The genetics of autoimmune diseases: a networked perspective

Lin, 1998, Familial clustering of rheumatoid arthritis with other autoimmune diseases, Hum Genet, 103, 475, 10.1007/s004390050853 Tait, 2004, Clustering of autoimmune disease in parents of siblings from the Type 1 diabetes Warren repository, Diabet Med, 21, 358, 10.1111/j.1464-5491.2004.01162.x Barcellos, 2006, Clustering of autoimmune diseases in families with a high-risk for multiple sclerosis: a descriptive study, Lancet Neurol, 5, 924, 10.1016/S1474-4422(06)70552-X IMSGC, The expanding genetic overlap between multiple sclerosis and type I diabetes. Genes Immun 2009, 10:11–14. Rzhetsky, 2007, Probing genetic overlap among complex human phenotypes, Proc Natl Acad Sci U S A, 104, 11694, 10.1073/pnas.0704820104 Hindorff, 2009, Potential etiologic and functional implications of genome-wide association loci for human diseases and traits, Proc Natl Acad Sci U S A, 106, 9362, 10.1073/pnas.0903103106 A Catalog of Published Genome-Wide Association Studies on World Wide Web URL, http://www.genome.gov/26525384. Oksenberg, 2008, The genetics of multiple sclerosis: SNPs to pathways to pathogenesis, Nat Rev Genet, 9, 516, 10.1038/nrg2395 Wellcome Trust Case Control Consortium 2 on World Wide Web URL, https://www.wtccc.org.uk/ccc2/index.shtml. Torkamani, 2008, Pathway analysis of seven common diseases assessed by genome-wide association, Genomics, 92, 265, 10.1016/j.ygeno.2008.07.011 Lesnick, 2007, A genomic pathway approach to a complex disease: axon guidance and Parkinson disease, PLoS Genet, 3, e98, 10.1371/journal.pgen.0030098 Wang, 2007, Pathway-based approaches for analysis of genomewide association studies, Am J Hum Genet, 81 Baranzini, 2009, Pathway and network-based analysis of genome-wide association studies in multiple sclerosis, Hum Mol Genet, 18, 2078, 10.1093/hmg/ddp120 Chen, 2007, Enriching the analysis of genomewide association studies with hierarchical modeling, Am J Hum Genet, 81, 397, 10.1086/519794 Forabosco, 2009, Meta-analysis of genome-wide linkage studies across autoimmune diseases, Eur J Hum Genet, 17, 236, 10.1038/ejhg.2008.163 De Jager, 2009, Meta-analysis of genome scans and replication identify CD6 IRF8 and TNFRSF1A as new multiple sclerosis susceptibility loci, Nat Genet, 41, 776, 10.1038/ng.401 Johnson, 2009, An open access database of genome-wide association results, BMC Med Genet, 10, 6, 10.1186/1471-2350-10-6 Fisher, 1948, Combining independent tests of significance, American Statistician, 2, 30 Goh, 2007, The human disease network, Proc Natl Acad Sci U S A, 104, 8685, 10.1073/pnas.0701361104 Kumar, 2005 Husebye, 2009, Pathogenesis of primary adrenal insufficiency, Best Pract Res Clin Endocrinol Metab, 23, 147, 10.1016/j.beem.2008.09.004 Smyth, 2004, Replication of an association between the lymphoid tyrosine phosphatase locus (LYP/PTPN22) with type 1 diabetes, and evidence for its role as a general autoimmunity locus, Diabetes, 53, 3020, 10.2337/diabetes.53.11.3020 Abraham, 2009, IL-23 and autoimmunity: new insights into the pathogenesis of inflammatory bowel disease, Annu Rev Med, 60, 97, 10.1146/annurev.med.60.051407.123757 Nelson, 2004, IL-2, regulatory T cells, and tolerance, J Immunol, 172, 3983, 10.4049/jimmunol.172.7.3983 Malek, 2004, Tolerance, not immunity, crucially depends on IL-2, Nat Rev Immunol, 4, 665, 10.1038/nri1435 Jones, 2009, IL-21 drives secondary autoimmunity in patients with multiple sclerosis, following therapeutic lymphocyte depletion with alemtuzumab (Campath-1H), J Clin Invest, 119, 2052 Ettinger, 2008, The role of IL-21 in regulating B-cell function in health and disease, Immunol Rev, 223, 60, 10.1111/j.1600-065X.2008.00631.x Ettinger, 2008, Interleukin 21 as a target of intervention in autoimmune disease, Ann Rheum Dis, 67, iii83, 10.1136/ard.2008.098400 Scalapino, 2008, CTLA-4: a key regulatory point in the control of autoimmune disease, Immunol Rev, 223, 143, 10.1111/j.1600-065X.2008.00639.x Maier, 2009, IL2RA genetic heterogeneity in multiple sclerosis and type 1 diabetes susceptibility and soluble interleukin-2 receptor production, PLoS Genet, 5, e1000322, 10.1371/journal.pgen.1000322 Dendrou, 2009, Cell-specific protein phenotypes for the autoimmune locus IL2RA using a genotype-selectable human bioresource, Nat Genet, 41, 1011, 10.1038/ng.434 Gregersen, 2009, REL, encoding a member of the NF-kappaB family of transcription factors, is a newly defined risk locus for rheumatoid arthritis, Nat Genet, 41, 820, 10.1038/ng.395 Raychaudhuri, 2008, Common variants at CD40 and other loci confer risk of rheumatoid arthritis, Nat Genet, 40, 1216, 10.1038/ng.233 Plenge, 2007, TRAF1-C5 as a risk locus for rheumatoid arthritis—a genomewide study, N Engl J Med, 357, 1199, 10.1056/NEJMoa073491 WTCCC, Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 2007, 447:661–678. Harley, 2008, Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility variants in ITGAM, PXK, KIAA1542 and other loci, Nat Genet, 40, 204, 10.1038/ng.81 Hom, 2008, Association of systemic lupus erythematosus with C8orf13-BLK and ITGAM-ITGAX, N Engl J Med, 358, 900, 10.1056/NEJMoa0707865 Barrett, 2008, Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease, Nat Genet, 40, 955, 10.1038/ng.175 Nejentsev, 2009, Rare variants of IFIH1, a gene implicated in antiviral responses, protect against type 1 diabetes, Science, 324, 387, 10.1126/science.1167728 Hunt, 2008, Newly identified genetic risk variants for celiac disease related to the immune response, Nat Genet, 40, 395, 10.1038/ng.102 van Heel, 2007, A genome-wide association study for celiac disease identifies risk variants in the region harboring IL2 and IL21, Nat Genet, 39, 827, 10.1038/ng2058 ANZgene, 2009, Genome-wide association study identifies new multiple sclerosis susceptibility loci on chromosomes 12 and 20, Nat Genet, 41, 824, 10.1038/ng.396 Comabella, 2008, Identification of a novel risk locus for multiple sclerosis at 13q31.3 by a pooled genome-wide scan of 500,000 single nucleotide polymorphisms, PLoS One, 3, e3490, 10.1371/journal.pone.0003490 Hafler, 2007, Risk alleles for multiple sclerosis identified by a genomewide study, N Engl J Med, 357, 851, 10.1056/NEJMoa073493 Nair, 2009, Genome-wide scan reveals association of psoriasis with IL-23 and NF-kappaB pathways, Nat Genet, 41, 199, 10.1038/ng.311 Liu, 2008, A genome-wide association study of psoriasis and psoriatic arthritis identifies new disease loci, PLoS Genet, 4, e1000041, 10.1371/journal.pgen.1000041 Capon, 2008, Identification of ZNF313/RNF114 as a novel psoriasis susceptibility gene, Hum Mol Genet, 17, 1938, 10.1093/hmg/ddn091 Zhang, 2009, Psoriasis genome-wide association study identifies susceptibility variants within LCE gene cluster at 1q21, Nat Genet, 41, 205, 10.1038/ng.310 Raelson, 2007, Genome-wide association study for Crohn's disease in the Quebec Founder Population identifies multiple validated disease loci, Proc Natl Acad Sci U S A, 104, 14747, 10.1073/pnas.0706645104 Rioux, 2007, Genome-wide association study identifies new susceptibility loci for Crohn disease and implicates autophagy in disease pathogenesis, Nat Genet, 39, 596, 10.1038/ng2032 Libioulle, 2007, Novel Crohn disease locus identified by genome-wide association maps to a gene desert on 5p13.1 and modulates expression of PTGER4, PLoS Genet, 3, e58, 10.1371/journal.pgen.0030058 Parkes, 2007, Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn's disease susceptibility, Nat Genet, 39, 830, 10.1038/ng2061 Plenge, 2007, Two independent alleles at 6q23 associated with risk of rheumatoid arthritis, Nat Genet, 39, 1477, 10.1038/ng.2007.27 Julia, 2008, Genome-wide association study of rheumatoid arthritis in the Spanish population: KLF12 as a risk locus for rheumatoid arthritis susceptibility, Arthritis Rheum, 58, 2275, 10.1002/art.23623 Graham, 2008, Genetic variants near TNFAIP3 on 6q23 are associated with systemic lupus erythematosus, Nat Genet, 40, 1059, 10.1038/ng.200 Kozyrev, 2008, Functional variants in the B-cell gene BANK1 are associated with systemic lupus erythematosus, Nat Genet, 40, 211, 10.1038/ng.79 Cooper, 2008, Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci, Nat Genet, 40, 1399, 10.1038/ng.249 Hakonarson, 2007, A genome-wide association study identifies KIAA0350 as a type 1 diabetes gene, Nature, 448, 591, 10.1038/nature06010 Todd, 2007, Robust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes, Nat Genet, 39, 857, 10.1038/ng2068 Hakonarson, 2008, A novel susceptibility locus for type 1 diabetes on Chr12q13 identified by a genome-wide association study, Diabetes, 57, 1143, 10.2337/db07-1305 Grant, 2009, Follow-up analysis of genome-wide association data identifies novel loci for type 1 diabetes, Diabetes, 58, 290, 10.2337/db08-1022 Franke, 2007, Systematic association mapping identifies NELL1 as a novel IBD disease gene, PLoS One, 2, e691, 10.1371/journal.pone.0000691 Duerr, 2006, A genome-wide association study identifies IL23R as an inflammatory bowel disease gene, Science, 314, 1461, 10.1126/science.1135245 Yamazaki, 2005, Single nucleotide polymorphisms in TNFSF15 confer susceptibility to Crohn's disease, Hum Mol Genet, 14, 3499, 10.1093/hmg/ddi379 Baranzini, 2009, Genome-wide association analysis of susceptibility and clinical phenotype in multiple sclerosis, Hum Mol Genet, 18, 767, 10.1093/hmg/ddn388 Capon, 2007, Sequence variants in the genes for the interleukin-23 receptor (IL23R) and its ligand (IL12B) confer protection against psoriasis, Hum Genet, 122, 201, 10.1007/s00439-007-0397-0 Steer, 2007, Genomic DNA pooling for whole-genome association scans in complex disease: empirical demonstration of efficacy in rheumatoid arthritis, Genes Immun, 8, 57, 10.1038/sj.gene.6364359 Kamatani, 2008, Identification of a significant association of a single nucleotide polymorphism in TNXB with systemic lupus erythematosus in a Japanese population, J Hum Genet, 53, 64, 10.1007/s10038-007-0219-1 Cervino, 2007, A genome-wide study of lupus: preliminary analysis and data release, Ann N Y Acad Sci, 1110, 131, 10.1196/annals.1423.015 Saxena, 2007, Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels, Science, 316, 1331, 10.1126/science.1142358 Hanson, 2007, A search for variants associated with young-onset type 2 diabetes in American Indians in a 100K genotyping array, Diabetes, 56, 3045, 10.2337/db07-0462 Hayes, 2007, Identification of type 2 diabetes genes in Mexican Americans through genome-wide association studies, Diabetes, 56, 3033, 10.2337/db07-0482 Rampersaud, 2007, Identification of novel candidate genes for type 2 diabetes from a genome-wide association scan in the Old Order Amish: evidence for replication from diabetes-related quantitative traits and from independent populations, Diabetes, 56, 3053, 10.2337/db07-0457 Salonen, 2007, Type 2 diabetes whole-genome association study in four populations: the DiaGen consortium, Am J Hum Genet, 81, 338, 10.1086/520599 Scott, 2007, A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants, Science, 316, 1341, 10.1126/science.1142382 Sladek, 2007, A genome-wide association study identifies novel risk loci for type 2 diabetes, Nature, 445, 881, 10.1038/nature05616 Steinthorsdottir, 2007, A variant in CDKAL1 influences insulin response and risk of type 2 diabetes, Nat Genet, 39, 770, 10.1038/ng2043 Zeggini, 2007, Replication of genome-wide association signals in UK samples reveals risk loci for type 2 diabetes, Science, 316, 1336, 10.1126/science.1142364 Florez, 2007, A 100K genome-wide association scan for diabetes and related traits in the Framingham Heart Study: replication and integration with other genome-wide datasets, Diabetes, 56, 3063, 10.2337/db07-0451 Meigs, 2007, Genome-wide association with diabetes-related traits in the Framingham Heart Study, BMC Med Genet, 8, S16, 10.1186/1471-2350-8-S1-S16