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Oketch JW, Wain LV, Hollox EJ. A comparison of software for analysis of rare and common short tandem repeat (STR) variation using human genome sequences from clinical and population-based samples. PLoS One 2024; 19:e0300545. [PMID: 38558075 PMCID: PMC10984476 DOI: 10.1371/journal.pone.0300545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 02/27/2024] [Indexed: 04/04/2024] Open
Abstract
Short tandem repeat (STR) variation is an often overlooked source of variation between genomes. STRs comprise about 3% of the human genome and are highly polymorphic. Some cause Mendelian disease, and others affect gene expression. Their contribution to common disease is not well-understood, but recent software tools designed to genotype STRs using short read sequencing data will help address this. Here, we compare software that genotypes common STRs and rarer STR expansions genome-wide, with the aim of applying them to population-scale genomes. By using the Genome-In-A-Bottle (GIAB) consortium and 1000 Genomes Project short-read sequencing data, we compare performance in terms of sequence length, depth, computing resources needed, genotyping accuracy and number of STRs genotyped. To ensure broad applicability of our findings, we also measure genotyping performance against a set of genomes from clinical samples with known STR expansions, and a set of STRs commonly used for forensic identification. We find that HipSTR, ExpansionHunter and GangSTR perform well in genotyping common STRs, including the CODIS 13 core STRs used for forensic analysis. GangSTR and ExpansionHunter outperform HipSTR for genotyping call rate and memory usage. ExpansionHunter denovo (EHdn), STRling and GangSTR outperformed STRetch for detecting expanded STRs, and EHdn and STRling used considerably less processor time compared to GangSTR. Analysis on shared genomic sequence data provided by the GIAB consortium allows future performance comparisons of new software approaches on a common set of data, facilitating comparisons and allowing researchers to choose the best software that fulfils their needs.
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Affiliation(s)
- John W. Oketch
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Louise V. Wain
- Department of Population Health Sciences, University of Leicester, Leicester, United Kingdom
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, United Kingdom
| | - Edward J. Hollox
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
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Jama M, Zhang M, Poile C, Nakas A, Sharkey A, Dzialo J, Dawson A, Kutywayo K, Fennell DA, Hollox EJ. Gene fusions during the early evolution of mesothelioma correlate with impaired DNA repair and Hippo pathways. Genes Chromosomes Cancer 2024; 63:e23189. [PMID: 37421230 DOI: 10.1002/gcc.23189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/23/2023] [Accepted: 06/27/2023] [Indexed: 07/10/2023] Open
Abstract
Malignant pleural mesothelioma (MPM), a rare cancer a long latency period (up to 40 years) between asbestos exposure and disease presentation. The mechanisms coupling asbestos to recurrent somatic alterations are poorly defined. Gene fusions arising through genomic instability may create novel drivers during early MPM evolution. We explored the gene fusions that occurred early in the evolutionary history of the tumor. We conducted multiregional whole exome sequencing (WES) of 106 samples from 20 patients undergoing pleurectomy decortication and identified 24 clonal nonrecurrent gene fusions, three of which were novel (FMO9P-OR2W5, GBA3, and SP9). The number of early gene fusion events detected varied from zero to eight per tumor, and presence of gene fusions was associated with clonal losses involving the Hippo pathway genes and homologous recombination DNA repair genes. Fusions involved known tumor suppressors BAP1, MTAP, and LRP1B, and a clonal oncogenic fusion involving CACNA1D-ERC2, PARD3B-NT5DC2, and STAB2-NT5DC2 fusions were also identified as clonal fusions. Gene fusions events occur early during MPM evolution. Individual fusions are rare as no recurrent truncal fusions event were found. This suggests the importance of early disruption of these pathways in generating genomic rearrangements resulting in potentially oncogenic gene fusions.
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Affiliation(s)
- Maymun Jama
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Min Zhang
- Mesothelioma Research Programme, Leicester Cancer Research Centre, University of Leicester, Leicester, UK
- Novogene Corpotation Ltd., Building 301, Beijing, China
| | - Charlotte Poile
- Mesothelioma Research Programme, Leicester Cancer Research Centre, University of Leicester, Leicester, UK
| | - Apostolos Nakas
- Thoracic Medical Oncology, University Hospitals of Leicester NHS Trust, Leicester, UK
| | - Annabel Sharkey
- Department of Cardio-Thoracic Surgery, Sheffield Teaching Hospital NHS Trust, Sheffield, UK
| | - Joanna Dzialo
- Mesothelioma Research Programme, Leicester Cancer Research Centre, University of Leicester, Leicester, UK
| | - Alan Dawson
- Thoracic Medical Oncology, University Hospitals of Leicester NHS Trust, Leicester, UK
| | - Kudazyi Kutywayo
- Mesothelioma Research Programme, Leicester Cancer Research Centre, University of Leicester, Leicester, UK
- Department of Cardio-Thoracic Surgery, Sheffield Teaching Hospital NHS Trust, Sheffield, UK
| | - Dean A Fennell
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
- Mesothelioma Research Programme, Leicester Cancer Research Centre, University of Leicester, Leicester, UK
- Thoracic Medical Oncology, University Hospitals of Leicester NHS Trust, Leicester, UK
| | - Edward J Hollox
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
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Guillen-Guio B, Paynton ML, Allen RJ, Chin DP, Donoghue LJ, Stockwell A, Leavy OC, Hernandez-Beeftink T, Reynolds C, Cullinan P, Martinez F, Booth HL, Fahy WA, Hall IP, Hart SP, Hill MR, Hirani N, Hubbard RB, McAnulty RJ, Millar AB, Navaratnam V, Oballa E, Parfrey H, Saini G, Sayers I, Tobin MD, Whyte MK, Adegunsoye A, Kaminski N, Ma SF, Strek ME, Zhang Y, Fingerlin TE, Molina-Molina M, Neighbors M, Sheng XR, Oldham JM, Maher TM, Molyneaux PL, Flores C, Noth I, Schwartz DA, Yaspan BL, Jenkins RG, Wain LV, Hollox EJ. Association study of human leukocyte antigen variants and idiopathic pulmonary fibrosis. ERJ Open Res 2024; 10:00553-2023. [PMID: 38375425 PMCID: PMC10875457 DOI: 10.1183/23120541.00553-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 11/05/2023] [Indexed: 02/21/2024] Open
Abstract
Introduction Idiopathic pulmonary fibrosis (IPF) is a chronic interstitial pneumonia marked by progressive lung fibrosis and a poor prognosis. Recent studies have highlighted the potential role of infection in the pathogenesis of IPF, and a prior association of the HLA-DQB1 gene with idiopathic fibrotic interstitial pneumonia (including IPF) has been reported. Owing to the important role that the human leukocyte antigen (HLA) region plays in the immune response, here we evaluated if HLA genetic variation was associated specifically with IPF risk. Methods We performed a meta-analysis of associations of the HLA region with IPF risk in individuals of European ancestry from seven independent case-control studies of IPF (comprising 5159 cases and 27 459 controls, including a prior study of fibrotic interstitial pneumonia). Single nucleotide polymorphisms, classical HLA alleles and amino acids were analysed and signals meeting a region-wide association threshold of p<4.5×10-4 and a posterior probability of replication >90% were considered significant. We sought to replicate the previously reported HLA-DQB1 association in the subset of studies independent of the original report. Results The meta-analysis of all seven studies identified four significant independent single nucleotide polymorphisms associated with IPF risk. However, none met the posterior probability for replication criterion. The HLA-DQB1 association was not replicated in the independent IPF studies. Conclusion Variation in the HLA region was not consistently associated with risk in studies of IPF. However, this does not preclude the possibility that other genomic regions linked to the immune response may be involved in the aetiology of IPF.
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Affiliation(s)
- Beatriz Guillen-Guio
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
- Joint first authors
| | - Megan L. Paynton
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- Joint first authors
| | - Richard J. Allen
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
| | - Daniel P.W. Chin
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
| | | | | | - Olivia C. Leavy
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
| | - Tamara Hernandez-Beeftink
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
| | - Carl Reynolds
- National Heart & Lung Institute, Imperial College London, London, UK
| | - Paul Cullinan
- National Heart & Lung Institute, Imperial College London, London, UK
| | | | - Helen L. Booth
- University College Hospital, University College London, London, UK
| | | | - Ian P. Hall
- School of Medicine, University of Nottingham, Nottingham, UK
- National Institute for Health Research, Nottingham Biomedical Research Centre, Nottingham, UK
| | - Simon P. Hart
- Hull York Medical School, University of Hull, Hull, UK
| | - Mike R. Hill
- MRC Population Health Unit, University of Oxford, Oxford, UK
| | - Nik Hirani
- Centre for Inflammation Research, University of Edinburgh, Edinburgh, UK
| | - Richard B. Hubbard
- School of Medicine, University of Nottingham, Nottingham, UK
- National Institute for Health Research, Nottingham Biomedical Research Centre, Nottingham, UK
| | | | - Ann B. Millar
- Bristol Medical School, University of Bristol, Bristol, UK
| | - Vidya Navaratnam
- Division of Epidemiology and Public Health, University of Nottingham, Nottingham, UK
- National Institute for Health Research, Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust, Nottingham, UK
- Queensland Lung Transplant Service, The Prince Charles Hospital, Brisbane, QLD, Australia
| | | | - Helen Parfrey
- Royal Papworth Hospital NHS Foundation Trust, Cambridge, UK
| | - Gauri Saini
- School of Medicine, University of Nottingham, Nottingham, UK
| | - Ian Sayers
- Centre for Respiratory Research, NIHR Nottingham Biomedical Research Centre, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham, UK
| | - Martin D. Tobin
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
| | - Moira K.B. Whyte
- Centre for Inflammation Research, University of Edinburgh, Edinburgh, UK
| | | | - Naftali Kaminski
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Shwu-Fan Ma
- Department of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Mary E. Strek
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Yingze Zhang
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Tasha E. Fingerlin
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO, USA
| | - Maria Molina-Molina
- Servei de Pneumologia, Laboratori de Pneumologia Experimental, Instituto de Investigación Biomédica de Bellvitge (IDIBELL), Barcelona, Spain
- Campus de Bellvitge, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | | | | | - Justin M. Oldham
- Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Toby M. Maher
- National Heart and Lung Institute, Imperial College London, London, UK
- Division of Pulmonary and Critical Care Medicine, University of Southern California, Los Angeles, USA
| | - Philip L. Molyneaux
- National Heart and Lung Institute, Imperial College London, London, UK
- Royal Brompton and Harefield Hospitals, Guy's and St Thomas’ NHS Foundation Trust, London, UK
| | - Carlos Flores
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
- Genomics Division, Instituto Tecnologico y de Energias Renovables, Santa Cruz de Tenerife, Spain
- Facultad de Ciencias de la Salud, Universidad Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | - Imre Noth
- Department of Medicine, University of Virginia, Charlottesville, VA, USA
| | | | | | - R. Gisli Jenkins
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Louise V. Wain
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
- Joint senior authors
| | - Edward J. Hollox
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
- Joint senior authors
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Williams AT, Chen J, Coley K, Batini C, Izquierdo A, Packer R, Abner E, Kanoni S, Shepherd DJ, Free RC, Hollox EJ, Brunskill NJ, Ntalla I, Reeve N, Brightling CE, Venn L, Adams E, Bee C, Wallace SE, Pareek M, Hansell AL, Esko T, Stow D, Jacobs BM, van Heel DA, Hennah W, Rao BS, Dudbridge F, Wain LV, Shrine N, Tobin MD, John C. Genome-wide association study of thyroid-stimulating hormone highlights new genes, pathways and associations with thyroid disease. Nat Commun 2023; 14:6713. [PMID: 37872160 PMCID: PMC10593800 DOI: 10.1038/s41467-023-42284-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 10/05/2023] [Indexed: 10/25/2023] Open
Abstract
Thyroid hormones play a critical role in regulation of multiple physiological functions and thyroid dysfunction is associated with substantial morbidity. Here, we use electronic health records to undertake a genome-wide association study of thyroid-stimulating hormone (TSH) levels, with a total sample size of 247,107. We identify 158 novel genetic associations, more than doubling the number of known associations with TSH, and implicate 112 putative causal genes, of which 76 are not previously implicated. A polygenic score for TSH is associated with TSH levels in African, South Asian, East Asian, Middle Eastern and admixed American ancestries, and associated with hypothyroidism and other thyroid disease in South Asians. In Europeans, the TSH polygenic score is associated with thyroid disease, including thyroid cancer and age-of-onset of hypothyroidism and hyperthyroidism. We develop pathway-specific genetic risk scores for TSH levels and use these in phenome-wide association studies to identify potential consequences of pathway perturbation. Together, these findings demonstrate the potential utility of genetic associations to inform future therapeutics and risk prediction for thyroid diseases.
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Affiliation(s)
- Alexander T Williams
- Department of Population Health Sciences, University of Leicester, Leicester, UK.
| | - Jing Chen
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Kayesha Coley
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Chiara Batini
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- University Hospitals of Leicester NHS Trust, Infirmary Square, Leicester, UK
| | - Abril Izquierdo
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- University Hospitals of Leicester NHS Trust, Infirmary Square, Leicester, UK
| | - Richard Packer
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- University Hospitals of Leicester NHS Trust, Infirmary Square, Leicester, UK
| | - Erik Abner
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Stavroula Kanoni
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - David J Shepherd
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Robert C Free
- University Hospitals of Leicester NHS Trust, Infirmary Square, Leicester, UK
- School of Computing and Mathematical Sciences, University of Leicester, Leicester, UK
| | - Edward J Hollox
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Nigel J Brunskill
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
| | - Ioanna Ntalla
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Nicola Reeve
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- Division of Population Medicine, School of Medicine, Cardiff University, Cardiff, UK
| | - Christopher E Brightling
- University Hospitals of Leicester NHS Trust, Infirmary Square, Leicester, UK
- Institute for Lung Health, Leicester NIHR BRC, University of Leicester, Leicester, UK
| | - Laura Venn
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Emma Adams
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Catherine Bee
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Susan E Wallace
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Manish Pareek
- University Hospitals of Leicester NHS Trust, Infirmary Square, Leicester, UK
- Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - Anna L Hansell
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Tõnu Esko
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Daniel Stow
- Wolfson Institute of Population Health, Queen Mary University of London, London, UK
| | - Benjamin M Jacobs
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University of London, London, UK
- Department of Neurology, Royal London Hospital, Barts Health NHS Trust, London, UK
| | - David A van Heel
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - William Hennah
- Orion Pharma, Espoo, Finland
- Neuroscience Center, HiLIFE, University of Helsinki, Helsinki, Finland
- Institute for Molecular Medicine FIMM, HiLIFE, University of Helsinki, Helsinki, Finland
| | | | - Frank Dudbridge
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Louise V Wain
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- University Hospitals of Leicester NHS Trust, Infirmary Square, Leicester, UK
| | - Nick Shrine
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Martin D Tobin
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- University Hospitals of Leicester NHS Trust, Infirmary Square, Leicester, UK
| | - Catherine John
- Department of Population Health Sciences, University of Leicester, Leicester, UK.
- University Hospitals of Leicester NHS Trust, Infirmary Square, Leicester, UK.
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5
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Grove JI, Lo PC, Shrine N, Barwell J, Wain LV, Tobin MD, Salter AM, Borkar AN, Cuevas-Ocaña S, Bennett N, John C, Ntalla I, Jones GE, Neal CP, Thomas MG, Kuht H, Gupta P, Vemala VM, Grant A, Adewoye AB, Shenoy KT, Balakumaran LK, Hollox EJ, Hannan NR, Aithal GP. Identification and characterisation of a rare MTTP variant underlying hereditary non-alcoholic fatty liver disease. JHEP Rep 2023; 5:100764. [PMID: 37484212 PMCID: PMC10362796 DOI: 10.1016/j.jhepr.2023.100764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/28/2023] [Accepted: 04/11/2023] [Indexed: 07/25/2023] Open
Abstract
Background & Aims Non-alcoholic fatty liver disease (NAFLD) is a complex trait with an estimated prevalence of 25% globally. We aimed to identify the genetic variant underlying a four-generation family with progressive NAFLD leading to cirrhosis, decompensation, and development of hepatocellular carcinoma in the absence of common risk factors such as obesity and type 2 diabetes. Methods Exome sequencing and genome comparisons were used to identify the likely causal variant. We extensively characterised the clinical phenotype and post-prandial metabolic responses of family members with the identified novel variant in comparison with healthy non-carriers and wild-type patients with NAFLD. Variant-expressing hepatocyte-like cells (HLCs) were derived from human-induced pluripotent stem cells generated from homozygous donor skin fibroblasts and restored to wild-type using CRISPR-Cas9. The phenotype was assessed using imaging, targeted RNA analysis, and molecular expression arrays. Results We identified a rare causal variant c.1691T>C p.I564T (rs745447480) in MTTP, encoding microsomal triglyceride transfer protein (MTP), associated with progressive NAFLD, unrelated to metabolic syndrome and without characteristic features of abetalipoproteinaemia. HLCs derived from a homozygote donor had significantly lower MTP activity and lower lipoprotein ApoB secretion than wild-type cells, while having similar levels of MTP mRNA and protein. Cytoplasmic triglyceride accumulation in HLCs triggered endoplasmic reticulum stress, secretion of pro-inflammatory mediators, and production of reactive oxygen species. Conclusions We have identified and characterised a rare causal variant in MTTP, and homozygosity for MTTP p.I564T is associated with progressive NAFLD without any other manifestations of abetalipoproteinaemia. Our findings provide insights into mechanisms driving progressive NAFLD. Impact and Implications A rare genetic variant in the gene MTTP has been identified as responsible for the development of severe non-alcoholic fatty liver disease in a four-generation family with no typical disease risk factors. A cell line culture created harbouring this variant gene was characterised to understand how this genetic variation leads to a defect in liver cells, which results in accumulation of fat and processes that promote disease. This is now a useful model for studying the disease pathways and to discover new ways to treat common types of fatty liver disease.
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Affiliation(s)
- Jane I. Grove
- National Institute of Health Research (NIHR) Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust & University of Nottingham, Nottingham, UK
- Nottingham Digestive Diseases Centre, Translational Medical Sciences, School of Medicine, University of Nottingham, Nottingham, UK
| | - Peggy C.K. Lo
- Translational Medical Sciences, School of Medicine, University of Nottingham, Nottingham, UK
- University of Nottingham Biodiscovery Institute, University of Nottingham, Nottingham, UK
| | - Nick Shrine
- Genetic Epidemiology Group, Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Julian Barwell
- Clinical Genetics Department, University Hospitals Leicester NHS Trust, Leicester, UK
| | - Louise V. Wain
- Genetic Epidemiology Group, Department of Population Health Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Martin D. Tobin
- Genetic Epidemiology Group, Department of Population Health Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | | | - Aditi N. Borkar
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
| | - Sara Cuevas-Ocaña
- Translational Medical Sciences, School of Medicine, University of Nottingham, Nottingham, UK
- University of Nottingham Biodiscovery Institute, University of Nottingham, Nottingham, UK
| | - Neil Bennett
- Genetic Epidemiology Group, Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Catherine John
- Genetic Epidemiology Group, Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Ioanna Ntalla
- Clinical Genetics Department, University Hospitals Leicester NHS Trust, Leicester, UK
| | - Gabriela E. Jones
- Clinical Genetics Department, University Hospitals Leicester NHS Trust, Leicester, UK
| | | | - Mervyn G. Thomas
- Ulverscroft Eye Unit, Department of Neuroscience, Psychology and Behaviour, University of Leicester, Leicester, UK
| | - Helen Kuht
- Ulverscroft Eye Unit, Department of Neuroscience, Psychology and Behaviour, University of Leicester, Leicester, UK
| | - Pankaj Gupta
- Department of Chemical Pathology and Metabolic Diseases, University Hospitals of Leicester NHS Trust, Leicester, UK
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
| | - Vishwaraj M. Vemala
- Department of Gastroenterology, University Hospitals of Leicester NHS Trust, Leicester, UK
| | - Allister Grant
- Department of Gastroenterology, University Hospitals of Leicester NHS Trust, Leicester, UK
| | - Adeolu B. Adewoye
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | | | | | - Edward J. Hollox
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Nicholas R.F. Hannan
- Translational Medical Sciences, School of Medicine, University of Nottingham, Nottingham, UK
- University of Nottingham Biodiscovery Institute, University of Nottingham, Nottingham, UK
| | - Guruprasad P. Aithal
- National Institute of Health Research (NIHR) Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust & University of Nottingham, Nottingham, UK
- Nottingham Digestive Diseases Centre, Translational Medical Sciences, School of Medicine, University of Nottingham, Nottingham, UK
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6
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Guillen-Guio B, Paynton ML, Allen RJ, Chin DP, Donoghue LJ, Stockwell A, Leavy OC, Hernandez-Beeftink T, Reynolds C, Cullinan P, Martinez F, Booth HL, Fahy WA, Hall IP, Hart SP, Hill MR, Hirani N, Hubbard RB, McAnulty RJ, Millar AB, Navaratnam V, Oballa E, Parfrey H, Saini G, Sayers I, Tobin MD, Whyte MKB, Adegunsoye A, Kaminski N, Shwu-Fan M, Strek ME, Zhang Y, Fingerlin TE, Molina-Molina M, Neighbors M, Sheng XR, Oldham JM, Maher TM, Molyneaux PL, Flores C, Noth I, Schwartz DA, Yaspan BL, Jenkins RG, Wain LV, Hollox EJ. Association study of human leukocyte antigen (HLA) variants and idiopathic pulmonary fibrosis. medRxiv 2023:2023.07.20.23292940. [PMID: 37546732 PMCID: PMC10402235 DOI: 10.1101/2023.07.20.23292940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Introduction Idiopathic pulmonary fibrosis (IPF) is a chronic interstitial pneumonia marked by progressive lung fibrosis and a poor prognosis. Recent studies have highlighted the potential role of infection in the pathogenesis of IPF and a prior association of the HLA-DQB1 gene with idiopathic fibrotic interstitial pneumonia (including IPF) has been reported. Due to the important role that the Human Leukocyte Antigen (HLA) region plays in the immune response, here we evaluated if HLA genetic variation was associated specifically with IPF risk. Methods We performed a meta-analysis of associations of the HLA region with IPF risk in individuals of European ancestry from seven independent case-control studies of IPF (comprising a total of 5,159 cases and 27,459 controls, including the prior study of fibrotic interstitial pneumonia). Single nucleotide polymorphisms, classical HLA alleles and amino acids were analysed and signals meeting a region-wide association threshold p<4.5×10-4 and a posterior probability of replication >90% were considered significant. We sought to replicate the previously reported HLA-DQB1 association in the subset of studies independent of the original report. Results The meta-analysis of all seven studies identified four significant independent single nucleotide polymorphisms associated with IPF risk. However, none met the posterior probability for replication criterion. The HLA-DQB1 association was not replicated in the independent IPF studies. Conclusion Variation in the HLA region was not consistently associated with risk in studies of IPF. However, this does not preclude the possibility that other genomic regions linked to the immune response may be involved in the aetiology of IPF.
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Affiliation(s)
- Beatriz Guillen-Guio
- Department of Population Health Sciences, University of Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
| | - Megan L. Paynton
- Department of Population Health Sciences, University of Leicester, UK
| | - Richard J. Allen
- Department of Population Health Sciences, University of Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
| | - Daniel P.W. Chin
- Department of Population Health Sciences, University of Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
| | | | | | - Olivia C. Leavy
- Department of Population Health Sciences, University of Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
| | - Tamara Hernandez-Beeftink
- Department of Population Health Sciences, University of Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
| | | | | | | | | | | | | | - Ian P. Hall
- University of Nottingham, Nottingham, UK
- National Institute for Health Research, Nottingham Biomedical Research Centre, Nottingham, UK
| | | | | | | | - Richard B. Hubbard
- University of Nottingham, Nottingham, UK
- National Institute for Health Research, Nottingham Biomedical Research Centre, Nottingham, UK
| | | | | | - Vidya Navaratnam
- Division of Epidemiology and Public Health, University of Nottingham, Nottingham, UK
- National Institute for Health Research, Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust, Nottingham, UK
- Queensland Lung Transplant Service, The Prince Charles Hospital, Brisbane, QLD, Australia
| | | | - Helen Parfrey
- Royal Papworth Hospital NHS Foundation Trust, Cambridge, UK
| | | | - Ian Sayers
- Centre for Respiratory Research, NIHR Nottingham Biomedical Research Centre, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham, UK
| | - Martin D. Tobin
- Department of Population Health Sciences, University of Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
| | | | | | | | | | | | | | | | - Maria Molina-Molina
- Servei de Pneumologia, Laboratori de Pneumologia Experimental, Instituto de Investigación Biomédica de Bellvitge (IDIBELL), Barcelona, Spain
- Campus de Bellvitge, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigacion Biomedica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | | | | | | | - Toby M. Maher
- National Heart and Lung Institute, Imperial College London, London, UK
- Division of Pulmonary and Critical Care Medicine, University of Southern California, Los Angeles, USA
| | - Philip L. Molyneaux
- National Heart and Lung Institute, Imperial College London, London, UK
- Royal Brompton and Harefield Hospitals, Guy’s and St Thomas’ NHS Foundation Trust, London, UK
| | - Carlos Flores
- Centro de Investigacion Biomedica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
- Genomics Division, Instituto Tecnologico y de Energias Renovables, Santa Cruz de Tenerife, Spain
- Facultad de Ciencias de la Salud, Universidad Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | - Imre Noth
- University of Virginia, Virginia, USA
| | | | | | - R. Gisli Jenkins
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Louise V. Wain
- Department of Population Health Sciences, University of Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
| | - Edward J. Hollox
- Department of Genetics and Genome Biology, University of Leicester, UK
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Packer RJ, Williams AT, Hennah W, Eisenberg MT, Fawcett KA, Pearson W, Guyatt AL, Edris A, Hollox EJ, Marttila M, Rao BS, Bratty JR, Wain LV, Dudbridge F, Tobin MD. DeepPheWAS: an R package for phenotype generation and association analysis for phenome-wide association studies. Bioinformatics 2023; 39:7028485. [PMID: 36744935 PMCID: PMC10070035 DOI: 10.1093/bioinformatics/btad073] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 01/06/2023] [Accepted: 02/03/2023] [Indexed: 02/07/2023] Open
Abstract
SUMMARY DeepPheWAS is an R package for phenome wide association studies that creates clinically-curated composite phenotypes, and integrates quantitative phenotypes from primary care data, longitudinal trajectories of quantitative measures, disease progression, and drug response phenotypes. Tools are provided for efficient analysis of association with any genetic input, under any genetic model, with optional sex-stratified analysis, and for developing novel phenotypes. AVAILABILITY AND IMPLEMENTATION The DeepPheWAS R package is freely available under GNU general public licence v3.0 from at https://github.com/Richard-Packer/DeepPheWAS. SUPPLEMENTARY INFORMATION Supplementary methods and results are available at Bioinformatics online.
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Affiliation(s)
- Richard J Packer
- Department of Health Sciences, University of Leicester, Leicester, UK.,Leicester National Institute of Health and Care Research Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Alex T Williams
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - William Hennah
- Orion Pharma, Espoo, Finland.,Neuroscience Center, HiLIFE, University of Helsinki, Helsinki, Finland.,Institute for Molecular Medicine FIMM, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Micaela T Eisenberg
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | | | - Willow Pearson
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Anna L Guyatt
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Ahmed Edris
- Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium.,Department of Health Sciences, University of Leicester, Leicester, UK
| | - Edward J Hollox
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | | | | | | | - Louise V Wain
- Department of Health Sciences, University of Leicester, Leicester, UK.,Leicester National Institute of Health and Care Research Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Frank Dudbridge
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Martin D Tobin
- Department of Health Sciences, University of Leicester, Leicester, UK.,Leicester National Institute of Health and Care Research Biomedical Research Centre, Glenfield Hospital, Leicester, UK
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Pathak GA, Karjalainen J, Stevens C, Neale BM, Daly M, Ganna A, Andrews SJ, Kanai M, Cordioli M, Polimanti R, Harerimana N, Pirinen M, Liao RG, Chwialkowska K, Trankiem A, Balaconis MK, Nguyen H, Solomonson M, Veerapen K, Wolford B, Roberts G, Park D, Ball CA, Coignet M, McCurdy S, Knight S, Partha R, Rhead B, Zhang M, Berkowitz N, Gaddis M, Noto K, Ruiz L, Pavlovic M, Hong EL, Rand K, Girshick A, Guturu H, Baltzell AH, Niemi MEK, Rahmouni S, Guntz J, Beguin Y, Cordioli M, Pigazzini S, Nkambule L, Georges M, Moutschen M, Misset B, Darcis G, Guiot J, Azarzar S, Gofflot S, Claassen S, Malaise O, Huynen P, Meuris C, Thys M, Jacques J, Léonard P, Frippiat F, Giot JB, Sauvage AS, Frenckell CV, Belhaj Y, Lambermont B, Nakanishi T, Morrison DR, Mooser V, Richards JB, Butler-Laporte G, Forgetta V, Li R, Ghosh B, Laurent L, Belisle A, Henry D, Abdullah T, Adeleye O, Mamlouk N, Kimchi N, Afrasiabi Z, Rezk N, Vulesevic B, Bouab M, Guzman C, Petitjean L, Tselios C, Xue X, Afilalo J, Afilalo M, Oliveira M, Brenner B, Brassard N, Durand M, Schurr E, Lepage P, Ragoussis J, Auld D, Chassé M, Kaufmann DE, Lathrop GM, Adra D, Hayward C, Glessner JT, Shaw DM, Campbell A, Morris M, Hakonarson H, Porteous DJ, Below J, Richmond A, Chang X, Polikowski H, Lauren PE, Chen HH, Wanying Z, Fawns-Ritchie C, North K, McCormick JB, Chang X, Glessner JR, Hakonarson H, Gignoux CR, Wicks SJ, Crooks K, Barnes KC, Daya M, Shortt J, Rafaels N, Chavan S, Timmers PRHJ, Wilson JF, Tenesa A, Kerr SM, D’Mellow K, Shahin D, El-Sherbiny YM, von Hohenstaufen KA, Sobh A, Eltoukhy MM, Nkambul L, Elhadidy TA, Abd Elghafar MS, El-Jawhari JJ, Mohamed AAS, Elnagdy MH, Samir A, Abdel-Aziz M, Khafaga WT, El-Lawaty WM, Torky MS, El-shanshory MR, Yassen AM, Hegazy MAF, Okasha K, Eid MA, Moahmed HS, Medina-Gomez C, Ikram MA, Uitterlinden AG, Mägi R, Milani L, Metspalu A, Laisk T, Läll K, Lepamets M, Esko T, Reimann E, Naaber P, Laane E, Pesukova J, Peterson P, Kisand K, Tabri J, Allos R, Hensen K, Starkopf J, Ringmets I, Tamm A, Kallaste A, Alavere H, Metsalu K, Puusepp M, Batini C, Tobin MD, Venn LD, Lee PH, Shrine N, Williams AT, Guyatt AL, John C, Packer RJ, Ali A, Free RC, Wang X, Wain LV, Hollox EJ, Bee CE, Adams EL, Palotie A, Ripatti S, Ruotsalainen S, Kristiansson K, Koskelainen S, Perola M, Donner K, Kivinen K, Palotie A, Kaunisto M, Rivolta C, Bochud PY, Bibert S, Boillat N, Nussle SG, Albrich W, Quinodoz M, Kamdar D, Suh N, Neofytos D, Erard V, Voide C, Bochud PY, Rivolta C, Bibert S, Quinodoz M, Kamdar D, Neofytos D, Erard V, Voide C, Friolet R, Vollenweider P, Pagani JL, Oddo M, zu Bentrup FM, Conen A, Clerc O, Marchetti O, Guillet A, Guyat-Jacques C, Foucras S, Rime M, Chassot J, Jaquet M, Viollet RM, Lannepoudenx Y, Portopena L, Bochud PY, Vollenweider P, Pagani JL, Desgranges F, Filippidis P, Guéry B, Haefliger D, Kampouri EE, Manuel O, Munting A, Papadimitriou-Olivgeris M, Regina J, Rochat-Stettler L, Suttels V, Tadini E, Tschopp J, Van Singer M, Viala B, Boillat-Blanco N, Brahier T, Hügli O, Meuwly JY, Pantet O, Gonseth Nussle S, Bochud M, D’Acremont V, Estoppey Younes S, Albrich WC, Suh N, Cerny A, O’Mahony L, von Mering C, Bochud PY, Frischknecht M, Kleger GR, Filipovic M, Kahlert CR, Wozniak H, Negro TR, Pugin J, Bouras K, Knapp C, Egger T, Perret A, Montillier P, di Bartolomeo C, Barda B, de Cid R, Carreras A, Moreno V, Kogevinas M, Galván-Femenía I, Blay N, Farré X, Sumoy L, Cortés B, Mercader JM, Guindo-Martinez M, Torrents D, Garcia-Aymerich J, Castaño-Vinyals G, Dobaño C, Gori M, Renieri A, Mari F, Mondelli MU, Castelli F, Vaghi M, Rusconi S, Montagnani F, Bargagli E, Franchi F, Mazzei MA, Cantarini L, Tacconi D, Feri M, Scala R, Spargi G, Nencioni C, Bandini M, Caldarelli GP, Canaccini A, Ognibene A, D’Arminio Monforte A, Girardis M, Antinori A, Francisci D, Schiaroli E, Scotton PG, Panese S, Scaggiante R, Monica MD, Capasso M, Fiorentino G, Castori M, Aucella F, Biagio AD, Masucci L, Valente S, Mandalà M, Zucchi P, Giannattasio F, Coviello DA, Mussini C, Tavecchia L, Crotti L, Rizzi M, Rovere MTL, Sarzi-Braga S, Bussotti M, Ravaglia S, Artuso R, Perrella A, Romani D, Bergomi P, Catena E, Vincenti A, Ferri C, Grassi D, Pessina G, Tumbarello M, Pietro MD, Sabrina R, Luchi S, Furini S, Dei S, Benetti E, Picchiotti N, Sanarico M, Ceri S, Pinoli P, Raimondi F, Biscarini F, Stella A, Zguro K, Capitani K, Nkambule L, Tanfoni M, Fallerini C, Daga S, Baldassarri M, Fava F, Frullanti E, Valentino F, Doddato G, Giliberti A, Tita R, Amitrano S, Bruttini M, Croci S, Meloni I, Mencarelli MA, Rizzo CL, Pinto AM, Beligni G, Tommasi A, Sarno LD, Palmieri M, Carriero ML, Alaverdian D, Busani S, Bruno R, Vecchia M, Belli MA, Mantovani S, Ludovisi S, Quiros-Roldan E, Antoni MD, Zanella I, Siano M, Emiliozzi A, Fabbiani M, Rossetti B, Bergantini L, D’Alessandro M, Cameli P, Bennett D, Anedda F, Marcantonio S, Scolletta S, Guerrini S, Conticini E, Frediani B, Spertilli C, Donati A, Guidelli L, Corridi M, Croci L, Piacentini P, Desanctis E, Cappelli S, Verzuri A, Anemoli V, Pancrazzi A, Lorubbio M, Miraglia FG, Venturelli S, Cossarizza A, Vergori A, Gabrieli A, Riva A, Paciosi F, Andretta F, Gatti F, Parisi SG, Baratti S, Piscopo C, Russo R, Andolfo I, Iolascon A, Carella M, Merla G, Squeo GM, Raggi P, Marciano C, Perna R, Bassetti M, Sanguinetti M, Giorli A, Salerni L, Parravicini P, Menatti E, Trotta T, Coiro G, Lena F, Martinelli E, Mancarella S, Gabbi C, Maggiolo F, Ripamonti D, Bachetti T, Suardi C, Parati G, Bottà G, Domenico PD, Rancan I, Bianchi F, Colombo R, Barbieri C, Acquilini D, Andreucci E, Segala FV, Tiseo G, Falcone M, Lista M, Poscente M, Vivo OD, Petrocelli P, Guarnaccia A, Baroni S, Hayward C, Porteous DJ, Fawns-Ritchie C, Richmond A, Campbell A, van Heel DA, Hunt KA, Trembath RC, Huang QQ, Martin HC, Mason D, Trivedi B, Wright J, Finer S, Akhtar S, Anwar M, Arciero E, Ashraf S, Breen G, Chung R, Curtis CJ, Chowdhury M, Colligan G, Deloukas P, Durham C, Finer S, Griffiths C, Huang QQ, Hurles M, Hunt KA, Hussain S, Islam K, Khan A, Khan A, Lavery C, Lee SH, Lerner R, MacArthur D, MacLaughlin B, Martin H, Mason D, Miah S, Newman B, Safa N, Tahmasebi F, Trembath RC, Trivedi B, van Heel DA, Wright J, Griffiths CJ, Smith AV, Boughton AP, Li KW, LeFaive J, Annis A, Niavarani A, Aliannejad R, Sharififard B, Amirsavadkouhi A, Naderpour Z, Tadi HA, Aleagha AE, Ahmadi S, Moghaddam SBM, Adamsara A, Saeedi M, Abdollahi H, Hosseini A, Chariyavilaskul P, Jantarabenjakul W, Hirankarn N, Chamnanphon M, Suttichet TB, Shotelersuk V, Pongpanich M, Phokaew C, Chetruengchai W, Putchareon O, Torvorapanit P, Puthanakit T, Suchartlikitwong P, Nilaratanakul V, Sodsai P, Brumpton BM, Hveem K, Willer C, Wolford B, Zhou W, Rogne T, Solligard E, Åsvold BO, Franke L, Boezen M, Deelen P, Claringbould A, Lopera E, Warmerdam R, Vonk JM, van Blokland I, Lanting P, Ori APS, Feng YCA, Mercader J, Weiss ST, Karlson EW, Smoller JW, Murphy SN, Meigs JB, Woolley AE, Green RC, Perez EF, Wolford B, Zöllner S, Wang J, Beck A, Sloofman LG, Ascolillo S, Sebra RP, Collins BL, Levy T, Buxbaum JD, Sealfon SC, Jordan DM, Thompson RC, Gettler K, Chaudhary K, Belbin GM, Preuss M, Hoggart C, Choi S, Underwood SJ, Salib I, Britvan B, Keller K, Tang L, Peruggia M, Hiester LL, Niblo K, Aksentijevich A, Labkowsky A, Karp A, Zlatopolsky M, Zyndorf M, Charney AW, Beckmann ND, Schadt EE, Abul-Husn NS, Cho JH, Itan Y, Kenny EE, Loos RJF, Nadkarni GN, Do R, O’Reilly P, Huckins LM, Ferreira MAR, Abecasis GR, Leader JB, Cantor MN, Justice AE, Carey DJ, Chittoor G, Josyula NS, Kosmicki JA, Horowitz JE, Baras A, Gass MC, Yadav A, Mirshahi T, Hottenga JJ, Bartels M, de geus EEJC, Nivard MMG, Verma A, Ritchie MD, Rader D, Li B, Verma SS, Lucas A, Bradford Y, Abedalthagafi M, Alaamery M, Alshareef A, Sawaji M, Massadeh S, AlMalik A, Alqahtani S, Baraka D, Harthi FA, Alsolm E, Safieh LA, Alowayn AM, Alqubaishi F, Mutairi AA, Mangul S, Almutairi M, Aljawini N, Albesher N, Arabi YM, Mahmoud ES, Khattab AK, Halawani RT, Alahmadey ZZ, Albakri JK, Felemban WA, Suliman BA, Hasanato R, Al-Awdah L, Alghamdi J, AlZahrani D, AlJohani S, Al-Afghani H, AlDhawi N, AlBardis H, Alkwai S, Alswailm M, Almalki F, Albeladi M, Almohammed I, Barhoush E, Albader A, Alotaibi S, Alghamdi B, Jung J, fawzy MS, Alrashed M, Zeberg H, Nkambul L, Frithiof R, Hultström M, Lipcsey M, Tardif N, Rooyackers O, Grip J, Maricic T, Helgeland Ø, Magnus P, Trogstad LIS, Lee Y, Harris JR, Mangino M, Spector TD, Emma D, Moutsianas L, Caulfield MJ, Scott RH, Kousathanas A, Pasko D, Walker S, Stuckey A, Odhams CA, Rhodes D, Fowler T, Rendon A, Chan G, Arumugam P, Karczewski KJ, Martin AR, Wilson DJ, Spencer CCA, Crook DW, Wyllie DH, O’Connell AM, Atkinson EG, Kanai M, Tsuo K, Baya N, Turley P, Gupta R, Walters RK, Palmer DS, Sarma G, Solomonson M, Cheng N, Lu W, Churchhouse C, Goldstein JI, King D, Zhou W, Seed C, Daly MJ, Neale BM, Finucane H, Bryant S, Satterstrom FK, Band G, Earle SG, Lin SK, Arning N, Koelling N, Armstrong J, Rudkin JK, Callier S, Bryant S, Cusick C, Soranzo N, Zhao JH, Danesh J, Angelantonio ED, Butterworth AS, Sun YV, Huffman JE, Cho K, O’Donnell CJ, Tsao P, Gaziano JM, Peloso G, Ho YL, Smieszek SP, Polymeropoulos C, Polymeropoulos V, Polymeropoulos MH, Przychodzen BP, Fernandez-Cadenas I, Planas AM, Perez-Tur J, Llucià-Carol L, Cullell N, Muiño E, Cárcel-Márquez J, DeDiego ML, Iglesias LL, Soriano A, Rico V, Agüero D, Bedini JL, Lozano F, Domingo C, Robles V, Ruiz-Jaén F, Márquez L, Gomez J, Coto E, Albaiceta GM, García-Clemente M, Dalmau D, Arranz MJ, Dietl B, Serra-Llovich A, Soler P, Colobrán R, Martín-Nalda A, Martínez AP, Bernardo D, Rojo S, Fiz-López A, Arribas E, de la Cal-Sabater P, Segura T, González-Villa E, Serrano-Heras G, Martí-Fàbregas J, Jiménez-Xarrié E, de Felipe Mimbrera A, Masjuan J, García-Madrona S, Domínguez-Mayoral A, Villalonga JM, Menéndez-Valladares P, Chasman DI, Sesso HD, Manson JE, Buring JE, Ridker PM, Franco G, Davis L, Lee S, Priest J, Sankaran VG, van Heel D, Biesecker L, Kerchberger VE, Baillie JK. A first update on mapping the human genetic architecture of COVID-19. Nature 2022; 608:E1-E10. [PMID: 35922517 PMCID: PMC9352569 DOI: 10.1038/s41586-022-04826-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 04/29/2022] [Indexed: 01/04/2023]
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Fawcett KA, Demidov G, Shrine N, Paynton ML, Ossowski S, Sayers I, Wain LV, Hollox EJ. Exome-wide analysis of copy number variation shows association of the human leukocyte antigen region with asthma in UK Biobank. BMC Med Genomics 2022; 15:119. [PMID: 35597955 PMCID: PMC9124406 DOI: 10.1186/s12920-022-01268-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 05/10/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The role of copy number variants (CNVs) in susceptibility to asthma is not well understood. This is, in part, due to the difficulty of accurately measuring CNVs in large enough sample sizes to detect associations. The recent availability of whole-exome sequencing (WES) in large biobank studies provides an unprecedented opportunity to study the role of CNVs in asthma. METHODS We called common CNVs in 49,953 individuals in the first release of UK Biobank WES using ClinCNV software. CNVs were tested for association with asthma in a stage 1 analysis comprising 7098 asthma cases and 36,578 controls from the first release of sequencing data. Nominally-associated CNVs were then meta-analysed in stage 2 with an additional 17,280 asthma cases and 115,562 controls from the second release of UK Biobank exome sequencing, followed by validation and fine-mapping. RESULTS Five of 189 CNVs were associated with asthma in stage 2, including a deletion overlapping the HLA-DQA1 and HLA-DQB1 genes, a duplication of CHROMR/PRKRA, deletions within MUC22 and TAP2, and a duplication in FBRSL1. The HLA-DQA1, HLA-DQB1, MUC22 and TAP2 genes all reside within the human leukocyte antigen (HLA) region on chromosome 6. In silico analyses demonstrated that the deletion overlapping HLA-DQA1 and HLA-DQB1 is likely to be an artefact arising from under-mapping of reads from non-reference HLA haplotypes, and that the CHROMR/PRKRA and FBRSL1 duplications represent presence/absence of pseudogenes within the HLA region. Bayesian fine-mapping of the HLA region suggested that there are two independent asthma association signals. The variants with the largest posterior inclusion probability in the two credible sets were an amino acid change in HLA-DQB1 (glutamine to histidine at residue 253) and a multi-allelic amino acid change in HLA-DRB1 (presence/absence of serine, glycine or leucine at residue 11). CONCLUSIONS At least two independent loci characterised by amino acid changes in the HLA-DQA1, HLA-DQB1 and HLA-DRB1 genes are likely to account for association of SNPs and CNVs in this region with asthma. The high divergence of haplotypes in the HLA can give rise to spurious CNVs, providing an important, cautionary tale for future large-scale analyses of sequencing data.
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Affiliation(s)
- Katherine A Fawcett
- Department of Health Sciences, University of Leicester, Leicester, LE1 7RH, UK.
| | - German Demidov
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Nick Shrine
- Department of Health Sciences, University of Leicester, Leicester, LE1 7RH, UK
| | - Megan L Paynton
- Department of Health Sciences, University of Leicester, Leicester, LE1 7RH, UK
| | - Stephan Ossowski
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Ian Sayers
- Translational Medical Sciences, NIHR Respiratory Biomedical Research Centre, School of Medicine, Biodiscovery Institute, University of Nottingham, University Park, Nottingham, UK
| | - Louise V Wain
- Department of Health Sciences, University of Leicester, Leicester, LE1 7RH, UK.,Leicester Respiratory Biomedical Research Centre, National Institute for Health Research, Glenfield Hospital, Leicester, LE3 9QP, UK
| | - Edward J Hollox
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
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Alharbi AF, Sheng N, Nicol K, Strömberg N, Hollox EJ. Balancing selection at the human salivary agglutinin gene (DMBT1) driven by host-microbe interactions. iScience 2022; 25:104189. [PMID: 35494225 PMCID: PMC9038570 DOI: 10.1016/j.isci.2022.104189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 02/07/2022] [Accepted: 03/30/2022] [Indexed: 11/19/2022] Open
Abstract
Discovering loci under balancing selection in humans can identify loci with alleles that affect response to the environment and disease. Genome variation data have identified the 5′ region of the DMBT1 gene as undergoing balancing selection in humans. DMBT1 encodes the pattern-recognition glycoprotein DMBT1, also known as SALSA, gp340, or salivary agglutinin. DMBT1 binds to a variety of pathogens through a tandemly arranged scavenger receptor cysteine-rich (SRCR) domain, with the number of domains polymorphic in humans. We show that the signal of balancing selection is driven by one haplotype usually carrying a shorter SRCR repeat and another usually carrying a longer SRCR repeat. DMBT1 encoded by a shorter SRCR repeat allele does not bind a cariogenic and invasive Streptococcus mutans strain, in contrast to the long SRCR allele that shows binding. Our results suggest that balancing selection at DMBT1 is due to host-microbe interactions of encoded SRCR tandem repeat alleles. Clear evidence from many analyses show balancing selection at DMBT1 Scavenger-receptor cysteine-rich domain array associated with balancing selection Genetic variation, not alternative splicing, responsible for protein isoforms Long, but not short, DMBT1 isoforms bind a cariogenic strain of Streptococcus mutans
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Affiliation(s)
- Adel F. Alharbi
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
- Medina Regional Laboratory, General Directorate of Health Affairs, Ministry of Health, Medina, Saudi Arabia
| | - Nongfei Sheng
- Department of Odontology, Umeå University, Umeå, Sweden
| | - Katie Nicol
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | | | - Edward J. Hollox
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
- Corresponding author
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Nonnecke EB, Castillo PA, Johansson MEV, Hollox EJ, Shen B, Lönnerdal B, Bevins CL. Human intelectin-2 (ITLN2) is selectively expressed by secretory Paneth cells. FASEB J 2022; 36:e22200. [PMID: 35182405 PMCID: PMC9262044 DOI: 10.1096/fj.202101870r] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/20/2022] [Accepted: 01/26/2022] [Indexed: 01/04/2023]
Abstract
Intelectins (intestinal lectins) are highly conserved across chordate evolution and have been implicated in various human diseases, including Crohn's disease (CD). The human genome encodes two intelectin genes, intelectin-1 (ITLN1) and intelectin-2 (ITLN2). Other than its high sequence similarity with ITLN1, little is known about ITLN2. To address this void in knowledge, we report that ITLN2 exhibits discrete, yet notable differences from ITLN1 in primary structure, including a unique amino terminus, as well as changes in amino acid residues associated with the glycan-binding activity of ITLN1. We identified that ITLN2 is a highly abundant Paneth cell-specific product, which localizes to secretory granules, and is expressed as a multimeric protein in the small intestine. In surgical specimens of ileal CD, ITLN2 mRNA levels were reduced approximately five-fold compared to control specimens. The ileal expression of ITLN2 was unaffected by previously reported disease-associated variants in ITLN2 and CD-associated variants in neighboring ITLN1 as well as NOD2 and ATG16L1. ITLN2 mRNA expression was undetectable in control colon tissue; however, in both ulcerative colitis (UC) and colonic CD, metaplastic Paneth cells were found to express ITLN2. Together, the data reported establish the groundwork for understanding ITLN2 function(s) in the intestine, including its possible role in CD.
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Affiliation(s)
- Eric B Nonnecke
- Department of Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, California, USA
| | - Patricia A Castillo
- Department of Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, California, USA
| | - Malin E V Johansson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Edward J Hollox
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Bo Shen
- Department of Gastroenterology, Hepatology and Nutrition, Digestive Diseases and Surgery Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Bo Lönnerdal
- Department of Nutrition, University of California, Davis, Davis, California, USA
| | - Charles L Bevins
- Department of Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, California, USA
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12
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Lee PH, Guyatt AL, John C, Ali A, Wang X, Williams AT, Zhao B, Batini C, Bee C, Adams E, Melbourne CA, Brightling CE, Hsu R, Bethea J, Reeve N, Ntalla I, Terry S, Pareek M, Brunskill NJ, Barwell J, Hollox EJ, Miola J, Wallace SE, Shepherd DJ, Packer R, Venn L, Wain LV, Free RC, Tobin MD. Extended Cohort for E-health, Environment and DNA (EXCEED) COVID-19 focus. Wellcome Open Res 2021. [DOI: 10.12688/wellcomeopenres.17437.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background: New data collection in established longitudinal population studies provides an opportunity for studying the risk factors and sequelae of the novel coronavirus disease 2019 (COVID-19), plus the indirect impacts of the COVID-19 pandemic on wellbeing. The Extended Cohort for E-health, Environment and DNA (EXCEED) cohort is a population-based cohort (N>11,000), recruited from 2013 in Leicester, Leicestershire and Rutland. EXCEED includes consent for electronic healthcare record (EHR) linkage, spirometry, genomic data, and questionnaire data. Methods: Between May 2020 and July 2021, a new questionnaire was deployed in EXCEED, which captured COVID-19 symptoms, general physical and mental health, plus socioeconomic and environmental factors during the pandemic. An online system was developed to invite new participants to join EXCEED, with informed consent being provided online. New and existing participants then completed the COVID-19 questionnaire online. A subset of the new questionnaire respondents were invited to participate in COVID-19 serology substudies, using home antibody testing kits. Results: In total, 3,693 participants provided COVID-19 infection status (median age 62.9 (IQR 54.7-69.2), 58.9% female). Trends of monthly incidence proportions of COVID-19 in EXCEED (self-report or symptom-predicted) approximated local and national figures. Regression analysis of 2,768 participants with linked EHR data showed no obvious monotonic relationship between number of chronic diseases (of 16 pre-specified diseases) and COVID-19 infection. There were 2,144 participants with valid results from a kit allowing differentiation between antibodies due to vaccination or infection. Of these, 8.5% had results consistent with previous COVID-19 infection, and 85.9% had evidence of COVID-19 vaccination, but without evidence of infection. Conclusions: Enriching EXCEED with a new COVID-19 questionnaire and serology data may improve understanding of the risk factors, clinical sequelae and broader impacts of the COVID-19 pandemic in the general population. Controlled access to these data for bona fide researchers is via application to the EXCEED study.
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13
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Hollox EJ, Zuccherato LW, Tucci S. Genome structural variation in human evolution. Trends Genet 2021; 38:45-58. [PMID: 34284881 DOI: 10.1016/j.tig.2021.06.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 01/01/2023]
Abstract
Structural variation (SV) is a large difference (typically >100 bp) in the genomic structure of two genomes and includes both copy number variation and variation that does not change copy number of a genomic region, such as an inversion. Improved reference genomes, combined with widespread genome sequencing using short-read sequencing technology, and increasingly using long-read sequencing, have reignited interest in SV. Recent large-scale studies and functional focused analyses have highlighted the role of SV in human evolution. In this review, we highlight human-specific SVs involved in changes in the brain, population-specific SVs that affect response to the environment, including adaptation to diet and infectious diseases, and summarise the contribution of archaic hominin admixture to present-day human SV.
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Affiliation(s)
- Edward J Hollox
- Department of Genetics and Genome Biology, University of Leicester, UK.
| | - Luciana W Zuccherato
- Núcleo de Ensino e Pesquisa, Instituto Mário Penna, Belo Horizonte, Brazil; Departmento de Bioquímica e Imunologia, Universidade de Minas Gerais, Belo Horizonte, Brazil
| | - Serena Tucci
- Department of Anthropology, Yale University, New Haven, CT, USA
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14
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Hains DS, Polley S, Liang D, Saxena V, Arregui S, Ketz J, Barr-Beare E, Rawson A, Spencer JD, Cohen A, Hansen PL, Tuttolomondo M, Casella C, Ditzel HJ, Cohen D, Hollox EJ, Schwaderer AL. Deleted in malignant brain tumor 1 genetic variation confers urinary tract infection risk in children and mice. Clin Transl Med 2021; 11:e477. [PMID: 34323417 PMCID: PMC8255058 DOI: 10.1002/ctm2.477] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 12/03/2022] Open
Affiliation(s)
- David S Hains
- Department of Pediatrics, Indiana University, Indianapolis, Indiana, USA
| | - Shamik Polley
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Dong Liang
- Department of Pediatrics, Indiana University, Indianapolis, Indiana, USA
| | - Vijay Saxena
- Department of Pediatrics, Indiana University, Indianapolis, Indiana, USA
| | - Samuel Arregui
- Department of Pediatrics, Indiana University, Indianapolis, Indiana, USA
| | - John Ketz
- The Center for Clinical and Translational Research, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | | | - Ashley Rawson
- Department of Pediatrics, Indiana University, Indianapolis, Indiana, USA
| | - John D Spencer
- The Center for Clinical and Translational Research, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Ariel Cohen
- The Center for Clinical and Translational Research, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Pernille L Hansen
- Lundbeckfonden Center of Excellence NanoCAN, University of Southern Denmark, Odense, Denmark.,Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Martina Tuttolomondo
- Lundbeckfonden Center of Excellence NanoCAN, University of Southern Denmark, Odense, Denmark.,Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Cinzia Casella
- Lundbeckfonden Center of Excellence NanoCAN, University of Southern Denmark, Odense, Denmark.,Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Henrik J Ditzel
- Lundbeckfonden Center of Excellence NanoCAN, University of Southern Denmark, Odense, Denmark.,Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark.,Department of Oncology, Odense University Hospital, Odense, Denmark
| | - Daniel Cohen
- Emergency Department, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Edward J Hollox
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
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15
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Nonnecke EB, Castillo PA, Dugan AE, Almalki F, Underwood MA, De La Motte CA, Yuan W, Lu W, Shen B, Johansson MEV, Kiessling LL, Hollox EJ, Lönnerdal B, Bevins CL. Human intelectin-1 (ITLN1) genetic variation and intestinal expression. Sci Rep 2021; 11:12889. [PMID: 34145348 PMCID: PMC8213764 DOI: 10.1038/s41598-021-92198-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 06/07/2021] [Indexed: 12/13/2022] Open
Abstract
Intelectins are ancient carbohydrate binding proteins, spanning chordate evolution and implicated in multiple human diseases. Previous GWAS have linked SNPs in ITLN1 (also known as omentin) with susceptibility to Crohn's disease (CD); however, analysis of possible functional significance of SNPs at this locus is lacking. Using the Ensembl database, pairwise linkage disequilibrium (LD) analyses indicated that several disease-associated SNPs at the ITLN1 locus, including SNPs in CD244 and Ly9, were in LD. The alleles comprising the risk haplotype are the major alleles in European (67%), but minor alleles in African superpopulations. Neither ITLN1 mRNA nor protein abundance in intestinal tissue, which we confirm as goblet-cell derived, was altered in the CD samples overall nor when samples were analyzed according to genotype. Moreover, the missense variant V109D does not influence ITLN1 glycan binding to the glycan β-D-galactofuranose or protein-protein oligomerization. Taken together, our data are an important step in defining the role(s) of the CD-risk haplotype by determining that risk is unlikely to be due to changes in ITLN1 carbohydrate recognition, protein oligomerization, or expression levels in intestinal mucosa. Our findings suggest that the relationship between the genomic data and disease arises from changes in CD244 or Ly9 biology, differences in ITLN1 expression in other tissues, or an alteration in ITLN1 interaction with other proteins.
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Affiliation(s)
- Eric B Nonnecke
- Department of Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, CA, 95616, USA.
| | - Patricia A Castillo
- Department of Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, CA, 95616, USA
- Elanco Animal Health, Fort Dodge, IA, 50501, USA
| | - Amanda E Dugan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Faisal Almalki
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
- Medical Laboratories Technology Department, College of Applied Medical Sciences, Taibah University, Almadinah Almunwarah, Saudi Arabia
| | - Mark A Underwood
- Department of Pediatrics, School of Medicine, University of California, Davis, Sacramento, CA, 95817, USA
| | - Carol A De La Motte
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA
| | - Weirong Yuan
- Institute of Human Virology, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Wuyuan Lu
- Institute of Human Virology, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
- Fudan University, Shanghai, China
| | - Bo Shen
- Department of Gastroenterology, Hepatology and Nutrition, Digestive Diseases and Surgery Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
- Department of Surgery, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, 10032, USA
| | - Malin E V Johansson
- Institute of Biomedicine, Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | - Laura L Kiessling
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Edward J Hollox
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Bo Lönnerdal
- Department of Nutrition, University of California, Davis, Davis, CA, 95616, USA
| | - Charles L Bevins
- Department of Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, CA, 95616, USA.
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16
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Zhang M, Luo JL, Sun Q, Harber J, Dawson AG, Nakas A, Busacca S, Sharkey AJ, Waller D, Sheaff MT, Richards C, Wells-Jordan P, Gaba A, Poile C, Baitei EY, Bzura A, Dzialo J, Jama M, Le Quesne J, Bajaj A, Martinson L, Shaw JA, Pritchard C, Kamata T, Kuse N, Brannan L, De Philip Zhang P, Yang H, Griffiths G, Wilson G, Swanton C, Dudbridge F, Hollox EJ, Fennell DA. Author Correction: Clonal architecture in mesothelioma is prognostic and shapes the tumour microenvironment. Nat Commun 2021; 12:3569. [PMID: 34099722 PMCID: PMC8185116 DOI: 10.1038/s41467-021-23867-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Min Zhang
- Novogene Co., Ltd, Building 301, Beijing, China
| | - Jin-Li Luo
- Bioinformatics and Biostatistics Support Hub, University of Leicester, Leicester, UK
| | | | - James Harber
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Alan G Dawson
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK.,Department of Cardiothoracic Surgery, Glenfield Hospital, Leicester, UK
| | - Apostolos Nakas
- Department of Cardiothoracic Surgery, Glenfield Hospital, Leicester, UK
| | - Sara Busacca
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | | | - David Waller
- Barts Health NHS Trust, The Royal London Hospital, London, UK
| | | | - Cathy Richards
- Department of Pathology, Leicester Royal Infirmary, Infirmary Square, Leicester, Leicestershire, UK
| | - Peter Wells-Jordan
- Department of Pathology, Leicester Royal Infirmary, Infirmary Square, Leicester, Leicestershire, UK
| | - Aarti Gaba
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Charlotte Poile
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Essa Y Baitei
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK.,Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Aleksandra Bzura
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Joanna Dzialo
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Maymun Jama
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - John Le Quesne
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Bearsden, UK
| | - Amrita Bajaj
- Department of Radiology, Glenfield Hospital, Leicester, UK
| | - Luke Martinson
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Jacqui A Shaw
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Catrin Pritchard
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Tamihiro Kamata
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Nathaniel Kuse
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Lee Brannan
- Department of Health Sciences, University of Leicester, Leicester, UK
| | | | - Hongji Yang
- Department of Informatics, University of Leicester, Leicester, UK
| | - Gareth Griffiths
- Southampton Clinical Trials Unit, University of Southampton, Southampton, UK
| | | | | | - Frank Dudbridge
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Edward J Hollox
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Dean A Fennell
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK.
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17
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Zhang M, Luo JL, Sun Q, Harber J, Dawson AG, Nakas A, Busacca S, Sharkey AJ, Waller D, Sheaff MT, Richards C, Wells-Jordan P, Gaba A, Poile C, Baitei EY, Bzura A, Dzialo J, Jama M, Le Quesne J, Bajaj A, Martinson L, Shaw JA, Pritchard C, Kamata T, Kuse N, Brannan L, De Philip Zhang P, Yang H, Griffiths G, Wilson G, Swanton C, Dudbridge F, Hollox EJ, Fennell DA. Clonal architecture in mesothelioma is prognostic and shapes the tumour microenvironment. Nat Commun 2021; 12:1751. [PMID: 33741915 PMCID: PMC7979861 DOI: 10.1038/s41467-021-21798-w] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 02/04/2021] [Indexed: 01/31/2023] Open
Abstract
Malignant Pleural Mesothelioma (MPM) is typically diagnosed 20-50 years after exposure to asbestos and evolves along an unknown evolutionary trajectory. To elucidate this path, we conducted multi-regional exome sequencing of 90 tumour samples from 22 MPMs acquired at surgery. Here we show that exomic intratumour heterogeneity varies widely across the cohort. Phylogenetic tree topology ranges from linear to highly branched, reflecting a steep gradient of genomic instability. Using transfer learning, we detect repeated evolution, resolving 5 clusters that are prognostic, with temporally ordered clonal drivers. BAP1/-3p21 and FBXW7/-chr4 events are always early clonal. In contrast, NF2/-22q events, leading to Hippo pathway inactivation are predominantly late clonal, positively selected, and when subclonal, exhibit parallel evolution indicating an evolutionary constraint. Very late somatic alteration of NF2/22q occurred in one patient 12 years after surgery. Clonal architecture and evolutionary clusters dictate MPM inflammation and immune evasion. These results reveal potentially drugable evolutionary bottlenecking in MPM, and an impact of clonal architecture on shaping the immune landscape, with potential to dictate the clinical response to immune checkpoint inhibition.
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Affiliation(s)
- Min Zhang
- Novogene Co., Ltd, Building 301, Beijing, China
| | - Jin-Li Luo
- Bioinformatics and Biostatistics Support Hub, University of Leicester, Leicester, UK
| | | | - James Harber
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Alan G Dawson
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
- Department of Cardiothoracic Surgery, Glenfield Hospital, Leicester, UK
| | - Apostolos Nakas
- Department of Cardiothoracic Surgery, Glenfield Hospital, Leicester, UK
| | - Sara Busacca
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | | | - David Waller
- Barts Health NHS Trust, The Royal London Hospital, London, UK
| | | | - Cathy Richards
- Department of Pathology, Leicester Royal Infirmary, Infirmary Square, Leicester, Leicestershire, UK
| | - Peter Wells-Jordan
- Department of Pathology, Leicester Royal Infirmary, Infirmary Square, Leicester, Leicestershire, UK
| | - Aarti Gaba
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Charlotte Poile
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Essa Y Baitei
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Aleksandra Bzura
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Joanna Dzialo
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Maymun Jama
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - John Le Quesne
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Bearsden, UK
| | - Amrita Bajaj
- Department of Radiology, Glenfield Hospital, Leicester, UK
| | - Luke Martinson
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Jacqui A Shaw
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Catrin Pritchard
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Tamihiro Kamata
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Nathaniel Kuse
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Lee Brannan
- Department of Health Sciences, University of Leicester, Leicester, UK
| | | | - Hongji Yang
- Department of Informatics, University of Leicester, Leicester, UK
| | - Gareth Griffiths
- Southampton Clinical Trials Unit, University of Southampton, Southampton, UK
| | | | | | - Frank Dudbridge
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Edward J Hollox
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Dean A Fennell
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK.
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18
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Algady W, Weyell E, Mateja D, Garcia A, Courtin D, Hollox EJ. Genotyping complex structural variation at the malaria-associated human glycophorin locus using a PCR-based strategy. Ann Hum Genet 2020; 85:7-17. [PMID: 32895931 DOI: 10.1111/ahg.12405] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/23/2020] [Accepted: 08/15/2020] [Indexed: 02/06/2023]
Abstract
Structural variation in the human genome can affect risk of disease. An example is a complex structural variant of the human glycophorin gene cluster, called DUP4, which is associated with a clinically significant level of protection against severe malaria. The human glycophorin gene cluster harbours at least 23 distinct structural variants, and accurate genotyping of this complex structural variation remains a challenge. Here, we use a polymerase chain reaction-based strategy to genotype structural variation at the human glycophorin gene cluster, including the alleles responsible for the U- blood group. We validate our approach, based on a triplex paralogue ratio test, on publically available samples from the 1000 Genomes project. We then genotype 574 individuals from a longitudinal birth cohort (Tori-Bossito cohort) using small amounts of DNA at low cost. Our approach readily identifies known deletions and duplications, and can potentially identify novel variants for further analysis. It will allow exploration of genetic variation at the glycophorin locus, and investigation of its relationship with malaria, in large sample sets at minimal cost, using standard molecular biology equipment.
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Affiliation(s)
- Walid Algady
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Eleanor Weyell
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Daria Mateja
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - André Garcia
- UMR 261 MERIT, Institut de Recherche pour le Développement (IRD), Université de Paris, Paris, France
| | - David Courtin
- UMR 261 MERIT, Institut de Recherche pour le Développement (IRD), Université de Paris, Paris, France
| | - Edward J Hollox
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
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19
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Louzada S, Algady W, Weyell E, Zuccherato LW, Brajer P, Almalki F, Scliar MO, Naslavsky MS, Yamamoto GL, Duarte YAO, Passos-Bueno MR, Zatz M, Yang F, Hollox EJ. Structural variation of the malaria-associated human glycophorin A-B-E region. BMC Genomics 2020; 21:446. [PMID: 32600246 PMCID: PMC7325229 DOI: 10.1186/s12864-020-06849-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 06/18/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Approximately 5% of the human genome shows common structural variation, which is enriched for genes involved in the immune response and cell-cell interactions. A well-established region of extensive structural variation is the glycophorin gene cluster, comprising three tandemly-repeated regions about 120 kb in length and carrying the highly homologous genes GYPA, GYPB and GYPE. Glycophorin A (encoded by GYPA) and glycophorin B (encoded by GYPB) are glycoproteins present at high levels on the surface of erythrocytes, and they have been suggested to act as decoy receptors for viral pathogens. They are receptors for the invasion of the protist parasite Plasmodium falciparum, a causative agent of malaria. A particular complex structural variant, called DUP4, creates a GYPB-GYPA fusion gene known to confer resistance to malaria. Many other structural variants exist across the glycophorin gene cluster, and they remain poorly characterised. RESULTS Here, we analyse sequences from 3234 diploid genomes from across the world for structural variation at the glycophorin locus, confirming 15 variants in the 1000 Genomes project cohort, discovering 9 new variants, and characterising a selection of these variants using fibre-FISH and breakpoint mapping at the sequence level. We identify variants predicted to create novel fusion genes and a common inversion duplication variant at appreciable frequencies in West Africans. We show that almost all variants can be explained by non-allelic homologous recombination and by comparing the structural variant breakpoints with recombination hotspot maps, confirm the importance of a particular meiotic recombination hotspot on structural variant formation in this region. CONCLUSIONS We identify and validate large structural variants in the human glycophorin A-B-E gene cluster which may be associated with different clinical aspects of malaria.
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Affiliation(s)
- Sandra Louzada
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
- Present address: Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal
- Present address: BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Lisbon, Portugal
| | - Walid Algady
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Eleanor Weyell
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Luciana W Zuccherato
- Department of Pathology, Faculty of Medicine, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Paulina Brajer
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Faisal Almalki
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Marilia O Scliar
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Michel S Naslavsky
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Guilherme L Yamamoto
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Yeda A O Duarte
- School of Nursing, Universidade de São Paulo, São Paulo, Brazil
| | - Maria Rita Passos-Bueno
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Mayana Zatz
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | | | - Edward J Hollox
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK.
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20
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John C, Reeve NF, Free RC, Williams AT, Ntalla I, Farmaki AE, Bethea J, Barton LM, Shrine N, Batini C, Packer R, Terry S, Hargadon B, Wang Q, Melbourne CA, Adams EL, Bee CE, Harrington K, Miola J, Brunskill NJ, Brightling CE, Barwell J, Wallace SE, Hsu R, Shepherd DJ, Hollox EJ, Wain LV, Tobin MD. Cohort profile: Extended Cohort for E-health, Environment and DNA (EXCEED). Int J Epidemiol 2019; 48:1734. [PMID: 31365084 PMCID: PMC6857747 DOI: 10.1093/ije/dyz175] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Affiliation(s)
- Catherine John
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Nicola F Reeve
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Robert C Free
- NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
- Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | | | - Ioanna Ntalla
- Department of Health Sciences, University of Leicester, Leicester, UK
- Department of Clinical Pharmacology, William Harvey Research Institute, Barts & The London Medical School, Queen Mary University of London, Charterhouse Square, London, UK
| | - Aliki-Eleni Farmaki
- Department of Health Sciences, University of Leicester, Leicester, UK
- Department of Population Science and Experimental Medicine, Institute of Cardiovascular Science, University College London, London, UK
| | - Jane Bethea
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Linda M Barton
- Department of Haematology, University Hospitals of Leicester NHS Trust, Leicester, UK
| | - Nick Shrine
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Chiara Batini
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Richard Packer
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Sarah Terry
- NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Beverley Hargadon
- NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Qingning Wang
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Carl A Melbourne
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Emma L Adams
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Catherine E Bee
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Kyla Harrington
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - José Miola
- Leicester Law School, University of Leicester, Leicester, UK
| | - Nigel J Brunskill
- Department of Cardiovascular Sciences University of Leicester, Leicester, UK
| | - Christopher E Brightling
- NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
- Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - Julian Barwell
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Susan E Wallace
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Ron Hsu
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - David J Shepherd
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Edward J Hollox
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Louise V Wain
- Department of Health Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Martin D Tobin
- Department of Health Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
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21
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John C, Reeve NF, Free RC, Williams AT, Ntalla I, Farmaki AE, Bethea J, Barton LM, Shrine N, Batini C, Packer R, Terry S, Hargadon B, Wang Q, Melbourne CA, Adams EL, Bee CE, Harrington K, Miola J, Brunskill NJ, Brightling CE, Barwell J, Wallace SE, Hsu R, Shepherd DJ, Hollox EJ, Wain LV, Tobin MD. Cohort Profile: Extended Cohort for E-health, Environment and DNA (EXCEED). Int J Epidemiol 2019; 48:678-679j. [PMID: 31062032 PMCID: PMC6659362 DOI: 10.1093/ije/dyz073] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/26/2019] [Indexed: 12/22/2022] Open
Affiliation(s)
- Catherine John
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Nicola F Reeve
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Robert C Free
- NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
- Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | | | - Ioanna Ntalla
- Department of Health Sciences, University of Leicester, Leicester, UK
- Department of Clinical Pharmacology, William Harvey Research Institute, Barts & The London Medical School, Queen Mary University of London, Charterhouse Square, London, UK
| | - Aliki-Eleni Farmaki
- Department of Health Sciences, University of Leicester, Leicester, UK
- Department of Population Science and Experimental Medicine, Institute of Cardiovascular Science, University College London, London, UK
| | - Jane Bethea
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Linda M Barton
- Department of Haematology, University Hospitals of Leicester NHS Trust, Leicester, UK
| | - Nick Shrine
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Chiara Batini
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Richard Packer
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Sarah Terry
- NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Beverley Hargadon
- NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Qingning Wang
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Carl A Melbourne
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Emma L Adams
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Catherine E Bee
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Kyla Harrington
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - José Miola
- Leicester Law School, University of Leicester, Leicester, UK
| | - Nigel J Brunskill
- Department of Cardiovascular Sciences University of Leicester, Leicester, UK
| | - Christopher E Brightling
- NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
- Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - Julian Barwell
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Susan E Wallace
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Ron Hsu
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - David J Shepherd
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Edward J Hollox
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Louise V Wain
- Department of Health Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Martin D Tobin
- Department of Health Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
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22
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Zuccherato LW, Elói-Santos SM, Jardim LL, Camelo RM, Chaves DG, Souza RP, Hollox EJ, Rezende SM. Variation of rs3754689 at lactase gene and inhibitors in admixed Brazilian patients with hemophilia A. Haematologica 2019; 104:e527-e529. [PMID: 30872367 DOI: 10.3324/haematol.2019.220608] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Luciana W Zuccherato
- Complementary Propedeutic Department, Faculty of Medicine, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Silvana M Elói-Santos
- Complementary Propedeutic Department, Faculty of Medicine, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Letícia L Jardim
- Department of Internal Medicine, Faculty of Medicine, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Ricardo M Camelo
- Department of Internal Medicine, Faculty of Medicine, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | - Renan P Souza
- Department of General Biology, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Edward J Hollox
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Suely M Rezende
- Department of Internal Medicine, Faculty of Medicine, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
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23
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Algady W, Louzada S, Carpenter D, Brajer P, Färnert A, Rooth I, Ngasala B, Yang F, Shaw MA, Hollox EJ. The Malaria-Protective Human Glycophorin Structural Variant DUP4 Shows Somatic Mosaicism and Association with Hemoglobin Levels. Am J Hum Genet 2018; 103:769-776. [PMID: 30388403 PMCID: PMC6218809 DOI: 10.1016/j.ajhg.2018.10.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 10/04/2018] [Indexed: 01/23/2023] Open
Abstract
Glycophorin A and glycophorin B are red blood cell surface proteins and are both receptors for the parasite Plasmodium falciparum, which is the principal cause of malaria in sub-Saharan Africa. DUP4 is a complex structural genomic variant that carries extra copies of a glycophorin A-glycophorin B fusion gene and has a dramatic effect on malaria risk by reducing the risk of severe malaria by up to 40%. Using fiber-FISH and Illumina sequencing, we validate the structural arrangement of the glycophorin locus in the DUP4 variant and reveal somatic variation in copy number of the glycophorin B-glycophorin A fusion gene. By developing a simple, specific, PCR-based assay for DUP4, we show that the DUP4 variant reaches a frequency of 13% in the population of a malaria-endemic village in south-eastern Tanzania. We genotype a substantial proportion of that village and demonstrate an association of DUP4 genotype with hemoglobin levels, a phenotype related to malaria, using a family-based association test. Taken together, we show that DUP4 is a complex structural variant that may be susceptible to somatic variation and show that DUP4 is associated with a malarial-related phenotype in a longitudinally followed population.
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Affiliation(s)
- Walid Algady
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Sandra Louzada
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Danielle Carpenter
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Paulina Brajer
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Anna Färnert
- Division of Infectious Diseases, Department of Medicine Solna, Karolinska Institutet, 17176 Stockholm, Sweden; Department of Infectious Diseases, Karolinska University Hospital, Stockholm 17176, Sweden
| | - Ingegerd Rooth
- Nyamisati Malaria Research, Rufiji, National Institute for Medical Research, Dar-es-Salaam, Tanzania
| | - Billy Ngasala
- Department of Parasitology and Medical Entomology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania; Department of Women's and Children's Health, International Maternal and Child Health (IMCH), Uppsala Universitet, 75185 Uppsala, Sweden
| | - Fengtang Yang
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Marie-Anne Shaw
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds LS9 7TF, UK
| | - Edward J Hollox
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK.
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24
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Adewoye AB, Shrine N, Odenthal-Hesse L, Welsh S, Malarstig A, Jelinsky S, Kilty I, Tobin MD, Hollox EJ, Wain LV. Human CCL3L1 copy number variation, gene expression, and the role of the CCL3L1-CCR5 axis in lung function. Wellcome Open Res 2018; 3:13. [PMID: 29682616 PMCID: PMC5883389 DOI: 10.12688/wellcomeopenres.13902.2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/09/2018] [Indexed: 01/21/2023] Open
Abstract
Background: The CCL3L1-CCR5 signaling axis is important in a number of inflammatory responses, including macrophage function, and T-cell-dependent immune responses. Small molecule CCR5 antagonists exist, including the approved antiretroviral drug maraviroc, and therapeutic monoclonal antibodies are in development. Repositioning of drugs and targets into new disease areas can accelerate the availability of new therapies and substantially reduce costs. As it has been shown that drug targets with genetic evidence supporting their involvement in the disease are more likely to be successful in clinical development, using genetic association studies to identify new target repurposing opportunities could be fruitful. Here we investigate the potential of perturbation of the CCL3L1-CCR5 axis as treatment for respiratory disease. Europeans typically carry between 0 and 5 copies of CCL3L1 and this multi-allelic variation is not detected by widely used genome-wide single nucleotide polymorphism studies. Methods: We directly measured the complex structural variation of CCL3L1 using the Paralogue Ratio Test and imputed (with validation) CCR5del32 genotypes in 5,000 individuals from UK Biobank, selected from the extremes of the lung function distribution, and analysed DNA and RNAseq data for CCL3L1 from the 1000 Genomes Project. Results: We confirmed the gene dosage effect of CCL3L1 copy number on CCL3L1 mRNA expression levels. We found no evidence for association of CCL3L1 copy number or CCR5del32 genotype with lung function. Conclusions: These results suggest that repositioning CCR5 antagonists is unlikely to be successful for the treatment of airflow obstruction.
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Affiliation(s)
- Adeolu B. Adewoye
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Nick Shrine
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Linda Odenthal-Hesse
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | | | | | - Scott Jelinsky
- Pfizer Worldwide Research and Development, Cambridge, MA, USA
| | - Iain Kilty
- Pfizer Worldwide Research and Development, Cambridge, MA, USA
| | - Martin D. Tobin
- Department of Health Sciences, University of Leicester, Leicester, UK,National Institute of Health Research Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Edward J. Hollox
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK,
| | - Louise V. Wain
- Department of Health Sciences, University of Leicester, Leicester, UK,National Institute of Health Research Biomedical Research Centre, University of Leicester, Leicester, UK,
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25
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Adewoye AB, Shrine N, Odenthal-Hesse L, Welsh S, Malarstig A, Jelinsky S, Kilty I, Tobin MD, Hollox EJ, Wain LV. Human CCL3L1 copy number variation, gene expression, and the role of the CCL3L1-CCR5 axis in lung function. Wellcome Open Res 2018. [DOI: 10.12688/wellcomeopenres.13902.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background: The CCL3L1-CCR5 signaling axis is important in a number of inflammatory responses, including macrophage function, and T-cell-dependent immune responses. Small molecule CCR5 antagonists exist, including the approved antiretroviral drug maraviroc, and therapeutic monoclonal antibodies are in development. Repositioning of drugs and targets into new disease areas can accelerate the availability of new therapies and substantially reduce costs. As it has been shown that drug targets with genetic evidence supporting their involvement in the disease are more likely to be successful in clinical development, using genetic association studies to identify new target repurposing opportunities could be fruitful. Here we investigate the potential of perturbation of the CCL3L1-CCR5 axis as treatment for respiratory disease. Europeans typically carry between 0 and 5 copies of CCL3L1 and this multi-allelic variation is not detected by widely used genome-wide single nucleotide polymorphism studies. Methods: We directly measured the complex structural variation of CCL3L1 using the Paralogue Ratio Test and imputed (with validation) CCR5del32 genotypes in 5,000 individuals from UK Biobank, selected from the extremes of the lung function distribution, and analysed DNA and RNAseq data for CCL3L1 from the 1000 Genomes Project. Results: We confirmed the gene dosage effect of CCL3L1 copy number on CCL3L1 mRNA expression levels. We found no evidence for association of CCL3L1 copy number or CCR5del32 genotype with lung function. Conclusions: These results suggest that repositioning CCR5 antagonists is unlikely to be successful for the treatment of airflow obstruction.
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26
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Zuccherato LW, Schneider S, Tarazona-Santos E, Hardwick RJ, Berg DE, Bogle H, Gouveia MH, Machado LR, Machado M, Rodrigues-Soares F, Soares-Souza GB, Togni DL, Zamudio R, Gilman RH, Duarte D, Hollox EJ, Rodrigues MR. Population genetics of immune-related multilocus copy number variation in Native Americans. J R Soc Interface 2017; 14:rsif.2017.0057. [PMID: 28356540 DOI: 10.1098/rsif.2017.0057] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 03/02/2017] [Indexed: 12/22/2022] Open
Abstract
While multiallelic copy number variation (mCNV) loci are a major component of genomic variation, quantifying the individual copy number of a locus and defining genotypes is challenging. Few methods exist to study how mCNV genetic diversity is apportioned within and between populations (i.e. to define the population genetic structure of mCNV). These inferences are critical in populations with a small effective size, such as Amerindians, that may not fit the Hardy-Weinberg model due to inbreeding, assortative mating, population subdivision, natural selection or a combination of these evolutionary factors. We propose a likelihood-based method that simultaneously infers mCNV allele frequencies and the population structure parameter f, which quantifies the departure of homozygosity from the Hardy-Weinberg expectation. This method is implemented in the freely available software CNVice, which also infers individual genotypes using information from both the population and from trios, if available. We studied the population genetics of five immune-related mCNV loci associated with complex diseases (beta-defensins, CCL3L1/CCL4L1, FCGR3A, FCGR3B and FCGR2C) in 12 traditional Native American populations and found that the population structure parameters inferred for these mCNVs are comparable to but lower than those for single nucleotide polymorphisms studied in the same populations.
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Affiliation(s)
- Luciana W Zuccherato
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Silvana Schneider
- Departamento de Estatística, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Eduardo Tarazona-Santos
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | - Douglas E Berg
- Department of Molecular Microbiology, Washington University in Saint Louis School of Medicine, St Louis, MO, USA.,Department of Medicine, University of California San Diego, CA, USA
| | - Helen Bogle
- Department of Genetics, University of Leicester, Leicester, UK
| | - Mateus H Gouveia
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Lee R Machado
- Department of Genetics, University of Leicester, Leicester, UK.,School of Health, University of Northampton, Northampton, UK
| | - Moara Machado
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Fernanda Rodrigues-Soares
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Giordano B Soares-Souza
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Diego L Togni
- Departamento de Estatística, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Roxana Zamudio
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Robert H Gilman
- Johns Hopkins School of Public Health, Johns Hopkins University, Baltimore, MD, USA.,Asociación Benéfica PRISMA, Lima, Peru.,Universidade Peruana Cayetano Heredia, Lima, Peru
| | - Denise Duarte
- Departamento de Estatística, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Edward J Hollox
- Department of Genetics, University of Leicester, Leicester, UK
| | - Maíra R Rodrigues
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
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27
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Abujaber R, Shea PR, McLaren PJ, Lakhi S, Gilmour J, Allen S, Fellay J, Hollox EJ. No Evidence for Association of β-Defensin Genomic Copy Number with HIV Susceptibility, HIV Load during Clinical Latency, or Progression to AIDS. Ann Hum Genet 2017; 81:27-34. [PMID: 28084001 DOI: 10.1111/ahg.12182] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 11/30/2016] [Indexed: 11/28/2022]
Abstract
Common single-nucleotide variation in the host accounts for 25% of the variability in the plasma levels of HIV during the clinical latency stage (viral load set point). However, the role of rare variants and copy number variants remains relatively unexplored. Previous work has suggested copy number variation of a cluster of β-defensin genes affects HIV load in treatment-naïve sub-Saharan Africans and rate of response to antiretroviral treatment. Here we analyse a total of 1827 individuals from two cohorts of HIV-infected individuals from Europe and sub-Saharan Africa to investigate the role of β-defensin copy number variation on HIV load at set point. We find no evidence for association of copy number with viral load. We also compare distribution of β-defensin copy number between European cases and controls and find no differences, arguing against a role of β-defensin copy number in HIV acquisition. Taken together, our data argue against an effect of copy number variation of the β-defensin region in the spontaneous control of HIV infection.
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Affiliation(s)
- Razan Abujaber
- Department of Genetics, University of Leicester, Leicester, UK
| | - Patrick R Shea
- Institute for Genomic Medicine, Columbia University, New York, New York, USA
| | - Paul J McLaren
- National HIV and Retrovirology Laboratory, Public Health Agency of Canada, Winnipeg, Canada.,Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - Shabir Lakhi
- International AIDS Vaccine Initiative (IAVI), New York, New York, USA.,Zambia-Emory HIV Research Project, Lusaka and Copperbelt, Zambia
| | - Jill Gilmour
- International AIDS Vaccine Initiative (IAVI), New York, New York, USA.,IAVI Human Immunology Laboratory, Imperial College, London, United Kingdom
| | - Susan Allen
- International AIDS Vaccine Initiative (IAVI), New York, New York, USA.,School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | | | - Edward J Hollox
- Department of Genetics, University of Leicester, Leicester, UK
| | -
- Department of Genetics, University of Leicester, Leicester, UK
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28
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Rahbari R, Zuccherato LW, Tischler G, Chihota B, Ozturk H, Saleem S, Tarazona-Santos E, Machado LR, Hollox EJ. Understanding the Genomic Structure of Copy-Number Variation of the Low-Affinity Fcγ Receptor Region Allows Confirmation of the Association of FCGR3B Deletion with Rheumatoid Arthritis. Hum Mutat 2017; 38:390-399. [PMID: 27995740 PMCID: PMC5363352 DOI: 10.1002/humu.23159] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 12/14/2016] [Indexed: 11/23/2022]
Abstract
Fcγ receptors are a family of cell–surface receptors that are expressed by a host of different innate and adaptive immune cells, and mediate inflammatory responses by binding the Fc portion of immunoglobulin G. In humans, five low‐affinity receptors are encoded by the genes FCGR2A, FCGR2B, FCGR2C, FCGR3A, and FCGR3B, which are located in an 82.5‐kb segmental tandem duplication on chromosome 1q23.3, which shows extensive copy‐number variation (CNV). Deletions of FCGR3B have been suggested to increase the risk of inflammatory diseases such as systemic lupus erythematosus and rheumatoid arthritis (RA). In this study, we identify the deletion breakpoints of FCGR3B deletion alleles in the UK population and endogamous native American population, and show that some but not all alleles are likely to be identical‐by‐descent. We also localize a duplication breakpoint, confirming that the mechanism of CNV generation is nonallelic homologous recombination, and identify several alleles with gene conversion events using fosmid sequencing data. We use information on the structure of the deletion alleles to distinguish FCGR3B deletions from FCGR3A deletions in whole‐genome array comparative genomic hybridization (aCGH) data. Reanalysis of published aCGH data using this approach supports association of FCGR3B deletion with increased risk of RA in a large cohort of 1,982 cases and 3,271 controls (odds ratio 1.61, P = 2.9×10−3).
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Affiliation(s)
- Raheleh Rahbari
- Department of Genetics, University of Leicester, Leicester, United Kingdom.,Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Luciana W Zuccherato
- Department of Genetics, University of Leicester, Leicester, United Kingdom.,Departmento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Belinda Chihota
- School of Health, University of Northampton, Northampton, United Kingdom
| | - Hasret Ozturk
- Department of Genetics, University of Leicester, Leicester, United Kingdom
| | - Sara Saleem
- Department of Genetics, University of Leicester, Leicester, United Kingdom
| | - Eduardo Tarazona-Santos
- Departmento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Lee R Machado
- Department of Genetics, University of Leicester, Leicester, United Kingdom.,School of Health, University of Northampton, Northampton, United Kingdom
| | - Edward J Hollox
- Department of Genetics, University of Leicester, Leicester, United Kingdom
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29
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Barber JCK, Sharp AJ, Hollox EJ, Tyson C. Copy number variation of the REXO1L1 gene cluster; euchromatic deletion variant or susceptibility factor? Eur J Hum Genet 2016; 25:8-9. [PMID: 27485411 DOI: 10.1038/ejhg.2016.104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- John C K Barber
- Department of Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK.
| | - Andrew J Sharp
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York City, NY, USA
| | - Edward J Hollox
- Department of Genetics, University of Leicester, Leicester, UK
| | - Christine Tyson
- Department of Pathology, Cytogenetics Laboratory, Royal Columbian Hospital, New Westminster, British Columbia, Canada
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30
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Polley S, Cipriani V, Khan JC, Shahid H, Moore AT, Yates JRW, Hollox EJ. Analysis of copy number variation at DMBT1 and age-related macular degeneration. BMC Med Genet 2016; 17:44. [PMID: 27416785 PMCID: PMC4946147 DOI: 10.1186/s12881-016-0311-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 07/07/2016] [Indexed: 12/22/2022]
Abstract
BACKGROUND DMBT1 is a gene that shows extensive copy number variation (CNV) that alters the number of bacteria-binding domains in the protein and has been shown to activate the complement pathway. It lies next to the ARMS2/HTRA1 genes in a region of chromosome 10q26, where single nucleotide variants have been strongly associated with age-related macular degeneration (AMD), the commonest cause of blindness in Western populations. Complement activation is thought to be a key factor in the pathogenesis of this condition. We sought to investigate whether DMBT1 CNV plays any role in the susceptibility to AMD. METHODS We analysed long-range linkage disequilibrium of DMBT1 CNV1 and CNV2 with flanking single nucleotide polymorphisms (SNPs) using our previously published CNV and HapMap Phase 3 SNP data in the CEPH Europeans from Utah (CEU). We then typed a large cohort of 860 AMD patients and 419 examined age-matched controls for copy number at DMBT1 CNV1 and CNV2 and combined these data with copy numbers from a further 480 unexamined controls. RESULTS We found weak linkage disequilibrium between DMBT1 CNV1 and CNV2 with the SNPs rs1474526 and rs714816 in the HTRA1/ARMS2 region. By directly analysing copy number variation, we found no evidence of association of CNV1 or CNV2 with AMD. CONCLUSIONS We have shown that copy number variation at DMBT1 does not affect risk of developing age-related macular degeneration and can therefore be ruled out from future studies investigating the association of structural variation at 10q26 with AMD.
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Affiliation(s)
- Shamik Polley
- Department of Genetics, University of Leicester, Leicester, UK
| | - Valentina Cipriani
- UCL Institute of Ophthalmology, University College London, London, UK
- UCL Genetics Institute, University College London, London, UK
- Moorfields Eye Hospital, London, UK
| | - Jane C Khan
- Department of Medical Genetics, University of Cambridge, Cambridge, UK
- Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, Australia
- Department of Ophthalmology, Royal Perth Hospital, Perth, Australia
| | - Humma Shahid
- Department of Medical Genetics, University of Cambridge, Cambridge, UK
- Department of Ophthamology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Anthony T Moore
- UCL Institute of Ophthalmology, University College London, London, UK
- Moorfields Eye Hospital, London, UK
- Department of Ophthalmology UCSF Medical School, San Francisco, USA
| | - John R W Yates
- UCL Institute of Ophthalmology, University College London, London, UK
- Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Edward J Hollox
- Department of Genetics, University of Leicester, Leicester, UK.
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Hargreaves CE, Iriyama C, Rose-Zerilli MJJ, Nagelkerke SQ, Hussain K, Ganderton R, Lee C, Machado LR, Hollox EJ, Parker H, Latham KV, Kuijpers TW, Potter KN, Coupland SE, Davies A, Stackpole M, Oates M, Pettitt AR, Glennie MJ, Cragg MS, Strefford JC. Correction: Evaluation of High-Throughput Genomic Assays for the Fc Gamma Receptor Locus. PLoS One 2016; 11:e0145040. [PMID: 27007921 PMCID: PMC4805206 DOI: 10.1371/journal.pone.0145040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Hargreaves CE, Iriyama C, Rose-Zerilli MJJ, Nagelkerke SQ, Hussain K, Ganderton R, Lee C, Machado LR, Hollox EJ, Parker H, Latham KV, Kuijpers TW, Potter KN, Coupland SE, Davies A, Stackpole M, Oates M, Pettitt AR, Glennie MJ, Cragg MS, Strefford JC. Evaluation of High-Throughput Genomic Assays for the Fc Gamma Receptor Locus. PLoS One 2015; 10:e0142379. [PMID: 26545243 PMCID: PMC4636148 DOI: 10.1371/journal.pone.0142379] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 10/21/2015] [Indexed: 11/18/2022] Open
Abstract
Cancer immunotherapy has been revolutionised by the use monoclonal antibodies (mAb) that function through their interaction with Fc gamma receptors (FcγRs). The low-affinity FcγR genes are highly homologous, map to a complex locus at 1p23 and harbour single nucleotide polymorphisms (SNPs) and copy number variation (CNV) that can impact on receptor function and response to therapeutic mAbs. This complexity can hinder accurate characterisation of the locus. We therefore evaluated and optimised a suite of assays for the genomic analysis of the FcγR locus amenable to peripheral blood mononuclear cells and formalin-fixed paraffin-embedded (FFPE) material that can be employed in a high-throughput manner. Assessment of TaqMan genotyping for FCGR2A-131H/R, FCGR3A-158F/V and FCGR2B-232I/T SNPs demonstrated the need for additional methods to discriminate genotypes for the FCGR3A-158F/V and FCGR2B-232I/T SNPs due to sequence homology and CNV in the region. A multiplex ligation-dependent probe amplification assay provided high quality SNP and CNV data in PBMC cases, but there was greater data variability in FFPE material in a manner that was predicted by the BIOMED-2 multiplex PCR protocol. In conclusion, we have evaluated a suite of assays for the genomic analysis of the FcγR locus that are scalable for application in large clinical trials of mAb therapy. These assays will ultimately help establish the importance of FcγR genetics in predicting response to antibody therapeutics.
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Affiliation(s)
- Chantal E. Hargreaves
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, United Kingdom
| | - Chisako Iriyama
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, United Kingdom
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | | | - Sietse Q. Nagelkerke
- Department of Blood Cell Research, Sanquin Research and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, 1066 CX, Amsterdam, The Netherlands
| | - Khiyam Hussain
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, United Kingdom
| | - Rosalind Ganderton
- Molecular Pathology, University Hospital Southampton NHS Foundation Trust, Southampton, SO16 6YD, United Kingdom
| | - Charlotte Lee
- Molecular Pathology, University Hospital Southampton NHS Foundation Trust, Southampton, SO16 6YD, United Kingdom
| | - Lee R. Machado
- Department of Genetics, University of Leicester, Leicester, LE1 7RH, United Kingdom
- School of Health, University of Northampton, Northampton, NN2 7AL, United Kingdom
| | - Edward J. Hollox
- Department of Genetics, University of Leicester, Leicester, LE1 7RH, United Kingdom
| | - Helen Parker
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, United Kingdom
| | - Kate V. Latham
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, United Kingdom
| | - Taco W. Kuijpers
- Department of Blood Cell Research, Sanquin Research and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, 1066 CX, Amsterdam, The Netherlands
- Department of Pediatric Hematology, Immunology and Infectious Disease, Emma Children’s Hospital, Academic Medical Center, University of Amsterdam, 1105 AZ, Amsterdam, The Netherlands
| | - Kathleen N. Potter
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, United Kingdom
| | - Sarah E. Coupland
- Department of Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, University of Liverpool, Liverpool, L69 3GA, United Kingdom
| | - Andrew Davies
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, United Kingdom
| | - Michael Stackpole
- Department of Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, University of Liverpool, Liverpool, L69 3GA, United Kingdom
| | - Melanie Oates
- Department of Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, University of Liverpool, Liverpool, L69 3GA, United Kingdom
| | - Andrew R. Pettitt
- Department of Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, University of Liverpool, Liverpool, L69 3GA, United Kingdom
| | - Martin J. Glennie
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, United Kingdom
| | - Mark S. Cragg
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, United Kingdom
| | - Jonathan C. Strefford
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, United Kingdom
- * E-mail:
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Forni D, Martin D, Abujaber R, Sharp AJ, Sironi M, Hollox EJ. Determining multiallelic complex copy number and sequence variation from high coverage exome sequencing data. BMC Genomics 2015; 16:891. [PMID: 26526070 PMCID: PMC4630827 DOI: 10.1186/s12864-015-2123-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 10/22/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Copy number variation (CNV) is a major component of genomic variation, yet methods to accurately type genomic CNV lag behind methods that type single nucleotide variation. High-throughput sequencing can contribute to these methods by using sequence read depth, which takes the number of reads that map to a given part of the reference genome as a proxy for copy number of that region, and compares across samples. Furthermore, high-throughput sequencing also provides information on the sequence differences between copies within and between individuals. METHODS In this study we use high-coverage phase 3 exome sequences of the 1000 Genomes project to infer diploid copy number of the beta-defensin genomic region, a well-studied CNV that carries several beta-defensin genes involved in the antimicrobial response, signalling, and fertility. We also use these data to call sequence variants, a particular challenge given the multicopy nature of the region. RESULTS We confidently call copy number and sequence variation of the beta-defensin genes on 1285 samples from 26 global populations, validate copy number using Nanostring nCounter and triplex paralogue ratio test data. We use the copy number calls to verify the genomic extent of the CNV and validate sequence calls using analysis of cloned PCR products. We identify novel variation, mostly individually rare, predicted to alter amino-acid sequence in the beta-defensin genes. Such novel variants may alter antimicrobial properties or have off-target receptor interactions, and may contribute to individuality in immunological response and fertility. CONCLUSIONS Given that 81% of identified sequence variants were not previously in dbSNP, we show that sequence variation in multiallelic CNVs represent an unappreciated source of genomic diversity.
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Affiliation(s)
- Diego Forni
- Department of Genetics, University of Leicester, Leicester, UK.,Bioinformatics, Scientific Institute IRCCS E.MEDEA, Bosisio, Parini, Italy
| | - Diana Martin
- Department of Genetics, University of Leicester, Leicester, UK
| | - Razan Abujaber
- Department of Genetics, University of Leicester, Leicester, UK
| | - Andrew J Sharp
- Department of Genetics and Genome Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Manuela Sironi
- Bioinformatics, Scientific Institute IRCCS E.MEDEA, Bosisio, Parini, Italy
| | - Edward J Hollox
- Department of Genetics, University of Leicester, Leicester, UK.
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Hargreaves CE, Rose-Zerilli MJJ, Machado LR, Iriyama C, Hollox EJ, Cragg MS, Strefford JC. Fcγ receptors: genetic variation, function, and disease. Immunol Rev 2015; 268:6-24. [DOI: 10.1111/imr.12341] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Chantal E. Hargreaves
- Cancer Genomics Group; Cancer Sciences; Faculty of Medicine; University of Southampton; Southampton UK
- Antibody and Vaccine Group; Cancer Sciences; Faculty of Medicine; University of Southampton; Southampton UK
| | | | - Lee R. Machado
- Department of Genetics; University of Leicester; Leicester UK
- School of Health; University of Northampton; Northampton UK
| | - Chisako Iriyama
- Department of Hematology and Oncology; Nagoya University Graduate School of Medicine; Nagoya Japan
| | | | - Mark S. Cragg
- Antibody and Vaccine Group; Cancer Sciences; Faculty of Medicine; University of Southampton; Southampton UK
| | - Jonathan C. Strefford
- Cancer Genomics Group; Cancer Sciences; Faculty of Medicine; University of Southampton; Southampton UK
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Pal RP, Kockelbergh RC, Pringle JH, Cresswell L, Hew R, Dormer JP, Cooper C, Mellon JK, Barwell JG, Hollox EJ. Immunocytochemical detection of ERG expression in exfoliated urinary cells identifies with high specificity patients with prostate cancer. BJU Int 2015; 117:686-96. [DOI: 10.1111/bju.13184] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Raj P. Pal
- Department of Cancer Studies and Molecular Medicine; University of Leicester; Leicester UK
- Department of Urology; University Hospitals of Leicester NHS Trust; Leicester UK
| | - Roger C. Kockelbergh
- Department of Urology; University Hospitals of Leicester NHS Trust; Leicester UK
| | - John Howard Pringle
- Department of Cancer Studies and Molecular Medicine; University of Leicester; Leicester UK
| | - Lara Cresswell
- Department of Cytogenetics; University Hospitals of Leicester NHS Trust; Leicester UK
| | - Roger Hew
- Department of Cellular Pathology; University Hospitals of Leicester NHS Trust; Leicester UK
| | - John P. Dormer
- Department of Cellular Pathology; University Hospitals of Leicester NHS Trust; Leicester UK
| | - Colin Cooper
- Department of Cancer Genetics; University of East Anglia; Norwich UK
| | - John Kilian Mellon
- Department of Urology; University Hospitals of Leicester NHS Trust; Leicester UK
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Haridan US, Mokhtar U, Machado LR, Abdul Aziz AT, Shueb RH, Zaid M, Sim B, Mustafa M, Nik Yusof NK, Lee CKC, Abu Bakar S, AbuBakar S, Hollox EJ, Boon Peng H. A comparison of assays for accurate copy number measurement of the low-affinity Fc gamma receptor genes FCGR3A and FCGR3B. PLoS One 2015; 10:e0116791. [PMID: 25594501 PMCID: PMC4297192 DOI: 10.1371/journal.pone.0116791] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 12/16/2014] [Indexed: 11/18/2022] Open
Abstract
The FCGR3 locus encoding the low affinity activating receptor FcγRIII, plays a vital role in immunity triggered by cellular effector and regulatory functions. Copy number of the genes FCGR3A and FCGR3B has previously been reported to affect susceptibility to several autoimmune diseases and chronic inflammatory conditions. However, such genetic association studies often yield inconsistent results; hence require assays that are robust with low error rate. We investigated the accuracy and efficiency in estimating FCGR3 CNV by comparing Sequenom MassARRAY and paralogue ratio test-restriction enzyme digest variant ratio (PRT-REDVR). In addition, since many genetic association studies of FCGR3B CNV were carried out using real-time quantitative PCR, we have also included the evaluation of that method’s performance in estimating the multi-allelic CNV of FCGR3B. The qPCR assay exhibited a considerably broader distribution of signal intensity, potentially introducing error in estimation of copy number and higher false positive rates. Both Sequenom and PRT-REDVR showed lesser systematic bias, but Sequenom skewed towards copy number normal (CN = 2). The discrepancy between Sequenom and PRT-REDVR might be attributed either to batch effects noise in individual measurements. Our study suggests that PRT-REDVR is more robust and accurate in genotyping the CNV of FCGR3, but highlights the needs of multiple independent assays for extensive validation when performing a genetic association study with multi-allelic CNVs.
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Affiliation(s)
- Umi Shakina Haridan
- Institute of Medical Molecular Biotechnology (IMMB), Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, Selangor, Malaysia
| | - Umairah Mokhtar
- Institute of Medical Molecular Biotechnology (IMMB), Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, Selangor, Malaysia
| | - Lee R. Machado
- Department of Genetics, University of Leicester, Leicester, United Kingdom
| | - Abu Thalhah Abdul Aziz
- Institute of Medical Molecular Biotechnology (IMMB), Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, Selangor, Malaysia
| | - Rafidah Hanim Shueb
- Department of Microbiology and Parasitology, School of Medical Science, Health Campus, Universiti Sains Malaysia, Kubang Kerian, Kelantan, Malaysia
| | - Masliza Zaid
- Department of Medicine, Hospital Sungai Buloh, Jalan Hospital, Sungai Buloh, Selangor, Malaysia
| | - Benedict Sim
- Department of Medicine, Hospital Sungai Buloh, Jalan Hospital, Sungai Buloh, Selangor, Malaysia
| | - Mahiran Mustafa
- Hospital Raja Perempuan Zainab II, Kota Bharu, Kelantan, Malaysia
| | | | - Christopher K. C. Lee
- Department of Medicine, Hospital Sungai Buloh, Jalan Hospital, Sungai Buloh, Selangor, Malaysia
| | - Suhaili Abu Bakar
- Department of Biomedical Science, Faculty of Medicine and Health Science, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Sazaly AbuBakar
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
- Tropical Infectious Disease Research and Education Centre, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Edward J. Hollox
- Department of Genetics, University of Leicester, Leicester, United Kingdom
| | - Hoh Boon Peng
- Institute of Medical Molecular Biotechnology (IMMB), Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, Selangor, Malaysia
- * E-mail:
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Ottolini B, Hornsby MJ, Abujaber R, MacArthur JAL, Badge RM, Schwarzacher T, Albertson DG, Bevins CL, Solnick JV, Hollox EJ. Evidence of convergent evolution in humans and macaques supports an adaptive role for copy number variation of the β-defensin-2 gene. Genome Biol Evol 2014; 6:3025-38. [PMID: 25349268 PMCID: PMC4255768 DOI: 10.1093/gbe/evu236] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
β-defensins are a family of important peptides of innate immunity, involved in host defense, immunomodulation, reproduction, and pigmentation. Genes encoding β-defensins show evidence of birth-and-death evolution, adaptation by amino acid sequence changes, and extensive copy number variation (CNV) within humans and other species. The role of CNV in the adaptation of β-defensins to new functions remains unclear, as does the adaptive role of CNV in general. Here, we fine-map CNV of a cluster of β-defensins in humans and rhesus macaques. Remarkably, we found that the structure of the CNV is different between primates, with distinct mutational origins and CNV boundaries defined by retroviral long terminal repeat elements. Although the human β-defensin CNV region is 322 kb and encompasses several genes, including β-defensins, a long noncoding RNA gene, and testes-specific zinc-finger transcription factors, the orthologous region in the rhesus macaque shows CNV of a 20-kb region, containing only a single gene, the ortholog of the human β-defensin-2 gene. Despite its independent origins, the range of gene copy numbers in the rhesus macaque is similar to humans. In addition, the rhesus macaque gene has been subject to divergent positive selection at the amino acid level following its initial duplication event between 3 and 9.5 Ma, suggesting adaptation of this gene as the macaque successfully colonized novel environments outside Africa. Therefore, the molecular phenotype of β-defensin-2 CNV has undergone convergent evolution, and this gene shows evidence of adaptation at the amino acid level in rhesus macaques.
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Affiliation(s)
| | - Michael J Hornsby
- Department of Microbiology and Immunology, University of California Davis School of Medicine
| | - Razan Abujaber
- Department of Genetics, University of Leicester, United Kingdom
| | - Jacqueline A L MacArthur
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco Present address: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Richard M Badge
- Department of Genetics, University of Leicester, United Kingdom
| | | | - Donna G Albertson
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco Present address: Bluestone Center for Clinical Research, New York University College of Dentistry, New York, New York
| | - Charles L Bevins
- Department of Microbiology and Immunology, University of California Davis School of Medicine
| | - Jay V Solnick
- Department of Microbiology and Immunology, University of California Davis School of Medicine Department of Medicine, Center for Comparative Medicine, and the California National Primate Research Center, University of California
| | - Edward J Hollox
- Department of Genetics, University of Leicester, United Kingdom
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Jones EA, Kananurak A, Bevins CL, Hollox EJ, Bakaletz LO. Copy number variation of the beta defensin gene cluster on chromosome 8p influences the bacterial microbiota within the nasopharynx of otitis-prone children. PLoS One 2014; 9:e98269. [PMID: 24867293 PMCID: PMC4035277 DOI: 10.1371/journal.pone.0098269] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 04/29/2014] [Indexed: 12/13/2022] Open
Abstract
As there is increasing evidence that aberrant defensin expression is related to susceptibility for infectious disease and inflammatory disorders, we sought to determine if copy number of the beta-defensin gene cluster located on chromosome 8p23.1 (DEFB107, 106, 105, 104, 103, DEFB4 and SPAG11), that shows copy number variation as a block, was associated with susceptibility to otitis media (OM). The gene DEFB103 within this complex encodes human beta defensin-3 (hBD-3), an antimicrobial peptide (AP) expressed by epithelial cells that line the mammalian airway, important for defense of mucosal surfaces and previously shown to have bactericidal activity in vitro against multiple human pathogens, including the three that predominate in OM. To this end, we conducted a retrospective case-control study of 113 OM prone children and 267 controls aged five to sixty months. We identified the copy number of the above defined beta-defensin gene cluster (DEFB-CN) in each study subject by paralogue ratio assays. The mean DEFB-CN was indistinguishable between subjects classified as OM prone based on a recent history of multiple episodes of OM and control subjects who had no history of OM (4.4 ± 0.96 versus 4.4 ± 1.08, respectively: Odds Ratio [OR]: 1.16 (95% CI: 0.61, 2.20). Despite a lack of direct association, we observed a statistically significant correlation between DEFB-CN and nasopharyngeal bacterial colonization patterns. Collectively, our findings suggested that susceptibility to OM might be mediated by genetic variation among individuals, wherein a DEFB-CN less than 4 exerts a marked influence on the microbiota of the nasopharynx, specifically with regard to colonization by the three predominant bacterial pathogens of OM.
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Affiliation(s)
- Eric A. Jones
- Center for Microbial Pathogenesis, Department of Pediatrics, College of Medicine, The Research Institute at Nationwide Children's Hospital, The Ohio State University, Columbus, Ohio, United States of America
| | - Anchasa Kananurak
- Department of Microbiology and Immunology, School of Medicine, University of California Davis, Davis, California, United States of America
| | - Charles L. Bevins
- Department of Microbiology and Immunology, School of Medicine, University of California Davis, Davis, California, United States of America
| | - Edward J. Hollox
- Department of Genetics, University of Leicester, Leicester, United Kingdom
| | - Lauren O. Bakaletz
- Center for Microbial Pathogenesis, Department of Pediatrics, College of Medicine, The Research Institute at Nationwide Children's Hospital, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail:
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Wain LV, Sayers I, Soler Artigas M, Portelli MA, Zeggini E, Obeidat M, Sin DD, Bossé Y, Nickle D, Brandsma CA, Malarstig A, Vangjeli C, Jelinsky SA, John S, Kilty I, McKeever T, Shrine NRG, Cook JP, Patel S, Spector TD, Hollox EJ, Hall IP, Tobin MD. Whole exome re-sequencing implicates CCDC38 and cilia structure and function in resistance to smoking related airflow obstruction. PLoS Genet 2014; 10:e1004314. [PMID: 24786987 PMCID: PMC4006731 DOI: 10.1371/journal.pgen.1004314] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 03/06/2014] [Indexed: 11/19/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a leading cause of global morbidity and mortality and, whilst smoking remains the single most important risk factor, COPD risk is heritable. Of 26 independent genomic regions showing association with lung function in genome-wide association studies, eleven have been reported to show association with airflow obstruction. Although the main risk factor for COPD is smoking, some individuals are observed to have a high forced expired volume in 1 second (FEV1) despite many years of heavy smoking. We hypothesised that these "resistant smokers" may harbour variants which protect against lung function decline caused by smoking and provide insight into the genetic determinants of lung health. We undertook whole exome re-sequencing of 100 heavy smokers who had healthy lung function given their age, sex, height and smoking history and applied three complementary approaches to explore the genetic architecture of smoking resistance. Firstly, we identified novel functional variants in the "resistant smokers" and looked for enrichment of these novel variants within biological pathways. Secondly, we undertook association testing of all exonic variants individually with two independent control sets. Thirdly, we undertook gene-based association testing of all exonic variants. Our strongest signal of association with smoking resistance for a non-synonymous SNP was for rs10859974 (P = 2.34 × 10(-4)) in CCDC38, a gene which has previously been reported to show association with FEV1/FVC, and we demonstrate moderate expression of CCDC38 in bronchial epithelial cells. We identified an enrichment of novel putatively functional variants in genes related to cilia structure and function in resistant smokers. Ciliary function abnormalities are known to be associated with both smoking and reduced mucociliary clearance in patients with COPD. We suggest that genetic influences on the development or function of cilia in the bronchial epithelium may affect growth of cilia or the extent of damage caused by tobacco smoke.
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Affiliation(s)
- Louise V. Wain
- University of Leicester, Department of Health Sciences, Leicester, United Kingdom
- * E-mail:
| | - Ian Sayers
- Division of Respiratory Medicine, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom
| | - María Soler Artigas
- University of Leicester, Department of Health Sciences, Leicester, United Kingdom
| | - Michael A. Portelli
- Division of Respiratory Medicine, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom
| | | | - Ma'en Obeidat
- University of British Columbia Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, Canada
| | - Don D. Sin
- University of British Columbia Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, Canada
| | - Yohan Bossé
- Institut universitaire de cardiologie et de pneumologie de Québec, Department of Molecular Medicine, Laval University, Québec, Canada
| | - David Nickle
- Merck Research Laboratories, Boston, Massachusetts, United States of America
- Merck, Rahway, New Jersey, United States of America
| | - Corry-Anke Brandsma
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, GRIAC Research Institute, Groningen, The Netherlands
| | | | | | - Scott A. Jelinsky
- Pfizer Worldwide R&D, Cambridge, Massachusetts, United States of America
| | - Sally John
- Pfizer Worldwide R&D, Cambridge, Massachusetts, United States of America
| | - Iain Kilty
- Pfizer Worldwide R&D, Cambridge, Massachusetts, United States of America
| | - Tricia McKeever
- School of Community Health Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Nick R. G. Shrine
- University of Leicester, Department of Health Sciences, Leicester, United Kingdom
| | - James P. Cook
- University of Leicester, Department of Health Sciences, Leicester, United Kingdom
| | - Shrina Patel
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Tim D. Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Edward J. Hollox
- University of Leicester, Department of Genetics, Leicester, United Kingdom
| | - Ian P. Hall
- Division of Respiratory Medicine, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom
| | - Martin D. Tobin
- University of Leicester, Department of Health Sciences, Leicester, United Kingdom
- National Institute for Health Research (NIHR) Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, United Kingdom
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Vittori A, Breda C, Repici M, Orth M, Roos RAC, Outeiro TF, Giorgini F, Hollox EJ. Copy-number variation of the neuronal glucose transporter gene SLC2A3 and age of onset in Huntington's disease. Hum Mol Genet 2014; 23:3129-37. [PMID: 24452335 PMCID: PMC4030768 DOI: 10.1093/hmg/ddu022] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Huntington's disease (HD) is a devastating neurodegenerative disorder which is inherited in an autosomal dominant manner. HD is caused by a trinucleotide CAG repeat expansion that encodes a polyglutamine stretch in the huntingtin (HTT) protein. Mutant HTT expression leads to a myriad of cellular dysfunctions culminating in neuronal loss and consequent motor, cognitive and psychiatric disturbances in HD patients. The length of the CAG repeat is inversely correlated with age of onset (AO) in HD patients, while environmental and genetic factors can further modulate this parameter. Here, we explored whether the recently described copy-number variation (CNV) of the gene SLC2A3-which encodes the neuronal glucose transporter GLUT3-could modulate AO in HD. Strikingly, we found that increased dosage of SLC2A3 delayed AO in an HD cohort of 987 individuals, and that this correlated with increased levels of GLUT3 in HD patient cells. To our knowledge this is the first time that CNV of a candidate gene has been found to modulate HD pathogenesis. Furthermore, we found that increasing dosage of Glut1-the Drosophila melanogaster homologue of this glucose transporter-ameliorated HD-relevant phenotypes in fruit flies, including neurodegeneration and life expectancy. As alterations in glucose metabolism have been implicated in HD pathogenesis, this study may have important therapeutic relevance for HD.
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Affiliation(s)
- Angelica Vittori
- Department of Genetics, University of Leicester, Leicester, UK Cell and Molecular Neuroscience Unit, Instituto de Medicina Molecular, Lisbon, Portugal
| | - Carlo Breda
- Department of Genetics, University of Leicester, Leicester, UK
| | | | - Michael Orth
- Department of Neurology, University of Ulm, Ulm, Germany
| | - Raymund A C Roos
- Department of Neurology, Leiden University Medical Center, Leiden, The Netherlands
| | - Tiago F Outeiro
- Cell and Molecular Neuroscience Unit, Instituto de Medicina Molecular, Lisbon, Portugal Instituto de Fisiologia, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal Department of NeuroDegeneration and Restorative Research, University Medical Center Göttingen, Göttingen, Germany
| | | | - Edward J Hollox
- Department of Genetics, University of Leicester, Leicester, UK
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Wain LV, Odenthal-Hesse L, Abujaber R, Sayers I, Beardsmore C, Gaillard EA, Chappell S, Dogaru CM, McKeever T, Guetta-Baranes T, Kalsheker N, Kuehni CE, Hall IP, Tobin MD, Hollox EJ. Copy number variation of the beta-defensin genes in europeans: no supporting evidence for association with lung function, chronic obstructive pulmonary disease or asthma. PLoS One 2014; 9:e84192. [PMID: 24404154 PMCID: PMC3880289 DOI: 10.1371/journal.pone.0084192] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 11/13/2013] [Indexed: 12/23/2022] Open
Abstract
Lung function measures are heritable, predict mortality and are relevant in diagnosis of chronic obstructive pulmonary disease (COPD). COPD and asthma are diseases of the airways with major public health impacts and each have a heritable component. Genome-wide association studies of SNPs have revealed novel genetic associations with both diseases but only account for a small proportion of the heritability. Complex copy number variation may account for some of the missing heritability. A well-characterised genomic region of complex copy number variation contains beta-defensin genes (DEFB103, DEFB104 and DEFB4), which have a role in the innate immune response. Previous studies have implicated these and related genes as being associated with asthma or COPD. We hypothesised that copy number variation of these genes may play a role in lung function in the general population and in COPD and asthma risk. We undertook copy number typing of this locus in 1149 adult and 689 children using a paralogue ratio test and investigated association with COPD, asthma and lung function. Replication of findings was assessed in a larger independent sample of COPD cases and smoking controls. We found evidence for an association of beta-defensin copy number with COPD in the adult cohort (OR = 1.4, 95%CI:1.02-1.92, P = 0.039) but this finding, and findings from a previous study, were not replicated in a larger follow-up sample(OR = 0.89, 95%CI:0.72-1.07, P = 0.217). No robust evidence of association with asthma in children was observed. We found no evidence for association between beta-defensin copy number and lung function in the general populations. Our findings suggest that previous reports of association of beta-defensin copy number with COPD should be viewed with caution. Suboptimal measurement of copy number can lead to spurious associations. Further beta-defensin copy number measurement in larger sample sizes of COPD cases and children with asthma are needed.
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Affiliation(s)
- Louise V. Wain
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
| | | | - Razan Abujaber
- Department of Genetics, University of Leicester, Leicester, United Kingdom
| | - Ian Sayers
- Division of Respiratory Medicine, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Caroline Beardsmore
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, United Kingdom
- Institute for Lung Health, National Institute for Health Research (NIHR) Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, United Kingdom
| | - Erol A. Gaillard
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, United Kingdom
- Institute for Lung Health, National Institute for Health Research (NIHR) Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, United Kingdom
| | - Sally Chappell
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Cristian M. Dogaru
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Tricia McKeever
- School of Community Health Sciences, University of Nottingham, Nottingham, United Kingdom
| | | | - Noor Kalsheker
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Claudia E. Kuehni
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Ian P. Hall
- Division of Respiratory Medicine, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Martin D. Tobin
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
- Department of Genetics, University of Leicester, Leicester, United Kingdom
- Institute for Lung Health, National Institute for Health Research (NIHR) Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, United Kingdom
| | - Edward J. Hollox
- Department of Genetics, University of Leicester, Leicester, United Kingdom
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43
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Aklillu E, Odenthal-Hesse L, Bowdrey J, Habtewold A, Ngaimisi E, Yimer G, Amogne W, Mugusi S, Minzi O, Makonnen E, Janabi M, Mugusi F, Aderaye G, Hardwick R, Fu B, Viskaduraki M, Yang F, Hollox EJ. CCL3L1 copy number, HIV load, and immune reconstitution in sub-Saharan Africans. BMC Infect Dis 2013; 13:536. [PMID: 24219137 PMCID: PMC3829100 DOI: 10.1186/1471-2334-13-536] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 10/28/2013] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The role of copy number variation of the CCL3L1 gene, encoding MIP1α, in contributing to the host variation in susceptibility and response to HIV infection is controversial. Here we analyse a sub-Saharan African cohort from Tanzania and Ethiopia, two countries with a high prevalence of HIV-1 and a high co-morbidity of HIV with tuberculosis. METHODS We use a form of quantitative PCR called the paralogue ratio test to determine CCL3L1 gene copy number in 1134 individuals and validate our copy number typing using array comparative genomic hybridisation and fiber-FISH. RESULTS We find no significant association of CCL3L1 gene copy number with HIV load in antiretroviral-naïve patients prior to initiation of combination highly active anti-retroviral therapy. However, we find a significant association of low CCL3L1 gene copy number with improved immune reconstitution following initiation of highly active anti-retroviral therapy (p = 0.012), replicating a previous study. CONCLUSIONS Our work supports a role for CCL3L1 copy number in immune reconstitution following antiretroviral therapy in HIV, and suggests that the MIP1α -CCR5 axis might be targeted to aid immune reconstitution.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Edward J Hollox
- Department of Genetics, University of Leicester, University Road, Leicester, LE1 7RH, UK.
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Machado LR, Bowdrey J, Ngaimisi E, Habtewold A, Minzi O, Makonnen E, Yimer G, Amogne W, Mugusi S, Janabi M, Aderaye G, Mugusi F, Viskaduraki M, Aklillu E, Hollox EJ. Copy number variation of Fc gamma receptor genes in HIV-infected and HIV-tuberculosis co-infected individuals in sub-Saharan Africa. PLoS One 2013; 8:e78165. [PMID: 24250791 PMCID: PMC3826734 DOI: 10.1371/journal.pone.0078165] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 09/14/2013] [Indexed: 11/21/2022] Open
Abstract
AIDS, caused by the retrovirus HIV, remains the largest cause of morbidity in sub-Saharan Africa yet almost all genetic studies have focused on cohorts from Western countries. HIV shows high co-morbidity with tuberculosis (TB), as HIV stimulates the reactivation of latent tuberculosis (TB). Recent clinical trials suggest that an effective anti-HIV response correlates with non-neutralising antibodies. Given that Fcγ receptors are critical in mediating the non-neutralising effects of antibodies, analysis of the extensive variation at Fcγ receptor genes is important. Single nucleotide variation and copy number variation (CNV) of Fcγ receptor genes affects the expression profile, activatory/inhibitory balance, and IgG affinity of the Fcγ receptor repertoire of each individual. In this study we investigated whether CNV of FCGR2C, FCGR3A and FCGR3B as well as the HNA1 allotype of FCGR3B is associated with HIV load, response to highly-active antiretroviral therapy (HAART) and co-infection with TB. We confirmed an effect of TB-co-infection status on HIV load and response to HAART, but no conclusive effect of the genetic variants we tested. We observed a small effect, in Ethiopians, of FCGR3B copy number, where deletion was more frequent in HIV-TB co-infected patients than those infected with HIV alone.
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Affiliation(s)
- Lee R. Machado
- Department of Genetics, University of Leicester, Leicester, United Kingdom
| | - Jennifer Bowdrey
- Department of Genetics, University of Leicester, Leicester, United Kingdom
| | - Eliford Ngaimisi
- Division of Clinical Pharmacology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- Unit of Pharmacology, School of Pharmacy, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Abiy Habtewold
- Division of Clinical Pharmacology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Pharmacology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Omary Minzi
- Unit of Pharmacology, School of Pharmacy, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Eyasu Makonnen
- Department of Pharmacology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Getnet Yimer
- Division of Clinical Pharmacology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Pharmacology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Wondwossen Amogne
- Internal Medicine, Addis Ababa University, Addis Ababa, Ethiopia
- Institution of Medicine, Unit of Infectious Diseases, Karolinska Institutet, Karolinska University Hospital, Huddinge, Sweden
| | - Sabina Mugusi
- Department of Internal Medicine, Muhimbili National Hospital, Dar es Salaam, Tanzania
| | - Mohammed Janabi
- Department of Internal Medicine, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Getachew Aderaye
- Internal Medicine, Addis Ababa University, Addis Ababa, Ethiopia
| | - Ferdinand Mugusi
- Department of Internal Medicine, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Maria Viskaduraki
- College of Medicine, Biological Sciences and Psychology, University of Leicester, Leicester, United Kingdom
| | - Eleni Aklillu
- Division of Clinical Pharmacology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Edward J. Hollox
- Department of Genetics, University of Leicester, Leicester, United Kingdom
- * E-mail:
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45
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Veal CD, Xu H, Reekie K, Free R, Hardwick RJ, McVey D, Brookes AJ, Hollox EJ, Talbot CJ. Automated design of paralogue ratio test assays for the accurate and rapid typing of copy number variation. ACTA ACUST UNITED AC 2013; 29:1997-2003. [PMID: 23742985 PMCID: PMC3722521 DOI: 10.1093/bioinformatics/btt330] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Motivation: Genomic copy number variation (CNV) can influence susceptibility to common diseases. High-throughput measurement of gene copy number on large numbers of samples is a challenging, yet critical, stage in confirming observations from sequencing or array Comparative Genome Hybridization (CGH). The paralogue ratio test (PRT) is a simple, cost-effective method of accurately determining copy number by quantifying the amplification ratio between a target and reference amplicon. PRT has been successfully applied to several studies analyzing common CNV. However, its use has not been widespread because of difficulties in assay design. Results: We present PRTPrimer (www.prtprimer.org) software for automated PRT assay design. In addition to stand-alone software, the web site includes a database of pre-designed assays for the human genome at an average spacing of 6 kb and a web interface for custom assay design. Other reference genomes can also be analyzed through local installation of the software. The usefulness of PRTPrimer was tested within known CNV, and showed reproducible quantification. This software and database provide assays that can rapidly genotype CNV, cost-effectively, on a large number of samples and will enable the widespread adoption of PRT. Availability: PRTPrimer is available in two forms: a Perl script (version 5.14 and higher) that can be run from the command line on Linux systems and as a service on the PRTPrimer web site (www.prtprimer.org). Contact:cjt14@le.ac.uk Supplementary Information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Colin D Veal
- Department of Genetics, University of Leicester, Leicester, UK
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46
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Vittori A, Orth M, Roos RAC, Outeiro TF, Giorgini F, Hollox EJ. β-Defensin Genomic Copy Number Does Not Influence the Age of Onset in Huntington's Disease. J Huntingtons Dis 2013; 2:107-124. [PMID: 24587836 DOI: 10.3233/jhd-130047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND Huntington's disease (HD) is an autosomal dominant neurodegenerative disorder caused by the abnormal expansion of a CAG triplet repeat tract in the huntingtin gene. While the length of this CAG expansion is the major determinant of the age of onset (AO), other genetic factors have also been shown to play a modulatory role. Recent evidence suggests that neuroinflammation is a pivotal factor in the pathogenesis of HD, and that targeting this process may have important therapeutic ramifications. The human β-defensin 2 (hBD2) - encoded by DEFB4 - is an antimicrobial peptide that exhibits inducible expression in astrocytes during inflammation and is an important regulator of innate and adaptive immune response. Therefore, DEFB4 may contribute to the neuroinflammatory processes observed in HD. OBJECTIVE In this study we tested the hypothesis that copy number variation (CNV) of the β-defensin region, including DEFB4, modifies the AO in HD. METHODS AND RESULTS We genotyped β-defensin CNV in 490 HD individuals using the paralogue ratio test and found no association between β-defensin CNV and onset of HD. CONCLUSIONS We conclude that it is unlikely that DEFB4 plays a role in HD pathogenesis.
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Affiliation(s)
- Angelica Vittori
- Department of Genetics, University of Leicester, Leicester, UK ; Cell and Molecular Neuroscience Unit, Instituto de Medicina Molecular, Lisboa, Portugal
| | - Michael Orth
- Department of Neurology, University of Ulm, Ulm, Germany
| | - Raymund A C Roos
- Leiden University Medical Center, Department of Neurology, The Netherlands
| | - Tiago F Outeiro
- Cell and Molecular Neuroscience Unit, Instituto de Medicina Molecular, Lisboa, Portugal ; Faculdade de Medicina da Universidade de Lisboa, Instituto de Fisiologia, Lisboa, Portugal ; University Medical Center Göttingen, Department of NeuroDegeneration and Restorative Research, Göttingen, Germany
| | | | - Edward J Hollox
- Department of Genetics, University of Leicester, Leicester, UK
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47
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Hardwick RJ, Amogne W, Mugusi S, Yimer G, Ngaimisi E, Habtewold A, Minzi O, Makonnen E, Janabi M, Machado LR, Viskaduraki M, Mugusi F, Aderaye G, Lindquist L, Hollox EJ, Aklillu E. β-defensin genomic copy number is associated with HIV load and immune reconstitution in sub-saharan Africans. J Infect Dis 2012; 206:1012-9. [PMID: 22837491 DOI: 10.1093/infdis/jis448] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
AIDS, caused by the retrovirus human immunodeficiency virus (HIV), is the leading cause of death of economically active people (age, 15-59 years) in sub-Saharan Africa. The host genetic variability of immune response to HIV and immune reconstitution following initiation of highly active antiretroviral therapy (HAART) is poorly understood. Here we focused on copy number variation of the β-defensin genes, which have been shown to have anti-HIV activity, and are important chemoattractants for Th17 lymphocytes via the chemokine receptor CCR6. We determined β-defensin gene copy number for 1002 Ethiopian and Tanzanian patients. We show that higher β-defensin copy number variation is associated with increased HIV load prior to HAART (P=.005) and poor immune reconstitution following initiation of HAART (P=.003). We suggest a model where variable amounts of β-defensin expression by mucosal cells, due to gene copy number variation, alters the efficacy of recruitment of Th17 lymphocytes to the site of infection, altering the dynamics of infection.
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48
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Machado LR, Hardwick RJ, Bowdrey J, Bogle H, Knowles TJ, Sironi M, Hollox EJ. Evolutionary history of copy-number-variable locus for the low-affinity Fcγ receptor: mutation rate, autoimmune disease, and the legacy of helminth infection. Am J Hum Genet 2012; 90:973-85. [PMID: 22608500 DOI: 10.1016/j.ajhg.2012.04.018] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Revised: 03/22/2012] [Accepted: 04/10/2012] [Indexed: 11/18/2022] Open
Abstract
Both sequence variation and copy-number variation (CNV) of the genes encoding receptors for immunoglobulin G (Fcγ receptors) have been genetically and functionally associated with a number of autoimmune diseases. However, the molecular nature and evolutionary context of this variation is unknown. Here, we describe the structure of the CNV, estimate its mutation rate and diversity, and place it in the context of the known functional alloantigen variation of these genes. Deletion of Fcγ receptor IIIB, associated with systemic lupus erythematosus, is a result of independent nonallelic homologous recombination events with a frequency of approximately 0.1%. We also show that pathogen diversity, in particular helminth diversity, has played a critical role in shaping the functional variation at these genes both between mammalian species and between human populations. Positively selected amino acids are involved in the interaction with IgG and include some amino acids that are known polymorphic alloantigens in humans. This supports a genetic contribution to the hygiene hypothesis, which states that past evolution in the context of helminth diversity has left humans with an array of susceptibility alleles for autoimmune disease in the context of a helminth-free environment. This approach shows the link between pathogens and autoimmune disease at the genetic level and provides a strategy for interrogating the genetic variation underlying autoimmune-disease risk and infectious-disease susceptibility.
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Abstract
Recent work has emphasised that the human genome is not simple and static, but complex and dynamic. This review focuses on the regions that are particularly hard to dissect and analyse, yet hold clues to how the genome changes during evolution and disease. I begin by summarising recent key advances in the understanding of the variable structure of our genome, and then I discuss a medley of methods that may allow us to analyse this structure in fine detail. In the final part, I describe potential future developments in this field, and make an argument that, just as we routinely genotype single-nucleotide polymorphisms now and will routinely re-sequence genomes in the near future, we should be aiming to physically re-map the individual human genome for each individual we study.
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Affiliation(s)
- Edward J Hollox
- Department of Genetics, University of Leicester, Adrian Building, University Road, Leicester, UK.
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50
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Tollner TL, Venners SA, Hollox EJ, Yudin AI, Liu X, Tang G, Xing H, Kays RJ, Lau T, Overstreet JW, Xu X, Bevins CL, Cherr GN. A common mutation in the defensin DEFB126 causes impaired sperm function and subfertility. Sci Transl Med 2012; 3:92ra65. [PMID: 21775668 DOI: 10.1126/scitranslmed.3002289] [Citation(s) in RCA: 110] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A glycosylated polypeptide, β-defensin 126 (DEFB126), derived from the epididymis and adsorbed onto the sperm surface, has been implicated in immunoprotection and efficient movement of sperm in mucosal fluids of the female reproductive tract. Here, we report a sequence variant in DEFB126 that has a two-nucleotide deletion in the open reading frame, which generates an abnormal mRNA. The allele frequency of this variant sequence was high in both a European (0.47) and a Chinese (0.45) population cohort. Binding of the Agaricus bisporus lectin to the sperm surface glycocalyx was significantly lower in men with the homozygous variant (del/del) genotype than in those with either a del/wt or a wt/wt genotype, suggesting an altered sperm glycocalyx with fewer O-linked oligosaccharides in del/del men. Moreover, sperm from del/del carriers exhibited an 84% reduction in the rate of penetration of a hyaluronic acid gel, a surrogate for cervical mucus, compared to the other genotypes. This reduction in sperm performance in hyaluronic acid gels was not a result of decreased progressive motility (average curvilinear velocity) or morphological deficits. Nevertheless, DEFB126 genotype and lectin binding were correlated with sperm performance in the penetration assays. In a prospective cohort study of newly married couples who were trying to conceive by natural means, couples were less likely to become pregnant and took longer to achieve a live birth if the male partner was homozygous for the variant sequence. This common sequence variation in DEFB126, and its apparent effect of impaired reproductive function, will allow a better understanding, clinical evaluation, and possibly treatment of human infertility.
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Affiliation(s)
- Theodore L Tollner
- Department of Obstetrics and Gynecology, School of Medicine, University of California, Davis, CA 95817, USA
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