52 results on '"Mayor NP"'
Search Results
2. A donor-specific epigenetic classifier for acute graft-versus-host disease severity in hematopoietic stem cell
- Author
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Paul, DS, Jones, A, Sellar, RS, Mayor, NP, Feber, A, Webster, AP, Afonso, N, Sergeant, R, Szydlo, RM, Apperley, JF, Widschwendter, M, Mackinnon, S, Marsh, SGE, Madrigal, JA, Rakyan, VK, Peggs, KS, Beck, S, and National Institute for Health Research
- Subjects
Genetics & Heredity ,EPIGENOME-WIDE ASSOCIATION ,EXPRESSION ,0604 Genetics ,Science & Technology ,BLOOD ,SYSTEMATIC ANNOTATION ,BIOMARKERS ,1103 Clinical Sciences ,CANCER ,SHRUNKEN CENTROIDS ,surgical procedures, operative ,immune system diseases ,hemic and lymphatic diseases ,DISCOVERY ,T-CELLS ,Life Sciences & Biomedicine ,DNA METHYLATION - Abstract
Background Allogeneic hematopoietic stem cell transplantation (HSCT) is a curative treatment for many hematological conditions. Acute graft-versus-host disease (aGVHD) is a prevalent immune-mediated complication following HSCT. Current diagnostic biomarkers that correlate with aGVHD severity, progression, and therapy response in graft recipients are insufficient. Here, we investigated whether epigenetic marks measured in peripheral blood of healthy graft donors stratify aGVHD severity in human leukocyte antigen (HLA)-matched sibling recipients prior to T cell-depleted HSCT. Methods We measured DNA methylation levels genome-wide at single-nucleotide resolution in peripheral blood of 85 HSCT donors, matched to recipients with various transplant outcomes, with Illumina Infinium HumanMethylation450 BeadChips. Results Using genome-wide DNA methylation profiling, we showed that epigenetic signatures underlying aGVHD severity in recipients correspond to immune pathways relevant to aGVHD etiology. We discovered 31 DNA methylation marks in donors that associated with aGVHD severity status in recipients, and demonstrated strong predictive performance of these markers in internal cross-validation experiments (AUC = 0.98, 95 % CI = 0.96–0.99). We replicated the top-ranked CpG classifier using an alternative, clinical DNA methylation assay (P = 0.039). In an independent cohort of 32 HSCT donors, we demonstrated the utility of the epigenetic classifier in the context of a T cell-replete conditioning regimen (P = 0.050). Conclusions Our findings suggest that epigenetic typing of HSCT donors in a clinical setting may be used in conjunction with HLA genotyping to inform both donor selection and transplantation strategy, with the ultimate aim of improving patient outcome.
- Published
- 2015
3. Single nucleotide polymorphisms in the NOD2/CARD15 gene are associated with an increased risk of relapse and death for patients with acute leukemia after hematopoietic stem-cell transplantation with unrelated donors.
- Author
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Mayor NP, Shaw BE, Hughes DA, Maldonado-Torres H, Madrigal JA, Keshav S, Marsh SG, Mayor, Neema P, Shaw, Bronwen E, Hughes, Derralynn A, Maldonado-Torres, Hazael, Madrigal, J Alejandro, Keshav, Satish, and Marsh, Steven G E
- Published
- 2007
4. KIR2DS2+ NK cells in cancer patients demonstrate high activation in response to tumour-targeting antibodies.
- Author
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Graham LV, Fisher JG, Doyle ADP, Sale B, Del Rio L, French AJE, Mayor NP, Turner TR, Marsh SGE, Cragg MS, Forconi F, Khakoo SI, and Blunt MD
- Abstract
Strategies to mobilise natural killer (NK) cells against cancer include tumour-targeting antibodies, NK cell engagers (NKCEs) and the adoptive transfer of ex vivo expanded healthy donor-derived NK cells. Genetic and functional studies have revealed that expression of the activating killer immunoglobulin-like receptor KIR2DS2 is associated with enhanced function in NK cells from healthy donors and improved outcome in several different malignancies. The optimal strategy to leverage KIR2DS2+ NK cells therapeutically is however currently unclear. In this study, we therefore evaluated the response of KIR2DS2-expressing NK cells to activation against cancer with clinically relevant tumour-targeting antibodies and following ex vivo expansion. We identified that KIR2DS2
high NK cells from patients with chronic lymphocytic leukaemia and hepatocellular carcinoma had enhanced activation in response to tumour-targeting antibodies compared to KIR2DS2- NK cells. However, the superior function of healthy donor derived KIR2DS2high NK cells was lost following ex vivo expansion which is required for adoptive transfer-based therapeutic strategies. These data provide evidence that targeting KIR2DS2 directly in cancer patients may allow for the utilisation of their enhanced effector function, however such activity may be lost following their ex vivo expansion., Competing Interests: MB and SK have applied for a patent for peptide mediated NK cell activation. MB has received research funding from Karyopharm Therapeutics. MC is a retained consultant for BioInvent International and has performed educational and advisory roles for Baxalta and Boehringer Ingleheim. He has consulted for GSK, Radiant, iTeos Therapeutics, Surrozen, Hanall and Mestag and received research funding from BioInvent, Surrozen, GSK, UCB and iTeos. FF has received research support from Abbvie and has performed consultancies or educational activities for AstraZeneca, AbbVie, Janssen-Cilag, BC-Platform and Beigene. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Graham, Fisher, Doyle, Sale, Del Rio, French, Mayor, Turner, Marsh, Cragg, Forconi, Khakoo and Blunt.)- Published
- 2024
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5. Identification of 43 novel HLA alleles by PacBio single molecule real-time sequencing in haematopoietic cell donors.
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French AJE, Lucas JAM, Cooper MA, Marsh SGE, and Mayor NP
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- Humans, Sequence Analysis, DNA methods, Hematopoietic Stem Cell Transplantation, High-Throughput Nucleotide Sequencing methods, Hematopoietic Stem Cells metabolism, Alleles, Tissue Donors, HLA Antigens genetics, Histocompatibility Testing methods
- Abstract
A total of 43 novel HLA alleles detected in haematopoietic cell donors using single molecule real-time DNA sequencing., (© 2024 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)
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- 2024
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6. 60 HLA class I and 115 HLA class II sequence confirmations submitted to the IPD-IMGT/HLA Database.
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Lucas JAM, Hopper SJF, Robinson J, Marsh SGE, and Mayor NP
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- Humans, Sequence Analysis, DNA, Histocompatibility Testing, Alleles, Databases, Genetic, Histocompatibility Antigens Class II genetics, Histocompatibility Antigens Class II immunology, Histocompatibility Antigens Class I genetics, Histocompatibility Antigens Class I immunology
- Abstract
Sequence confirmations of 175 HLA class I and II alleles in the IPD-IMGT/HLA Database., (© 2024 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)
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- 2024
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7. The 18th International HLA & Immunogenetics workshop project report: Creating fully representative MHC reference haplotypes.
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Pollock NR, Farias TDJ, Kichula KM, Sauter J, Scholz S, Nii-Trebi NI, Khor SS, Tokunaga K, Voorter CE, Groeneweg M, Augusto DG, Arrieta-Bolaños E, Mayor NP, Edinur HA, ElGhazali G, Issler HC, Petzl-Erler ML, Oksenberg JR, Marin WM, Hollenbach JA, Gendzekhadze K, Cita R, Stelet V, Rajalingam R, Koskela S, Clancy J, Chatzistamatiou T, Houwaart T, Kulski J, Guethlein LA, Parham P, Schmidt AH, Dilthey A, and Norman PJ
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- Humans, Histocompatibility Testing, Major Histocompatibility Complex genetics, Haplotypes, HLA Antigens genetics, Immunogenetics methods
- Published
- 2024
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8. HLA typing: A review of methodologies and clinical impact on haematopoietic cell transplantation.
- Author
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Mayor NP and Marsh SGE
- Subjects
- Humans, Polymorphism, Genetic, Hematopoietic Stem Cell Transplantation, Histocompatibility Testing methods, HLA Antigens genetics, HLA Antigens immunology
- Abstract
The importance of the HLA gene system in haematopoietic cell transplant outcomes was established early on and advances in both fields have led to ever increasing success of this clinical therapy. In large part, improvements in the understanding of HLA have been driven by the advancement in typing technologies. Each iteration of typing technology has improved the resolution of HLA typing, and often enabled the identification of polymorphism within the HLA loci. The discovery of the enormous amount of variation in the HLA genes, and the need to be able to characterise this for clinical HLA typing, has often resulted in a move away from one typing method to another more suited to typing of this complexity. Today, the gold standard for HLA typing are methods that can produce definitive HLA typing results., (Copyright © 2024 Elsevier Ltd. All rights reserved.)
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- 2024
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9. The novel alleles, HLA-G*01:04:09 and HLA-DPB1*04:01:01:136, detected in a hematopoietic cell donor.
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French AJE, Lucas JAM, Turner TR, Marsh SGE, and Mayor NP
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- Humans, Alleles, HLA-DP beta-Chains genetics, HLA-G Antigens, Genes, MHC Class I
- Abstract
Two novel alleles, HLA-G*01:04:09 and HLA-DPB1*04:01:01:136, were identified in a single healthy individual., (© 2024 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)
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- 2024
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10. Fifty novel HLA-DPB1 alleles identified in a UK cohort of unrelated hematopoietic cell donors and recipients.
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Cambridge CA, Turner TR, Georgiou X, Robinson J, Mayor NP, and Marsh SGE
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- Humans, Alleles, HLA-DP beta-Chains genetics, Genotype, United Kingdom, Unrelated Donors
- 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., (© 2023 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)
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- 2024
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11. The novel HLA-F*01:16 and HLA-F*01:17 alleles identified in hematopoietic cell donors.
- Author
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Rowley MV, Lucas JAM, Turner TR, Marsh SGE, and Mayor NP
- Subjects
- Humans, Alleles, Genes, MHC Class I, Tissue Donors
- Abstract
Two novel non-classical HLA class I alleles have been characterized, HLA-F*01:16 and -F*01:17., (© 2023 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)
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- 2024
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12. 86 novel HLA-E alleles discovered through full-gene sequencing of 6227 hematopoietic cell transplant patients and unrelated donors.
- Author
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Lucas JAM, Georgiou X, Cooper MA, Robinson J, Marsh SGE, and Mayor NP
- Subjects
- Humans, Alleles, HLA-E Antigens, Hematopoietic Stem Cell Transplantation
- Abstract
Until recently the number of alleles of the nonclassical HLA class I gene HLA-E documented in the IPD-IMGT/HLA Database was small and as a result, the gene was often not considered to be notably polymorphic. Here, we describe our work in identifying and submitting 86 novel HLA-E alleles after full-gene single-molecule real-time (SMRT) DNA sequencing of 6227 DNA samples. These samples were comprised of 2468 patients undergoing hematopoietic cell transplantation and 3759 unrelated potential donors. A total of 111 unique HLA-E alleles were detected in this cohort. The majority of novel alleles (79.1%) contained polymorphisms in intronic regions, highlighting the significant undiscovered variation present in the noncoding regions of the HLA-E gene., (© 2022 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)
- Published
- 2023
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13. Characterization of the novel HLA-A*02:01:01:206 allele in a Northern European individual.
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Williams HB, Lucas JAM, Cambridge CA, Marsh SGE, and Mayor NP
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- Alleles, High-Throughput Nucleotide Sequencing, Humans, Sequence Analysis, DNA, HLA-A Antigens genetics, White People
- Abstract
Pacific Biosciences SMRT sequencing used to identify the novel allele, HLA-A*02:01:02:206., (© 2022 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)
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- 2022
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14. Identification of the novel HLA-E*01:03:02:25 allele in an acute lymphoblastic leukemia patient.
- Author
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Williams HB, Lucas JAM, Georgiou X, Marsh SGE, and Mayor NP
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- Alleles, Histocompatibility Testing, Humans, HLA-E Antigens, Histocompatibility Antigens Class I genetics, Precursor Cell Lymphoblastic Leukemia-Lymphoma genetics, Precursor Cell Lymphoblastic Leukemia-Lymphoma therapy
- Abstract
HLA-E*01:03:02:25 sequenced from blood and buccal samples of an ALL patient., (© 2022 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)
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- 2022
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15. The novel HLA-DRB1*03:01:01:05 and -DPB1*04:02:01:21 alleles identified in patients with acute leukemia.
- Author
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Williams HB, Turner TR, Cambridge CA, Marsh SGE, and Mayor NP
- Subjects
- Alleles, Gene Frequency, HLA-DQ beta-Chains, HLA-DRB1 Chains genetics, Humans, Polymorphism, Genetic, HLA-DQ Antigens genetics, Leukemia genetics, Leukemia therapy
- Abstract
Two novel HLA class II alleles were characterized, HLA-DRB1*03:01:01:05 and HLA-DPB1*04:02:01:21., (© 2022 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)
- Published
- 2022
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16. Widespread non-coding polymorphism in HLA class II genes of International HLA and Immunogenetics Workshop cell lines.
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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, and Marsh SGE
- Subjects
- Alleles, Cell Line, Gene Frequency, Haplotypes, Humans, Genes, MHC Class II, Immunogenetics
- Abstract
As the primary genetic determinant of immune recognition of self and non-self, the hyperpolymorphic HLA genes play key roles in disease association and transplantation. The large, variably sized HLA class II genes have historically been less well characterized than the shorter HLA class I genes. Here, we have used Pacific Biosciences Single Molecule Real-Time (SMRT®) DNA sequencing to perform four-field resolution HLA typing of HLA-DRB1/3/4/5, -DQA1, -DQB1, -DPA1 and -DPB1 from a panel of 181 B-lymphoblastoid cell lines from the International HLA and Immunogenetics Workshops. By interrogating all exons, introns, and the untranslated regions of these important reference cells, we have improved their HLA typing resolution on the IPD-IMGT/HLA database. We observed widespread non-coding polymorphism, with over twice as many unique genomic sequences identified compared with coding sequences (CDS). We submitted 263 unique sequences to the IPD-IMGT/HLA Database, often from multiple cell lines, including 114 confirmations of existing alleles, of which 30 were also extensions to full-length genomic sequences where only CDS was available previously. A total of 149 novel alleles were identified, largely differing from their closest reference allele sequences by a single nucleotide polymorphism (SNP). However, some highly divergent alleles were deemed to be recombinants, only detectable by full-length sequencing with long, phased reads. The fourth-field variation we observed allowed fine mapping of linkage disequilibrium patterns and haplotypes to particular ancestries. This study has highlighted the under-appreciated non-coding diversity in HLA class II genes, with potential implications for population genetic and clinical studies., (© 2022 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)
- Published
- 2022
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17. Impact of Previously Unrecognized HLA Mismatches Using Ultrahigh Resolution Typing in Unrelated Donor Hematopoietic Cell Transplantation.
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Mayor NP, Wang T, Lee SJ, Kuxhausen M, Vierra-Green C, Barker DJ, Auletta J, Bhatt VR, Gadalla SM, Gragert L, Inamoto Y, Morris GP, Paczesny S, Reshef R, Ringdén O, Shaw BE, Shaw P, Spellman SR, and Marsh SGE
- Subjects
- Adolescent, Adult, Child, Child, Preschool, Female, Humans, Infant, Infant, Newborn, Male, Unrelated Donors, Young Adult, Hematopoietic Stem Cell Transplantation methods, Histocompatibility Testing methods, Transplantation Conditioning methods
- Abstract
Purpose: Ultrahigh resolution (UHR) HLA matching is reported to result in better outcomes following unrelated donor hematopoietic cell transplantation, improving survival and reducing post-transplant complications. However, most studies included relatively small numbers of patients. Here we report the findings from a large, multicenter validation study., Methods: UHR HLA typing was available on 5,140 conventionally 10 out of 10 HLA-matched patients with malignant disease transplanted between 2008 and 2017., Results: After UHR HLA typing, 82% of pairs remained 10 out of 10 UHR-matched; 12.3% of patients were 12 out of 12 UHR HLA-matched. Compared with 12 out of 12 UHR-matched patients, probabilities of grade 2-4 acute graft-versus-host disease (aGVHD) were significantly increased with UHR mismatches (overall P = .0019) and in those patients who were HLA-DPB1 T-cell epitope permissively mismatched or nonpermissively mismatched (overall P = .0011). In the T-cell-depleted subset, the degree of UHR HLA mismatch was only associated with increased transplant-related mortality (TRM) (overall P = .0068). In the T-cell-replete subset, UHR HLA matching was associated with a lower probability of aGVHD (overall P = .0020); 12 out of 12 UHR matching was associated with reduced TRM risk when compared with HLA-DPB1 T-cell epitope permissively mismatched patients, whereas nonpermissive mismatching resulted in a greater risk (overall P = .0003)., Conclusion: This study did not confirm that UHR 12 out of 12 HLA matching increases the probability of overall survival but does demonstrate that aGVHD risk, and in certain settings TRM, is lowest in UHR HLA-matched pairs and thus warrants consideration when multiple 10 out of 10 HLA-matched donors of equivalent age are available., Competing Interests: Stephanie J. LeeHonoraria: Wolters KluwerConsulting or Advisory Role: Incyte, Pfizer, EMD Serono, Kadmon, MSD Oncology, Sanofi, Genzyme, Regeneron, 4SCResearch Funding: Kadmon, Takeda, Amgen, Bristol-Myers Squibb, EMD Serono, MSD, Novartis, Incyte, Syndax, Pfizer, AstraZenecaPatents, Royalties, Other Intellectual Property: Patent pending for high-affinity T-cell receptors that target the Merkel polyomavirus Jeffrey AulettaConsulting or Advisory Role: MORE Health, AlloVir, AscellaHealth Vijaya R. BhattConsulting or Advisory Role: Abbvie, Incyte, Agios, Genentech, Rigel, Partnership for Health Analytic Research, LLC, Omeros, TakedaResearch Funding: Incyte, Tolero Pharmaceuticals, National Marrow Donor Program, Abbvie, Pfizer, Jazz PharmaceuticalsOther Relationship: Oncoceutics, Novartis, Pfizer Loren GragertOther Relationship: National Marrow Donor Program/Be The Match, United Network For Organ Sharing Yoshihiro InamotoHonoraria: Kyowa Kirin Co, Ltd, Astellas Pharma, Sumitomo Dainippon, Novartis, Chugai Pharma, Bristol-Myers Squibb, MSD K.K.Consulting or Advisory Role: Novartis, Janssen, Meiji Seika Kaisha Gerald P. MorrisResearch Funding: Ferring Inc, AmgenTravel, Accommodations, Expenses: Thermo Fisher Scientific Sophie PaczesnyPatents, Royalties, Other Intellectual Property: Dr Paczesny has a patent on “Methods of detection of graft-versus-host disease” licensed to Viracor-IBT Laboratories Ran ReshefConsulting or Advisory Role: Atara Biotherapeutics, Novartis, Bristol-Myers Squibb, Gilead Sciences, TScan TherapeuticsResearch Funding: Atara Biotherapeutics, Incyte, Pharmacyclics, Shire, Immatics, Takeda, Gilead Sciences, Precision Biosciences, Astellas Pharma, Bristol-Myers Squibb Bronwen E. ShawHonoraria: TherakosConsulting or Advisory Role: Orcabio Peter ShawConsulting or Advisory Role: NovartisOther Relationship: Link PharmaNo other potential conflicts of interest were reported.
- Published
- 2021
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18. The novel HLA-C*03:04:01:47 allele sequence identified using Pacific biosciences SMRT sequencing.
- Author
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Comerford AG, Lucas JAM, Turner TR, Marsh SGE, and Mayor NP
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- Alleles, Genes, MHC Class I, Humans, Sequence Analysis, DNA, HLA-C Antigens genetics, High-Throughput Nucleotide Sequencing
- Abstract
A novel variant of HLA-C*03:04:01:47 was identified using Pacific Biosciences SMRT sequencing platform., (© 2020 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)
- Published
- 2020
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19. Presence of donor-encoded centromeric KIR B content increases the risk of infectious mortality in recipients of myeloablative, T-cell deplete, HLA-matched HCT to treat AML.
- Author
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Bultitude WP, Schellekens J, Szydlo RM, Anthias C, Cooley SA, Miller JS, Weisdorf DJ, Shaw BE, Roberts CH, Garcia-Sepulveda CA, Lee J, Pearce RM, Wilson MC, Potter MN, Byrne JL, Russell NH, MacKinnon S, Bloor AJ, Patel A, McQuaker IG, Malladi R, Tholouli E, Orchard K, Potter VT, Madrigal JA, Mayor NP, and Marsh SGE
- Subjects
- Adult, HLA Antigens, Humans, Neoplasm Recurrence, Local, Retrospective Studies, T-Lymphocytes, Hematopoietic Stem Cell Transplantation, Leukemia, Myeloid, Acute therapy, Receptors, KIR genetics
- Abstract
The reported influence of donor Killer-cell Immunoglobulin-like Receptor (KIR) genes on the outcomes of haematopoietic cell transplantation (HCT) are contradictory, in part due to diversity of disease, donor sources, era and conditioning regimens within and between different studies. Here, we describe the results of a retrospective clinical analysis establishing the effect of donor KIR motifs on the outcomes of 119 HLA-matched, unrelated donor HCT for adult acute myeloid leukaemia (AML) using myeloablative conditioning (MAC) in a predominantly T-cell deplete (TCD) cohort. We observed that HCT involving donors with at least one KIR B haplotype were more likely to result in non-relapse mortality (NRM) than HCT involving donors with two KIR A haplotypes (p = 0.019). Upon separation of KIR haplotypes into their centromeric (Cen) and telomeric (Tel) motif structures, we demonstrated that the Cen-B motif was largely responsible for this effect (p = 0.001). When the cause of NRM was investigated further, infection was the dominant cause of death (p = 0.006). No evidence correlating donor KIR B haplotype with relapse risk was observed. The results from this analysis confirm previous findings in the unrelated, TCD, MAC transplant setting and imply a protective role for donor-encoded Cen-A motifs against infection in allogeneic HCT recipients.
- Published
- 2020
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20. Single molecule real-time DNA sequencing of the full HLA-E gene for 212 reference cell lines.
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Lucas JAM, Hayhurst JD, Turner TR, Gymer AW, Leen G, Robinson J, Marsh SGE, and Mayor NP
- Subjects
- Alleles, Cell Line, Genotype, HLA Antigens, Histocompatibility Testing, Sequence Analysis, DNA, High-Throughput Nucleotide Sequencing, Histocompatibility Antigens Class II genetics
- Abstract
We have developed a genotyping assay that produces fully phased, unambiguous HLA-E genotyping using Pacific Biosciences' single molecule real-time DNA sequencing. In total 212 cell lines were genotyped, including the panel of 107 established at the 10th International Histocompatibility Workshop. Our results matched the previously known HLA-E genotype in 94 (44.3%) cell lines, in all cases either improving or equalling previous genotyping resolution. Three (1.4%) cells had discrepant HLA-E genotyping data and 115 (54.2%) had no previous HLA-E data. The HLA-E genotypes for four (1.9%) cell lines resulted in a change of zygosity by identifying two distinct haplotypes. We discovered eight novel HLA-E alleles, extended the known reference sequence of seven and confirmed the existence of a further 10., (© 2020 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)
- Published
- 2020
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21. Extending the sequences of HLA class I alleles without full-length genomic coverage using single molecule real-time DNA sequencing.
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Hassall KB, Latham K, Robinson J, Gymer A, Goodall R, Merlo D, Marsh SGE, and Mayor NP
- Subjects
- Alleles, Genomics, Humans, Sequence Analysis, DNA, High-Throughput Nucleotide Sequencing, Histocompatibility Antigens Class I genetics
- Abstract
The assignment of an HLA allele name to a sequence requires a comparison between the generated target sequence and a reference sequence on the IPD-IMGT/HLA database. Absence of a full-length reference sequence can result in the inability of HLA typing software to accurately compare and assign the sequence. We sequenced the most frequently seen HLA class I alleles on the Anthony Nolan register present in the database with only a partial genomic sequence, with the aim of increasing the number of complete reference sequences. We successfully extended 95 full-length HLA class I sequences and identified 13 novel variants. Increasing the number of full-length HLA class I reference sequences in the database has aided accuracy of HLA analysis tools for all histocompatibility and immunogenetics laboratories., (© 2020 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)
- Published
- 2020
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22. A novel allele, HLA-C*07:01:01:30 identified using third-generation sequencing.
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Liu YL, Turner TR, Georgiou X, Marsh SGE, and Mayor NP
- Subjects
- Alleles, Amino Acid Substitution, Base Sequence, Humans, Sequence Homology, HLA-C Antigens genetics, High-Throughput Nucleotide Sequencing methods, Polymorphism, Single Nucleotide, Sequence Analysis, DNA methods
- Abstract
The novel allele, HLA-C*07:01:01:30 differs by one nucleotide substitution with HLA-C*07:01:01:01 at gDNA 627., (© 2019 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)
- Published
- 2019
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23. Identification of a new allele, HLA-DRB1*01:01:01:02 discovered using third-generation sequencing.
- Author
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Liu YL, Macpherson HL, Pryke OL, Marsh SGE, and Mayor NP
- Subjects
- Alleles, Amino Acid Substitution, Base Sequence, Humans, Sequence Homology, HLA-DRB1 Chains genetics, High-Throughput Nucleotide Sequencing methods, Introns genetics, Polymorphism, Single Nucleotide, Sequence Analysis, DNA methods
- Abstract
HLA-DRB1*01:01:01:02 is the first reported intronic variant of DRB1*01:01:01, differing by a single nucleotide substitution., (© 2019 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)
- Published
- 2019
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24. A genomic extension to the sequence of HLA-A*02:13, identified using third-generation sequencing.
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Liu YL, Lucas JAM, Turner TR, Marsh SGE, and Mayor NP
- Subjects
- Alleles, Humans, Genomics methods, HLA-A2 Antigen genetics, High-Throughput Nucleotide Sequencing methods, Sequence Analysis, DNA methods
- Abstract
Pacific Biosciences' SMRT sequencing method was used to extend the sequence of HLA-A*02:13., (© 2019 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)
- Published
- 2019
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25. A reply to Hurley et al. regarding Recipients Receiving Better HLA-Matched Hematopoietic Cell Transplantation Grafts, Uncovered by a Novel HLA Typing Method, Have Superior Survival: A Retrospective Study.
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Mayor NP, Hayhurst JD, Turner TR, Szydlo RM, Shaw BE, Bultitude WP, Sayno JR, Tavarozzi F, Latham K, Anthias C, Robinson J, Braund H, Danby R, Perry J, Wilson MC, Bloor AJ, McQuaker IG, MacKinnon S, Marks DI, Pagliuca A, Potter MN, Potter VT, Russell NH, Thomson KJ, Madrigal JA, and Marsh SGE
- Subjects
- Histocompatibility Testing, Retrospective Studies, Hematopoietic Stem Cell Transplantation
- Published
- 2019
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26. Next-generation HLA typing of 382 International Histocompatibility Working Group reference B-lymphoblastoid cell lines: Report from the 17th International HLA and Immunogenetics Workshop.
- Author
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Creary LE, Guerra SG, Chong W, Brown CJ, Turner TR, Robinson J, Bultitude WP, Mayor NP, Marsh SGE, Saito K, Lam K, Duke JL, Mosbruger TL, Ferriola D, Monos D, Willis A, Askar M, Fischer G, Saw CL, Ragoussis J, Petrek M, Serra-Pagés C, Juan M, Stavropoulos-Giokas C, Dinou A, Ameen R, Al Shemmari S, Spierings E, Gendzekhadze K, Morris GP, Zhang Q, Kashi Z, Hsu S, Gangavarapu S, Mallempati KC, Yamamoto F, Osoegawa K, Vayntrub T, Chang CJ, Hansen JA, and Fernández-Viňa MA
- Subjects
- Alleles, Cell Line, Transformed, Cell Transformation, Viral, Data Accuracy, Exons genetics, Genetic Loci, Genetic Variation, Genotype, Haplotypes genetics, High-Throughput Nucleotide Sequencing methods, Histocompatibility, Homozygote, Humans, Sequence Analysis, DNA methods, Single-Blind Method, B-Lymphocytes virology, HLA Antigens genetics, Herpesvirus 4, Human immunology, Histocompatibility Antigens Class I genetics, Histocompatibility Antigens Class II genetics, Histocompatibility Testing methods
- Abstract
Extended molecular characterization of HLA genes in the IHWG reference B-lymphoblastoid cell lines (B-LCLs) was one of the major goals for the 17th International HLA and Immunogenetics Workshop (IHIW). Although reference B-LCLs have been examined extensively in previous workshops complete high-resolution typing was not completed for all the classical class I and class II HLA genes. To address this, we conducted a single-blind study where select panels of B-LCL genomic DNA samples were distributed to multiple laboratories for HLA genotyping by next-generation sequencing methods. Identical cell panels comprised of 24 and 346 samples were distributed and typed by at least four laboratories in order to derive accurate consensus HLA genotypes. Overall concordance rates calculated at both 2- and 4-field allele-level resolutions ranged from 90.4% to 100%. Concordance for the class I genes ranged from 91.7 to 100%, whereas concordance for class II genes was variable; the lowest observed at HLA-DRB3 (84.2%). At the maximum allele-resolution 78 B-LCLs were defined as homozygous for all 11 loci. We identified 11 novel exon polymorphisms in the entire cell panel. A comparison of the B-LCLs NGS HLA genotypes with the HLA genotypes catalogued in the IPD-IMGT/HLA Database Cell Repository, revealed an overall allele match at 68.4%. Typing discrepancies between the two datasets were mostly due to the lower-resolution historical typing methods resulting in incomplete HLA genotypes for some samples listed in the IPD-IMGT/HLA Database Cell Repository. Our approach of multiple-laboratory NGS HLA typing of the B-LCLs has provided accurate genotyping data. The data generated by the tremendous collaborative efforts of the 17th IHIW participants is useful for updating the current cell and sequence databases and will be a valuable resource for future studies., (Copyright © 2019. Published by Elsevier Inc.)
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- 2019
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27. Recipients Receiving Better HLA-Matched Hematopoietic Cell Transplantation Grafts, Uncovered by a Novel HLA Typing Method, Have Superior Survival: A Retrospective Study.
- Author
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Mayor NP, Hayhurst JD, Turner TR, Szydlo RM, Shaw BE, Bultitude WP, Sayno JR, Tavarozzi F, Latham K, Anthias C, Robinson J, Braund H, Danby R, Perry J, Wilson MC, Bloor AJ, McQuaker IG, MacKinnon S, Marks DI, Pagliuca A, Potter MN, Potter VT, Russell NH, Thomson KJ, Madrigal JA, and Marsh SGE
- Subjects
- Adult, Alleles, Female, Hematopoietic Stem Cell Transplantation methods, Histocompatibility genetics, Histocompatibility Testing methods, Humans, Male, Middle Aged, Retrospective Studies, Survival Analysis, Unrelated Donors, Hematopoietic Stem Cell Transplantation mortality, Histocompatibility immunology, Histocompatibility Testing standards, Sequence Analysis, DNA standards
- Abstract
HLA matching at an allelic-level resolution for volunteer unrelated donor (VUD) hematopoietic cell transplantation (HCT) results in improved survival and fewer post-transplant complications. Limitations in typing technologies used for the hyperpolymorphic HLA genes have meant that variations outside of the antigen recognition domain (ARD) have not been previously characterized in HCT. Our aim was to explore the extent of diversity outside of the ARD and determine the impact of this diversity on transplant outcome. Eight hundred ninety-one VUD-HCT donors and their recipients transplanted for a hematologic malignancy in the United Kingdom were retrospectively HLA typed at an ultra-high resolution (UHR) for HLA-A, -B, -C, -DRB1, -DQB1, and -DPB1 using next-generation sequencing technology. Matching was determined at full gene level for HLA class I and at a coding DNA sequence level for HLA class II genes. The HLA matching status changed in 29.1% of pairs after UHR HLA typing. The 12/12 UHR HLA matched patients had significantly improved 5-year overall survival when compared with those believed to be 12/12 HLA matches based on their original HLA typing but were found to be mismatched after UHR HLA typing (54.8% versus 30.1%, P = .022). Survival was also significantly better in 12/12 UHR HLA-matched patients when compared with those with any degree of mismatch at this level of resolution (55.1% versus 40.1%, P = .005). This study shows that better HLA matching, found when typing is done at UHR that includes exons outside of the ARD, introns, and untranslated regions, can significantly improve outcomes for recipients of a VUD-HCT for a hematologic malignancy and should be prospectively performed at donor selection., (Copyright © 2019 American Society for Blood and Marrow Transplantation. Published by Elsevier Inc. All rights reserved.)
- Published
- 2019
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28. HLA-DPB1*64:01N and DPB1*701:01 sequence extensions by single molecule real-time DNA sequencing.
- Author
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Cambridge CA, Turner TR, Abraham JP, Marsh SGE, and Mayor NP
- Subjects
- Base Sequence, Codon chemistry, Gene Expression, Genotype, HLA-DP beta-Chains immunology, Hematopoietic Stem Cell Transplantation, High-Throughput Nucleotide Sequencing, Histocompatibility Testing, Humans, Polymerase Chain Reaction methods, Protein Isoforms genetics, Protein Isoforms immunology, Sequence Alignment, Sequence Analysis, DNA, Tissue Donors, Alleles, Exons, HLA-DP beta-Chains genetics, Polymorphism, Single Nucleotide
- Abstract
Pacific Bioscience's SMRT sequencing was used to confirm and extend HLA-DPB1*64:01N and 701:01., (© 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)
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- 2018
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29. Two novel alleles, HLA-A*32:01:01:09 and 32:01:01:10, identified by Pacific Bioscience's SMRT sequencing.
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Cambridge CA, Turner TR, Georgiou X, Marsh SGE, and Mayor NP
- Subjects
- B-Lymphocytes immunology, B-Lymphocytes pathology, Base Sequence, Cell Line, Tumor, Codon chemistry, Gene Expression, Genotype, HLA-A Antigens immunology, Hematopoietic Stem Cell Transplantation, Histocompatibility Testing, Humans, Polymerase Chain Reaction, Precursor Cell Lymphoblastic Leukemia-Lymphoma immunology, Precursor Cell Lymphoblastic Leukemia-Lymphoma pathology, Precursor Cell Lymphoblastic Leukemia-Lymphoma therapy, Protein Isoforms genetics, Protein Isoforms immunology, Sequence Alignment, Sequence Analysis, DNA, Transplant Recipients, Alleles, HLA-A Antigens genetics, Introns, Polymorphism, Single Nucleotide, Precursor Cell Lymphoblastic Leukemia-Lymphoma genetics
- Abstract
Pacific Bioscience's SMRT DNA sequencing was used to identify two novel intronic variants of HLA-A*32:01:01:01., (© 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)
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- 2018
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30. The novel KIR2DL1 allele, KIR2DL1*037, defined in the cell line SPO010 (IHW9036).
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Bultitude WP, Gymer AW, Robinson J, Mayor NP, and Marsh SGE
- Subjects
- Alleles, Cell Line, Consanguinity, High-Throughput Nucleotide Sequencing, Histocompatibility Testing, Homozygote, Humans, Polymorphism, Genetic, Sequence Alignment, World Health Organization, Genotype, Killer Cells, Natural physiology, Receptors, KIR2DL1 genetics, White People
- Abstract
The novel KIR2DL1*037 allele discovered and characterised by single molecule real-time (SMRT) DNA sequencing., (© 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)
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- 2018
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31. KIR2DL1 allele sequence extensions and discovery of 2DL1*0010102 and 2DL1*0010103 alleles by DNA sequencing.
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Bultitude WP, Gymer AW, Robinson J, Mayor NP, and Marsh SGE
- Subjects
- Alleles, Cohort Studies, High-Throughput Nucleotide Sequencing, Humans, Polymorphism, Single Nucleotide, United Kingdom, World Health Organization, Genotype, Introns genetics, Receptors, KIR2DL1 genetics
- Abstract
Full-length KIR2DL1 allele sequence extensions characterised by single molecule real-time (SMRT) DNA sequencing., (© 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)
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- 2018
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32. Single molecule real-time DNA sequencing of HLA genes at ultra-high resolution from 126 International HLA and Immunogenetics Workshop cell lines.
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Turner TR, Hayhurst JD, Hayward DR, Bultitude WP, Barker DJ, Robinson J, Madrigal JA, Mayor NP, and Marsh SGE
- Subjects
- Alleles, Cell Line, Humans, Linkage Disequilibrium genetics, Computer Systems, HLA Antigens genetics, Immunogenetics, Internationality, Sequence Analysis, DNA, Single Molecule Imaging
- Abstract
The hyperpolymorphic HLA genes play important roles in disease and transplantation and act as genetic markers of migration and evolution. A panel of 107 B-lymphoblastoid cell lines (B-LCLs) was established in 1987 at the 10th International Histocompatibility Workshop as a resource for the immunogenetics community. These B-LCLs are well characterised and represent diverse ethnicities and HLA haplotypes. Here we have applied Pacific Biosciences' Single Molecule Real-Time (SMRT) DNA sequencing to HLA type 126 B-LCL, including the 107 International HLA and Immunogenetics Workshop (IHIW) cells, to ultra-high resolution. Amplicon sequencing of full-length HLA class I genes (HLA-A, -B and -C) and partial length HLA class II genes (HLA-DRB1, -DQB1 and -DPB1) was performed. We typed a total of 931 HLA alleles, 895 (96%) of which were consistent with the typing in the IPD-IMGT/HLA Database (Release 3.27.0, January 20, 2017), with 595 (64%) typed at a higher resolution. Discrepant types, including novel alleles (n = 10) and changes in zygosity (n = 13), as well as previously unreported types (n = 34) were observed. In addition, patterns of linkage disequilibrium were distinguished by four-field resolution typing of HLA-B and HLA-C. By improving and standardising the HLA typing of these B-LCLs, we have ensured their continued usefulness as a resource for the immunogenetics community in the age of next generation DNA sequencing., (© 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)
- Published
- 2018
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33. Recipient/donor HLA and CMV matching in recipients of T-cell-depleted unrelated donor haematopoietic cell transplants.
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Shaw BE, Mayor NP, Szydlo RM, Bultitude WP, Anthias C, Kirkland K, Perry J, Clark A, Mackinnon S, Marks DI, Pagliuca A, Potter MN, Russell NH, Thomson K, Madrigal JA, and Marsh SGE
- Subjects
- Adolescent, Adult, Aged, Child, Child, Preschool, Female, Histocompatibility, Humans, Lymphocyte Depletion, Male, Middle Aged, Risk Factors, Serologic Tests, Survival Analysis, Young Adult, Cytomegalovirus immunology, HLA Antigens immunology, Hematologic Neoplasms therapy, Hematopoietic Stem Cell Transplantation methods, Unrelated Donors supply & distribution
- Abstract
Improving haematopoietic cell transplantation outcomes by selection of an HLA-matched unrelated donor is best practice; however, donor selection by secondary characteristics is controversial. We studied 1271 recipients with haematological malignancies who underwent T-cell-depleted allografts and had complete data on HLA-matching status for six loci (HLA-A, -B, -C, -DRB1, -DQB1, -DPB1) and clinical outcome data. Five-year overall survival was 40.6%. HLA mismatching (at HLA-A, -B, -C, -DRB1, -DQB1) relative risk (RR) 1.22, 95% confidence interval (CI) 1.2-1.5, P=0.033 for 1 mismatch and RR 1.46, 95% CI 1.1-1.9, P=0.009 for >1 mismatch) and CMV mismatching (RR 1.37, 95% CI 1.2-1.6, P<0.001) were significantly associated with inferior survival. Donors aged <30 years showed a trend towards better survival. The multivariate model for mortality, combining CMV and HLA-match status, found an RR of 1.36 (95% CI 1.1-1.7, P=0.003) for HLA matched/CMV mismatched, an RR of 1.22 (95% CI 0.99-1.5, P=0.062) for HLA mismatched/CMV matched and an RR of 1.81 (95% CI 1.4-2.3, P=<0.001) for HLA/ CMV mismatched, compared with the HLA/CMV-matched recipients. These data suggest that HLA and CMV matching status should be considered when selecting unrelated donors and that CMV matching may abrogate the effect of an HLA mismatch.
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- 2017
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34. Polymorphism in TGFB1 is associated with worse non-relapse mortality and overall survival after stem cell transplantation with unrelated donors.
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Arrieta-Bolaños E, Mayor NP, Marsh SG, Madrigal JA, Apperley JF, Kirkland K, Mackinnon S, Marks DI, McQuaker G, Perry J, Potter MN, Russell NH, Thomson K, and Shaw BE
- Subjects
- Adolescent, Adult, Alleles, Child, Child, Preschool, Female, Gene Expression, Genotype, Hematologic Neoplasms mortality, Hematologic Neoplasms therapy, Humans, Infant, Male, Middle Aged, Prognosis, Regulatory Sequences, Nucleic Acid, Risk Assessment, Sequence Analysis, DNA, Siblings, Survival Analysis, Transplant Recipients, Transplantation, Homologous, Unrelated Donors, Hematologic Neoplasms diagnosis, Hematologic Neoplasms genetics, Hematopoietic Stem Cell Transplantation, Polymorphism, Genetic, Transforming Growth Factor beta1 genetics
- Abstract
Transforming growth factor β-1, encoded by the TGFB1 gene, is a cytokine that plays a central role in many physiological and pathogenic processes. We have sequenced TGFB1 regulatory region and assigned allelic genotypes in a large cohort of hematopoietic stem cell transplantation patients and donors. In this study, we analyzed 522 unrelated donor-patient pairs and examined the combined effect of all the common polymorphisms in this genomic region. In univariate analysis, we found that patients carrying a specific allele, 'p001', showed significantly reduced overall survival (5-year overall survival 30.7% for p001/p001 patients vs. 41.6% others; P=0.032) and increased non-relapse mortality (1-year non-relapse mortality: 39.0% vs. 25.4%; P=0.039) after transplantation. In multivariate analysis, the presence of a p001/p001 genotype in patients was confirmed as an independent factor for reduced overall survival [hazard ratio=1.53 (1.04-2.24); P=0.031], and increased non-relapse mortality [hazard ratio=1.73 (1.06-2.83); P=0.030]. In functional experiments we found a trend towards a higher percentage of surface transforming growth factor β-1-positive regulatory T cells after activation when the cells had a p001 allele (P=0.07). Higher or lower production of transforming growth factor β-1 in the inflammatory context of hematopoietic stem cell transplantation may influence the development of complications in these patients. Findings indicate that TGFB1 genotype could potentially be of use as a prognostic factor in hematopoietic stem cell transplantation risk assessment algorithms., (Copyright© Ferrata Storti Foundation.)
- Published
- 2016
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35. A donor-specific epigenetic classifier for acute graft-versus-host disease severity in hematopoietic stem cell transplantation.
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Paul DS, Jones A, Sellar RS, Mayor NP, Feber A, Webster AP, Afonso N, Sergeant R, Szydlo RM, Apperley JF, Widschwendter M, Mackinnon S, Marsh SG, Madrigal JA, Rakyan VK, Peggs KS, and Beck S
- Subjects
- Adolescent, Adult, Aged, DNA Methylation, Epigenomics, Female, Genotype, Graft vs Host Disease blood, Graft vs Host Disease etiology, Graft vs Host Disease immunology, HLA Antigens genetics, HLA Antigens immunology, Humans, Male, Middle Aged, Siblings, T-Lymphocytes immunology, Transplantation Conditioning adverse effects, Young Adult, Graft vs Host Disease genetics, Hematopoietic Stem Cell Transplantation adverse effects, Tissue Donors
- Abstract
Background: Allogeneic hematopoietic stem cell transplantation (HSCT) is a curative treatment for many hematological conditions. Acute graft-versus-host disease (aGVHD) is a prevalent immune-mediated complication following HSCT. Current diagnostic biomarkers that correlate with aGVHD severity, progression, and therapy response in graft recipients are insufficient. Here, we investigated whether epigenetic marks measured in peripheral blood of healthy graft donors stratify aGVHD severity in human leukocyte antigen (HLA)-matched sibling recipients prior to T cell-depleted HSCT., Methods: We measured DNA methylation levels genome-wide at single-nucleotide resolution in peripheral blood of 85 HSCT donors, matched to recipients with various transplant outcomes, with Illumina Infinium HumanMethylation450 BeadChips., Results: Using genome-wide DNA methylation profiling, we showed that epigenetic signatures underlying aGVHD severity in recipients correspond to immune pathways relevant to aGVHD etiology. We discovered 31 DNA methylation marks in donors that associated with aGVHD severity status in recipients, and demonstrated strong predictive performance of these markers in internal cross-validation experiments (AUC = 0.98, 95% CI = 0.96-0.99). We replicated the top-ranked CpG classifier using an alternative, clinical DNA methylation assay (P = 0.039). In an independent cohort of 32 HSCT donors, we demonstrated the utility of the epigenetic classifier in the context of a T cell-replete conditioning regimen (P = 0.050)., Conclusions: Our findings suggest that epigenetic typing of HSCT donors in a clinical setting may be used in conjunction with HLA genotyping to inform both donor selection and transplantation strategy, with the ultimate aim of improving patient outcome.
- Published
- 2015
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36. The novel HLA-B*44 allele, HLA-B*44:220, identified by Single Molecule Real-Time DNA sequencing in a British Caucasoid male.
- Author
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Hayward DR, Bultitude WP, Mayor NP, Madrigal JA, and Marsh SG
- Subjects
- Base Sequence, Codon, Exons, Gene Expression, HLA-B44 Antigen immunology, Histocompatibility Testing, Humans, Male, Molecular Sequence Data, Sequence Alignment, United Kingdom, White People, Alleles, Amino Acid Substitution, HLA-B44 Antigen genetics, Polymorphism, Single Nucleotide
- Abstract
The genomic sequence of the novel HLA-B*44:220 allele identified in a British Caucasoid male., (© 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)
- Published
- 2015
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37. Proof-of-Principle for Immune Control of Global HIV-1 Reactivation In Vivo.
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Smith NM, Mlcochova P, Watters SA, Aasa-Chapman MM, Rabin N, Moore S, Edwards SG, Garson JA, Grant PR, Ferns RB, Kashuba A, Mayor NP, Schellekens J, Marsh SG, McMichael AJ, Perelson AS, Pillay D, Goonetilleke N, and Gupta RK
- Subjects
- Antibodies, Neutralizing blood, CD4-Positive T-Lymphocytes virology, CD8-Positive T-Lymphocytes immunology, Cytokines analysis, Enzyme-Linked Immunospot Assay, HIV Antibodies blood, HIV Infections complications, Humans, Leukocytes, Mononuclear immunology, Leukocytes, Mononuclear virology, Melphalan adverse effects, Melphalan therapeutic use, Middle Aged, Models, Theoretical, Multiple Myeloma drug therapy, Myeloablative Agonists adverse effects, Myeloablative Agonists therapeutic use, Stem Cell Transplantation adverse effects, T-Lymphocyte Subsets immunology, Transplantation, Autologous, HIV Infections immunology, HIV Infections virology, HIV-1 immunology, HIV-1 physiology, Virus Activation immunology
- Abstract
Background: Emerging data relating to human immunodeficiency virus type 1 (HIV-1) cure suggest that vaccination to stimulate the host immune response, particularly cytotoxic cells, may be critical to clearing of reactivated HIV-1-infected cells. However, evidence for this approach in humans is lacking, and parameters required for a vaccine are unknown because opportunities to study HIV-1 reactivation are rare., Methods: We present observations from a HIV-1 elite controller, not treated with combination antiretroviral therapy, who experienced viral reactivation following treatment for myeloma with melphalan and autologous stem cell transplantation. Mathematical modeling was performed using a standard viral dynamic model. Enzyme-linked immunospot, intracellular cytokine staining, and tetramer staining were performed on peripheral blood mononuclear cells; in vitro CD8 T-cell-mediated control of virion production by autologous CD4 T cells was quantified; and neutralizing antibody titers were measured., Results: Viral rebound was measured at 28,000 copies/mL on day 13 post-transplant before rapid decay to <50 copies/mL in 2 distinct phases with t1/2 of 0.71 days and 4.1 days. These kinetics were consistent with an expansion of cytotoxic effector cells and killing of productively infected CD4 T cells. Following transplantation, innate immune cells, including natural killer cells, recovered with virus rebound. However, most striking was the expansion of highly functional HIV-1-specific cytotoxic CD8 T cells, at numbers consistent with those applied in modeling, as virus control was regained., Conclusions: These observations provide evidence that the human immune response is capable of controlling coordinated global HIV-1 reactivation, remarkably with potency equivalent to combination antiretroviral therapy. These data will inform design of vaccines for use in HIV-1 curative interventions., (© The Author 2015. Published by Oxford University Press on behalf of the Infectious Diseases Society of America.)
- Published
- 2015
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38. HLA Typing for the Next Generation.
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Mayor NP, Robinson J, McWhinnie AJ, Ranade S, Eng K, Midwinter W, Bultitude WP, Chin CS, Bowman B, Marks P, Braund H, Madrigal JA, Latham K, and Marsh SG
- Subjects
- Alleles, Genomics, Humans, High-Throughput Nucleotide Sequencing methods, Histocompatibility Testing methods, Sequence Analysis, DNA methods
- Abstract
Allele-level resolution data at primary HLA typing is the ideal for most histocompatibility testing laboratories. Many high-throughput molecular HLA typing approaches are unable to determine the phase of observed DNA sequence polymorphisms, leading to ambiguous results. The use of higher resolution methods is often restricted due to cost and time limitations. Here we report on the feasibility of using Pacific Biosciences' Single Molecule Real-Time (SMRT) DNA sequencing technology for high-resolution and high-throughput HLA typing. Seven DNA samples were typed for HLA-A, -B and -C. The results showed that SMRT DNA sequencing technology was able to generate sequences that spanned entire HLA Class I genes that allowed for accurate allele calling. Eight novel genomic HLA class I sequences were identified, four were novel alleles, three were confirmed as genomic sequence extensions and one corrected an existing genomic reference sequence. This method has the potential to revolutionize the field of HLA typing. The clinical impact of achieving this level of resolution HLA typing data is likely to considerable, particularly in applications such as organ and blood stem cell transplantation where matching donors and recipients for their HLA is of utmost importance.
- Published
- 2015
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39. Caspase-8 polymorphisms result in reduced Alemtuzumab-induced T-cell apoptosis and worse survival after transplantation.
- Author
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Shaw BE, Lee F, Krishnamurthy S, Byrne JL, Seedhouse C, Mayor NP, Maldonado-Torres H, Saudemont A, Marsh SG, Madrigal JA, and Russell NH
- Subjects
- Adolescent, Adult, Aged, Alemtuzumab, Allografts, Child, Child, Preschool, Female, Humans, Lymphocyte Depletion, Male, Middle Aged, Stem Cell Transplantation, Antibodies, Monoclonal, Humanized administration & dosage, Antibodies, Monoclonal, Humanized adverse effects, Antineoplastic Agents administration & dosage, Antineoplastic Agents adverse effects, Apoptosis drug effects, Apoptosis genetics, Caspase 8 genetics, Hematologic Neoplasms genetics, Hematologic Neoplasms mortality, Hematologic Neoplasms therapy, Polymorphism, Genetic, T-Lymphocytes, Transplantation Conditioning adverse effects
- Abstract
Allo-SCT using unrelated donors is a curative treatment for patients with hematological disorders. The best donor is one matched for 10/10 HLA alleles, however studies have shown an additional survival benefit when considering other genetic factors. It has been shown that a six-nucleotide insertion/deletion polymorphism in the CASP8 gene promoter results in reduced susceptibility of T lymphocytes to undergo apoptosis. In 186 SCT recipients, we found a significantly better OS in those who received a transplant from a WT/WT donor compared with donors with a deletion (3 years: 52 vs 34%; P=0.03; multivariate analysis; RR 0.61; 95% CI 0.38-0.98, P=0.04). This was more marked when both the patient and the donor had a deletion (3 years OS: 62% compared with 36%, P=0.01). As the majority of these patients received Alemtuzumab during conditioning, we went on to analyze the in vitro effect of the polymorphism on Alemtuzumab-induced apoptosis. We showed statistically significantly higher percentages of apoptotic naïve CD4 (P<0.0005) and CD8 (P<0.0005) T cells in WT/WT donors in comparison with donors with a deletion. These data imply an unrecognized role for the CASP8 promoter polymorphism on survival following unrelated SCT particularly in the context of T-cell depletion with Alemtuzumab.
- Published
- 2015
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40. Genomic sequence of the rare HLA-A*02:95 allele identified by sequence-based typing and cloning.
- Author
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Bultitude WP, Mayor NP, McWhinnie AJ, Madrigal JA, and Marsh SG
- Subjects
- Base Sequence, Cloning, Molecular, Genome, Histocompatibility Testing, Humans, Molecular Sequence Data, Mutation genetics, Sequence Analysis, DNA, United Kingdom, Alleles, Exons genetics, HLA-A Antigens genetics
- Abstract
Genomic sequence of HLA-A*02:95 identified in an Anthony Nolan volunteer donor., (© 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)
- Published
- 2014
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41. NOD2 Polymorphisms and Their Impact on Haematopoietic Stem Cell Transplant Outcome.
- Author
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Mayor NP, Shaw BE, Madrigal JA, and Marsh SG
- Abstract
Haematopoietic stem cell transplantation (HSCT) is a valuable tool in the treatment of many haematological disorders. Advances in understanding HLA matching have improved prognoses. However, many recipients of well-matched HSCT develop posttransplant complications, and survival is far from absolute. The pursuit of novel genetic factors that may impact on HSCT outcome has resulted in the publication of many articles on a multitude of genes. Three NOD2 polymorphisms, identified as disease-associated variants in Crohn's disease, have recently been suggested as important candidate gene markers in the outcome of HSCT. It was originally postulated that as the clinical manifestation of inflammatory responses characteristic of several post-transplant complications was of notable similarity to those seen in Crohn's disease, it was possible that they shared a common cause. Since the publication of this first paper, numerous studies have attempted to replicate the results in different transplant settings. The data has varied considerably between studies, and as yet no consensus on the impact of NOD2 SNPs on HSCT outcome has been achieved. Here, we will review the existing literature, summarise current theories as to why the data differs, and suggest possible mechanisms by which the SNPs affect HSCT outcome.
- Published
- 2012
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42. Short template amplicon and multiplex megaprimer-enabled relay (STAMMER) sequencing, a simultaneous approach to higher throughput sequence-based typing of polymorphic genes.
- Author
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Roberts CH, Mayor NP, Madrigal JA, and Marsh SG
- Subjects
- DNA Primers chemistry, Humans, DNA Primers genetics, Genes genetics, Polymerase Chain Reaction methods, Polymorphism, Genetic, Sequence Analysis, DNA methods
- Abstract
Sequence-based typing (SBT) is a powerful method of genotyping in highly polymorphic gene systems. In standard SBT methods, both strands of a double-stranded template amplicon are sequenced in separate reactions in order to achieve high quality data across the region of interest. The amount of informative data that is obtained from the second strand sequence is often low, whilst the impact of performing second strand sequencing on costs and throughput are significant. Here we present short template amplicon and multiplex megaprimer-enabled relay (STAMMER) sequencing, a novel simultaneous sequence-based typing methodology that allows the detection of any practical amount of useful sequence from a plurality of distinct polymerase chain reaction products in a single sequencing reaction. In addition to simultaneous bidirectional sequencing, we show how the STAMMER approach can be used to simultaneously sequence a number of regions of interest that are not physically linked within the range of a single sequencing reaction. The efficiencies of this method could impact significantly on the output of SBT laboratories.
- Published
- 2010
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43. Association of functional polymorphisms of the transforming growth factor B1 gene with survival and graft-versus-host disease after unrelated donor hematopoietic stem cell transplantation.
- Author
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Berro M, Mayor NP, Maldonado-Torres H, Cooke L, Kusminsky G, Marsh SG, Madrigal JA, and Shaw BE
- Subjects
- Adult, Cohort Studies, Female, Humans, Male, Survival Analysis, Transforming Growth Factor beta1 blood, Transplantation, Homologous, Treatment Outcome, Graft vs Host Disease genetics, Hematopoietic Stem Cell Transplantation, Polymorphism, Single Nucleotide, Transforming Growth Factor beta1 genetics
- Abstract
Background: Many genetic factors play major roles in the outcome of hematopoietic stem cell transplants from unrelated donors. Transforming growth factor beta1 is a member of a highly pleiotrophic family of growth factors involved in the regulation of numerous immunomodulatory processes., Design and Methods: We investigated the impact of single nucleotide polymorphisms at codons 10 and 25 of TGFB1, the gene encoding for transforming growth factor beta1, on outcomes in 427 mye-loablative-conditioned transplanted patients. In addition, transforming growth factor beta1 plasma levels were measured in 263 patients and 327 donors., Results: Patients homozygous for the single nucleotide polymorphism at codon 10 had increased non-relapse mortality (at 3 years: 46.8% versus 29.4%, P=0.014) and reduced overall survival (at 5 years 29.3% versus 42.2%, P=0.013); the differences remained statistically significant in multivariate analysis. Donor genotype alone had no impact, although multiple single nucleotide polymorphisms within the pair were significantly associated with higher non-relapse mortality (at 3 years: 44% versus 29%, P=0.021) and decreased overall survival (at 5 years: 33.8% versus 41.9%, P=0.033). In the 10/10 HLA matched transplants (n=280), recipients of non-wild type grafts tended to have a higher incidence of acute graft-versus-host disease grades II-IV (P=0.052). In multivariate analysis, when analyzed with patients' genotype, the incidences of both overall and grades II-IV acute graft-versus-host disease were increased (P=0.025 and P=0.009, respectively) in non-wild-type pairs., Conclusions: We conclude that increasing numbers of single nucleotide polymorphisms in codon 10 of TGFB1 in patients and donors are associated with a worse outcome following hematopoietic stem cell transplantation from unrelated donors.
- Published
- 2010
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44. Diverging effects of HLA-DPB1 matching status on outcome following unrelated donor transplantation depending on disease stage and the degree of matching for other HLA alleles.
- Author
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Shaw BE, Mayor NP, Russell NH, Apperley JF, Clark RE, Cornish J, Darbyshire P, Ethell ME, Goldman JM, Little AM, Mackinnon S, Marks DI, Pagliuca A, Thomson K, Marsh SG, and Madrigal JA
- Subjects
- Adolescent, Adult, Aged, Alleles, Child, Child, Preschool, Female, Graft vs Host Disease etiology, HLA-DP beta-Chains, Humans, Leukemia immunology, Male, Middle Aged, Recurrence, Tissue Donors, HLA Antigens genetics, HLA-DP Antigens immunology, Hematopoietic Stem Cell Transplantation, Histocompatibility Testing, Leukemia therapy
- Abstract
Disease stage and recipient/donor human leukocyte antigen (HLA) matching are important determinants of outcome in transplantation using volunteer-unrelated donors (VUD). Matching for HLA-A, -B, -C, -DRB1, -DQB1 is beneficial, whereas the importance of DPB1 matching is more controversial. The impact of HLA matching status may differ dependent on disease stage. We investigated the outcome according to the degree of HLA matching at 6 loci, in 488 recipients of predominantly T-cell depleted bone marrow VUD transplants for leukaemia. Survival was significantly better in 12/12-matched transplants in those with early leukaemia (5 years: 63 versus 41% in 10/10 matched, P=0.006), but not late stage disease. Conversely, within the HLA-mismatched group (< or =9/10), there was a significant survival advantage to DPB1 mismatching (5 years: 39 versus 21% in DPB1 matched, P=0.008), particularly in late leukaemia (P=0.01), persisting in multivariate analysis (odds ratio 0.478; 95% confidence interval 0.30, 0.75; P=0.001). These novel findings suggest that the best outcome for patients with early leukaemia, with a 10/10-matched donor, is achieved by matching for DPB1. Conversely, our results suggest that in patients receiving an HLA-mismatched graft, the outcome is significantly better if they are also mismatched for DPB1. We recommend validation of these results in independent datasets.
- Published
- 2010
- Full Text
- View/download PDF
45. No impact of NOD2/CARD15 on outcome after SCT: a reply.
- Author
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Mayor NP, Shaw BE, Madrigal JA, and Marsh SG
- Subjects
- Cohort Studies, Genetic Predisposition to Disease, Humans, Survival Analysis, Transplantation, Homologous adverse effects, Hematopoietic Stem Cell Transplantation adverse effects, Neoplasm Recurrence, Local genetics, Nod2 Signaling Adaptor Protein genetics, Polymorphism, Single Nucleotide genetics, Precursor Cell Lymphoblastic Leukemia-Lymphoma therapy
- Published
- 2008
- Full Text
- View/download PDF
46. A novel technique for NOD2/CARD15 genotyping using PCR-SSP.
- Author
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Mayor NP, Shaw BE, Keshav S, Madrigal JA, and Marsh SG
- Subjects
- Biomarkers, DNA Primers, Exons, Genetic Predisposition to Disease, Genotype, Graft vs Host Disease genetics, Humans, Inflammatory Bowel Diseases genetics, Nod2 Signaling Adaptor Protein analysis, Transplantation, Homologous, Hematopoietic Stem Cell Transplantation, Nod2 Signaling Adaptor Protein genetics, Polymerase Chain Reaction methods, Polymorphism, Single Nucleotide
- Abstract
The Nucleotide-binding Oligomerisation Domain (NOD) 2 protein is encoded by the Caspase Recruitment Domain (CARD) 15 gene and has a critical role in innate immunity. Recent studies have implicated Single Nucleotide Polymorphisms (SNPs) of the NOD2/CARD15 gene with the onset of several Inflammatory Bowel Disorders (Crohn's Disease, Blau syndrome) and the progression of several malignant diseases. The identification of SNPs in the genotypes of donor and recipient pairs prior to haematopoietic stem cell transplantation have also been shown to predict for a worse outcome, specifically causing increases in the incidence and severity of acute Graft-versus-Host disease, disease relapse and mortality. In light of these widespread areas of interest, we have developed a Polymerase Chain Reaction assay using Sequence Specific Primers (PCR-SSP) to identify the three SNPs that have been implicated, (SNPs 8, 12 and 13). The assay has proven to be a rapid and accurate method of performing NOD2/CARD15 genotyping when compared to other techniques described to date.
- Published
- 2007
- Full Text
- View/download PDF
47. HLA-DPB1 matching status has significant implications for recipients of unrelated donor stem cell transplants.
- Author
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Shaw BE, Marsh SG, Mayor NP, Russell NH, and Madrigal JA
- Subjects
- Adolescent, Adult, Aged, Child, Child, Preschool, Disease-Free Survival, Female, HLA-DP beta-Chains, Humans, Infant, Leukemia therapy, Lymphocyte Depletion, Male, Middle Aged, Recurrence, Risk Factors, HLA-DP Antigens, Hematopoietic Stem Cell Transplantation, Histocompatibility Testing, Leukemia mortality, Tissue Donors
- Abstract
Studies in unrelated donor (UD) hematopoietic stem cell transplantations (HSCT) show an effect of the matching status of HLA-DPB1 on complications. We analyzed 423 UD-HSCT pairs. Most protocols included T-cell depletion (TCD). All pairs had high-resolution tissue typing performed for 6 HLA loci. Two hundred eighty-two pairs were matched at 10 of 10 alleles (29% were DPB1 matched). In 141 HLA-mismatched pairs, 28% were matched for DPB1. In the 10 of 10 matched pairs (n = 282), the 3-year probability of relapse was 61%. This was significantly higher in DPB1-matched pairs (74%) as compared with DPB1-mismatched pairs (56%) (log rank, P = .001). This finding persisted in multivariate analysis. In the group overall (n = 423), relapse was also significantly increased if DPB1 was matched (log rank; P < .001). These results were similar in chronic myeloid leukemia (CML; P < .001) and acute lymphoblastic leukemia (ALL; P = .013). In ALL, DPB1-matched pairs had a significantly worse overall survival (log rank; P = .025). Thus, in recipients of TCD UD-HSCT, a match for DPB1 is associated with a significantly increased risk of disease relapse, irrespective of the matching status for the other HLA molecules. It is possible that this effect is especially apparent following TCD transplantations and invites speculation about the function of DPB1 within the immune system.
- Published
- 2006
- Full Text
- View/download PDF
48. Sequence of a novel HLA-A*0301 intronic variant (A*03010103).
- Author
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Mayor NP, Cox ST, McWhinnie AJ, Argüello JR, Shaw BE, Little AM, Madrigal JA, and Marsh SG
- Subjects
- Base Sequence, HLA-A Antigens immunology, HLA-A3 Antigen, Humans, Molecular Sequence Data, HLA-A Antigens genetics, Introns
- Abstract
We report here the full-length sequence of a novel HLA-A*0301 allele, A*03010103, which differs from A*03010101 by a single nucleotide substitution (G>T) at position 492 within intron 2. The variant was originally identified by Reference Strand-mediated Conformational Analysis (RSCA) and was confirmed by cloning and sequencing. The difference in RSCA mobility between A*03010101 and A*03010103 demonstrates the sensitivity of RSCA to detect single nucleotide polymorphisms.
- Published
- 2005
- Full Text
- View/download PDF
49. Polymorphisms in the TNFA gene promoter region show evidence of strong linkage disequilibrium with HLA and are associated with delayed neutrophil engraftment in unrelated donor hematopoietic stem cell transplantation.
- Author
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Shaw BE, Maldonado H, Madrigal JA, Smith C, Petronzelli F, Mayor NP, Potter MN, Bodmer JG, and Marsh SG
- Subjects
- Adolescent, Adult, Base Sequence, Cell Line, Tumor, Child, Child, Preschool, Haplotypes, Humans, Infant, Leukocyte Count, Middle Aged, Molecular Sequence Data, Polymorphism, Genetic, HLA Antigens genetics, Hematopoietic Stem Cell Transplantation, Linkage Disequilibrium, Neutrophils pathology, Promoter Regions, Genetic, Tumor Necrosis Factor-alpha genetics
- Abstract
Sustained myeloid engraftment is an important determinant of outcome in hematopoietic stem cell transplantation (HSCT). Human tumor necrosis factor (TNF)-alpha is encoded by a gene, TNFA, located in the class III region of the major histocompatibility complex on chromosome 6, flanked by the human leukocyte antigen (HLA) class I and II regions. A number of polymorphisms in the promoter region of the TNFA gene have been associated with increased production of TNF-alphain vivo. Additionally, raised TNF-alpha levels have been reported to have a detrimental effect on the outcome in HSCT, in particular on early complications such as acute graft vs host disease, failure to engraft, and transplant-related mortality. There is evidence of linkage disequilibrium (LD) between TNFA promoter polymorphisms and extended HLA haplotypes. We have genotyped 73 cell lines and 189 donor/recipient pairs (undergoing HSCT) for their TNFA polymorphism, all of which had been well characterized with respect to their HLA genes. We found evidence of strong LD between HLA genes and TNFA; however, there was also evidence for recombination events having taken place, as we found that a number of transplant pairs who were matched for their HLA haplotypes were not matched for their TNFA alleles. We analyzed early outcomes in the transplant recipients and found a significant delay in engraftment in those pairs where both donor and recipients possessed an AG allele (associated with higher TNF-alpha levels). Our results suggest a functional effect of TNFA polymorphisms on myeloid engraftment in unrelated HSCT.
- Published
- 2004
- Full Text
- View/download PDF
50. The degree of matching at HLA-DPB1 predicts for acute graft-versus-host disease and disease relapse following haematopoietic stem cell transplantation.
- Author
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Shaw BE, Potter MN, Mayor NP, Pay AL, Smith C, Goldman JM, Prentice HG, Marsh SG, and Madrigal JA
- Subjects
- Acute Disease, Adolescent, Adult, Child, Child, Preschool, Cytomegalovirus Infections epidemiology, Female, Graft vs Host Disease mortality, HLA-DP beta-Chains, Hematopoietic Stem Cell Transplantation mortality, Humans, Infant, Leukemia mortality, Leukemia therapy, Lymphocyte Depletion methods, Male, Middle Aged, Parity, Predictive Value of Tests, Probability, Recurrence, Survival Rate, T-Lymphocytes immunology, Time Factors, Graft vs Host Disease epidemiology, HLA-DP Antigens immunology, Hematopoietic Stem Cell Transplantation methods, Histocompatibility Testing methods
- Abstract
The importance of matching for HLA-DPB1 in unrelated donor haematopoietic stem cell (HSC) transplantation is little understood. Most transplant centres do not, currently, prospectively match for DPB1, but emerging data show that DPB1 matching does play a role in determining outcome. We studied the impact of HLA-DPB1 matching on outcome in 143 recipients of T-cell depletion transplants, who matched with their respective unrelated donors (allelic level) at HLA-A, -B, -C, -DRB1 and -DQB1. Of those matched at DPB1, 47.2% (17/36) developed acute graft-versus-host disease (aGvHD) as compared to 66.3% (55/83) of those who were mismatched. This led to a 19.1% (95% CI 0.1-38.3%) increase in the chance of developing aGvHD in mismatched patients (P=0.049). Relapse of the original disease occurred in 51 recipients; 23 of 37 (62%) matched at both DPB1 alleles, 28 of 82 (34%) were mismatched at one or two DPB1 alleles. Thus, there was a significantly higher relapse rate (P=0.0011) in transplant recipients who matched at both DPB1 alleles. In conclusion, a donor/recipient DPB1 match was associated with a significantly lower incidence of aGvHD and a significantly higher incidence of disease relapse. This study provides further evidence for an immunogenic role of HLA-DPB1 in HSC transplants.
- Published
- 2003
- Full Text
- View/download PDF
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