public HLA class I and/or II epitopes accounting for 70-100% of serum's total reactivity. More than 2,000 complement dependent cytotoxicity (CDC) and 200 flow crossmatches (FLXM) were performed using sera from these patients and deceased donor T and B lymphocytes. RESULTS Luminex serum analysis was able to correctly predict outcomes of 95% of T and B cell FLXM. In contrast, predictive values for the CDC T and B cell crossmatches by Luminex serum analysis were only 77% and 75%, respectively. The use of serum analysis in donor selection would have reduced the total number of required FLXM by more than 50%. The frequency of negative T cell FLXM was 56% when donors were selected randomly; however, if serum antibody analysis had been used to preselect the donors by excluding donors that were likely to be positive, the frequency of corresponding negative crossmatches would have increased up to 93%. CONCLUSION This approach to donor selection may allow wider geographic sharing of cadaver donor organs without actually performing the crossmatch.
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Affiliation(s)
- Smita Vaidya
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA.
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Cano P, Klitz W, Mack SJ, Maiers M, Marsh SGE, Noreen H, Reed EF, Senitzer D, Setterholm M, Smith A, Fernández-Viña M. Common and well-documented HLA alleles: report of the Ad-Hoc committee of the american society for histocompatiblity and immunogenetics. Hum Immunol 2007; 68:392-417. [PMID: 17462507 DOI: 10.1016/j.humimm.2007.01.014] [Citation(s) in RCA: 166] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2007] [Accepted: 01/17/2007] [Indexed: 10/23/2022]
Abstract
In histocompatibility testing some genotype ambiguities are almost always resolved into the genotype with the most common alleles. To achieve unambiguous assignments additional unwieldy tests are performed. The American Society for Histocompatibility and Immunogenetics formed a committee to define what human leukocyte antigen (HLA) genotypes do not need to be resolved in external proficiency testing. The tasks included detailed analysis of large datasets of high-resolution typing and thorough review of the pertinent scientific literature. Strict criteria were used to create a catalogue of common and well-documented (CWD) alleles. In total, 130, 245, 81, and 143 of the highly polymorphic HLA-A, -B, -C, and DRB1 loci fell into the CWD category; these represent 27%-30% of all alleles recognized. For the loci DRB3/4/5, DQA1, DQB1, and DPB1, a total of 29, 16, 26, and 52 CWD alleles were identified. A recommendation indicated that an acceptable report should only include one possible genotype; multiple genotypes can only be reported if only one of these includes two alleles of the CWD group. Exceptions in which resolution is not necessary are ambiguities involving functional alleles with identical sequences in the antigen recognition site. The criteria were established for proficiency testing, which could be a valuable tool when making clinical histocompatibility decisions.
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Affiliation(s)
- Pedro Cano
- University of Texas M. D. Anderson Cancer Center, HLA Typing Laboratory, Houston, Texas 77054, USA
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Balas A, Vilches C, Rodríguez MA, Fernández B, Martinez MP, de Pablo R, García-Sánchez F, Vicario JL. Group-specific amplification of cDNA from DRB1 genes. Complete coding sequences of partially defined alleles and identification of the new alleles DRB1*040602, DRB1*111102, DRB1*080103, and DRB1*0113. Hum Immunol 2006; 67:1008-16. [PMID: 17174751 DOI: 10.1016/j.humimm.2006.09.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2006] [Revised: 09/01/2006] [Accepted: 09/28/2006] [Indexed: 10/24/2022]
Abstract
We present here the complete coding sequences, previously unavailable, of the DRB1 alleles DRB1*030102, *0306, *040701, *0408, *1327, *1356, *1411, *1446, *1503, *1504, *0806, *0813, and *0818. For cDNA isolation, new group-specific primers located at the 5'UT and 3'UT regions were used to carry out allele-specific amplification and a convenient method for determining full-length sequences for DRB1 alleles. Complete coding sequencing of samples previously typed as DRB1*0406, DRB1*080101, and DRB1*1111 revealed new alleles with noncoding nucleotide changes at exons 1 and 3. In addition, we found a novel allele, DRB1*0113, whose second exon carries a sequence motif characteristic of DRB1*07 alleles. The predicted class II haplotypic associations of all alleles are reported and discussed.
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Affiliation(s)
- Antonio Balas
- Departamento de Histocompatibilidad, Centro de Transfusión de la Comunidad de Madrid, Madrid, Spain.
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Rizzuto G, Li L, Steiner N, Slack R, Tang T, Heine U, Lin YS, Ng J, Hartzman R, Hurley CK. Diversity within the DRB1*08 allele family in four populations from a United States hematopoietic stem cell donor database and characterization of five novel DRB1*08 alleles. Hum Immunol 2003; 64:607-13. [PMID: 12770791 DOI: 10.1016/s0198-8859(03)00069-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The frequencies of DRB1*08 alleles within four major United States populations found within a hematopoietic stem cell volunteer donor database were determined by DNA sequencing of over 60 DRB1*08 positive individuals from each group. Seven of 30 known DRB1*08 alleles were identified within this study population (080101, 080201, 080302, 080401, 0806, 0807, and 0811). Each ethnic group was characterized by a different highly prevalent allele: DRB1*080101 in Caucasians; DRB1*080401 in African-Americans; DRB1*080302 in Asians; and DRB1*080201 in Hispanics. The alleles DRB1*080101, DRB1*080201, and DRB1*080401 were present in all four populations. This report also describes five novel DRB1*08 alleles uncovered during routine human leukocyte antigen typing.
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Affiliation(s)
- Gabrielle Rizzuto
- Department of Oncology, Georgetown University Medical Center, Washington, DC 20057, USA
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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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