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Cambridge CA, Turner TR, Georgiou X, Robinson J, Mayor NP, Marsh SGE. Fifty novel HLA-DPB1 alleles identified in a UK cohort of unrelated hematopoietic cell donors and recipients. HLA 2024; 103:e15261. [PMID: 37850248 DOI: 10.1111/tan.15261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/14/2023] [Accepted: 10/06/2023] [Indexed: 10/19/2023]
Abstract
HLA-DPB1 is the classical HLA class II genes with the least recorded variation on the IPD-IMGT/HLA Database, suggesting the full extent of its diversity is perhaps yet to be characterized. Here, a full-gene typing strategy was employed to genotype a UK cohort of 1470 HCT recipients (n = 744) and donors (n = 726). In total, 2940 full-length HLA-DPB1 sequences were generated, comprising 193 distinct alleles. Of these, 107 sequences contained novel variation, totaling 49 unique intronic HLA-DPB1 alleles, and one coding variant (HLA-DPB1*1188:01). Full-gene sequencing resulted in zygosity changes for 129 individuals by identifying two distinct intronic variants of the same coding allele. We verified the existence of nine unconfirmed alleles and extended the sequence of two existing alleles on the IPD-IMGT/HLA Database.
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Affiliation(s)
| | - Thomas R Turner
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK
- UCL Cancer Institute, University College London, London, UK
| | - Xenia Georgiou
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK
| | - James Robinson
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK
- UCL Cancer Institute, University College London, London, UK
| | - Neema P Mayor
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK
- UCL Cancer Institute, University College London, London, UK
| | - Steven G E Marsh
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK
- UCL Cancer Institute, University College London, London, UK
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Truong L, Matern BM, El-Lagta N, Mobegi FM, Askar M, Ogret Y, Oguz FS, Kwok J, D'Orsogna L, Martinez P, Petersdorf E, Tilanus MGJ, De Santis D. Report from the extended HLA-DPA1 ~ promoter ~ HLA-DPB1 haplotype of the 18th international HLA and immunogenetics workshop. HLA 2023; 102:690-706. [PMID: 37452528 DOI: 10.1111/tan.15155] [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: 03/27/2023] [Revised: 06/04/2023] [Accepted: 06/29/2023] [Indexed: 07/18/2023]
Abstract
The primary goal of the HLA-DPA1 ~ promoter ~ HLA-DPB1 haplotype component of the 18th IHIWS was to characterise the extended haplotypes within the HLA-DP region and survey the extent of genetic diversity in this region across human populations. In this report, we analysed single-nucleotide polymorphisms (SNPs) in 255 subjects from 6 different cohorts. The results from the HLA-DP haplotype component have validated findings from the initial pilot study. SNPs in this region were inherited in strong linkage, particularly HLA-DPA1, SNP-linked promoter haplotypes and motifs in exon 2 of HLA-DPB1. We reported 17 SNP-linked haplotypes in the promoter region. Together with HLA-DPA1 and HLA-DPB1 alleles, they formed 74 distinct extended HLA-DP haplotypes in 438 sequences. We also observed the presence of region-specific alleles and promoter haplotypes. Our approach involved phasing extended SNPs including promoter SNPs, HLA-DPA1 and HLA-DPB1 alleles, in a 22 kb region, GRCh38/hg38 (chr6:33,064,111-33,086,679), followed by clustering of these SNPs as one extended haplotype. This hierarchical clustering revealed four major clades, suggesting that haplotypes within each clade may have diverged from a common ancestral haplotype and undergone similar evolutionary processes. The correlation between HLA-DPA1 and the promoter region raises questions about the role of HLA-DPA1 antigen in the heterodimer. This finding requires validation on a larger sample size specifically designed for anthropological analysis. Nevertheless, the results from this study highlight the clinical potential of selecting better-matched donors for patients awaiting haematopoietic stem cell transplants from genetically overlapping groups that share common ancestral haplotypes.
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Affiliation(s)
- Linh Truong
- Department of Clinical Immunology, PathWest, Fiona Stanley Hospital, Perth, Western Australia, Australia
- UWA Medical School, The University of Western Australia, Perth, Western Australia, Australia
| | - Benedict M Matern
- Central Diagnostic Laboratory, University Medical Center Utrecht, Utrecht, Netherlands
| | - Naser El-Lagta
- Department of Clinical Immunology, PathWest, Fiona Stanley Hospital, Perth, Western Australia, Australia
| | - Fredrick M Mobegi
- Department of Clinical Immunology, PathWest, Fiona Stanley Hospital, Perth, Western Australia, Australia
| | - Medhat Askar
- QU Health Cluster & Department of Basic Sciences, College of Medicine, Qatar University, Doha, Qatar
| | - Yeliz Ogret
- Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Fatma S Oguz
- Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Janette Kwok
- Division of Transplantation and Immunogenetics, Queen Mary Hospital, Hong Kong, China
| | - Lloyd D'Orsogna
- Department of Clinical Immunology, PathWest, Fiona Stanley Hospital, Perth, Western Australia, Australia
- UWA Medical School, The University of Western Australia, Perth, Western Australia, Australia
| | - Patricia Martinez
- Department of Clinical Immunology, PathWest, Fiona Stanley Hospital, Perth, Western Australia, Australia
- UWA Medical School, The University of Western Australia, Perth, Western Australia, Australia
| | - Effie Petersdorf
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Marcel G J Tilanus
- School for Oncology and Reproduction, GROW, Maastricht University, Maastricht, Netherlands
| | - Dianne De Santis
- Department of Clinical Immunology, PathWest, Fiona Stanley Hospital, Perth, Western Australia, Australia
- UWA Medical School, The University of Western Australia, Perth, Western Australia, Australia
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3
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Turner TR, Hayward DR, Gymer AW, Barker DJ, Leen G, Cambridge CA, Macpherson HL, Georgiou X, Cooper MA, Lucas JAM, Nadeem D, Robinson J, Mayor NP, Marsh SGE. Widespread non‐coding polymorphism in
HLA
class
II
genes of International
HLA
and Immunogenetics Workshop cell lines. HLA 2022; 99:328-356. [DOI: 10.1111/tan.14571] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 12/01/2022]
Affiliation(s)
- Thomas R. Turner
- Anthony Nolan Research Institute, Royal Free Hospital London UK
- UCL Cancer Institute, Royal Free Campus London UK
| | | | - Arthur W. Gymer
- Anthony Nolan Research Institute, Royal Free Hospital London UK
| | | | - Gayle Leen
- Anthony Nolan Research Institute, Royal Free Hospital London UK
- UCL Cancer Institute, Royal Free Campus London UK
| | | | | | - Xenia Georgiou
- Anthony Nolan Research Institute, Royal Free Hospital London UK
| | | | | | - Daud Nadeem
- Anthony Nolan Research Institute, Royal Free Hospital London UK
| | - James Robinson
- Anthony Nolan Research Institute, Royal Free Hospital London UK
- UCL Cancer Institute, Royal Free Campus London UK
| | - Neema P. Mayor
- Anthony Nolan Research Institute, Royal Free Hospital London UK
- UCL Cancer Institute, Royal Free Campus London UK
| | - Steven G. E. Marsh
- Anthony Nolan Research Institute, Royal Free Hospital London UK
- UCL Cancer Institute, Royal Free Campus London UK
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