A Large-Scale Rheumatoid Arthritis Genetic Study Identifies Association at Chromosome 9q33.2

Rheumatoid arthritis (RA) is a chronic, systemic autoimmune disease affecting both joints and extra-articular tissues. Although some genetic risk factors for RA are well-established, most notably HLA-DRB1 and PTPN22, these markers do not fully account for the observed heritability. To identify additional susceptibility loci, we carried out a multi-tiered, case-control association study, genotyping 25,966 putative functional SNPs in 475 white North American RA patients and 475 matched controls. Significant markers were genotyped in two additional, independent, white case-control sample sets (661 cases/1322 controls from North America and 596 cases/705 controls from The Netherlands) identifying a SNP, rs1953126, on chromosome 9q33.2 that was significantly associated with RA (ORcommon = 1.28, trend Pcomb = 1.45E-06). Through a comprehensive fine-scale-mapping SNP-selection procedure, 137 additional SNPs in a 668 kb region from MEGF9 to STOM on 9q33.2 were chosen for follow-up genotyping in a staged-approach. Significant single marker results (Pcomb<0.01) spanned a large 525 kb region from FBXW2 to GSN. However, a variety of analyses identified SNPs in a 70 kb region extending from the third intron of PHF19 across TRAF1 into the TRAF1-C5 intergenic region, but excluding the C5 coding region, as the most interesting (trend Pcomb: 1.45E-06 → 5.41E-09). The observed association patterns for these SNPs had heightened statistical significance and a higher degree of consistency across sample sets. In addition, the allele frequencies for these SNPs displayed reduced variability between control groups when compared to other SNPs. Lastly, in combination with the other two known genetic risk factors, HLA-DRB1 and PTPN22, the variants reported here generate more than a 45-fold RA-risk differential.

[1]  Judy H. Cho,et al.  A Genome-Wide Association Study Identifies IL23R as an Inflammatory Bowel Disease Gene , 2006, Science.

[2]  C. Y. Wang,et al.  NF-kappaB antiapoptosis: induction of TRAF1 and TRAF2 and c-IAP1 and c-IAP2 to suppress caspase-8 activation. , 1998, Science.

[3]  D. Strachan,et al.  Rheumatoid arthritis association at 6q23 , 2007, Nature Genetics.

[4]  N Risch,et al.  The Future of Genetic Studies of Complex Human Diseases , 1996, Science.

[5]  K. Mossman.  The Wellcome Trust Case Control Consortium, U.K. , 2008 .

[6]  T. Pincus,et al.  Mortality in the rheumatic diseases : The impact of arthritis , 1995 .

[7]  M. Kendall.  Statistical Methods for Research Workers , 1937, Nature.

[8]  J. Hazes,et al.  Diagnostic and prognostic characteristics of the enzyme linked immunosorbent rheumatoid factor assays in rheumatoid arthritis. , 1996, Annals of the rheumatic diseases.

[9]  H. Heimpel,et al.  Tumor necrosis factor receptor-associated factor 1 gene overexpression in B-cell chronic lymphocytic leukemia: analysis of NF-kappa B/Rel-regulated inhibitors of apoptosis. , 2002, Blood.

[10]  S. Gabriel,et al.  Two independent alleles at 6q23 associated with risk of rheumatoid arthritis , 2007, Nature Genetics.

[11]  Yusuke Nakamura,et al.  Functional haplotypes of PADI4, encoding citrullinating enzyme peptidylarginine deiminase 4, are associated with rheumatoid arthritis , 2003, Nature Genetics.

[12]  Jinho Yoo,et al.  SNPAnalyzer : a web-based integrated workbench for single-nucleotide polymorphism analysis , 2005 .

[13]  S. Alkan,et al.  Expression of the Tumor Necrosis Factor Receptor-Associated Factors (TRAFs) 1 and 2 is a Characteristic Feature of Hodgkin and Reed-Sternberg Cells , 2000, Modern Pathology.

[14]  Steven J. Schrodi,et al.  A missense single-nucleotide polymorphism in a gene encoding a protein tyrosine phosphatase (PTPN22) is associated with rheumatoid arthritis. , 2004, American journal of human genetics.

[15]  R. Fisher,et al.  Statistical Methods for Research Workers. , 1955 .

[16]  Anbupalam Thalamuthu,et al.  TRAF1-C5 as a risk locus for rheumatoid arthritis--a genomewide study. , 2007, The New England journal of medicine.

[17]  J. Trent,et al.  Clustering of non-major histocompatibility complex susceptibility candidate loci in human autoimmune diseases. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[18]  P. Armitage.  Tests for Linear Trends in Proportions and Frequencies , 1955 .

[19]  T. Pincus,et al.  Mortality in the rheumatic diseases. , 1995, Arthritis care and research : the official journal of the Arthritis Health Professions Association.

[20]  D. Clayton,et al.  A unified stepwise regression procedure for evaluating the relative effects of polymorphisms within a gene using case/control or family data: application to HLA in type 1 diabetes. , 2002, American journal of human genetics.

[21]  G. Robertson,et al.  A novel human homologue of Drosophila polycomblike gene is up-regulated in multiple cancers. , 2004, Gene.

[22]  A. Barton,et al.  Investigation of association between the TRAF family genes and RA susceptibility , 2007, Annals of the rheumatic diseases.

[23]  R. Ward,et al.  HLA-linked rheumatoid arthritis. , 1994, American journal of human genetics.

[24]  Lars Alfredsson,et al.  A Candidate Gene Approach Identifies the TRAF1/C5 Region as a Risk Factor for Rheumatoid Arthritis , 2007, PLoS Medicine.

[25]  P. Stastny.  Association of the B-cell alloantigen DRw4 with rheumatoid arthritis. , 1978, The New England journal of medicine.

[26]  Steven J. Schrodi,et al.  PTPN22 genetic variation: evidence for multiple variants associated with rheumatoid arthritis. , 2005, American journal of human genetics.

[27]  A. Clark,et al.  The role of haplotypes in candidate gene studies , 2004, Genetic epidemiology.

[28]  P. Gregersen,et al.  Dissecting the heterogeneity of rheumatoid arthritis through linkage analysis of quantitative traits. , 2007, Arthritis and rheumatism.

[29]  C. Allaart,et al.  The Leiden Early Arthritis Clinic. , 2003, Clinical and experimental rheumatology.

[30]  Olivia T. Abar,et al.  A 7 gene signature identifies the risk of developing cirrhosis in patients with chronic hepatitis C , 2007, Hepatology.

[31]  Yusuke Nakamura,et al.  An intronic SNP in a RUNX1 binding site of SLC22A4, encoding an organic cation transporter, is associated with rheumatoid arthritis , 2003, Nature Genetics.

[32]  Jonathan C. Cohen,et al.  A Common Allele on Chromosome 9 Associated with Coronary Heart Disease , 2007, Science.

[33]  N. Breslow,et al.  Statistical methods in cancer research. Vol. 1. The analysis of case-control studies. , 1981 .

[34]  A S Rigby,et al.  Characterizing the quantitative genetic contribution to rheumatoid arthritis using data from twins. , 2000, Arthritis and rheumatism.

[35]  D. Gauguier,et al.  Genetic Influences on the End-Stage Effector Phase of Arthritis , 2001, The Journal of experimental medicine.

[36]  Paola Sebastiani,et al.  Genetic dissection and prognostic modeling of overt stroke in sickle cell anemia , 2005, Nature Genetics.

[37]  M. Liang,et al.  The American Rheumatism Association 1987 revised criteria for the classification of rheumatoid arthritis. , 1988, Arthritis and rheumatism.

[38]  Elizabeth W Karlson,et al.  Replication of putative candidate-gene associations with rheumatoid arthritis in >4,000 samples from North America and Sweden: association of susceptibility with PTPN22, CTLA4, and PADI4. , 2005, American journal of human genetics.

[39]  G. Firestein.  Evolving concepts of rheumatoid arthritis , 2003, Nature.

[40]  F. Arnett.  Revised criteria for the classification of rheumatoid arthritis. , 1990, Orthopedic nursing.

[41]  M. Olivier.  A haplotype map of the human genome. , 2003, Nature.

[42]  B Müller-Myhsok,et al.  Genetic analysis of complex diseases. , 1997, Science.

[43]  C I Amos,et al.  A genomewide screen in multiplex rheumatoid arthritis families suggests genetic overlap with other autoimmune diseases. , 2001, American journal of human genetics.

[44]  Stephen B. Johnson,et al.  The New York cancer project: Rationale, organization, design, and baseline characteristics , 2004, Journal of Urban Health.

[45]  S. Bae,et al.  The -169C/T polymorphism in FCRL3 is not associated with susceptibility to rheumatoid arthritis or systemic lupus erythematosus in a case-control study of Koreans. , 2006, Arthritis and rheumatism.

[46]  Pablo Villoslada,et al.  European Population Substructure: Clustering of Northern and Southern Populations , 2006, PLoS genetics.

[47]  Steven J. Schrodi,et al.  A large-scale genetic association study confirms IL12B and leads to the identification of IL23R as psoriasis-risk genes. , 2007, American journal of human genetics.

[48]  E. Topol,et al.  A Polymorphism in the Protease-Like Domain of Apolipoprotein(a) Is Associated With Severe Coronary Artery Disease , 2007, Arteriosclerosis, thrombosis, and vascular biology.

[49]  P. Gregersen,et al.  The shared epitope hypothesis. An approach to understanding the molecular genetics of susceptibility to rheumatoid arthritis. , 1987, Arthritis and rheumatism.

[50]  Ralph Weissleder,et al.  Arthritis critically dependent on innate immune system players. , 2002, Immunity.

[51]  W. Haenszel,et al.  Statistical aspects of the analysis of data from retrospective studies of disease. , 1959, Journal of the National Cancer Institute.

[52]  L. Young,et al.  Expression of the tumour necrosis factor receptor‐associated factors 1 and 2 in Hodgkin's disease , 2001, The Journal of pathology.

[53]  J. Kremer,et al.  A trial of etanercept, a recombinant tumor necrosis factor receptor:Fc fusion protein, in patients with rheumatoid arthritis receiving methotrexate. , 1999, The New England journal of medicine.

[54]  L. Matis,et al.  A Role for Complement in Antibody-Mediated Inflammation: C5-Deficient DBA/1 Mice Are Resistant to Collagen-Induced Arthritis , 2000, The Journal of Immunology.

[55]  A. Silman,et al.  Epidemiology and genetics of rheumatoid arthritis , 2002, Arthritis research.

[56]  Gonçalo R. Abecasis,et al.  GOLD-Graphical Overview of Linkage Disequilibrium , 2000, Bioinform..

[57]  Paul Wordsworth,et al.  Polygenic susceptibility in rheumatoid arthritis. , 1991, Annals of the rheumatic diseases.

[58]  Javier Martín,et al.  SLC22A4, RUNX1, and SUMO4 polymorphisms are not associated with rheumatoid arthritis: a case-control study in a Spanish population. , 2006, The Journal of rheumatology.

[59]  D. Schaid,et al.  Score tests for association between traits and haplotypes when linkage phase is ambiguous. , 2002, American journal of human genetics.

[60]  Simon C. Potter,et al.  Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls , 2007, Nature.

[61]  S. Hwang,et al.  Regulation of TNF-α-mediated hyperplasia through TNF receptors, TRAFs, and NF-κB in synoviocytes obtained from patients with rheumatoid arthritis , 2002 .

[62]  S. Germer,et al.  High-throughput SNP allele-frequency determination in pooled DNA samples by kinetic PCR. , 2000, Genome research.

[63]  H. Stein,et al.  Tumor necrosis factor receptor-associated factor 1 is overexpressed in Reed-Sternberg cells of Hodgkin's disease and Epstein-Barr virus-transformed lymphoid cells. , 1999, Blood.

[64]  M. Olivier.  A haplotype map of the human genome , 2003, Nature.

[65]  Y. Lee,et al.  PADI4 polymorphisms and rheumatoid arthritis susceptibility: a meta-analysis , 2007, Rheumatology International.

[66]  N. Breslow,et al.  Statistical methods in cancer research: volume 1- The analysis of case-control studies , 1980 .

[67]  L. Matis,et al.  Anti-C5 monoclonal antibody therapy prevents collagen-induced arthritis and ameliorates established disease. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[68]  P. Reitsma,et al.  Factor VII and Fibrinogen Levels as Risk Factors for Venous Thrombosis , 1994, Thrombosis and Haemostasis.

[69]  B. Morgan,et al.  Complement activation and inhibition in experimental models of arthritis. , 1999, Molecular immunology.

[70]  F. Breedveld,et al.  Tumour necrosis factor alpha gene polymorphisms in rheumatoid arthritis: association with susceptibility to, or severity of, disease? , 1997, British journal of rheumatology.

[71]  Jeffrey Ross-Ibarra,et al.  Genetic Data Analysis II. Methods for Discrete Population Genentic Data , 2002 .

[72]  Johanna M Seddon,et al.  Common variation in three genes, including a noncoding variant in CFH, strongly influences risk of age-related macular degeneration , 2006, Nature Genetics.

[73]  Nunzio Bottini,et al.  A functional variant of lymphoid tyrosine phosphatase is associated with type I diabetes , 2004, Nature Genetics.

[74]  Ryan D. Hernandez,et al.  Natural selection on protein-coding genes in the human genome , 2005, Nature.

[75]  A. Iliadou,et al.  Association of chronic inflammation, not its treatment, with increased lymphoma risk in rheumatoid arthritis. , 2006, Arthritis and rheumatism.

[76]  J. Woody,et al.  Randomised double-blind comparison of chimeric monoclonal antibody to tumour necrosis factor α (cA2) versus placebo in rheumatoid arthritis , 1994, The Lancet.

[77]  L. Jorde.  Linkage disequilibrium as a gene-mapping tool. , 1995, American journal of human genetics.

[78]  Yusuke Nakamura,et al.  A functional variant in FCRL3, encoding Fc receptor-like 3, is associated with rheumatoid arthritis and several autoimmunities , 2005, Nature Genetics.

[79]  M. Cargill,et al.  Selecting Tagging SNPs for Association Studies Using Power Calculations from Genotype Data , 2004, Human Heredity.

[80]  T. Golub,et al.  The molecular signature of mediastinal large B-cell lymphoma differs from that of other diffuse large B-cell lymphomas and shares features with classical Hodgkin lymphoma. , 2003, Blood.

[81]  P. Gregersen,et al.  Clustering of disease features within 512 multicase rheumatoid arthritis families. , 2004, Arthritis and rheumatism.

[82]  Ann Morgan,et al.  Re-evaluation of putative rheumatoid arthritis susceptibility genes in the post-genome wide association study era and hypothesis of a key pathway underlying susceptibility , 2008, Human molecular genetics.

[83]  P. Gregersen,et al.  PTPN22: setting thresholds for autoimmunity. , 2006, Seminars in immunology.

[84]  K. Ikari,et al.  Supportive evidence for a genetic association of the FCRL3 promoter polymorphism with rheumatoid arthritis , 2005, Annals of the rheumatic diseases.

[85]  R. Kaiser.  Incidence of lymphoma in patients with rheumatoid arthritis: a systematic review of the literature. , 2008, Clinical lymphoma & myeloma.

[86]  Wentian Li,et al.  STAT4 and the risk of rheumatoid arthritis and systemic lupus erythematosus. , 2007, The New England journal of medicine.

[87]  F. Alt,et al.  TRAF1 is a negative regulator of TNF signaling. enhanced TNF signaling in TRAF1-deficient mice. , 2001, Immunity.

[88]  Steven J. Schrodi,et al.  Meta-analysis evidence of a differential risk of the FCRL3 -169T-->C polymorphism in white and East Asian rheumatoid arthritis patients. , 2007, Arthritis and rheumatism.

[89]  Kari Stefansson,et al.  A common variant on chromosome 9p21 affects the risk of myocardial infarction. , 2007, Science.

[90]  R. Gascoyne,et al.  TNFR-Associated Factor Family Protein Expression in Normal Tissues and Lymphoid Malignancies , 2000, The Journal of Immunology.

[91]  M. Gill,et al.  Evidence for novel susceptibility genes for late-onset Alzheimer's disease from a genome-wide association study of putative functional variants. , 2007, Human molecular genetics.

[92]  E. Topol,et al.  Identification of four gene variants associated with myocardial infarction. , 2005, American journal of human genetics.

[93]  Margaret A. Pericak-Vance,et al.  Genetic Analysis of Complex Disease , 2006 .

[94]  H. Okamoto.  Tumor necrosis factor inhibitors for rheumatoid arthritis. , 2006, The New England journal of medicine.