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Lanata CM, Blazer A, Criswell LA. The Contribution of Genetics and Epigenetics to Our Understanding of Health Disparities in Rheumatic Diseases. Rheum Dis Clin North Am 2020; 47:65-81. [PMID: 34042055 DOI: 10.1016/j.rdc.2020.09.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Socioeconomic determinants of health are associated with worse outcomes in the rheumatic diseases and contribute significantly to health disparities. However, genetic and epigenetic risk factors may affect different populations disproportionally and further exacerbate health disparities. We discuss the role of genetics and epigenetics to the health disparities observed in rheumatic diseases. We review concepts of population genetics and natural selection, current genome-wide genetic and epigenetic studies of several autoimmune diseases, and environmental exposures associated with disease risk in different populations. To understand how genomics influence health disparities in the rheumatic diseases, further studies in different populations worldwide are needed.
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Affiliation(s)
- Cristina M Lanata
- Russell/Engleman Rheumatology Research Center, University of California, San Francisco, 513 Parnassus Avenue, MSB S865, San Francisco, CA, USA
| | - Ashira Blazer
- Department of Medicine, Division of Rheumatology, NYU Langone Health, 550 1st Avenue, MSB 606, New York, NY 10029, USA
| | - Lindsey A Criswell
- Russell/Engleman Rheumatology Research Center, University of California, San Francisco, 513 Parnassus Avenue, MSB S864, San Francisco, CA, USA.
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Lanata CM, Paranjpe I, Nititham J, Taylor KE, Gianfrancesco M, Paranjpe M, Andrews S, Chung SA, Rhead B, Barcellos LF, Trupin L, Katz P, Dall'Era M, Yazdany J, Sirota M, Criswell LA. A phenotypic and genomics approach in a multi-ethnic cohort to subtype systemic lupus erythematosus. Nat Commun 2019; 10:3902. [PMID: 31467281 PMCID: PMC6715644 DOI: 10.1038/s41467-019-11845-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 07/13/2019] [Indexed: 01/05/2023] Open
Abstract
Systemic lupus erythematous (SLE) is a heterogeneous autoimmune disease in which outcomes vary among different racial groups. Here, we aim to identify SLE subgroups within a multiethnic cohort using an unsupervised clustering approach based on the American College of Rheumatology (ACR) classification criteria. We identify three patient clusters that vary according to disease severity. Methylation association analysis identifies a set of 256 differentially methylated CpGs across clusters, including 101 CpGs in genes in the Type I Interferon pathway, and we validate these associations in an external cohort. A cis-methylation quantitative trait loci analysis identifies 744 significant CpG-SNP pairs. The methylation signature is enriched for ethnic-associated CpGs suggesting that genetic and non-genetic factors may drive outcomes and ethnic-associated methylation differences. Our computational approach highlights molecular differences associated with clusters rather than single outcome measures. This work demonstrates the utility of applying integrative methods to address clinical heterogeneity in multifactorial multi-ethnic disease settings.
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Affiliation(s)
- Cristina M Lanata
- Russell/Engleman Rheumatology Research Center, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Ishan Paranjpe
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joanne Nititham
- Russell/Engleman Rheumatology Research Center, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Kimberly E Taylor
- Russell/Engleman Rheumatology Research Center, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Milena Gianfrancesco
- Russell/Engleman Rheumatology Research Center, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Manish Paranjpe
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
| | - Shan Andrews
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
| | - Sharon A Chung
- Russell/Engleman Rheumatology Research Center, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | | | | | - Laura Trupin
- Russell/Engleman Rheumatology Research Center, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Patricia Katz
- Russell/Engleman Rheumatology Research Center, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Maria Dall'Era
- Russell/Engleman Rheumatology Research Center, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Jinoos Yazdany
- Russell/Engleman Rheumatology Research Center, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Marina Sirota
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
| | - Lindsey A Criswell
- Russell/Engleman Rheumatology Research Center, Department of Medicine, University of California San Francisco, San Francisco, CA, USA.
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.
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Genetic contributions to lupus nephritis in a multi-ethnic cohort of systemic lupus erythematous patients. PLoS One 2018; 13:e0199003. [PMID: 29953444 PMCID: PMC6023154 DOI: 10.1371/journal.pone.0199003] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 05/30/2018] [Indexed: 01/02/2023] Open
Abstract
OBJECTIVE African Americans, East Asians, and Hispanics with systemic lupus erythematous (SLE) are more likely to develop lupus nephritis (LN) than are SLE patients of European descent. The etiology of this difference is not clear, and this study was undertaken to investigate how genetic variants might explain this effect. METHODS In this cross-sectional study, 1244 SLE patients from multiethnic case collections were genotyped for 817,810 single-nucleotide polymorphisms (SNPs) across the genome. Continental genetic ancestry was estimated utilizing the program ADMIXTURE. Gene-based testing and pathway analysis was performed within each ethnic group and meta-analyzed across ethnicities. We also performed candidate SNP association tests with SNPs previously established as risk alleles for SLE, LN, and chronic kidney disease (CKD). Association testing and logistic regression models were performed with LN as the outcome, adjusted for continental ancestries, sex, disease duration, and age. RESULTS We studied 255 North European, 263 South European, 238 Hispanic, 224 African American and 264 East Asian SLE patients, of whom 606 had LN (48.7%). In genome-wide gene-based and candidate SNP analyses, we found distinct genes, pathways and established risk SNPs associated with LN for each ethnic group. Gene-based analyses showed significant associations between variation in ZNF546 (p = 1.0E-06), TRIM15 (p = 1.0E-06), and TRIMI0 (p = 1.0E-06) and LN among South Europeans, and TTC34 (p = 8.0E-06) was significantly associated with LN among Hispanics. The SNP rs8091180 in NFATC1 was associated with LN (OR 1.43, p = 3.3E-04) in the candidate SNP meta-analysis with the highest OR among African-Americans (OR 2.17, p = 0.0035). CONCLUSION Distinct genetic factors are associated with the risk of LN in SLE patients of different ethnicities. CKD risk alleles may play a role in the development of LN in addition to SLE-associated risk variants. These findings may further explain the clinical heterogeneity of LN risk and response to therapy observed between different ethnic groups.
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Taylor KE, Wong Q, Levine DM, McHugh C, Laurie C, Doheny K, Lam MY, Baer AN, Challacombe S, Lanfranchi H, Schiødt M, Srinivasan M, Umehara H, Vivino FB, Zhao Y, Shiboski SC, Daniels TE, Greenspan JS, Shiboski CH, Criswell LA. Genome-Wide Association Analysis Reveals Genetic Heterogeneity of Sjögren's Syndrome According to Ancestry. Arthritis Rheumatol 2017; 69:1294-1305. [PMID: 28076899 PMCID: PMC5449251 DOI: 10.1002/art.40040] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 01/05/2017] [Indexed: 01/10/2023]
Abstract
OBJECTIVE The Sjögren's International Collaborative Clinical Alliance (SICCA) is an international data registry and biorepository derived from a multisite observational study of participants in whom genotyping was performed on the Omni2.5M platform and who had undergone deep phenotyping using common protocol-directed methods. The aim of this study was to examine the genetic etiology of Sjögren's syndrome (SS) across ancestry and disease subsets. METHODS We performed genome-wide association study analyses using SICCA subjects and external controls obtained from dbGaP data sets, one using all participants (1,405 cases, 1,622 SICCA controls, and 3,125 external controls), one using European participants (585, 966, and 580, respectively), and one using Asian participants (460, 224, and 901, respectively) with ancestry adjustments via principal components analyses. We also investigated whether subphenotype distributions differ by ethnicity, and whether this contributes to the heterogeneity of genetic associations. RESULTS We observed significant associations in established regions of the major histocompatibility complex (MHC), IRF5, and STAT4 (P = 3 × 10-42 , P = 3 × 10-14 , and P = 9 × 10-10 , respectively), and several novel suggestive regions (those with 2 or more associations at P < 1 × 10-5 ). Two regions have been previously implicated in autoimmune disease: KLRG1 (P = 6 × 10-7 [Asian cluster]) and SH2D2A (P = 2 × 10-6 [all participants]). We observed striking differences between the associations in Europeans and Asians, with high heterogeneity especially in the MHC; representative single-nucleotide polymorphisms from established and suggestive regions had highly significant differences in the allele frequencies in the study populations. We showed that SSA/SSB autoantibody production and the labial salivary gland focus score criteria were associated with the first worldwide principal component, indicative of higher non-European ancestry (P = 4 × 10-15 and P = 4 × 10-5 , respectively), but that subphenotype differences did not explain most of the ancestry differences in genetic associations. CONCLUSION Genetic associations with SS differ markedly according to ancestry; however, this is not explained by differences in subphenotypes.
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Affiliation(s)
| | | | | | | | | | | | - Mi Y. Lam
- University of CaliforniaSan Francisco
| | | | - Stephen Challacombe
- Guy's, King's, and St. Thomas' Dental Institute, King's College LondonLondonUK
| | | | | | | | | | | | - Yan Zhao
- Peking Union Medical College HospitalBeijingChina
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Abstract
INTRODUCTION Systemic lupus erythematosus (SLE) is a disease distributed worldwide, which occurs in both genders, and across racial/ethnic and age groups; however, higher rates are observed in adults, in women and in non-Caucasians. Genetic, environmental, sociodemographic and methodological issues are responsible not only for these differences but for the variable course and outcome of the disease. Non-Caucasians have a more severe disease with a higher risk for early mortality and damage accrual. Males also have a more severe disease; however, a negative impact of male gender on lupus outcomes has not been firmly established. Childhood-onset is associated with a more severe disease; moreover, it is also associated with higher damage and diminished survival; finally, late-onset lupus is mild but it is associated with higher damage accrual and a diminished survival. Areas covered: In this review, we discuss the incidence and prevalence of SLE, the impact of age, gender and race/ethnicity in SLE and in the survival of those affected. Expert commentary: Age, gender and race/ethnicity impact disease expression in SLE patients; despite improvements in survival, mortality in SLE remains almost three times higher than in the general population.
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Affiliation(s)
- Guillermo J Pons-Estel
- a Department of Autoimmune Diseases , Institut Clinic de Medicina I Dermatologia, Hospital Clinic , Barcelona , Catalonia , Spain.,b Division of Rheumatology and Autoimmune Diseases , Sanatorio Parque, Grupo Oroño , Rosario , Argentina
| | - Manuel F Ugarte-Gil
- c Servicio de Reumatología , Hospital Nacional Guillermo Almenara Irigoyen, EsSalud , Lima , Perú.,d School of Medicine , Universidad Científica del Sur , Lima , Perú
| | - Graciela S Alarcón
- e Division of Clinical Immunology and Rheumatology, School of Medicine , The University of Alabama at Birmingham , Birmingham , AL , USA.,f Department of Medicine, School of Medicine , Universidad Peruana Cayetano Heredia , Lima , Perú
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Seldin MF. The genetics of human autoimmune disease: A perspective on progress in the field and future directions. J Autoimmun 2015; 64:1-12. [PMID: 26343334 PMCID: PMC4628839 DOI: 10.1016/j.jaut.2015.08.015] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 08/23/2015] [Indexed: 12/18/2022]
Abstract
Progress in defining the genetics of autoimmune disease has been dramatically enhanced by large scale genetic studies. Genome-wide approaches, examining hundreds or for some diseases thousands of cases and controls, have been implemented using high throughput genotyping and appropriate algorithms to provide a wealth of data over the last decade. These studies have identified hundreds of non-HLA loci as well as further defining HLA variations that predispose to different autoimmune diseases. These studies to identify genetic risk loci are also complemented by progress in gene expression studies including definition of expression quantitative trait loci (eQTL), various alterations in chromatin structure including histone marks, DNase I sensitivity, repressed chromatin regions as well as transcript factor binding sites. Integration of this information can partially explain why particular variations can alter proclivity to autoimmune phenotypes. Despite our incomplete knowledge base with only partial definition of hereditary factors and possible functional connections, this progress has and will continue to facilitate a better understanding of critical pathways and critical changes in immunoregulation. Advances in defining and understanding functional variants potentially can lead to both novel therapeutics and personalized medicine in which therapeutic approaches are chosen based on particular molecular phenotypes and genomic alterations.
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Affiliation(s)
- Michael F Seldin
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Tupper Hall Room 4453, Davis, CA 95616, USA; Division of Rheumatology and Allergy, Department of Medicine, University of California, Davis, Tupper Hall Room 4453, Davis, CA 95616, USA.
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Petit A, Dadzie O. Multisystemic diseases and ethnicity: a focus on lupus erythematosus, systemic sclerosis, sarcoidosis and Behçet disease. Br J Dermatol 2013; 169 Suppl 3:1-10. [PMID: 24098896 DOI: 10.1111/bjd.12533] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/16/2013] [Indexed: 01/15/2023]
Affiliation(s)
- A. Petit
- Service de Dermatologie; APHP Hôpital Saint-Louis; 1 avenue Claude Vellefaux 75010 Paris France
| | - O.E. Dadzie
- Department of Dermatology and Histopathology; The North West London Hospitals NHS Trust; Northwick Park Hospital; Watford Road Harrow HA1 3UJ U.K
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Levy DM, Peschken CA, Tucker LB, Chédeville G, Huber AM, Pope JE, Silverman ED. Influence of ethnicity on childhood-onset systemic lupus erythematosus: results from a multiethnic multicenter Canadian cohort. Arthritis Care Res (Hoboken) 2013; 65:152-60. [PMID: 22744999 DOI: 10.1002/acr.21779] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2012] [Accepted: 06/16/2012] [Indexed: 11/09/2022]
Abstract
OBJECTIVE To determine the influence of ethnicity and sociodemographic factors on disease characteristics of the Canadian pediatric lupus population. METHODS Childhood-onset systemic lupus erythematosus (SLE) patients at 4 pediatric centers in Halifax, Montreal, Toronto, and Vancouver were consecutively recruited. Sociodemographics and disease data were collected. Patients were categorized by their primary self-selected ethnicity, and exploratory cluster analyses were examined for disease expression by ethnicity. RESULTS We enrolled 213 childhood-onset SLE patients, and ethnicity data were available for 206 patients: white (31%), Asian (30%), South Asian (15%), black (10%), Latino/Hispanic (4%), Aboriginal (4%), and Arab/Middle Eastern (3%). The frequency of clinical classification criteria (malar rash, arthritis, serositis, and renal disease) and autoantibodies significantly differed among ethnicities. Medications were prescribed equally across ethnicities: 76% were taking prednisone, 86% antimalarials, and 56% required additional immunosuppressants. Cluster analysis partitioned into 3 main groups: mild (n = 50), moderate (n = 82), and severe (n = 68) disease clusters. Only 20% of white patients were in the severe cluster compared to 51% of Asian and 41% of black patients (P = 0.03). However, disease activity indices and damage scores were similar across ethnicities. CONCLUSION Canadian childhood-onset SLE patients reflect our multiethnic population, with differences in disease manifestations, autoantibody profiles, and severity of disease expression by ethnicity.
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Affiliation(s)
- Deborah M Levy
- Hospital for Sick Children and University of Toronto, Toronto, Ontario, Canada.
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Richman IB, Taylor KE, Chung SA, Trupin L, Petri M, Yelin E, Graham RR, Lee A, Behrens TW, Gregersen PK, Seldin MF, Criswell LA. European genetic ancestry is associated with a decreased risk of lupus nephritis. ARTHRITIS AND RHEUMATISM 2012; 64:3374-82. [PMID: 23023776 PMCID: PMC3865923 DOI: 10.1002/art.34567] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
OBJECTIVE African Americans, East Asians, and Hispanics with systemic lupus erythematosus (SLE) are more likely to develop renal disease than are SLE patients of European descent. This study was undertaken to investigate whether European genetic ancestry protects against the development of lupus nephritis, with the aim of exploring the genetic and socioeconomic factors that might explain this effect. METHODS This was a cross-sectional study of SLE patients from a multiethnic case collection. Participants were genotyped for 126 single-nucleotide polymorphisms (SNPs) informative for ancestry. A subset of participants was also genotyped for 80 SNPs in 14 candidate genes for renal disease in SLE. Logistic regression was used to test the association between European ancestry and renal disease. Analyses were adjusted for continental ancestries, socioeconomic status (SES), and candidate genes. RESULTS Participants (n = 1,906) had, on average, 62.4% European, 15.8% African, 11.5% East Asian, 6.5% Amerindian, and 3.8% South Asian ancestry. Among the participants, 656 (34%) had renal disease. A 10% increase in the proportion of European ancestry estimated in each participant was associated with a 15% reduction in the odds of having renal disease, after adjustment for disease duration and sex (odds ratio 0.85, 95% confidence interval 0.82-0.87; P = 1.9 × 10(-30) ). Adjustment for other genetic ancestries, measures of SES, or SNPs in the genes most associated with renal disease (IRF5 [rs4728142], BLK [rs2736340], STAT4 [rs3024912], and HLA-DRB1*0301 and DRB1*1501) did not substantively alter this relationship. CONCLUSION European ancestry is protective against the development of renal disease in SLE, an effect that is independent of other genetic ancestries, candidate risk alleles, and socioeconomic factors.
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Alonso-Perez E, Suarez-Gestal M, Calaza M, Ordi-Ros J, Balada E, Bijl M, Papasteriades C, Carreira P, Skopouli FN, Witte T, Endreffy E, Marchini M, Migliaresi S, Sebastiani GD, Santos MJ, Suarez A, Blanco FJ, Barizzone N, Pullmann R, Ruzickova S, Lauwerys BR, Gomez-Reino JJ, Gonzalez A. Further evidence of subphenotype association with systemic lupus erythematosus susceptibility loci: a European cases only study. PLoS One 2012; 7:e45356. [PMID: 23049788 PMCID: PMC3458859 DOI: 10.1371/journal.pone.0045356] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Accepted: 08/14/2012] [Indexed: 11/24/2022] Open
Abstract
Introduction Systemic Lupus Erythematosus (SLE) shows a spectrum of clinical manifestations that complicate its diagnosis, treatment and research. This variability is likely related with environmental exposures and genetic factors among which known SLE susceptibility loci are prime candidates. The first published analyses seem to indicate that this is the case for some of them, but results are still inconclusive and we aimed to further explore this question. Methods European SLE patients, 1444, recruited at 17 centres from 10 countries were analyzed. Genotypes for 26 SLE associated SNPs were compared between patients with and without each of 11 clinical features: ten of the American College of Rheumatology (ACR) classification criteria (except ANAs) and age of disease onset. These analyses were adjusted for centre of recruitment, top ancestry informative markers, gender and time of follow-up. Overlap of samples with previous studies was excluded for assessing replication. Results There were three new associations: the SNPs in XKR6 and in FAM167A-BLK were associated with lupus nephritis (OR = 0.76 and 1.30, Pcorr = 0.007 and 0.03, respectively) and the SNP of MECP2, which is in chromosome X, with earlier age of disease onset in men. The previously reported association of STAT4 with early age of disease onset was replicated. Some other results were suggestive of the presence of additional associations. Together, the association signals provided support to some previous findings and to the characterization of lupus nephritis, autoantibodies and age of disease onset as the clinical features more associated with SLE loci. Conclusion Some of the SLE loci shape the disease phenotype in addition to increase susceptibility to SLE. This influence is more prominent for some clinical features than for others. However, results are only partially consistent between studies and subphenotype specific GWAS are needed to unravel their genetic component.
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Affiliation(s)
- Elisa Alonso-Perez
- Laboratorio de Investigacion 10 and Rheumatology Unit, Instituto de Investigacion Sanitaria - Hospital Clinico Universitario de Santiago, Santiago de Compostela, Spain
| | - Marian Suarez-Gestal
- Laboratorio de Investigacion 10 and Rheumatology Unit, Instituto de Investigacion Sanitaria - Hospital Clinico Universitario de Santiago, Santiago de Compostela, Spain
| | - Manuel Calaza
- Laboratorio de Investigacion 10 and Rheumatology Unit, Instituto de Investigacion Sanitaria - Hospital Clinico Universitario de Santiago, Santiago de Compostela, Spain
| | - Josep Ordi-Ros
- Internal Medicine, Research Laboratory in Autoimmune Diseases, Hospital Vall d’Hebron, Barcelona, Spain
| | - Eva Balada
- Internal Medicine, Research Laboratory in Autoimmune Diseases, Hospital Vall d’Hebron, Barcelona, Spain
| | - Marc Bijl
- Department of Internal Medicine and Rheumatology, Martini Hospital, Groningen, The Netherlands
| | - Chryssa Papasteriades
- Department of Histocompatibility and Immunology, Evangelismos Hospital, Athens, Greece
| | | | - Fotini N. Skopouli
- Pathophysiology Department, Athens University Medical School, Athens, Greece
| | - Torsten Witte
- Division of Clinical Immunology, Department of Internal Medicine of the Hannover Medical School, Hannover, Germany
| | - Emöke Endreffy
- Paediatrics Department, Albert Szent-Györgyi Medical Centre, University of Szeged, Szeged, Hungary
| | - Maurizio Marchini
- Referral Center for Systemic Autoimmune Diseases, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico and University of Milan, Milan, Italy
| | | | | | - Maria Jose Santos
- Rheumatology Department, Hospital Garcia de Orta and Rheumatology Research Unit, Instituto Medicina Molecular, Lisboa, Portugal
| | - Ana Suarez
- Department of Functional Biology, Hospital Universitario Central de Asturias, Universidad de Oviedo, Oviedo, Spain
| | | | - Nadia Barizzone
- Department of Medical Sciences and IRCAD, Eastern Piedmont University, Novara, Italy
| | - Rudolf Pullmann
- Institute of Clinical Biochemistry, Martin Faculty Hospital, Jessenius Medical Faculty, Martin, Slovakia
| | - Sarka Ruzickova
- Institute of Biotechnology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Bernard R. Lauwerys
- Cliniques Universitaires Saint-Luc and Université Catholique de Louvain, Brussels, Belgium
| | - Juan J. Gomez-Reino
- Laboratorio de Investigacion 10 and Rheumatology Unit, Instituto de Investigacion Sanitaria - Hospital Clinico Universitario de Santiago, Santiago de Compostela, Spain
- Department of Medicine, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Antonio Gonzalez
- Laboratorio de Investigacion 10 and Rheumatology Unit, Instituto de Investigacion Sanitaria - Hospital Clinico Universitario de Santiago, Santiago de Compostela, Spain
- * E-mail:
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Alonso-Perez E, Suarez-Gestal M, Calaza M, Sebastiani GD, Pullmann R, Papasteriades C, Kovacs A, Skopouli FN, Bijl M, Suarez A, Marchini M, Migliaresi S, Carreira P, Ordi-Ros J, Witte T, Ruzickova S, Santos MJ, Barizzone N, Blanco FJ, Lauwerys BR, Gomez-Reino JJ, Gonzalez A. Bias in effect size of systemic lupus erythematosus susceptibility loci across Europe: a case-control study. Arthritis Res Ther 2012; 14:R94. [PMID: 22541939 PMCID: PMC3446468 DOI: 10.1186/ar3818] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Revised: 03/27/2012] [Accepted: 04/27/2012] [Indexed: 01/11/2023] Open
Abstract
Introduction We aimed to investigate whether the effect size of the systemic lupus erythematosus (SLE) risk alleles varies across European subpopulations. Methods European SLE patients (n = 1,742) and ethnically matched healthy controls (n = 2,101) were recruited at 17 centres from 10 different countries. Only individuals with self-reported ancestry from the country of origin were included. In addition, participants were genotyped for top ancestry informative markers and for 25 SLE associated SNPs. The results were used to compare effect sizes between the Central Eureopan and Southern European subgroups. Results Twenty of the 25 SNPs showed independent association with SLE, These SNPs showed a significant bias to larger effect sizes in the Southern subgroup, with 15/20 showing this trend (P = 0.019) and a larger mean odds ratio of the 20 SNPs (1.46 vs. 1.34, P = 0.02) as well as a larger difference in the number of risk alleles (2.06 vs. 1.63, P = 0.027) between SLE patients and controls than for Central Europeans. This bias was reflected in a very significant difference in the cumulative genetic risk score (4.31 vs. 3.48, P = 1.8 × 10-32). Effect size bias was accompanied by a lower number of SLE risk alleles in the Southern subjects, both patients and controls, the difference being more marked between the controls (P = 1.1 × 10-8) than between the Southern and Central European patients (P = 0.016). Seven of these SNPs showed significant allele frequency clines. Conclusion Our findings showed a bias to larger effect sizes of SLE loci in the Southern Europeans relative to the Central Europeans together with clines of SLE risk allele frequencies. These results indicate the need to study risk allele clines and the implications of the polygenic model of inheritance in SLE.
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Affiliation(s)
- Elisa Alonso-Perez
- Laboratorio de Investigacion 10 and Rheumatology Unit, Instituto de Investigacion Sanitaria - Hospital Clinico Universitario de Santiago, Choupana s/n, Santiago de Compostela 15706, Spain
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Association of systemic lupus erythematosus clinical features with European population genetic substructure. PLoS One 2011; 6:e29033. [PMID: 22194982 PMCID: PMC3237589 DOI: 10.1371/journal.pone.0029033] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Accepted: 11/19/2011] [Indexed: 11/18/2022] Open
Abstract
Systemic Lupus Erythematosus (SLE) is an autoimmune disease with a very varied spectrum of clinical manifestations that could be partly determined by genetic factors. We aimed to determine the relationship between prevalence of 11 clinical features and age of disease onset with European population genetic substructure. Data from 1413 patients of European ancestry recruited in nine countries was tested for association with genotypes of top ancestry informative markers. This analysis was done with logistic regression between phenotypes and genotypes or principal components extracted from them. We used a genetic additive model and adjusted for gender and disease duration. Three clinical features showed association with ancestry informative markers: autoantibody production defined as immunologic disorder (P = 6.8×10(-4)), oral ulcers (P = 6.9×10(-4)) and photosensitivity (P = 0.002). Immunologic disorder was associated with genotypes more common in Southern European ancestries, whereas the opposite trend was observed for photosensitivity. Oral ulcers were specifically more common in patients of Spanish and Portuguese self-reported ancestry. These results should be taken into account in future research and suggest new hypotheses and possible underlying mechanisms to be investigated. A first hypothesis linking photosensitivity with variation in skin pigmentation is suggested.
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Galvan A, Fladvad T, Skorpen F, Gao X, Klepstad P, Kaasa S, Dragani TA. Genetic clustering of European cancer patients indicates that opioid-mediated pain relief is independent of ancestry. THE PHARMACOGENOMICS JOURNAL 2011; 12:412-6. [DOI: 10.1038/tpj.2011.27] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Kang G, Gao G, Shete S, Redden DT, Chang BL, Rebbeck TR, Barnholtz-Sloan JS, Pajewski NM, Allison DB. Capitalizing on admixture in genome-wide association studies: a two-stage testing procedure and application to height in African-Americans. Front Genet 2011; 2. [PMID: 21754915 PMCID: PMC3132882 DOI: 10.3389/fgene.2011.00011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
As genome-wide association studies expand beyond populations of European ancestry, the role of admixture will become increasingly important in the continued discovery and fine-mapping of variation influencing complex traits. Although admixture is commonly viewed as a confounding influence in association studies, approaches such as admixture mapping have demonstrated its ability to highlight disease susceptibility regions of the genome. In this study, we illustrate a powerful two-stage testing strategy designed to uncover trait-associated single nucleotide polymorphisms in the presence of ancestral allele frequency differentiation. In the first stage, we conduct an association scan by using predicted genotypic values based on regional admixture estimates. We then select a subset of promising markers for inclusion in a second-stage analysis, where association is tested between the observed genotype and the phenotype conditional on the predicted genotype. We prove that, under the null hypothesis, the test statistics used in each stage are orthogonal and asymptotically independent. Using simulated data designed to mimic African-American populations in the case of a quantitative trait, we show that our two-stage procedure maintains appropriate control of the family wise error rate and has higher power under realistic effect sizes than the one-stage testing procedure in which all markers are tested for association simultaneously with control of admixture. We apply the proposed procedure to a study of height in 201 African-Americans genotyped at 108 ancestry informative markers. The two-stage procedure identified two statistically significant markers rs1985080 (PTHB1/BBS9) and rs952718 (ABCA12). PTHB1/BBS9 is downregulated by parathyroid hormone in osteoblastic cells and is thought to be involved in parathyroid hormone action in bones and may play a role in height. ABCA12 is a member of the superfamily of ATP binding cassette transporters and its potential involvement in height is unclear.
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Affiliation(s)
- Guolian Kang
- Section on Statistical Genetics, Department of Biostatistics, The University of Alabama at Birmingham, Birmingham, AL, USA
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Abstract
Staggering advances have been made in our understanding of the genetic basis of human systemic lupus erythematosus (SLE), but has this been sufficient to fulfill early predictions that we could use genetics to provide personalized healthcare? Our current understanding of the genetic etiology of SLE indicates a strong underlying genetic predisposition, mediated by multiple gene variants. Compared with other complex genetic diseases, the disease risk imparted by many of these variants is strong. We argue that, for SLE, this particular combination of genetic effects means that the personalized prediction of disease onset or manifestation is certainly a realistic possibility, although further large-scale genetic studies will be required before this becomes a reality. We speculate that, in the future, genetic information could help guide targeted therapeutic intervention.
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