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Voorter CEM, Groeneweg M, Olieslagers TI, Fae I, Fischer GF, Andreani M, Troiano M, Vidan-Jeras B, Montanic S, Hepkema BG, Bungener LB, Tilanus MGJ, Wieten L. Resolving unknown nucleotides in the IPD-IMGT/HLA database by extended and full-length sequencing of HLA class I and II alleles. Immunogenetics 2024; 76:109-121. [PMID: 38400869 PMCID: PMC10944811 DOI: 10.1007/s00251-024-01333-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 01/16/2024] [Indexed: 02/26/2024]
Abstract
In the past, identification of HLA alleles was limited to sequencing the region of the gene coding for the peptide binding groove, resulting in a lack of sequence information in the HLA database, challenging HLA allele assignment software programs. We investigated full-length sequences of 19 HLA class I and 7 HLA class II alleles, and we extended another 47 HLA class I alleles with sequences of 5' and 3' UTR regions that were all not yet available in the IPD-IMGT/HLA database. We resolved 8638 unknown nucleotides in the coding sequence of HLA class I and 2139 of HLA class II. Furthermore, with full-length sequencing of the 26 alleles, more than 90 kb of sequence information was added to the non-coding sequences, whereas extension of the 47 alleles resulted in the addition of 5.5 kb unknown nucleotides to the 5' UTR and > 31.7 kb to the 3' UTR region. With this information, some interesting features were observed, like possible recombination events and lineage evolutionary origins. The continuing increase in the availability of full-length sequences in the HLA database will enable the identification of the evolutionary origin and will help the community to improve the alignment and assignment accuracy of HLA alleles.
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Affiliation(s)
- Christina E M Voorter
- Department of Transplantation Immunology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, The Netherlands.
- GROW School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands.
| | - Mathijs Groeneweg
- Department of Transplantation Immunology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, The Netherlands
- GROW School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Timo I Olieslagers
- Department of Transplantation Immunology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, The Netherlands
- GROW School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Ingrid Fae
- Department for Transfusion Medicine and Cell Therapy, Medical University Vienna, Vienna, Austria
| | - Gottfried F Fischer
- Department for Transfusion Medicine and Cell Therapy, Medical University Vienna, Vienna, Austria
| | - Marco Andreani
- Laboratorio di Immunogenetica dei Trapianti, Dipartimento di Oncoematologia, Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Maria Troiano
- Laboratorio di Immunogenetica dei Trapianti, Dipartimento di Oncoematologia, Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - 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
| | - Bouke G Hepkema
- Transplantation Immunology, Department of Laboratory Medicine, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Laura B Bungener
- Transplantation Immunology, Department of Laboratory Medicine, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Marcel G J Tilanus
- Department of Transplantation Immunology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, The Netherlands
- GROW School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Lotte Wieten
- Department of Transplantation Immunology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, The Netherlands
- GROW School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
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Asenjo J, Cisneros E, Vilches C. Hemizygous amplification and complete Sanger sequencing of HLA-C*07:37:01:02 from a South European Caucasoid. HLA 2020; 97:159-161. [PMID: 33034132 PMCID: PMC7894500 DOI: 10.1111/tan.14095] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 10/04/2020] [Accepted: 10/05/2020] [Indexed: 12/14/2022]
Abstract
The novel C*07:37:01:02 was completely sequenced after haplo-specific amplification from a European Caucasoid carrying B*07:02.
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Affiliation(s)
- Judit Asenjo
- Immunogenetics and Histocompatibility Laboratory, Instituto de Investigación Sanitaria Puerta de Hierro-Segovia de Arana, Majadahonda, Spain
| | - Elisa Cisneros
- Immunogenetics and Histocompatibility Laboratory, Instituto de Investigación Sanitaria Puerta de Hierro-Segovia de Arana, Majadahonda, Spain
| | - Carlos Vilches
- Immunogenetics and Histocompatibility Laboratory, Instituto de Investigación Sanitaria Puerta de Hierro-Segovia de Arana, Majadahonda, Spain
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Vayntrub TA, Mack SJ, Fernandez-Viña MA. Preface: 17th International HLA and Immunogenetics Workshop. Hum Immunol 2020; 81:52-58. [PMID: 32051104 DOI: 10.1016/j.humimm.2020.01.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Tamara A Vayntrub
- Histocompatibility, Immunogenetics, and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA.
| | - Steven J Mack
- Center for Genetics, Children's Hospital Oakland Research Institute, Oakland, CA, USA.
| | - Marcelo A Fernandez-Viña
- Histocompatibility, Immunogenetics, and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA; Department of Pathology, Stanford University Medical Center, Stanford, CA, USA.
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Faé I, Wenda S, Grill C, Fischer GF. HLA-B*44:138Q: Evidence for a confined deletion and recombination events in an otherwise unaffected HLA-haplotype. HLA 2019; 93:89-96. [PMID: 30488584 PMCID: PMC6590401 DOI: 10.1111/tan.13439] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 11/16/2018] [Accepted: 11/23/2018] [Indexed: 12/26/2022]
Abstract
We discovered a new HLA-B allele, HLA-B*44:138Q, and confirmed its segregation. For characterisation, we used serology, sequence specific oligonucleotide (SSO), sequence specific primer (SSP), and full length sequencing by Sanger and next-generation sequencing. From an evolutionary point the 5' part of the new allele is identical with alleles from the HLA-B*44:02 group, while its 3' part is identical to the HLA-B*15:18:01:02 allele, the breakpoint being located somewhere between intron 3 and exon 4. The salient feature of the new allele is a deletion of codon 94 in exon 3, which is unique for HLA-alleles reported so far. Gene conversion can be hypothesised in the generation of this HLA sequence; however, the deletion seems to have occurred additionally. Other HLA-alleles of the new allele's haplotype were common alleles.
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Affiliation(s)
- Ingrid Faé
- Department for Blood Group Serology and Transfusion Medicine, Medical University of Vienna, Vienna, Austria
| | - Sabine Wenda
- Department for Blood Group Serology and Transfusion Medicine, Medical University of Vienna, Vienna, Austria
| | - Cornelia Grill
- Department for Blood Group Serology and Transfusion Medicine, General Hospital of Vienna, Vienna, Austria
| | - Gottfried F Fischer
- Department for Blood Group Serology and Transfusion Medicine, Medical University of Vienna, Vienna, Austria
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