1
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Kløve-Mogensen K, Terp SK, Steffensen R. Comparison of real-time quantitative PCR and two digital PCR platforms to detect copy number variation in FCGR3B. J Immunol Methods 2024; 526:113628. [PMID: 38331313 DOI: 10.1016/j.jim.2024.113628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 02/02/2024] [Accepted: 02/05/2024] [Indexed: 02/10/2024]
Abstract
The importance of structural genetic variants, such as copy number variations (CNVs), in modulating human disease is being increasingly recognized. Several clinical conditions require investigation of human neutrophil antigen (HNA-1), which is encoded by the Fc gamma receptor IIIb gene (FCGR3B), including suspicion of neutropenia, infections, and proactive testing of blood component donors to reduce the potential risk in transfusion. In this study, we compared real-time quantitative polymerase chain reaction (qPCR) with two digital PCR (dPCR) platforms, namely droplet digital PCR and an array-based platform, to determine copy numbers (CNs) in FCGR3B. We initially tested 400 anonymous blood donors with qPCR using a commercially available TaqMan probe assay (Applied Biosystems) on a Quant Studio 12 Flex. CNs was determined for all 400 tested individuals with CNs ranging from zero to four. Zero copies were detected in 0.2% (1/400), one copy was detected in 3.8% (15/400), two copies were detected in 87.8% (351/400), three copies were detected in 8.0% (32/400), and four copies were detected in 0.2% (1/400) of tested individuals. From this cohort, we selected 32 donors with CNs from zero to four for analyses with Digital Real-Time PCR (dPCR) using Lab on an array (LOAA) on an On-Point analyzer from Optolane Technologies Inc. and the Droplet Digital PCR (ddPCR) platform from Bio-Rad Laboratories. We compared the obtained CNs of FCGR3B on the three platforms and found full concordance between the CNs obtained. We therefore conclude that all three platforms can be used for quantification of CNs for FCGR3B, and although dPCR has some advantages over qPCR, it was not necessary for reliably estimating CNs of the FCGR3B gene.
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Affiliation(s)
- Kirstine Kløve-Mogensen
- Department of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark; Department of Clinical Medicine, Aalborg University, Aalborg, Denmark.
| | - Simone Karlsson Terp
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark; Department of Molecular Diagnostics, Aalborg University Hospital, Aalborg, Denmark.
| | - Rudi Steffensen
- Department of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark.
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2
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Kløve-Mogensen K, Steffensen R, Masmas TN, Glenthøj A, Jensen CF, Haunstrup TM, Ratcliffe P, Höglund P, Hasle H, Nielsen KR. Genetic variations in low-to-medium-affinity Fcγ receptors and autoimmune neutropenia in early childhood in a Danish cohort. Int J Immunogenet 2023; 50:65-74. [PMID: 36754570 DOI: 10.1111/iji.12614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 01/09/2023] [Accepted: 01/22/2023] [Indexed: 02/10/2023]
Abstract
Autoimmune neutropenia (AIN) in early childhood is caused by autoantibodies directed against antigens on the neutrophil membrane and is a frequent cause of neutropenia in children. Association of AIN with Fcγ receptor (FCGR) 3B variants is well described. In this study, we investigate genetic variations in the FCGR locus and copy number variation of FCGR3B. A total of 130 antibody-positive AIN patients, 64 with specific anti-HNA-1a antibodies and 66 with broad-reacting anti-FcγRIIIb antibodies, were genotyped with a multiplex ligation probe assay and compared with healthy controls. Positive findings were confirmed with real-time q-PCR. We determined copy numbers of the FCGR2 and FCGR3 genes and the following SNPs: FCGR2A Q62W (rs201218628), FCGR2A H166R (rs1801274), FCGR2B I232T (rs1050501), FCGR3A V176F (rs396991), haplotypes for FCGR2B/C promoters (rs3219018/rs780467580), FCGR2C STOP/ORF and HNA-1 genotypes in FCGR3B (rs447536, rs448740, rs52820103, rs428888 and rs2290834). Generally, associations were antibody specific, with all associations being representative of the anti-HNA-1a-positive group, while the only association found in the anti-FcγRIIIb group was with the HNA-1 genotype. An increased risk of AIN was observed for patients with one copy of FCGR3B; the HNA genotypes HNA-1a, HNA-1aa or HNA-1aac; the FCGR2A 166H and FCGR2B 232I variations; and no copies of FCGR2B 2B.4. A decreased risk was observed for HNA genotype HNA-1bb; FCGR2A 166R; FCGR2B 232T; and one copy of FCGR2B promoter 2B.4. We conclude that in our Danish cohort, there was a strong association between variation in the FCGR locus and AIN. The findings of different genetic associations between autoantibody groups could indicate the presence of two different disease entities and disease heterogeneity.
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Affiliation(s)
- Kirstine Kløve-Mogensen
- Department of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark.,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Rudi Steffensen
- Department of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark
| | - Tania Nicole Masmas
- Pediatric Hematopoietic Stem Cell Transplantation and Immunodeficiency, Department of Pediatrics and Adolescent Medicine, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Andreas Glenthøj
- Department of Hematology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Christina Friis Jensen
- Department of Pediatrics and Adolescent Medicine, Aalborg University Hospital, Aalborg, Denmark
| | - Thure Mors Haunstrup
- Department of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark
| | - Paul Ratcliffe
- Department of medicine Huddinge, Karolinska Institute, Stockholm, Sweden
| | - Petter Höglund
- Department of medicine Huddinge, Karolinska Institute, Stockholm, Sweden
| | - Henrik Hasle
- Department of Pediatrics and Adolescent Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Kaspar René Nielsen
- Department of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark.,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
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3
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Nassir N, Tambi R, Bankapur A, Al Heialy S, Karuvantevida N, Khansaheb HH, Zehra B, Begum G, Hameid RA, Ahmed A, Deesi Z, Alkhajeh A, Uddin KF, Akter H, Safizadeh Shabestari SA, Almidani O, Islam A, Gaudet M, Kandasamy RK, Loney T, Tayoun AA, Nowotny N, Woodbury-Smith M, Rahman P, Kuebler WM, Yaseen Hachim M, Casanova JL, Berdiev BK, Alsheikh-Ali A, Uddin M. Single-cell transcriptome identifies FCGR3B upregulated subtype of alveolar macrophages in patients with critical COVID-19. iScience 2021; 24:103030. [PMID: 34458692 PMCID: PMC8384759 DOI: 10.1016/j.isci.2021.103030] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 06/16/2021] [Accepted: 08/20/2021] [Indexed: 01/08/2023] Open
Abstract
Understanding host cell heterogeneity is critical for unraveling disease mechanism. Utilizing large-scale single-cell transcriptomics, we analyzed multiple tissue specimens from patients with life-threatening COVID-19 pneumonia, compared with healthy controls. We identified a subtype of monocyte-derived alveolar macrophages (MoAMs) where genes associated with severe COVID-19 comorbidities are significantly upregulated in bronchoalveolar lavage fluid of critical cases. FCGR3B consistently demarcated MoAM subset in different samples from severe COVID-19 cohorts and in CCL3L1-upregulated cells from nasopharyngeal swabs. In silico findings were validated by upregulation of FCGR3B in nasopharyngeal swabs of severe ICU COVID-19 cases, particularly in older patients and those with comorbidities. Additional lines of evidence from transcriptomic data and in vivo of severe COVID-19 cases suggest that FCGR3B may identify a specific subtype of MoAM in patients with severe COVID-19 that may present a novel biomarker for screening and prognosis, as well as a potential therapeutic target. Association of MoAM subtype with severe COVID-19 cases presented with comorbidities Upregulated FCGR3B in CCL3L1 positive MoAM cells in severe COVID-19 cases Upregulated FCGR3B within MoAM subtype as a potential marker for COVID-19 severity
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Affiliation(s)
- Nasna Nassir
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
| | - Richa Tambi
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
| | - Asma Bankapur
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
| | - Saba Al Heialy
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
- Meakins-Christie Laboratories, Research Institute of the McGill University Health Center, Montreal, QC, Canada
| | - Noushad Karuvantevida
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
| | - Hamda Hassan Khansaheb
- Dubai Health Authority, Microbiology and Infection Control Unit, Pathology and Genetics Department, Latifa Women and Children Hospital, Dubai, UAE
| | - Binte Zehra
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
| | - Ghausia Begum
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
| | - Reem Abdel Hameid
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
| | - Awab Ahmed
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
| | - Zulfa Deesi
- Dubai Health Authority, Microbiology and Infection Control Unit, Pathology and Genetics Department, Latifa Women and Children Hospital, Dubai, UAE
| | | | - K.M. Furkan Uddin
- Genetics and Genomic Medicine Centre, NeuroGen Children’s Healthcare, Dhaka, Bangladesh
| | - Hosneara Akter
- Genetics and Genomic Medicine Centre, NeuroGen Children’s Healthcare, Dhaka, Bangladesh
| | | | - Omar Almidani
- Nuffield Department of Surgical Science, University of Oxford, Oxford, UK
| | - Amirul Islam
- Genetics and Genomic Medicine Centre, NeuroGen Children’s Healthcare, Dhaka, Bangladesh
- Cellular Intelligence (Ci) Lab, GenomeArc Inc., Toronto, ON, Canada
| | - Mellissa Gaudet
- Meakins-Christie Laboratories, Research Institute of the McGill University Health Center, Montreal, QC, Canada
| | | | - Tom Loney
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
| | - Ahmad Abou Tayoun
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
- Al Jalila Genomics Center, Al Jalila Children’s Hospital, Dubai, UAE
| | - Norbert Nowotny
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
- Institute of Virology, University of Veterinary Medicine Vienna, Vienna, Austria
| | | | - Proton Rahman
- Department of Rheumatology, Memorial University of Newfoundland, St Johns, NL, Canada
| | - Wolfgang M. Kuebler
- Institute of Physiology, Charité - Universitätsmedizin Berlin, Berlin Germany
| | - Mahmood Yaseen Hachim
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University of Paris, Imagine Institute, Paris, France
- Howard Hughes Medical Institute, New York, NY, USA
| | - Bakhrom K. Berdiev
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
| | - Alawi Alsheikh-Ali
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
- Dubai Health Authority, Dubai, UAE
| | - Mohammed Uddin
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
- Cellular Intelligence (Ci) Lab, GenomeArc Inc., Toronto, ON, Canada
- Corresponding author
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4
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Nagelkerke SQ, Schmidt DE, de Haas M, Kuijpers TW. Genetic Variation in Low-To-Medium-Affinity Fcγ Receptors: Functional Consequences, Disease Associations, and Opportunities for Personalized Medicine. Front Immunol 2019; 10:2237. [PMID: 31632391 PMCID: PMC6786274 DOI: 10.3389/fimmu.2019.02237] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 09/04/2019] [Indexed: 12/23/2022] Open
Abstract
Fc-gamma receptors (FcγR) are the cellular receptors for Immunoglobulin G (IgG). Upon binding of complexed IgG, FcγRs can trigger various cellular immune effector functions, thereby linking the adaptive and innate immune systems. In humans, six classic FcγRs are known: one high-affinity receptor (FcγRI) and five low-to-medium-affinity FcγRs (FcγRIIA, -B and -C, FcγRIIIA and -B). In this review we describe the five genes encoding the low-to-medium -affinity FcγRs (FCGR2A, FCGR2B, FCGR2C, FCGR3A, and FCGR3B), including well-characterized functionally relevant single nucleotide polymorphisms (SNPs), haplotypes as well as copy number variants (CNVs), which occur in distinct copy number regions across the locus. The evolution of the locus is also discussed. Importantly, we recommend a consistent nomenclature of genetic variants in the FCGR2/3 locus. Next, we focus on the relevance of genetic variation in the FCGR2/3 locus in auto-immune and auto-inflammatory diseases, highlighting pathophysiological insights that are informed by genetic association studies. Finally, we illustrate how specific FcγR variants relate to variation in treatment responses and prognosis amongst autoimmune diseases, cancer and transplant immunology, suggesting novel opportunities for personalized medicine.
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Affiliation(s)
- Sietse Q Nagelkerke
- Sanquin Research and Landsteiner Laboratory, Department of Blood Cell Research, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.,Pediatric Hematology, Immunology and Infectious Diseases, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - David E Schmidt
- Sanquin Research and Landsteiner Laboratory, Department of Experimental Immunology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Masja de Haas
- Sanquin Diagnostic Services, Department of Immunohematology Diagnostics, Amsterdam, Netherlands.,Sanquin Research, Center for Clinical Transfusion Research, Leiden, Netherlands.,Jon J. van Rood Center for Clinical Transfusion Science, Leiden University Medical Center, Leiden, Netherlands.,Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
| | - Taco W Kuijpers
- Sanquin Research and Landsteiner Laboratory, Department of Blood Cell Research, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.,Pediatric Hematology, Immunology and Infectious Diseases, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
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5
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Zhou L, Wang Y, Wang K, Wang J, Ma A, Pan X. Potential therapeutic drugs for ischemic stroke based on bioinformatics analysis. Int J Neurosci 2019; 129:1098-1102. [PMID: 31387440 DOI: 10.1080/00207454.2019.1634072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Ischemic stroke (IS) is a complex disease affected by various environmental factors, genetic factors and their interactions. Because genetic factors occupy an irreplaceable place in the pathogenesis of IS, the identification of genetic factors has become one of the hot spots in the current research. In the present study, we aimed to identify possible gene targets and relevant drug molecules in the pathogenesis of IS. Microarray dataset of GSE16561 was downloaded from Gene Expression Omnibus database. The differentially expressed genes (DEGs) between IS group and control group were obtained using limma package in R. Ground-Operation Simulation package in R language was used to cluster DEGs according to their biological process, cellular components and molecular functions with respect to the GO annotation. The DEGs were analyzed by Search Tool for the Retrieval of Interacting Genes online database and Cytoscape software to predict their interaction relationship. Finally, the DEGs were submitted to DGIdb dataset and related drug molecules were retrieved. 20 DEGs were identified from IS group including 1 downregulated and 19 upregulated genes. The function enrichment analysis revealed that the DEGs were enriched in three GO terms, mainly including inflammatory response, positive regulation of protein kinase activity and innate immune response. Finally, 10 drug molecules were identified from the DEGs. Our study identified some potential biological targets and drug molecules for the treatment of IS.
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Affiliation(s)
- Lingyan Zhou
- Department of Neurology , The Affiliated Hospital of Qingdao University , Qingdao , China
| | - Yuan Wang
- Department of Neurology , The Affiliated Hospital of Qingdao University , Qingdao , China
| | - Kun Wang
- Department of Neurology , The Affiliated Hospital of Qingdao University , Qingdao , China
| | - Jing Wang
- Department of Neurology , The Affiliated Hospital of Qingdao University , Qingdao , China
| | - Aijun Ma
- Department of Neurology , The Affiliated Hospital of Qingdao University , Qingdao , China
| | - Xudong Pan
- Department of Neurology , The Affiliated Hospital of Qingdao University , Qingdao , China
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6
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Typiak M, Rębała K, Haraś A, Skotarczak M, Słomiński JM, Dubaniewicz A. Copy number variation of FCGR genes in etiopathogenesis of sarcoidosis. PLoS One 2017; 12:e0177194. [PMID: 28472129 PMCID: PMC5417662 DOI: 10.1371/journal.pone.0177194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 04/24/2017] [Indexed: 11/19/2022] Open
Abstract
We have previously revealed that, in contrast to polymorphism of FCGR2B and FCGR3B, polymorphism of FCGR2A, FCGR2C and FCGR3A genes, encoding receptors for Fc fragment of immunoglobulin G (Fcγ receptors), play a role in increased level of circulating immune complexes with occurrence of Mycobacterium tuberculosis heat shock proteins in patients with sarcoidosis. However, this immunocomplexemia might also be caused by decreased clearance by immune cells due to a changed copy number of FCGR genes. Thus, the next step of our study was to evaluate copy number variation of FCGR2A, FCGR2B, FCGR2C, FCGR3A and FCGR3B in this disease. The analysis was carried out by real-time quantitative PCR on 104 patients and 110 healthy volunteers. Despite previously detected variation in allele/genotype frequencies of FCGR in sarcoidosis and its particular stages, there was no copy number variation of the tested genes between sarcoidosis or its stages and healthy control, as well as between stages themselves. A relevant increase in copy number of FCGR2C and FCGR3B in Stage IV of sarcoidosis vs. other stages and controls was detected, but this observation was based on a limited number of Stage IV patients. Hence, polymorphism of FCGR genes seems to be more important than their copy number variation in etiopathogenesis of sarcoidosis in patients from the Polish population.
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Affiliation(s)
- Marlena Typiak
- Department of Pulmonology, Medical University of Gdansk, Gdansk, Poland
| | - Krzysztof Rębała
- Department of Forensic Medicine, Medical University of Gdansk, Gdansk, Poland
| | - Agnieszka Haraś
- Department of Forensic Medicine, Medical University of Gdansk, Gdansk, Poland
| | - Monika Skotarczak
- 2nd Department of Radiology, Medical University of Gdansk, Gdansk, Poland
| | | | - Anna Dubaniewicz
- Department of Pulmonology, Medical University of Gdansk, Gdansk, Poland
- * E-mail:
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7
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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: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [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 GeneticsUniversity of LeicesterLeicesterUnited Kingdom
- Wellcome Trust Sanger InstituteHinxtonUnited Kingdom
| | - Luciana W Zuccherato
- Department of GeneticsUniversity of LeicesterLeicesterUnited Kingdom
- Departmento de Biologia GeralInstituto de Ciências BiológicasUniversidade Federal de Minas GeraisBelo HorizonteBrazil
| | | | - Belinda Chihota
- School of HealthUniversity of NorthamptonNorthamptonUnited Kingdom
| | - Hasret Ozturk
- Department of GeneticsUniversity of LeicesterLeicesterUnited Kingdom
| | - Sara Saleem
- Department of GeneticsUniversity of LeicesterLeicesterUnited Kingdom
| | - Eduardo Tarazona‐Santos
- Departmento de Biologia GeralInstituto de Ciências BiológicasUniversidade Federal de Minas GeraisBelo HorizonteBrazil
| | - Lee R Machado
- Department of GeneticsUniversity of LeicesterLeicesterUnited Kingdom
- School of HealthUniversity of NorthamptonNorthamptonUnited Kingdom
| | - Edward J Hollox
- Department of GeneticsUniversity of LeicesterLeicesterUnited Kingdom
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8
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Qi Y, Zhou X, Bu D, Hou P, Lv J, Zhang H. Low copy numbers of FCGR3A and FCGR3B associated with Chinese patients with SLE and AASV. Lupus 2017; 26:1383-1389. [PMID: 28355982 DOI: 10.1177/0961203317700485] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Low-affinity Fcγ receptors (FcγR) act as key mediators of the pathogenic effects of autoantibodies. In this study, we aimed to determine whether copy number variations (CNVs) in FCGR3A and FCGR3B were associated with systemic lupus nephritis (SLE) and ANCA-associated systemic vasculitis (AASV) in Chinese individuals. A total of 1118 individuals were enrolled, including 415 SLE patients, 139 AASV patients, and 564 healthy controls. FCGR3A and FCGR3B copy numbers (CNs) were determined by both a paralogue ratio test and TaqMan quantitative PCR assay. In the susceptibility associations, a low FCGR3B CN was significantly associated with SLE ( p = 5.01 × 10-3; odds ratio (OR) 1.71; 95% confidence interval (CI) 1.17-2.48) and AASV ( p = 0.04; OR = 1.72; 95% CI 1.02-2.88). A low FCGR3A CN was also significantly associated with SLE ( p = 6.02 × 10-3; OR 2.72; 95% CI 1.30-5.71) and AASV ( p = 0.042; OR 2.64; 95% CI 1.00-6.93). Further subphenotype analysis revealed that low CNs of FCGR3A and FCGR3B were significantly associated with clinical manifestations in SLE and AASV patients. Therefore, in this case-control study, we identified low CNs of FCGR2A and FCGR3B to be common risk factors for SLE and AASV.
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Affiliation(s)
- Y Qi
- 1 Renal Division, Peking University First Hospital, People's Republic of China.,2 Peking University Institute of Nephrology, People's Republic of China.,3 Key Laboratory of Renal Disease, Ministry of Health of China, People's Republic of China.,4 Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, People's Republic of China
| | - X Zhou
- 1 Renal Division, Peking University First Hospital, People's Republic of China.,2 Peking University Institute of Nephrology, People's Republic of China.,3 Key Laboratory of Renal Disease, Ministry of Health of China, People's Republic of China.,4 Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, People's Republic of China
| | - D Bu
- 5 Research Central Institute, Peking University First Hospital, Beijing, People's Republic of China
| | - P Hou
- 1 Renal Division, Peking University First Hospital, People's Republic of China.,2 Peking University Institute of Nephrology, People's Republic of China.,3 Key Laboratory of Renal Disease, Ministry of Health of China, People's Republic of China.,4 Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, People's Republic of China
| | - J Lv
- 1 Renal Division, Peking University First Hospital, People's Republic of China.,2 Peking University Institute of Nephrology, People's Republic of China.,3 Key Laboratory of Renal Disease, Ministry of Health of China, People's Republic of China.,4 Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, People's Republic of China
| | - H Zhang
- 1 Renal Division, Peking University First Hospital, People's Republic of China.,2 Peking University Institute of Nephrology, People's Republic of China.,3 Key Laboratory of Renal Disease, Ministry of Health of China, People's Republic of China.,4 Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, People's Republic of China
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9
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Fischer J, Degenhardt F, Hofmann A, Redler S, Basmanav FB, Heilmann-Heimbach S, Hanneken S, Giehl KA, Wolff H, Moebus S, Kruse R, Lutz G, Blaumeiser B, Böhm M, Garcia Bartels N, Blume-Peytavi U, Petukhova L, Christiano AM, Nöthen MM, Betz RC. Genomewide analysis of copy number variants in alopecia areata in a Central European cohort reveals association with MCHR2. Exp Dermatol 2017; 26:536-541. [PMID: 27306922 DOI: 10.1111/exd.13123] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/08/2016] [Indexed: 12/13/2022]
Abstract
Alopecia areata (AA) is a common hair loss disorder of autoimmune aetiology, which often results in pronounced psychological distress. Understanding of the pathophysiology of AA is increasing, due in part to recent genetic findings implicating common variants at several genetic loci. To date, no study has investigated the contribution of copy number variants (CNVs) to AA, a prominent class of genomic variants involved in other autoimmune disorders. Here, we report a genomewide- and a candidate gene-focused CNV analysis performed in a cohort of 585 patients with AA and 1340 controls of Central European origin. A nominally significant association with AA was found for CNVs in the following five chromosomal regions: 4q35.2, 6q16.3, 9p23, 16p12.1 and 20p12.1. The most promising finding was a 342.5-kb associated region in 6q16.3 (duplications in 4/585 patients; 0/1340 controls). The duplications spanned the genes MCHR2 and MCHR2-AS1, implicated in melanin-concentrating hormone (MCH) signalling. These genes have not been implicated in previous studies of AA pathogenesis. However, previous research has shown that MCHR2 affects the scale colour of barfin flounder fish via the induction of melanin aggregation. AA preferentially affects pigmented hairs, and the hair of patients with AA frequently shows a change in colour when it regrows following an acute episode of AA. This might indicate a relationship between AA, pigmentation and MCH signalling. In conclusion, the present results provide suggestive evidence for the involvement of duplications in MCHR2 in AA pathogenesis.
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Affiliation(s)
| | - Franziska Degenhardt
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Andrea Hofmann
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Silke Redler
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | | | - Stefanie Heilmann-Heimbach
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Sandra Hanneken
- Department of Dermatology, University of Düsseldorf, Düsseldorf, Germany
| | - Kathrin A Giehl
- Department of Dermatology, University of Munich, Munich, Germany
| | - Hans Wolff
- Department of Dermatology, University of Munich, Munich, Germany
| | - Susanne Moebus
- Institute of Medical Informatics, Biometry and Epidemiology, University Duisburg-Essen, Duisburg, Germany
| | | | - Gerhard Lutz
- Hair & Nail, Dermatological Practice, Wesseling, Germany
| | - Bettina Blaumeiser
- Department of Medical Genetics, University and University Hospital of Antwerp, Antwerp, Belgium
| | - Markus Böhm
- Department of Dermatology, University of Münster, Münster, Germany
| | - Natalie Garcia Bartels
- Clinical Research Center for Hair and Skin Science, Department of Dermatology and Allergy, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Ulrike Blume-Peytavi
- Clinical Research Center for Hair and Skin Science, Department of Dermatology and Allergy, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Lynn Petukhova
- Department of Dermatology, Columbia University, New York, NY, USA
| | - Angela M Christiano
- Department of Dermatology, Columbia University, New York, NY, USA.,Department of Genetics and Development, Columbia University, New York, NY, USA
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Regina C Betz
- Institute of Human Genetics, University of Bonn, Bonn, Germany
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10
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Nguyen HT, Boocock J, Merriman TR, Black MA. SRBreak: A Read-Depth and Split-Read Framework to Identify Breakpoints of Different Events Inside Simple Copy-Number Variable Regions. Front Genet 2016; 7:160. [PMID: 27695476 PMCID: PMC5023681 DOI: 10.3389/fgene.2016.00160] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Accepted: 08/24/2016] [Indexed: 12/28/2022] Open
Abstract
Copy-number variation (CNV) has been associated with increased risk of complex diseases. High-throughput sequencing (HTS) technologies facilitate the detection of copy-number variable regions (CNVRs) and their breakpoints. This helps in understanding genome structure as well as their evolution process. Various approaches have been proposed for detecting CNV breakpoints, but currently it is still challenging for tools based on a single analysis method to identify breakpoints of CNVs. It has been shown, however, that pipelines which integrate multiple approaches are able to report more reliable breakpoints. Here, based on HTS data, we have developed a pipeline to identify approximate breakpoints (±10 bp) relating to different ancestral events within a specific CNVR. The pipeline combines read-depth and split-read information to infer breakpoints, using information from multiple samples to allow an imputation approach to be taken. The main steps involve using a normal mixture model to cluster samples into different groups, followed by simple kernel-based approaches to maximize information obtained from read-depth and split-read approaches, after which common breakpoints of groups are inferred. The pipeline uses split-read information directly from CIGAR strings of BAM files, without using a re-alignment step. On simulated data sets, it was able to report breakpoints for very low-coverage samples including those for which only single-end reads were available. When applied to three loci from existing human resequencing data sets (NEGR1, LCE3, IRGM) the pipeline obtained good concordance with results from the 1000 Genomes Project (92, 100, and 82%, respectively). The package is available at https://github.com/hoangtn/SRBreak, and also as a docker-based application at https://registry.hub.docker.com/u/hoangtn/srbreak/.
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Affiliation(s)
- Hoang T Nguyen
- Department of Biochemistry, University of OtagoDunedin, New Zealand; Virtual Institute of Statistical GeneticsDunedin, New Zealand; Department of Psychiatry, Mount Sinai School of Medicine, New YorkNY, USA; Department of Mathematics, Cao Thang College of TechnologyHo Chi Minh City, Vietnam
| | - James Boocock
- Department of Biochemistry, University of OtagoDunedin, New Zealand; Virtual Institute of Statistical GeneticsDunedin, New Zealand; Department of Psychiatry, Mount Sinai School of Medicine, New YorkNY, USA
| | - Tony R Merriman
- Department of Biochemistry, University of OtagoDunedin, New Zealand; Virtual Institute of Statistical GeneticsDunedin, New Zealand
| | - Michael A Black
- Department of Biochemistry, University of OtagoDunedin, New Zealand; Virtual Institute of Statistical GeneticsDunedin, New Zealand
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11
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Martorana D, Bonatti F, Alberici F, Gioffredi A, Reina M, Urban ML, Maritati F, Adorni A, Radice A, Pizzolato S, Gregorini G, Jeannin G, Guida G, Boita M, Pesci A, Moroni G, Neri TM, Sinico RA, Vaglio A. Fcγ-receptor 3B ( FCGR3B ) copy number variations in patients with eosinophilic granulomatosis with polyangiitis. J Allergy Clin Immunol 2016; 137:1597-1599.e8. [DOI: 10.1016/j.jaci.2015.09.053] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 08/13/2015] [Accepted: 09/30/2015] [Indexed: 10/22/2022]
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12
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Wu J, Li Y, Guan W, Viken K, Perlman DM, Bhargava M. FCGR3A and FCGR3B copy number variations are risk factors for sarcoidosis. Hum Genet 2016; 135:715-25. [PMID: 27059607 DOI: 10.1007/s00439-016-1669-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 04/05/2016] [Indexed: 12/12/2022]
Abstract
Sarcoidosis is a multisystem granulomatous disorder that causes significant morbidity. Genetic factors contribute to sarcoidosis risks. In this study, we investigated whether copy number variations (CNVs) of FCGR3A (coding for FcγRIIIA) and FCGR3B (coding for FcγRIIIB) genes are associated with sarcoidosis susceptibility and whether the expressions of FcγRIIIA on NK cells and FcγRIIIB on neutrophils are altered in sarcoidosis patients. TaqMan real-time PCR assays were used to analyze the CNV of FCGR3A and FCGR3B genes. FCGR3A and FCGR3B CNV genotypes were compared between 671 biopsy-proven sarcoidosis patients and the same number of healthy controls matched with age, sex, race, and geographic area from the ACCESS (A Case Control Etiologic Study of Sarcoidosis) cohort. Flow cytometry analyses were used to determine expressions of FcγRIIIA on NK cells and FcγRIIIB on neutrophils in phenotype analyses. We found that FCGR3A CNVs were significantly associated with sarcoidosis in females (CN = 1 vs. CN = 2 logistic regression adjusted for sex and race, OR 4.0156, SE = 2.2784, P = 0.0143; CN = 3 vs. CN = 2 logistic regression adjusted for sex and race, OR 2.8044, SE = 1.1065, P = 0.0090), suggesting that FCGR3A gene abnormality influences sarcoidosis development in a gender-specific manner. Furthermore, FcγRIIIA expressions were significantly decreased on NK cells from sarcoidosis patients compared to those from healthy controls (P = 0.0007). Additionally, low FCGR3B CN was associated with sarcoidosis (CN <2 vs. CN = 2 logistic regression adjusted for sex and race, OR 1.5025, SE = 0.2682, P = 0.0226), indicating that the functions of FCGR3B gene may also contribute to the pathogenesis of sarcoidosis. We conclude that FCGR3A CNVs are a major risk factor for female sarcoidosis and FCGR3B CNVs may also affect the development of sarcoidosis.
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Affiliation(s)
- Jianming Wu
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, 235B AnSc/VetMed Bldg., 1988 Fitch Avenue, St. Paul, MN, 55108, USA.
| | - Yunfang Li
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, 235B AnSc/VetMed Bldg., 1988 Fitch Avenue, St. Paul, MN, 55108, USA
| | - Weihua Guan
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, USA
| | - Kevin Viken
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of Minnesota, Minneapolis, USA
| | - David M Perlman
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of Minnesota, Minneapolis, USA
| | - Maneesh Bhargava
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of Minnesota, Minneapolis, USA
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13
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Franke L, el Bannoudi H, Jansen DTSL, Kok K, Trynka G, Diogo D, Swertz M, Fransen K, Knevel R, Gutierrez-Achury J, Ärlestig L, Greenberg JD, Kremer J, Pappas DA, Kanterakis A, Weersma RK, van der Helm-van Mil AHM, Guryev V, Rantapää-Dahlqvist S, Gregersen PK, Plenge RM, Wijmenga C, Huizinga TWJ, Ioan-Facsinay A, Toes REM, Zhernakova A. Association analysis of copy numbers of FC-gamma receptor genes for rheumatoid arthritis and other immune-mediated phenotypes. Eur J Hum Genet 2016; 24:263-70. [PMID: 25966632 PMCID: PMC4717214 DOI: 10.1038/ejhg.2015.95] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 03/27/2015] [Accepted: 04/15/2015] [Indexed: 12/20/2022] Open
Abstract
Segmental duplications (SDs) comprise about 5% of the human genome and are enriched for immune genes. SD loci often show copy numbers variations (CNV), which are difficult to tag with genotyping methods. CNV in the Fcγ receptor region (FCGR) has been suggested to be associated with rheumatic diseases. The objective of this study was to delineate association of FCGR-CNV with rheumatoid arthritis (RA), coeliac disease and Inflammatory bowel disease incidence. We developed a method to accurately quantify CNV in SD loci based on the intensity values from the Immunochip platform and applied it to the FCGR locus. We determined the method's validity using three independent assays: segregation analysis in families, arrayCGH, and whole genome sequencing. Our data showed the presence of two separate CNVs in the FCGR locus. The first region encodes FCGR2A, FCGR3A and part of FCGR2C gene, the second encodes another part of FCGR2C, FCGR3B and FCGR2B. Analysis of CNV status in 4578 individuals with RA and 5457 controls indicated association of duplications in the FCGR3B gene in antibody-negative RA (P=0.002, OR=1.43). Deletion in FCGR3B was associated with increased risk of antibody-positive RA, consistently with previous reports (P=0.023, OR=1.23). A clear genotype-phenotype relationship was observed: CNV polymorphisms of the FCGR3A gene correlated to CD16A expression (encoded by FCGR3A) on CD8 T-cells. In conclusion, our method allows determining the CNV status of the FCGR locus, we identified association of CNV in FCGR3B to RA and showed a functional relationship between CNV in the FCGR3A gene and CD16A expression.
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Affiliation(s)
- Lude Franke
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Hanane el Bannoudi
- Department of Rheumatology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Diahann T S L Jansen
- Department of Rheumatology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Klaas Kok
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Gosia Trynka
- Division of Rheumatology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Dorothee Diogo
- Division of Rheumatology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Morris Swertz
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
- Genomics Coordination Center, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Karin Fransen
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Rachel Knevel
- Department of Rheumatology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Javier Gutierrez-Achury
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Lisbeth Ärlestig
- Department of Public Health and Clinical Medicine/Rheumatology, Umeå University, Umeå, Sweden
| | - Jeffrey D Greenberg
- Department of Medicine, New York University School of Medicine, New York, New York, USA
| | - Joel Kremer
- Department of Medicine, Albany Medical College, Albany, New York, USA
| | - Dimitrios A Pappas
- Department of Medicine, Columbia University College of Physicians and Surgeons, New York, New York, USA
| | - Alexandros Kanterakis
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
- Genomics Coordination Center, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | | | - Viktor Guryev
- Laboratory of Genome Structure and Ageing, European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | | | | | - Robert M Plenge
- Division of Rheumatology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Tom W-J Huizinga
- Department of Rheumatology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Andreea Ioan-Facsinay
- Department of Rheumatology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Rene E M Toes
- Department of Rheumatology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
- Department of Rheumatology, Leiden University Medical Centre, Leiden, The Netherlands
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14
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Tsang-A-Sjoe MWP, Nagelkerke SQ, Bultink IEM, Geissler J, Tanck MWT, Tacke CE, Ellis JA, Zenz W, Bijl M, Berden JH, de Leeuw K, Derksen RH, Kuijpers TW, Voskuyl AE. Fc-gamma receptor polymorphisms differentially influence susceptibility to systemic lupus erythematosus and lupus nephritis. Rheumatology (Oxford) 2016; 55:939-48. [DOI: 10.1093/rheumatology/kev433] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Indexed: 01/09/2023] Open
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15
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Variability at the FCGR locus: characterization in Black South Africans and evidence for ethnic variation in and out of Africa. Genes Immun 2015; 17:93-104. [PMID: 26673965 DOI: 10.1038/gene.2015.60] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 11/17/2015] [Accepted: 11/18/2015] [Indexed: 01/07/2023]
Abstract
This study set out to comprehensively investigate all known functional FcγR variants in South African Black and Caucasian individuals. Population diversity was further assessed using data from the 1000 Genomes Project. In our cohort, Black South Africans neither possessed the haplotypes previously associated with increased surface densities of FcγRIIb and FcγRIIIa nor the FCGR2C haplotype recently associated with increased vaccine efficacy in the RV144 HIV-1 vaccine trial (despite 48.7% bearing the c.134-96T tag allele). Moreover, Africans (South Africans, Luhya Kenyans and Yoruba Nigerians) lack the FCGR2C c.798+1G splice-site allele required for the expression of functional FcγRIIc. Although the presence or absence of surface FcγRIIc did not affect natural killer cell-mediated antibody-dependent cellular cytotoxicity capability, this may be significant for other FcγRIIc-mediated functions. Overall, allele distribution and linkage disequilibrium in Africans and Caucasians differed in a manner that would suggest a differentially maintained balance of FcγR-mediated cell activation in these populations. Finally, significant variation observed among different African populations precludes the use of any one African population as a proxy for FcγR diversity in Africans. In conclusion, the findings of this study highlight further ethnic variation at the FCGR gene locus, in particular for FCGR2C, a gene with increasingly recognized clinical significance.
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16
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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] [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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17
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Lee YH, Bae SC, Seo YH, Kim JH, Choi SJ, Ji JD, Song GG. Association between FCGR3B copy number variations and susceptibility to autoimmune diseases: a meta-analysis. Inflamm Res 2015; 64:983-91. [PMID: 26407570 DOI: 10.1007/s00011-015-0882-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Revised: 09/15/2015] [Accepted: 09/16/2015] [Indexed: 01/24/2023] Open
Abstract
OBJECTIVE This study determined whether FCGR3B copy number variations (CNVs) were associated with susceptibility to autoimmune diseases. METHODS A meta-analysis was conducted to determine the association between FCGR3B CNVs and susceptibility to autoimmune diseases by comparing low FCGR3B CN (<2 to ≥2) and high FCGR3B CN (>2 to ≤2). RESULTS In all, 28 comparative studies from 15 reports involving 12,160 patients and 11,103 controls were included in this meta-analysis. The meta-analysis showed a significant association between low FCGR3B CN and autoimmune diseases (OR=1.496, 95% CI=1.301-1.716, p=1.0×10(-9)). Subgroup analysis according to ethnicity indicated an association between low FCGR3B CN and autoimmune diseases in Caucasians (OR=1.482, 95% CI=1.219-1.801, p=7.7×10(-6)) and Asians (OR=1.498, 95% CI=1.306-1.717, p=1.0×10(-9)). Meta-analysis according to the type of autoimmune disease indicated a significant association of low FCGR3B CN with systemic lupus erythematosus (SLE; OR=1.797, 95% CI=1.562-2.068, p<1.0×10(-9)), primary Sjogren's syndrome (pSS; OR=2.263, 95% CI=1.316-3.892, p=0.003), and Wegener's granulomatosis (WG; OR=1.973, 95% CI=1.178-3.302, p=0.010), but not with rheumatoid arthritis (RA; OR=1.333, 95% CI=0.947-1.877, p=0.099). However, the meta-analysis showed no association between high FCGR3B CN and SLE, RA, pSS, and WG. CONCLUSIONS Thus, the results of this meta-analysis indicated that low FCGR3B CN increased susceptibility to autoimmune diseases, especially SLE, pSS, and WG.
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Affiliation(s)
- Young Ho Lee
- Division of Rheumatology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, 72 Inchon-ro, Seongbuk-gu, Seoul, 136-705, Korea.
| | - Sang-Cheol Bae
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
| | - Young Ho Seo
- Division of Rheumatology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, 72 Inchon-ro, Seongbuk-gu, Seoul, 136-705, Korea
| | - Jae-Hoon Kim
- Division of Rheumatology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, 72 Inchon-ro, Seongbuk-gu, Seoul, 136-705, Korea
| | - Sung Jae Choi
- Division of Rheumatology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, 72 Inchon-ro, Seongbuk-gu, Seoul, 136-705, Korea
| | - Jong Dae Ji
- Division of Rheumatology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, 72 Inchon-ro, Seongbuk-gu, Seoul, 136-705, Korea
| | - Gwan Gyu Song
- Division of Rheumatology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, 72 Inchon-ro, Seongbuk-gu, Seoul, 136-705, Korea
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18
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Yim SH, Jung SH, Chung B, Chung YJ. Clinical implications of copy number variations in autoimmune disorders. Korean J Intern Med 2015; 30:294-304. [PMID: 25995659 PMCID: PMC4438283 DOI: 10.3904/kjim.2015.30.3.294] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 03/30/2015] [Indexed: 11/27/2022] Open
Abstract
Human genetic variation is represented by the genetic differences both within and among populations, and most genetic variants do not cause overt diseases but contribute to disease susceptibility and influence drug response. During the last century, various genetic variants, such as copy number variations (CNVs), have been associated with diverse human disorders. Here, we review studies on the associations between CNVs and autoimmune diseases to gain some insight. First, some CNV loci are commonly implicated in various autoimmune diseases, such as Fcγ receptors in patients with systemic lupus erythemoatosus or idiopathic thrombocytopenic purpura and β-defensin genes in patients with psoriasis or Crohn's disease. This means that when a CNV locus is associated with a particular autoimmune disease, we should examine its potential associations with other diseases. Second, interpopulation or interethnic differences in the effects of CNVs on phenotypes exist, including disease susceptibility, and evidence suggests that CNVs are important to understand susceptibility to and pathogenesis of autoimmune diseases. However, many findings need to be replicated in independent populations and different ethnic groups. The validity and reliability of detecting CNVs will improve quickly as genotyping technology advances, which will support the required replication.
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Affiliation(s)
- Seon-Hee Yim
- Department of Medical Education, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Seung-Hyun Jung
- Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea, Seoul, Korea
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Boram Chung
- Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea, Seoul, Korea
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Yeun-Jun Chung
- Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea, Seoul, Korea
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea
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19
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Abstract
Genome-wide association studies that scan the genome for common genetic variants associated with phenotype have greatly advanced medical knowledge. Hyperuricemia is no exception, with 28 loci identified. However, genetic control of pathways determining gout in the presence of hyperuricemia is still poorly understood. Two important pathways determining hyperuricemia have been confirmed (renal and gut excretion of uric acid with glycolysis now firmly implicated). Major urate loci are SLC2A9 and ABCG2. Recent studies show that SLC2A9 is involved in renal and gut excretion of uric acid and is implicated in antioxidant defense. Although etiological variants at SLC2A9 are yet to be identified, it is clear that considerable genetic complexity exists at the SLC2A9 locus, with multiple statistically independent genetic variants and local epistatic interactions. The positions of implicated genetic variants within or near chromatin regions involved in transcriptional control suggest that this mechanism (rather than structural changes in SLC2A9) is important in regulating the activity of SLC2A9. ABCG2 is involved primarily in extra-renal uric acid under-excretion with the etiological variant influencing expression. At the other 26 loci, probable causal genes can be identified at three (PDZK1, SLC22A11, and INHBB) with strong candidates at a further 10 loci. Confirmation of the causal gene will require a combination of re-sequencing, trans-ancestral mapping, and correlation of genetic association data with expression data. As expected, the urate loci associate with gout, although inconsistent effect sizes for gout require investigation. Finally, there has been no genome-wide association study using clinically ascertained cases to investigate the causes of gout in the presence of hyperuricemia. In such a study, use of asymptomatic hyperurcemic controls would be expected to increase the ability to detect genetic associations with gout.
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Affiliation(s)
- Tony R Merriman
- Department of Biochemistry, University of Otago, Box 56, Dunedin, 9054, New Zealand.
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20
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Chen JY, Wang CM, Chang SW, Cheng CH, Wu YJJ, Lin JC, Yang B, Ho HH, Wu J. Association of FCGR3A and FCGR3B copy number variations with systemic lupus erythematosus and rheumatoid arthritis in Taiwanese patients. Arthritis Rheumatol 2015; 66:3113-21. [PMID: 25154742 PMCID: PMC4232894 DOI: 10.1002/art.38813] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 07/31/2014] [Indexed: 12/12/2022]
Abstract
Objective To determine whether copy number variations (CNVs) in FCGR3A and FCGR3B are associated with systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA) in Taiwanese individuals. Methods FCGR3A and FCGR3B CNV genotypes were determined in 846 patients with SLE, 948 patients with RA, and 1,420 healthy control subjects, using custom TaqMan CNV assays. The FCGR3A and FCGR3B CNV genotypes were compared between healthy control subjects and patients and among patients stratified according to clinical characteristics. Results A low (<2) FCGR3A copy number was significantly associated with SLE (for <2 copies versus 2 copies, P = 5.06 × 10−4, false discovery rate–corrected P [PFDR] = 0.001, odds ratio [OR] 3.26, 95% confidence interval [95% CI] 1.68−6.35) and RA (for <2 copies versus 2 copies, P = 5.83 × 10−4, PFDR = 0.0012, OR 2.82, 95% CI 1.56−5.1). A low FCGR3B copy number was also significantly associated with SLE (for <2 copies versus 2 copies, P = 0.0032, PFDR = 0.0032, OR 1.59, 95% CI 1.17−2.18). Notably, a high (>2) FCGR3A copy number was also associated with SLE (for >2 copies versus 2 copies, P = 0.003, PFDR = 0.0061, OR 1.6, 95% CI 1.17−2.18). Additionally, the FCGR3A low copy number genotype was significantly enriched in subsets of patients with SLE (those with ulcer, arthritis, rash, discoid rash, photosensitivity, nephritis, leukopenia, thrombocytopenia, depressed complement levels, and autoantibody positivity) and patients with RA (those positive for rheumatoid factor) compared with healthy control subjects. The FCGR3B low copy number genotype was also significantly enriched in SLE patients with ulcer, rash, discoid rash, photosensitivity, ascites, nephritis, complement level depression, and anti–double-stranded DNA antibody positivity compared with control subjects. However, FCGR3B CNVs were not associated with RA susceptibility (for <2 copy numbers versus 2 copy numbers, P = 0.3584, OR 1.15, 95% CI 0.85–1.55) and clinical characteristics. Conclusion In Taiwanese individuals, a low FCGR3A copy number is a common risk factor for SLE and RA, while a low FCGR3B copy number confers a risk of SLE but not RA.
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Affiliation(s)
- Ji-Yih Chen
- Chang Gung University College of Medicine, Taiwan, Republic of China
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Almal SH, Padh H. Frequency distribution of autoimmunity associated FCGR3B gene copy number in Indian population. Int J Immunogenet 2014; 42:26-30. [PMID: 25428402 DOI: 10.1111/iji.12165] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 09/12/2014] [Accepted: 10/23/2014] [Indexed: 11/27/2022]
Abstract
Amongst several human genome variations, copy number variations (CNVs) are considered as an important source of variability contributing to susceptibility to wide range of diseases. Although CNV is scattered for genes throughout the human genome, several of autoimmunity related genes have CN variation and therefore play an important role in susceptibility to autoimmune diseases. The association of the Fc gamma receptor 3B (FCGR3B) gene copy number in autoimmunity is well characterized in various populations studied. The Fc gamma receptor is a low affinity, glycosylphosphatidylinositol-linked receptor for IgG molecule predominantly expressed on human neutrophils. The variable gene copy number of FCGR3B is found to be involved in the impaired clearance of immune complexes, which significantly contribute to the pathogenesis of several autoimmune diseases such as systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), type-1 diabetes and others. The FCGR3B copy number ranged from 0 to ≥ 2 copies per diploid genome in other populations, but yet not explored in Indian population. Hence, this study aims to evaluate the variation in the frequency distribution of FCGR3B CNV in Indian population. FCGR3B gene copy number varied significantly when compared to other population of the world. This observation will help us in exploring the potential role of CNV in FCGR3B gene and its association to autoimmune disorders in Indian population.
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Affiliation(s)
- S H Almal
- Department of Cell and Molecular Biology, B.V. Patel Pharmaceutical Education and Research Development (PERD) Centre, Thaltej, Ahmedabad, Gujarat, India
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Jung SH, Yim SH, Hu HJ, Lee KH, Lee JH, Sheen DH, Lim MK, Kim SY, Park SW, Kim SH, Han K, Kim TH, Shim SC, Chung YJ. Genome-wide copy number variation analysis identifies deletion variants associated with ankylosing spondylitis. Arthritis Rheumatol 2014; 66:2103-12. [PMID: 24692264 DOI: 10.1002/art.38650] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 03/27/2014] [Indexed: 01/16/2023]
Abstract
OBJECTIVE To identify ankylosing spondylitis (AS)-associated copy number variations (CNVs) in Korean subjects and their synergistic roles in the development of AS. METHODS A genome-wide association study (GWAS) was performed in 309 patients with AS and 309 control subjects, using a copy number variant (CNV) microarray. AS-associated CNV regions were replicated in 2 independent sets (625 patients and 891 control subjects) by quantitative polymerase chain reaction (PCR) and deletion-typing PCR. RESULTS In the CNV GWAS, 227 CNV regions were shown to be significantly associated with the risk of AS. Of the candidate CNV regions, 9 were successfully replicated in the first replication analysis: 1q32.2 (HHAT), 1p34.2 (BMP8A), 2q31.2 (PRKRA), 6p21.32 (HLA-DPB1), 11q22.1 (CNTN5), 13q13.1 (EEF1DP3), 14q24.2 (RGS6), 16p13.3, and 22q11.1 (IL17RA). The 5 deletion-type CNV regions, in 1q32.2, 2q31.2, 6p21.32, 13q13.1, and 16p13.3, were associated with an increased risk of AS, and the other 4 CNV regions were protective. In the second replication analysis, 4 CNV regions in 1q32.2, 2q31.2, 6p21.32, and 16p13.3 were replicated. Among patients with CNV regions in ≥4 risk-increasing loci, the risk was 18.0 times higher than that in patients without any deletions (odds ratio [OR] 17.98, P = 2.3 × 10(-7) ). Among patients with CNV regions in ≥2 protective loci, the risk was 5.2 times lower than that in those without any deletions (OR 0.19, P = 4.0 × 10(-10) ). The additive effects of simultaneous events were shown to be dependent on the frequency of CNV regions. Through deletion-typing PCR and sequencing, the exact sizes and breakpoint sequences were defined in 4 CNV regions. The mechanism of all 3 deletions was shown to be microhomology-based nonhomologous end joining. CONCLUSION The results of this study can help to identify pathogenic mechanisms of AS and can easily be applied in the development of algorithms estimating the risk of AS.
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Nguyen HT, Merriman TR, Black MA. The CNVrd2 package: measurement of copy number at complex loci using high-throughput sequencing data. Front Genet 2014; 5:248. [PMID: 25136349 PMCID: PMC4117933 DOI: 10.3389/fgene.2014.00248] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2014] [Accepted: 07/09/2014] [Indexed: 11/15/2022] Open
Abstract
Recent advances in high-throughout sequencing technologies have made it possible to accurately assign copy number (CN) at CN variable loci. However, current analytic methods often perform poorly in regions in which complex CN variation is observed. Here we report the development of a read depth-based approach, CNVrd2, for investigation of CN variation using high-throughput sequencing data. This methodology was developed using data from the 1000 Genomes Project from the CCL3L1 locus, and tested using data from the DEFB103A locus. In both cases, samples were selected for which paralog ratio test data were also available for comparison. The CNVrd2 method first uses observed read-count ratios to refine segmentation results in one population. Then a linear regression model is applied to adjust the results across multiple populations, in combination with a Bayesian normal mixture model to cluster segmentation scores into groups for individual CN counts. The performance of CNVrd2 was compared to that of two other read depth-based methods (CNVnator, cn.mops) at the CCL3L1 and DEFB103A loci. The highest concordance with the paralog ratio test method was observed for CNVrd2 (77.8/90.4% for CNVrd2, 36.7/4.8% for cn.mops and 7.2/1% for CNVnator at CCL3L1 and DEF103A). CNVrd2 is available as an R package as part of the Bioconductor project: http://www.bioconductor.org/packages/release/bioc/html/CNVrd2.html.
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Affiliation(s)
- Hoang T Nguyen
- Department of Biochemistry, University of Otago Dunedin, New Zealand ; Department of Mathematics and Statistics, University of Otago Dunedin, New Zealand ; Department of Biochemistry, Virtual Institute of Statistical Genetics, University of Otago Dunedin, New Zealand
| | - Tony R Merriman
- Department of Biochemistry, University of Otago Dunedin, New Zealand ; Department of Biochemistry, Virtual Institute of Statistical Genetics, University of Otago Dunedin, New Zealand
| | - Michael A Black
- Department of Biochemistry, University of Otago Dunedin, New Zealand ; Department of Biochemistry, Virtual Institute of Statistical Genetics, University of Otago Dunedin, New Zealand
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Human gene copy number variation and infectious disease. Hum Genet 2014; 133:1217-33. [PMID: 25110110 DOI: 10.1007/s00439-014-1457-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 05/20/2014] [Indexed: 01/05/2023]
Abstract
Variability in the susceptibility to infectious disease and its clinical manifestation can be determined by variation in the environment and by genetic variation in the pathogen and the host. Despite several successes based on candidate gene studies, defining the host variation affecting infectious disease has not been as successful as for other multifactorial diseases. Both single nucleotide variation and copy number variation (CNV) of the host contribute to the host's susceptibility to infectious disease. In this review we focus on CNV, particularly on complex multiallelic CNV that is often not well characterised either directly by hybridisation methods or indirectly by analysis of genotypes and flanking single nucleotide variants. We summarise the well-known examples, such as α-globin deletion and susceptibility to severe malaria, as well as more recent controversies, such as the extensive CNV of the chemokine gene CCL3L1 and HIV infection. We discuss the potential biological mechanisms that could underly any genetic association and reflect on the extensive complexity and functional variation generated by a combination of CNV and sequence variation, as illustrated by the Fc gamma receptor genes FCGR3A, FCGR3B and FCGR2C. We also highlight some understudied areas that might prove fruitful areas for further research.
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Compilation of copy number variants identified in phenotypically normal and parous Japanese women. J Hum Genet 2014; 59:326-31. [PMID: 24785687 DOI: 10.1038/jhg.2014.27] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Revised: 03/21/2014] [Accepted: 03/26/2014] [Indexed: 11/09/2022]
Abstract
With increasing public concern about infertility and the frequent involvement of chromosomal anomalies in miscarriage, analyses of copy number variations (CNVs) have been used to identify the genomic regions responsible for each process of childbearing. Although associations between CNVs and diseases have been reported, many CNVs have also been identified in healthy individuals. Like other types of mutations, phenotypically indefinite CNVs may have been retained and accumulated during anthropogenesis. Therefore to distinguish causative variants from other variants is a formidable task. Furthermore, because previous studies have predominantly focused on European and African populations, comprehensive detection of common Asian CNVs is eagerly awaited. Here, using a high-resolution genotyping array and samples from 411 Japanese women with normal parity without significant complications, we have compiled 1043 copy number variable regions. In total, the collected regions cover 164 Mb, or up to 0.5% of the genome. The copy number differences in these regions may be irrelevant not only to infertility but also to a wide range of diseases. The utility of this resource in reducing the candidate pathogenetic variants, especially in Japanese subjects, is also demonstrated.
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Association between HLA-DQA1 gene copy number polymorphisms and susceptibility to rheumatoid arthritis in Chinese Han population. J Genet 2014; 93:215-8. [DOI: 10.1007/s12041-014-0339-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Yuan J, Zhao D, Wu L, Xu X, Pang Y, Zhang J, Ma Y, Liu J, Wang J. FCGR3Bcopy number loss rather than gain is a risk factor for systemic lupus erythematous and lupus nephritis: a meta-analysis. Int J Rheum Dis 2014; 18:392-7. [PMID: 24673810 DOI: 10.1111/1756-185x.12342] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Jin Yuan
- Department of Dermatology; Huashan Hospital affiliated to Fudan University; Shanghai China
| | - Dongbao Zhao
- Department of Rheumatology and Immunology; Changhai Hospital affiliated to Second Military Medical University; Shanghai China
| | - Lijun Wu
- Department of Digestive Diseases; Huashan Hospital affiliated to Fudan University; Shanghai China
| | - Xia Xu
- Department of Rheumatology and Immunology; Changhai Hospital affiliated to Second Military Medical University; Shanghai China
| | - Yafei Pang
- Department of Rheumatology and Immunology; Changhai Hospital affiliated to Second Military Medical University; Shanghai China
| | - Jun Zhang
- Department of Digestive Diseases; Huashan Hospital affiliated to Fudan University; Shanghai China
| | - Yanyun Ma
- Ministry of Education Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering; School of Life Sciences; Fudan University; Shanghai China
| | - Jie Liu
- Department of Digestive Diseases; Huashan Hospital affiliated to Fudan University; Shanghai China
| | - Jiucun Wang
- Ministry of Education Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering; School of Life Sciences; Fudan University; Shanghai China
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Singer J, Jensen‐Jarolim E. IgE-based immunotherapy of cancer: challenges and chances. Allergy 2014; 69:137-49. [PMID: 24117861 PMCID: PMC4022995 DOI: 10.1111/all.12276] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2013] [Indexed: 12/16/2022]
Abstract
Passive immunotherapy with monoclonal antibodies is an indispensable cornerstone of clinical oncology. Notably, all FDA-approved antibodies comprise the IgG class, although numerous research articles proposed monoclonal antibodies of the IgM, IgG, IgA and IgE classes directed specifically against tumor-associated antigens. In particular, for the IgE isotype class, several recent studies could demonstrate high tumoricidic efficacy. Therefore, this review specifically highlights the latest developments toward IgE-based immunotherapy of cancer. Possible mechanisms and safety aspects of IgE-mediated tumor cell death are discussed with special focus on the attracted immune cells. An outlook is given on how especially comparative oncology could contribute to further developments. Humans and dogs have a highly comparable IgE biology, suggesting that translational AllergoOncology studies in patients with canine cancer could have predictive value for the potential of IgE-based anticancer immunotherapy in human clinical oncology.
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Affiliation(s)
- J. Singer
- Comparative Immunology and Oncology Institute of Pathophysiology and Allergy Research Medical University of Vienna Vienna Austria
| | - E. Jensen‐Jarolim
- Comparative Immunology and Oncology Institute of Pathophysiology and Allergy Research Medical University of Vienna Vienna Austria
- Comparative Medicine Messerli Research Institute of the University of Veterinary Medicine Vienna Medical University Vienna and University Vienna Vienna Austria
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29
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Comment on ‘No association of primary Sjögren’s syndrome with Fcγ receptor gene variants’. Genes Immun 2013; 14:530-1. [DOI: 10.1038/gene.2013.52] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Bullich G, Ballarín J, Oliver A, Ayasreh N, Silva I, Santín S, Díaz-Encarnación MM, Torra R, Ars E. HLA-DQA1 and PLA2R1 polymorphisms and risk of idiopathic membranous nephropathy. Clin J Am Soc Nephrol 2013; 9:335-43. [PMID: 24262501 DOI: 10.2215/cjn.05310513] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
BACKGROUND AND OBJECTIVES Single nucleotide polymorphisms (SNPs) within HLA complex class II HLA-DQ α-chain 1 (HLA-DQA1) and M-type phospholipase A2 receptor (PLA2R1) genes were identified as strong risk factors for idiopathic membranous nephropathy (IMN) development in a recent genome-wide association study. Copy number variants (CNVs) within the Fc gamma receptor III (FCGR3) locus have been associated with several autoimmune diseases, but their role in IMN has not been studied. This study aimed to validate the association of HLA-DQA1 and PLA2R1 risk alleles with IMN in a Spanish cohort, test the putative association of FCGR3A and FCGR3B CNVs with IMN, and assess the use of these genetic factors to predict the clinical outcome of the disease. DESIGN, SETTINGS, PARTICIPANTS, & MEASUREMENTS A Spanish cohort of 89 IMN patients and 286 matched controls without nephropathy was recruited between October of 2009 and July of 2012. Case-control studies for SNPs within HLA-DQA1 (rs2187668) and PLA2R1 (rs4664308) genes and CNVs for FCGR3A and FCGR3B genes were performed. The contribution of these polymorphisms to predict clinical outcome and renal function decline was analyzed. RESULTS This study validated the association of these HLA-DQA1 and PLA2R1 SNPs with IMN in a Spanish cohort and its increased risk when combining both risk genotypes. No significant association was found between FCGR3 CNVs and IMN. These results revealed that HLA-DQA1 and PLA2R1 genotype combination adjusted for baseline proteinuria strongly predicted response to immunosuppressive therapy. HLA-DQA1 genotype adjusted for proteinuria was also linked with renal function decline. CONCLUSION This study confirms that HLA-DQA1 and PLA2R1 genotypes are risk factors for IMN, whereas no association was identified for FCGR3 CNVs. This study provides, for the first time, evidence of the contribution of these HLA-DQA1 and PLA2R1 polymorphisms in predicting IMN response to immunosuppressors and disease progression. Future studies are needed to validate and identify prognostic markers.
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Affiliation(s)
- Gemma Bullich
- Molecular Biology Laboratory and, †Nephrology Department, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Universitat Autònoma de Barcelona, Red de Investigación Renal, Instituto de Investigación Carlos III, Barcelona, Spain
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Dunstan E, Lester S, Black R, Rischmueller M, Chan H, Hewitt AW, Hill CL. No Association between FC γ R3B Copy Number Variation and Susceptibility to Biopsy-Proven Giant Cell Arteritis. ARTHRITIS 2013; 2013:514914. [PMID: 24027635 PMCID: PMC3762162 DOI: 10.1155/2013/514914] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 07/21/2013] [Indexed: 11/18/2022]
Abstract
Objective. To determine the relationship between FCGR3B gene copy number variation (CNV) and biopsy proven giant cell arteritis (GCA). Methods. FCGR3B CNV was determined in 139 Australian biopsy proven GCA patients and 162 population matched controls, using a duplex qPCR assay and RNase P as the reference gene. Copy number was determined using Copy Caller software (v.1.0, Applied Biosystems, USA). CNV genotypes were classified into 3 groups (<2, 2, 3+) for analysis purposes, and analysis was performed using logistic regression. Results. All GCA patients had a positive temporal artery biopsy, and the most common presenting symptoms were visual disturbance and temporal headache. The mean age of patients at biopsy was 74 years (range 51-94) and 88/139 (63%) were female. The frequency of low (<2) FCGR3B copy number was comparable between GCA patients (9/139 = 6.5%) and controls (10/162 = 6.2%), as was the frequency of high (3+) FCGR3B copy number (15/130 (10.8%) in GCA patients versus 13/162 (8.0%) in controls). Overall there was no evidence that FCGR3B CNV frequencies differed between GCA patients and controls (χ (2) = 0.75, df = 2, P = 0.69). Conclusion. FCGR3B CNV is not associated with GCA; however, replicate studies are required.
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Affiliation(s)
- Emma Dunstan
- Rheumatology Department, The Queen Elizabeth Hospital, Woodville South, SA 5011, Australia
- The Health Observatory, Discipline of Medicine, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Sue Lester
- Rheumatology Department, The Queen Elizabeth Hospital, Woodville South, SA 5011, Australia
| | - Rachel Black
- Rheumatology Department, The Queen Elizabeth Hospital, Woodville South, SA 5011, Australia
| | - Maureen Rischmueller
- Rheumatology Department, The Queen Elizabeth Hospital, Woodville South, SA 5011, Australia
- Discipline of Medicine, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Helen Chan
- Centre for Eye Research, Royal Victorian Eye and Ear Hospital, University of Melbourne, East Melbourne, VIC 3002, Australia
| | - Alex W. Hewitt
- Centre for Eye Research, Royal Victorian Eye and Ear Hospital, University of Melbourne, East Melbourne, VIC 3002, Australia
- Lions Institute, University of Western Australia, Nedlands, WA 6009, Australia
| | - Catherine L. Hill
- Rheumatology Department, The Queen Elizabeth Hospital, Woodville South, SA 5011, Australia
- The Health Observatory, Discipline of Medicine, The University of Adelaide, Adelaide, SA 5005, Australia
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Nossent JC, Becker-Merok A, Rischmueller M, Lester S. Susceptibility for Lupus Nephritis by Low Copy Number of the FCGR3B Gene Is Linked to Increased Levels of Pathogenic Autoantibodies. Autoimmune Dis 2013; 2013:750814. [PMID: 23864940 PMCID: PMC3705838 DOI: 10.1155/2013/750814] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 06/03/2013] [Indexed: 12/14/2022] Open
Abstract
Low copy number (CN) of the FCGR3B gene reduces FCGR3B membrane expression on neutrophils and results in clearance of a smaller amount of immune complex. We investigated FCGR3B CN in relation to the clinical phenotype in a Caucasian SLE cohort (n = 107). FCGR3B CN was determined by three different qPCR parameter estimations (Ct-, Cy0, and cpD1) and confirmed by the FCGR2C/FCGR2A paralog ratio test. Clinical and serological data were then analyzed for their association with FCGR3B CN. Low FCGR3B CN (<2) was more frequent in SLE patients than in healthy controls (n = 162) (20% versus 6%, OR 4.15, P = 0.003) and associated with higher disease activity scores (SLEDAI 10.4 versus 6.1, P = 0.03), lupus nephritis (LN) (25 versus 5%, P = 0.03), and increased levels of antibodies against dsDNA (81 versus 37 IU, P = 0.03), C1q (22 versus 6 IU, P = 0.003), and ribosomal P (10 versus 5 IU, P = 0.01). No such associations were seen with antibodies against extractable nuclear antigens or high FCGR3B CN (>2). In multivariate analyses, LN was independently associated with anti-C1q-Ab levels (P = 0.03) and low FCGR3B CN (P = 0.09). We conclude that the susceptibility for LN in patients with low FCGR3B CN is linked to increased levels of pathogenic autoantibodies.
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Affiliation(s)
- Johannes C. Nossent
- Department of Rheumatology, Institute of Clinical Medicine, University of Tromsø, 9037 Tromsø, Norway
- Department of Rheumatology, University Hospital Northern Norway, P.O. Box 14, 9038 Tromsø, Norway
- Department of Rheumatology, Basil Hetzel Institute, The Queen Elizabeth Hospital, Adelaide, SA 5020, Australia
| | - Andrea Becker-Merok
- Department of Rheumatology, Institute of Clinical Medicine, University of Tromsø, 9037 Tromsø, Norway
- Department of Rheumatology, University Hospital Northern Norway, P.O. Box 14, 9038 Tromsø, Norway
| | - Maureen Rischmueller
- Department of Rheumatology, Basil Hetzel Institute, The Queen Elizabeth Hospital, Adelaide, SA 5020, Australia
- Division of Medicine, University of Adelaide, Adelaide, SA 5000, Australia
| | - Sue Lester
- Department of Rheumatology, Basil Hetzel Institute, The Queen Elizabeth Hospital, Adelaide, SA 5020, Australia
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CNVrd, a read-depth algorithm for assigning copy-number at the FCGR locus: population-specific tagging of copy number variation at FCGR3B. PLoS One 2013; 8:e63219. [PMID: 23646200 PMCID: PMC3640002 DOI: 10.1371/journal.pone.0063219] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 04/04/2013] [Indexed: 01/09/2023] Open
Abstract
The extent of contribution from common gene copy number (CN) variants in human disease is currently unresolved. Part of the reason for this is the technical difficulty in directly measuring CN variation (CNV) using molecular methods, and the lack of single nucleotide polymorphisms (SNPs) that can tag complex CNV that has arisen multiple times on different SNP haplotypes. One CNV locus implicated in human disease is FCGR. Here we aimed to use next-generation sequencing (NGS) data from the 1000 Genomes Project to assign CN at FCGR3A and FCGR3B and to comprehensively assess the ability of SNPs to tag specific CN variants. A read-depth algorithm was developed (CNVrd) and validated on a subset of HapMap samples using CN assignments that had previously been determined using molecular and microarray methods. At 7 out of 9 other complex loci there was >90% concordance with microarray data. However, given that some prior knowledge of CN is required, the generalizability of CNVrd is limited and should be applied to other complex CNV loci with caution. Subsequently, CN was assigned et FCGR3B using CNVrd in a total of 952 samples from the 1000 Genomes Project, using three classes and SNPs that correlated with duplication were identified. The best tag SNP was observed in the Mexican-American sample set for duplication at FCGR3B. This SNP (rs117435514, r2 = 0.79) also tagged similar duplication in Chinese and Japanese (r2 = 0.35–0.60), but not in Caucasian or African. No tag SNP for duplication at FCGR3A or deletion at FCGR3B was identified in any population. We conclude that it is possible to tag CNV at the FCGR locus, but CN and SNPs have to be characterized and correlated on a population-specific basis.
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Zhou XJ, Cheng FJ, Qi YY, Zhao YF, Hou P, Zhu L, Lv JC, Zhang H. FCGR2B and FCRLB gene polymorphisms associated with IgA nephropathy. PLoS One 2013; 8:e61208. [PMID: 23593433 PMCID: PMC3625155 DOI: 10.1371/journal.pone.0061208] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Accepted: 03/07/2013] [Indexed: 11/19/2022] Open
Abstract
Background IgA nephropathy (IgAN) is a complex syndrome characterized by deposition of IgA and IgA containing immune complexes (ICs) composed of IgG and complement C3 proteins in the mesangial area of glomeruli. The low-affinity receptors for the Fc region of IgG (FcγRs) are involved in autoantibody/immune complex-induced organ injury as well as ICs clearance. The aim of the study was to associate multiple polymorphisms within FCGR gene locus with IgAN in a large Chinese cohort. Patients and Methods 60 single nucleotide polymorphisms (SNPs) spanning a 400 kb range within FCGR gene locus were analyzed in 2100 DNA samples from patients with biopsy proven IgAN and healthy age- and sex-matched controls from the same population in Chinese. Results Among the 60 SNPs investigated, 15 gene polymorphisms within FCGR gene locus (25%) were associated with susceptibility to IgAN. The most significantly associated SNPs within individual genes were FCGR2B rs12118043 (p = 8.74*10−3, OR 0.76, 95% CI 0.62–0.93), and FCRLB rs4657093 (p = 2.28*10−3, OR 0.77, 95% CI 0.65–0.91). Both conditional analysis and linkage disequilibrium analysis suggested they were independent signals associated with IgAN. Associations between FCGR2B rs12118043 and proteinuria (p = 3.65×10−2) as well as gross hematuria (p = 4.53×10−2), between FCRLB rs4657093 and levels of serum creatinine (p = 2.67×10−2) as well as eGFR (p = 5.41*10−3) were also observed. Electronic cis-expression quantative trait loci analysis supported their possible functional significance, with protective genotypes correlating lower gene expressions. Conclusion Our data from genetic associations and expression associations revealed potentially pathogenic roles of Fc receptor gene polymorphisms in IgAN.
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Affiliation(s)
- Xu-jie Zhou
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Key Laboratory of Renal Disease, Ministry of Health of China, Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, People's Republic of China
| | - Fa-juan Cheng
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Key Laboratory of Renal Disease, Ministry of Health of China, Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, People's Republic of China
| | - Yuan-yuan Qi
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Key Laboratory of Renal Disease, Ministry of Health of China, Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, People's Republic of China
| | - Yan-feng Zhao
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Key Laboratory of Renal Disease, Ministry of Health of China, Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, People's Republic of China
| | - Ping Hou
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Key Laboratory of Renal Disease, Ministry of Health of China, Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, People's Republic of China
| | - Li Zhu
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Key Laboratory of Renal Disease, Ministry of Health of China, Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, People's Republic of China
| | - Ji-cheng Lv
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Key Laboratory of Renal Disease, Ministry of Health of China, Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, People's Republic of China
| | - Hong Zhang
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Key Laboratory of Renal Disease, Ministry of Health of China, Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, People's Republic of China
- * E-mail:
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Olsson LM, Holmdahl R. Copy number variation in autoimmunity--importance hidden in complexity? Eur J Immunol 2012; 42:1969-76. [PMID: 22865047 DOI: 10.1002/eji.201242601] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Copy number variation, namely regions of the genome that can be either deleted or duplicated in a variable way, has emerged as an important source of genetic variance in the human genome. Genes with immunological functions are particularly prone to copy number variation, in part because this is a mechanism to expand the recognition repertoire; however, immunological genes not directly involved in immune recognition are also copy number variable but, despite the link between immunological function and copy number variation, very few copy number variants (CNVs) have been found to be associated with autoimmune diseases, even in recent large genome-wide CNV-association studies. Nonetheless, CNVs in FCGR3B, DEFB4, CCL3L1, C4A/B and NCF1 have been suggested to be associated with autoimmune diseases, although there is conflicting evidence in all cases. The reasons for the lack of definitive data on CNV-autoimmunity associations, as well as the technical challenges for the field are the focus of this review.
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Affiliation(s)
- Lina M Olsson
- Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
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Cantsilieris S, White SJ. Correlating multiallelic copy number polymorphisms with disease susceptibility. Hum Mutat 2012; 34:1-13. [PMID: 22837109 DOI: 10.1002/humu.22172] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Accepted: 07/13/2012] [Indexed: 01/20/2023]
Abstract
The human genome contains a significant amount of sequence variation, from single nucleotide polymorphisms to large stretches of DNA that may be present in a range of different copies between individuals. Several such regions are variable in >1% of the population (referred to as copy number polymorphisms or CNPs), and many studies have looked for associations between the copy number of genes within multiallelic CNPs and disease susceptibility. Associations have indeed been described for several genes, including the β-defensins (DEFB4, DEFB103, DEFB104), chemokine ligand 3 like 1 (CCL3L1), Fc gamma receptor 3B (FCGR3B), and complement component C4 (C4). However, follow-up replication in independent cohorts has failed to reproduce a number of these associations. It is clear that replicated associations such as those between C4 and systemic lupus erythematosus, and β-defensin and psoriasis, have used robust genotyping methodologies. Technical issues associated with genotyping sequences of high identity may therefore account for failure to replicate other associations. Here, we compare and contrast the most popular approaches that have been used to genotype CNPs, describe how they have been applied in different situations, and discuss potential reasons for the difficulty in reproducibly linking multiallelic CNPs to complex diseases.
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Affiliation(s)
- Stuart Cantsilieris
- Centre for Reproduction and Development, Monash Institute of Medical Research, Monash University, Melbourne, Victoria, Australia
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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] [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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McKinney C, Broen JCA, Vonk MC, Beretta L, Hesselstrand R, Hunzelmann N, Riemekasten G, Scorza R, Simeon CP, Fonollosa V, Carreira PE, Ortego-Centeno N, Gonzalez-Gay MA, Airo P, Coenen M, Martin J, Radstake TRDJ, Merriman TR. Evidence that deletion at FCGR3B is a risk factor for systemic sclerosis. Genes Immun 2012; 13:458-60. [PMID: 22551723 DOI: 10.1038/gene.2012.15] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
There is increasing evidence that gene copy number (CN) variation influences clinical phenotype. The low-affinity Fc receptor 3B (FCGR3B) located in the FCGR gene cluster is a CN polymorphic gene involved in the recruitment of polymorphonuclear neutrophils to sites of inflammation and their activation. Given the genetic overlap between systemic lupus erythematosus and systemic sclerosis (SSc) and the strong evidence for FCGR3B CN in the pathology of SLE, we hypothesised that FCGR3B gene dosage influences susceptibility to SSc. We obtained FCGR3B deletion status in 777 European Caucasian cases and 1000 controls. There was an inverse relationship between FCGR3B CN and disease susceptibility. CN of ≤ 1 was a significant risk factor for SSc (OR=1.55 (1.13-2.14), P=0.007) relative to CN ≥ 2. Although requiring replication, these results suggest that impaired immune complex clearance arising from FCGR3B deficiency contributes to the pathology of SSc, and FCGR3B CN variation is a common risk factor for systemic autoimmunity.
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Affiliation(s)
- C McKinney
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
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