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Voorter CEM, Matern B, Tran TH, Fink A, Vidan-Jeras B, Montanic S, Fischer G, Fae I, de Santis D, Whidborne R, Andreani M, Testi M, Groeneweg M, Tilanus MGJ. Full-length extension of HLA allele sequences by HLA allele-specific hemizygous Sanger sequencing (SSBT). Hum Immunol 2018; 79:763-772. [PMID: 30107213 DOI: 10.1016/j.humimm.2018.08.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 08/09/2018] [Accepted: 08/09/2018] [Indexed: 12/27/2022]
Abstract
The gold standard for typing at the allele level of the highly polymorphic Human Leucocyte Antigen (HLA) gene system is sequence based typing. Since sequencing strategies have mainly focused on identification of the peptide binding groove, full-length sequence information is lacking for >90% of the HLA alleles. One of the goals of the 17th IHIWS workshop is to establish full-length sequences for as many HLA alleles as possible. In our component "Extension of HLA sequences by full-length HLA allele-specific hemizygous Sanger sequencing" we have used full-length hemizygous Sanger Sequence Based Typing to achieve this goal. We selected samples of which full length sequences were not available in the IPD-IMGT/HLA database. In total we have generated the full-length sequences of 48 HLA-A, 45 -B and 31 -C alleles. For HLA-A extended alleles, 39/48 showed no intron differences compared to the first allele of the corresponding allele group, for HLA-B this was 26/45 and for HLA-C 20/31. Comparing the intron sequences to other alleles of the same allele group revealed that in 5/48 HLA-A, 16/45 HLA-B and 8/31 HLA-C alleles the intron sequence was identical to another allele of the same allele group. In the remaining 10 cases, the sequence either showed polymorphism at a conserved nucleotide or was the result of a gene conversion event. Elucidation of the full-length sequence gives insight in the polymorphic content of the alleles and facilitates the identification of its evolutionary origin.
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Affiliation(s)
- Christina E M Voorter
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, The Netherlands.
| | - Ben Matern
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Thuong Hien Tran
- Transplantation Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Annette Fink
- Transplantation Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Blanka Vidan-Jeras
- Tissue Typing Center, Blood Transfusion Centre of Slovenia, Ljubljana, Slovenia
| | - Sendi Montanic
- Tissue Typing Center, Blood Transfusion Centre of Slovenia, Ljubljana, Slovenia
| | - Gottfried Fischer
- Department for Blood Group Serology and Blood Transfusion Medicine, Medical University Vienna, Vienna, Austria
| | - Ingrid Fae
- Department for Blood Group Serology and Blood Transfusion Medicine, Medical University Vienna, Vienna, Austria
| | - Dianne de Santis
- Department of Clinical Immunology, PathWest, Royal Perth Hospital, Perth, Australia
| | - Rebecca Whidborne
- Department of Clinical Immunology, PathWest, Royal Perth Hospital, Perth, Australia
| | - Marco Andreani
- Laboratory of Immunogenetics and Transplant Biology, IME Foundation, Policlinic of the University of Tor Vergata, Rome, Italy
| | - Manuela Testi
- Laboratory of Immunogenetics and Transplant Biology, IME Foundation, Policlinic of the University of Tor Vergata, Rome, Italy
| | - Mathijs Groeneweg
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Marcel G J Tilanus
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, The Netherlands
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2
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Sequence-based typing of HLA: an improved group-specific full-length gene sequencing approach. Methods Mol Biol 2014; 1109:101-14. [PMID: 24473781 DOI: 10.1007/978-1-4614-9437-9_7] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Matching for HLA at the allele level is crucial for stem cell transplantation. The golden standard approach for allele definition of full gene polymorphism, the so-called high-resolution HLA typing, is sequence-based typing (SBT). Although the majority of the polymorphism for class I is located in exons 2 and 3 and for class II in exon 2, for allele definition it is necessary to unravel the complete coding and intron sequences leading to an ultrahigh HLA typing resolution at the allele level, i.e., a full-length gene polymorphism identification.This chapter describes our recently developed SBT method for HLA-A, -B, -C, and -DQB1, that is based on full-length hemizygous Sanger sequencing of the alleles, separated by group-specific amplification using the low-resolution typing result as reference starting point. Group-specific amplification has already been established for DRB. This method enables a cost-efficient, user-friendly SBT approach resulting in a timely unambiguous HLA typing to an ultrahigh resolution level with minimal hands-on time.
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Verduin EP, Schonewille H, Brand A, Haasnoot GW, Claas FH, Lindenburg IT, Lopriore E, Oepkes D, Roelen DL, Doxiadis II. High anti-HLA response in women exposed to intrauterine transfusions for severe alloimmune hemolytic disease is associated with mother-child HLA triplet mismatches, high anti-D titer, and new red blood cell antibody formation. Transfusion 2012; 53:939-47. [DOI: 10.1111/j.1537-2995.2012.03862.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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4
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Holdsworth R, Hurley CK, Marsh SGE, Lau M, Noreen HJ, Kempenich JH, Setterholm M, Maiers M. The HLA dictionary 2008: a summary of HLA-A, -B, -C, -DRB1/3/4/5, and -DQB1 alleles and their association with serologically defined HLA-A, -B, -C, -DR, and -DQ antigens. ACTA ACUST UNITED AC 2009; 73:95-170. [DOI: 10.1111/j.1399-0039.2008.01183.x] [Citation(s) in RCA: 131] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Voorter CEM, Mulkers E, Liebelt P, Sleyster E, van den Berg-Loonen EM. Reanalysis of sequence-based HLA-A, -B and -Cw typings: how ambiguous is today?s SBT typing tomorrow. ACTA ACUST UNITED AC 2007; 70:383-9. [PMID: 17868258 DOI: 10.1111/j.1399-0039.2007.00921.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The permanently increasing number of human leukocyte antigen (HLA)-alleles and the growing list of ambiguities require continuous updating of high-resolution HLA typing results. Two different kinds of ambiguities exist: the first, when two or more allele combinations have identical heterozygous sequences, and the second, when differences are located outside the analyzed region. The number of HLA-A, B and C alleles recognized in 1999 was almost tripled in 2006. Two hundred individuals, sequence-based typing (SBT) typed in the period from 1999 to 2002, were reanalyzed using the 2006 database. A final allele typing result of at least four digits was obtained for HLA-A, -B and -C by heterozygous sequencing of exons 2 and 3 and, if necessary, additional exons and/or allele-specific sequencing. Storage of the individual sequences in a specially developed database enabled reanalysis with all present and future HLA releases. In the 5-year period HLA-A, -B and -C typing results became ambiguous in 37%, 46% and 41% of the cases. Most were because of differences outside the analyzed region; ambiguities because of different allele combinations with identical heterozygous sequences were present in 7%, 8% and 13% of the HLA-A, -B and -C typings. These results indicate that within 5 years, approximately half of the HLA SBT typings become ambiguous.
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Affiliation(s)
- C E M Voorter
- Tissue Typing Laboratory, University Hospital Maastricht, Maastricht, The Netherlands
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6
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Voorter CEM, Gervais T, Mulkers EMT, Latinne D, van den Berg-Loonen EM. Identification of the new allele B*3556 and extension of the sequences of B*4420 and B*4427. ACTA ACUST UNITED AC 2006; 68:253-6. [PMID: 16948648 DOI: 10.1111/j.1399-0039.2006.00654.x] [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: 11/28/2022]
Abstract
A new B*35 allele, B*3556, was identified in a Caucasian individual. Direct sequencing of exons 2 and 3 revealed that B*3556 was identical to B*3503, except for a nucleotide substitution from G to A at position 302, which causes a change from AGC to AAC at codon 101. This results in an amino acid change from Ser to Asn at position 77 of the mature protein. Two B*44 alleles, B*4420 and B*4427, were detected in a liver recipient and in an unrelated bone marrow donor, respectively, and their sequences were confirmed. The sequences of exons 1,4 and 5 were also elucidated; for B*4420, these exons proved to be identical to those of B*440201. The sequence of exon 5 of B*4427 showed three mismatches with that of B*440201, implicating that it probably arose from B*440201 by allele conversion with an allele of the B*15, 45, 46, 49 or 50 allele group. Elucidation of the sequence of introns 3 and 4 indicated that the breakpoint for allele conversion has to be located in intron 3 or exon 4.
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Affiliation(s)
- C E M Voorter
- Tissue Typing Laboratory, University Hospital Maastricht, PO Box 5800, 6202 AZ Maastricht, The Netherlands
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7
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Schreuder GMT, Hurley CK, Marsh SGE, Lau M, Fernandez-Vina M, Noreen HJ, Setterholm M, Maiers M. The HLA Dictionary 2004: a summary of HLA-A, -B, -C, -DRB1/3/4/5 and -DQB1 alleles and their association with serologically defined HLA-A, -B, -C, -DR and -DQ antigens. ACTA ACUST UNITED AC 2005; 65:1-55. [PMID: 15663741 DOI: 10.1111/j.1399-0039.2005.00350.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
This report presents serologic equivalents of human leucocyte antigen (HLA)-A, -B, -C, -DRB1, -DRB3, -DRB4, -DRB5 and -DQB1 alleles. The dictionary is an update of the one published in 2001. The data summarize equivalents obtained by the World Health Organization Nomenclature Committee for factors of the HLA System, the International Cell Exchange, the National Marrow Donor Program, recent publications and individual laboratories. This latest update of the dictionary is enhanced by the inclusion of results from studies performed during the 13th International Histocompatibility Workshop and from neural network analyses. A summary of the data as recommended serologic equivalents is presented as expert assigned types. The tables include remarks for alleles, which are or may be expressed as antigens with serologic reaction patterns that differ from the well-established HLA specificities. The equivalents provided will be useful in guiding searches for unrelated hematopoietic stem cell donors in which patients and/or potential donors are typed by either serology or DNA-based methods. The serological DNA equivalent dictionary will also aid in typing and matching procedures for organ transplant programs whose waiting lists of potential donors and recipients comprise of mixtures of serologic and DNA-based typings. The tables with HLA equivalents and a questionnaire for submission of serologic reaction patterns for poorly identified allelic products will be made available through the WMDA web page: www.worldmarrow.org. and in the near future also in a searchable form on the IMGT/HLA database.
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Affiliation(s)
- G M Th Schreuder
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands.
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8
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Swelsen WTN, Voorter CEM, Chak KY, van den Berg-Loonen EM. Elucidation of Exon 1, 4, and 5 Sequences of 39 Infrequent HLA-B Alleles. Hum Immunol 2005; 66:543-53. [PMID: 15935892 DOI: 10.1016/j.humimm.2005.01.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2004] [Revised: 12/22/2004] [Accepted: 01/03/2005] [Indexed: 11/17/2022]
Abstract
More than 590 human leukocyte antigen (HLA)-B alleles have been identified by sequence analysis. Although the polymorphic exon 2 and 3 sequences of all HLA-B alleles are described, the sequences of the other exons of a number of infrequent B-alleles are unknown. In this study, the exon 1, 4, and 5 sequences of 39 different HLA-B alleles were elucidated by allele-specific sequencing. Overall, these exon sequences showed identity with the majority of the known sequences from the corresponding allele groups, except for four alleles B*4010, B*4415, B*4416, and B*5606. The exon 1 sequence of B*4010 had nucleotide differences with all B*40 alleles, but was identical to the B*54, *55, *56, and *59 allele groups. B*4416 differed from B*440201 at position 988, which was previously considered a conserved position. B*4415 showed exon 1, 4, and 5 sequences deviating from the other B*44 alleles, but identical to B*4501. The exon 1 and 4 sequences of B*5606 differed from other B*56 alleles, but were in complete agreement with B*7801. The deviating exon sequences of B*4415 and B*5606 confirmed the evolutionary origin of these alleles suggested by the sequences of exons 2 and 3. The polymorphism observed in exons 1, 4, and 5 merely reflects the lineage-specificity of HLA-B.
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Affiliation(s)
- Wendy T N Swelsen
- Tissue Typing Laboratory, University Hospital Maastricht, Maastricht, The Netherlands
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9
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Schreuder GMT, Hurley CK, Marsh SGE, Lau M, Fernandez-Vina MA, Noreen HJ, Setterholm M, Maiers M. HLA dictionary 2004: summary of HLA-A, -B, -C, -DRB1/3/4/5, -DQB1 alleles and their association with serologically defined HLA-A, -B, -C, -DR, and -DQ antigens. Hum Immunol 2005; 66:170-210. [PMID: 15695003 DOI: 10.1016/j.humimm.2004.09.017] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2004] [Accepted: 09/30/2003] [Indexed: 11/20/2022]
Abstract
This report presents serologic equivalents of human leukocyte antigen (HLA)-A, -B, -C, -DRB1, -DRB3, -DRB4, -DRB5, and -DQB1 alleles. The dictionary is an update of the one published in 2001. The data summarize equivalents obtained by the World Health Organization (WHO) Nomenclature Committee for Factors of the HLA System, the International Cell Exchange (UCLA), the National Marrow Donor Program, recent publications, and individual laboratories. This latest update of the dictionary is enhanced by the inclusion of results from studies performed during the 13th International Histocompatibility Workshop and from neural network analyses. A summary of the data as recommended serologic equivalents is presented as expert assigned types. The tables include remarks for alleles, which are or may be expressed as antigens with serologic reaction patterns that differ from the well-established HLA specificities. The equivalents provided will be useful in guiding searches for unrelated hematopoietic stem cell donors in which patients and/or potential donors are typed by either serology or DNA-based methods. The serological-DNA equivalent dictionary will also aid in typing and matching procedures for organ transplant programs whose waiting lists of potential donors and recipients are comprised of mixtures of serologic and DNA-based typings. The tables with HLA equivalents and a questionnaire for submission of serologic reaction patterns for poorly identified allelic products will be made available through the World Marrow Donor Association Web page (www.worldmarrow.org).
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Affiliation(s)
- Geziena M Th Schreuder
- World Marrow Donor Association Quality Assurance and IT Working Groups Leiden, The Netherlands.
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10
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Schreuder GMT, Hurley CK, Marsh SGE, Lau M, Fernandez-Vina M, Noreen HJ, Setterholm M, Maiers M. The HLA Dictionary 2004: a summary of HLA-A, -B, -C, -DRB1/3/4/5 and -DQB1 alleles and their association with serologically defined HLA-A, -B, -C, -DR and -DQ antigens. Int J Immunogenet 2005; 32:19-69. [PMID: 15686589 DOI: 10.1111/j.1744-313x.2005.00497.x] [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: 11/30/2022]
Abstract
This report presents serological equivalents of HLA-A, -B, -C, -DRB1, -DRB3, -DRB4, -DRB5 and -DQB1 alleles. The dictionary is an update of that published in 2001. The data summarize equivalents obtained by the World Health Organization Nomenclature Committee for Factors of the HLA System, the International Cell Exchange (UCLA), the National Marrow Donor Program (NMDP), recent publications and individual laboratories. This latest update of the dictionary is enhanced by the inclusion of results from studies performed during the 13th International Histocompatibility Workshop and from neural network analyses. A summary of the data as recommended serological equivalents is presented as expert assigned types. The tables include remarks for alleles, which are or may be expressed as antigens with serological reaction patterns that differ from the well-established HLA specificities. The equivalents provided will be useful in guiding searches for unrelated haematopoietic stem cell donors in which patients and/or potential donors are typed by either serology or DNA-based methods. The serological DNA equivalent dictionary will also aid in typing and matching procedures for organ transplant programmes whose waiting lists of potential donors and recipients comprise mixtures of serological and DNA-based typings. The tables with HLA equivalents and a questionnaire for submission of serological reaction patterns for poorly identified allelic products will be made available through the WMDA web page (http://www.worldmarrow.org) and, in the near future, also in a searchable form on the IMGT/HLA database.
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Affiliation(s)
- G M Th Schreuder
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands.
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Swelsen WTN, Voorter CEM, van den Berg-Loonen EM. Ambiguities of human leukocyte antigen-B resolved by sequence-based typing of exons 1, 4, and 5. ACTA ACUST UNITED AC 2004; 63:248-54. [PMID: 14989714 DOI: 10.1111/j.1399-0039.2004.00181.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The elucidation of the sequences of human leukocyte antigen-B (HLA-B)-exons 1 through 5 has led to an increase of ambiguities with alleles having identical exon 2 and 3 sequences, but differences in other exons. At the moment, 26 HLA-B alleles show such ambiguities which can be resolved by sequencing the exons in which the differences are located. Here we report a sequence-based typing (SBT) strategy for heterozygous sequencing of exons 1, 4, and 5, in addition to the previously described exons 2 and 3. The strategy was validated against a panel of 25 individuals, carrying HLA-B alleles from 33 different allele groups. Correct assignment of all HLA-B alleles was obtained for exons 1 through 5. In addition, the SBT protocol was used to resolve ambiguities in 50 individuals. The ambiguous combinations studied were B*0705/06, B*0801/19N, B*1512/19, B*180101/17N, B*270502/13/0504, B*350101/42/40N, B*390101/0103, B*400102/0101, B*440201/19N/27, and B*510101/11N/0105/30/32. In all cases, sequencing revealed the first allele to be present, except for three individuals with B*07. One of them typed B*0705; the other two were B*0706. The described SBT protocol for sequencing exons 1, 4, and 5 is a valuable tool for resolving ambiguities of HLA-B alleles with differences in these exons, as well as for studying the polymorphism of HLA-B outside exons 2 and 3.
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Affiliation(s)
- W T N Swelsen
- Tissue Typing Laboratory, University Hospital Maastricht, the Netherlands.
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Shankarkumar U, Sridharan B, Pitchappan RM. HLA diversity among Nadars, a primitive Dravidian caste of South India. ACTA ACUST UNITED AC 2003; 62:542-7. [PMID: 14617038 DOI: 10.1046/j.1399-0039.2003.00118.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
South India is one of the oldest geophysical regions mainly occupied by Dravidian language-speaking people. Here a random panel of 61 unrelated Nadar healthy individual from Tamil Nadu State were analyzed and compared with other populations of India and the world. HLA-A, B and C alleles frequencies and their haplotype frequencies were determined by high-resolution typing of genomic DNA. The analysis revealed that the Nadar caste of South India have several characters shared with East Asian populations consistent with the demographic history of South India, as well as specific features including several unique alleles such as A*03011, A*31011, B*15011, B*3501, B*51011, Cw*02022. In addition, haplotypes such as A*31011-Cw*02022-B*3501, A*03011-Cw*04011-B*4406 and A*2402101-Cw*04011-B*51011 are of high frequency in both these populations but are rare or absent in other populations of India and the world. The study suggests that a comparatively lesser degree of genetic admixture occurred between the South Indian and North Indian racial groups than that between South Indian and East Asian groups.
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Affiliation(s)
- U Shankarkumar
- HLA Department, Institute of Immunohaematology (ICMR), K.E.M. Hospital, Parel, Mumbai, India.
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Swelsen WTN, Voorter CEM, van den Berg-Loonen EM. Polymorphism of intron 4 in HLA-A, -B and -C genes. TISSUE ANTIGENS 2003; 61:475-83. [PMID: 12823771 DOI: 10.1034/j.1399-0039.2003.00057.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The sequence database of HLA class I genes focuses on the coding sequences, the exons. Limited information is available on the non-coding sequences of the different class I alleles. In this study we have determined the intron 4 nucleotide sequence of at least one representative of each major allelic group of HLA-A, -B and -C. The intron 4 sequences were determined for 27 HLA-A, 81 HLA-B and 30 HLA-C alleles by allele-specific sequencing, using primers located in adjacent exons and introns. The sequences revealed that the length of intron 4 varies with a minimum of 93 and a maximum of 124 nucleotides as a result of insertions and deletions. There were remarkable similarities and differences within HLA-A, -B and -C, as well as between them. Within HLA-A, a deletion of three nucleotides was detected in several HLA-A alleles. The HLA-B alleles could be divided into two groups with one group having a deletion of 11 nucleotides compared with the second group. Within HLA-C, all Cw*07 alleles showed remarkable differences with the other Cw alleles. Cw*07 had an insertion of three nucleotides, shared only by the Cw*17 group. Moreover, Cw*07 was found to have an aberrant nucleotide sequence. Differences between HLA-A, -B and -C alleles were also observed. Remarkable was the deletion of 20 nucleotides in all HLA-A and -B alleles compared with HLA-C, whereas the HLA-A alleles showed an insertion of one nucleotide and a deletion of three nucleotides compared with HLA-B and -C. Furthermore, 32 different polymorphic positions were detected between HLA-A, -B and -C.
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Affiliation(s)
- W T N Swelsen
- Tissue Typing Laboratory, University Hospital Maastricht, 6202 AZ Maastricht, the Netherlands
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