publication . Article . 2009

Replication of recently identified associated single-nucleotide polymorphisms from six autoimmune diseases in Genetic Analysis Workshop 16 rheumatoid arthritis data.

Deshmukh, Harshal; Kim-Howard, Xana; Nath, Swapan K;
Open Access English
  • Published: 01 Dec 2009 Journal: BMC Proceedings, volume 3, issue Suppl 7, pages S31-S31 (eissn: 1753-6561, Copyright policy)
  • Publisher: BioMed Central
Abstract
<p>Abstract</p> <p>Many autoimmune diseases share similar underlying pathology and have a tendency to cluster within families, giving rise to the concept of shared susceptibility genes among them. In the Genetic Analysis Workshop 16 rheumatoid arthritis (RA) data we sought to replicate the genetic association between single-nucleotide polymorphisms (SNPs) identified in recent genome-wide association studies (GWAS) on RA and five other autoimmune diseases. We identified 164 significantly associated non-HLA SNPs (<it>p </it>< 10<sup>-5</sup>) from 16 GWAS and 13 candidate gene studies on six different autoimmune diseases, including RA, systemic lupus erythematosus...
Subjects
free text keywords: Proceedings, Medicine, R, Science, Q, General Biochemistry, Genetics and Molecular Biology, General Medicine, Autoimmunity, medicine.disease_cause, Genetics, Rheumatoid arthritis, medicine.disease, Genome-wide association study, Immunology, Single-nucleotide polymorphism, Candidate gene, Genetic association, business.industry, business, Lupus erythematosus, Disease
Funded by
NIH| Genetic Analysis of Common Diseases: An Evaluation
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01GM031575-22
  • Funding stream: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
,
WT
Project
  • Funder: Wellcome Trust (WT)
,
NIH| Identifying the novel SLE susceptibility gene on 5p15.3
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01AI063622-05
  • Funding stream: NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES
38 references, page 1 of 3

Marrack, P, Kappler, J, Kotzin, BL. Autoimmune disease: why and where it occurs. Nat Med. 2001; 7: 899-905 [OpenAIRE] [PubMed] [DOI]

Olsen, N, Sokka, T, Seehorn, CL, Kraft, B, Maas, K, Moore, J, Aune, TM. A gene expression signature for recent onset rheumatoid arthritis in peripheral blood mononuclear cells. Ann Rheum Dis. 2004; 63: 1387-1392 [OpenAIRE] [PubMed] [DOI]

Bennett, L, Palucka, AK, Arce, E, Cantrell, V, Borvak, J, Banchereau, J, Pascual, V. Interferon and granulopoiesis signatures in systemic lupus erythematosus blood. J Exp Med. 2003; 197: 711-723 [OpenAIRE] [PubMed] [DOI]

Alarcón-Riquelme, ME. A RUNX trio with a taste for autoimmunity. Nat Genet. 2003; 35: 299-300 [OpenAIRE] [PubMed] [DOI]

Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature. 2007; 447: 661-678 [OpenAIRE] [PubMed] [DOI]

Chang, M, Rowland, CM, Garcia, VE, Schrodi, SJ, Catanese, JJ, Helm-van Mil, AH van der, Ardlie, KG, Amos, CI, Criswell, LA, Kastner, DL, Gregersen, PK, Kurreeman, FA, Toes, RE, Huizinga, TW, Seldin, MF, Begovich, AB. A large-scale rheumatoid arthritis genetic study identifies association at chromosome 9q33.2. PLoS Genet. 2008; 4: e1000107 [OpenAIRE] [PubMed] [DOI]

Remmers, EF, Plenge, RM, Lee, AT, Graham, RR, Hom, G, Behrens, TW, de Bakker, PI, Le, JM, Lee, HS, Batliwalla, F, Li, W, Masters, SL, Booty, MG, Carulli, JP, Padyukov, L, Alfredsson, L, Klareskog, L, Chen, WV, Amos, CI, Criswell, LA, Seldin, MF, Kastner, DL, Gregersen, PK. STAT4 and the risk of rheumatoid arthritis and systemic lupus erythematosus. N Engl J Med. 2007; 357: 977-986 [OpenAIRE] [PubMed] [DOI]

Hom, G, Graham, RR, Modrek, B, Taylor, KE, Ortmann, W, Garnier, S, Lee, AT, Chung, SA, Ferreira, RC, Pant, PV, Ballinger, DG, Kosoy, R, Demirci, FY, Kamboh, MI, Kao, AH, Tian, C, Gunnarsson, I, Bengtsson, AA, Rantapää-Dahlqvist, S, Petri, M, Manzi, S, Seldin, MF, Rönnblom, L, Syvänen, AC, Criswell, LA, Gregersen, PK, Behrens, TW. Association of systemic lupus erythematosus with C8orf13-BLK and ITGAM-ITGAX. N Engl J Med. 2008; 358: 900-909 [PubMed] [DOI]

Graham, RR, Cotsapas, C, Davies, L, Hackett, R, Lessard, CJ, Leon, JM, Burtt, NP, Guiducci, C, Parkin, M, Gates, C, Plenge, RM, Behrens, TW, Wither, JE, Rioux, JD, Fortin, PR, Graham, DC, Wong, AK, Vyse, TJ, Daly, MJ, Altshuler, D, Moser, KL, Gaffney, PM. Genetic variants near TNFAIP3 on 6q23 are associated with systemic lupus erythematosus. Nat Genet. 2008; 40: 1059-1061 [OpenAIRE] [PubMed] [DOI]

Musone, SL, Taylor, KE, Lu, TT, Nititham, J, Ferreira, RC, Ortmann, W, Shifrin, N, Petri, MA, Kamboh, MI, Manzi, S, Seldin, MF, Gregersen, PK, Behrens, TW, Ma, A, Kwok, PY, Criswell, LA. Multiple polymorphisms in the TNFAIP3 region are independently associated with systemic lupus erythematosus. Nat Genet. 2008; 40: 1062-1064 [OpenAIRE] [PubMed] [DOI]

Harley, JB, Alarcón-Riquelme, ME, Criswell, LA, Jacob, CO, Kimberly, RP, Moser, KL, Tsao, BP, Vyse, TJ, Langefeld, CD, Nath, SK, Guthridge, JM, Cobb, BL, Mirel, DB, Marion, MC, Williams, AH, Divers, J, Wang, W, Frank, SG, Namjou, B, Gabriel, SB, Lee, AT, Gregersen, PK, Behrens, TW, Taylor, KE, Fernando, M, Zidovetzki, R, Gaffney, PM, Edberg, JC, Rioux, JD, Ojwang, JO, James, JA, Merrill, JT, Gilkeson, GS, Seldin, MF, Yin, H, Baechler, EC, Li, QZ, Wakeland, EK, Bruner, GR, Kaufman, KM, Kelly, JA. Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility variants in ITGAM, PXK, KIAA1542 and other loci. Nat Genet. 2008; 40: 204-210 [OpenAIRE] [PubMed] [DOI]

Barrett, JC, Hansoul, S, Nicolae, DL, Cho, JH, Duerr, RH, Rioux, JD, Brant, SR, Silverberg, MS, Taylor, KD, Barmada, MM, Bitton, A, Dassopoulos, T, Datta, LW, Green, T, Griffiths, AM, Kistner, EO, Murtha, MT, Regueiro, MD, Rotter, JI, Schumm, LP, Steinhart, AH, Targan, SR, Xavier, RJ, Libioulle, C, Sandor, C, Lathrop, M, Belaiche, J, Dewit, O, Gut, I, Heath, S, Laukens, D, Mni, M, Rutgeerts, P, Van Gossum, A, Zelenika, D, Franchimont, D, Hugot, JP, de Vos, M, Vermeire, S, Louis, E, Cardon, LR, Anderson, CA, Drummond, H, Nimmo, E, Ahmad, T, Prescott, NJ, Onnie, CM, Fisher, SA, Marchini, J, Ghori, J, Bumpstead, S, Gwilliam, R, Tremelling, M, Deloukas, P, Mansfield, J, Jewell, D, Satsangi, J, Mathew, CG, Parkes, M, Georges, M, Daly, MJ. Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease. Nat Genet. 2008; 40: 955-962 [OpenAIRE] [PubMed] [DOI]

van Heel, DA, Franke, L, Hunt, KA, Gwilliam, R, Zhernakova, A, Inouye, M, Wapenaar, MC, Barnardo, MC, Bethel, G, Holmes, GK, Feighery, C, Jewell, D, Kelleher, D, Kumar, P, Travis, S, Walters, JR, Sanders, DS, Howdle, P, Swift, J, Playford, RJ, McLaren, WM, Mearin, ML, Mulder, CJ, McManus, R, McGinnis, R, Cardon, LR, Deloukas, P, Wijmenga, C. A genome-wide association study for celiac disease identifies risk variants in the region harboring IL2 and IL21. Nat Genet. 2007; 39: 827-829 [OpenAIRE] [PubMed] [DOI]

Hafler, DA, Compston, A, Sawcer, S, Lander, ES, Daly, MJ, De Jager, PL, de Bakker, PI, Gabriel, SB, Mirel, DB, Ivinson, AJ, Pericak-Vance, MA, Gregory, SG, Rioux, JD, McCauley, JL, Haines, JL, Barcellos, LF, Cree, B, Oksenberg, JR, Hauser, SL. Risk alleles for multiple sclerosis identified by a genomewide study. N Engl J Med. 2007; 357: 851-862 [PubMed] [DOI]

Gregory, SG, Schmidt, S, Seth, P, Oksenberg, JR, Hart, J, Prokop, A, Caillier, SJ, Ban, M, Goris, A, Barcellos, LF, Lincoln, R, McCauley, JL, Sawcer, SJ, Compston, DA, Dubois, B, Hauser, SL, Garcia-Blanco, MA, Pericak-Vance, MA, Haines, JL. Interleukin 7 receptor alpha chain (IL7R) shows allelic and functional association with multiple sclerosis. Nat Genet. 2007; 39: 1083-1091 [OpenAIRE] [PubMed] [DOI]

38 references, page 1 of 3
Related research
Abstract
<p>Abstract</p> <p>Many autoimmune diseases share similar underlying pathology and have a tendency to cluster within families, giving rise to the concept of shared susceptibility genes among them. In the Genetic Analysis Workshop 16 rheumatoid arthritis (RA) data we sought to replicate the genetic association between single-nucleotide polymorphisms (SNPs) identified in recent genome-wide association studies (GWAS) on RA and five other autoimmune diseases. We identified 164 significantly associated non-HLA SNPs (<it>p </it>< 10<sup>-5</sup>) from 16 GWAS and 13 candidate gene studies on six different autoimmune diseases, including RA, systemic lupus erythematosus...
Subjects
free text keywords: Proceedings, Medicine, R, Science, Q, General Biochemistry, Genetics and Molecular Biology, General Medicine, Autoimmunity, medicine.disease_cause, Genetics, Rheumatoid arthritis, medicine.disease, Genome-wide association study, Immunology, Single-nucleotide polymorphism, Candidate gene, Genetic association, business.industry, business, Lupus erythematosus, Disease
Funded by
NIH| Genetic Analysis of Common Diseases: An Evaluation
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01GM031575-22
  • Funding stream: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
,
WT
Project
  • Funder: Wellcome Trust (WT)
,
NIH| Identifying the novel SLE susceptibility gene on 5p15.3
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01AI063622-05
  • Funding stream: NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES
38 references, page 1 of 3

Marrack, P, Kappler, J, Kotzin, BL. Autoimmune disease: why and where it occurs. Nat Med. 2001; 7: 899-905 [OpenAIRE] [PubMed] [DOI]

Olsen, N, Sokka, T, Seehorn, CL, Kraft, B, Maas, K, Moore, J, Aune, TM. A gene expression signature for recent onset rheumatoid arthritis in peripheral blood mononuclear cells. Ann Rheum Dis. 2004; 63: 1387-1392 [OpenAIRE] [PubMed] [DOI]

Bennett, L, Palucka, AK, Arce, E, Cantrell, V, Borvak, J, Banchereau, J, Pascual, V. Interferon and granulopoiesis signatures in systemic lupus erythematosus blood. J Exp Med. 2003; 197: 711-723 [OpenAIRE] [PubMed] [DOI]

Alarcón-Riquelme, ME. A RUNX trio with a taste for autoimmunity. Nat Genet. 2003; 35: 299-300 [OpenAIRE] [PubMed] [DOI]

Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature. 2007; 447: 661-678 [OpenAIRE] [PubMed] [DOI]

Chang, M, Rowland, CM, Garcia, VE, Schrodi, SJ, Catanese, JJ, Helm-van Mil, AH van der, Ardlie, KG, Amos, CI, Criswell, LA, Kastner, DL, Gregersen, PK, Kurreeman, FA, Toes, RE, Huizinga, TW, Seldin, MF, Begovich, AB. A large-scale rheumatoid arthritis genetic study identifies association at chromosome 9q33.2. PLoS Genet. 2008; 4: e1000107 [OpenAIRE] [PubMed] [DOI]

Remmers, EF, Plenge, RM, Lee, AT, Graham, RR, Hom, G, Behrens, TW, de Bakker, PI, Le, JM, Lee, HS, Batliwalla, F, Li, W, Masters, SL, Booty, MG, Carulli, JP, Padyukov, L, Alfredsson, L, Klareskog, L, Chen, WV, Amos, CI, Criswell, LA, Seldin, MF, Kastner, DL, Gregersen, PK. STAT4 and the risk of rheumatoid arthritis and systemic lupus erythematosus. N Engl J Med. 2007; 357: 977-986 [OpenAIRE] [PubMed] [DOI]

Hom, G, Graham, RR, Modrek, B, Taylor, KE, Ortmann, W, Garnier, S, Lee, AT, Chung, SA, Ferreira, RC, Pant, PV, Ballinger, DG, Kosoy, R, Demirci, FY, Kamboh, MI, Kao, AH, Tian, C, Gunnarsson, I, Bengtsson, AA, Rantapää-Dahlqvist, S, Petri, M, Manzi, S, Seldin, MF, Rönnblom, L, Syvänen, AC, Criswell, LA, Gregersen, PK, Behrens, TW. Association of systemic lupus erythematosus with C8orf13-BLK and ITGAM-ITGAX. N Engl J Med. 2008; 358: 900-909 [PubMed] [DOI]

Graham, RR, Cotsapas, C, Davies, L, Hackett, R, Lessard, CJ, Leon, JM, Burtt, NP, Guiducci, C, Parkin, M, Gates, C, Plenge, RM, Behrens, TW, Wither, JE, Rioux, JD, Fortin, PR, Graham, DC, Wong, AK, Vyse, TJ, Daly, MJ, Altshuler, D, Moser, KL, Gaffney, PM. Genetic variants near TNFAIP3 on 6q23 are associated with systemic lupus erythematosus. Nat Genet. 2008; 40: 1059-1061 [OpenAIRE] [PubMed] [DOI]

Musone, SL, Taylor, KE, Lu, TT, Nititham, J, Ferreira, RC, Ortmann, W, Shifrin, N, Petri, MA, Kamboh, MI, Manzi, S, Seldin, MF, Gregersen, PK, Behrens, TW, Ma, A, Kwok, PY, Criswell, LA. Multiple polymorphisms in the TNFAIP3 region are independently associated with systemic lupus erythematosus. Nat Genet. 2008; 40: 1062-1064 [OpenAIRE] [PubMed] [DOI]

Harley, JB, Alarcón-Riquelme, ME, Criswell, LA, Jacob, CO, Kimberly, RP, Moser, KL, Tsao, BP, Vyse, TJ, Langefeld, CD, Nath, SK, Guthridge, JM, Cobb, BL, Mirel, DB, Marion, MC, Williams, AH, Divers, J, Wang, W, Frank, SG, Namjou, B, Gabriel, SB, Lee, AT, Gregersen, PK, Behrens, TW, Taylor, KE, Fernando, M, Zidovetzki, R, Gaffney, PM, Edberg, JC, Rioux, JD, Ojwang, JO, James, JA, Merrill, JT, Gilkeson, GS, Seldin, MF, Yin, H, Baechler, EC, Li, QZ, Wakeland, EK, Bruner, GR, Kaufman, KM, Kelly, JA. Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility variants in ITGAM, PXK, KIAA1542 and other loci. Nat Genet. 2008; 40: 204-210 [OpenAIRE] [PubMed] [DOI]

Barrett, JC, Hansoul, S, Nicolae, DL, Cho, JH, Duerr, RH, Rioux, JD, Brant, SR, Silverberg, MS, Taylor, KD, Barmada, MM, Bitton, A, Dassopoulos, T, Datta, LW, Green, T, Griffiths, AM, Kistner, EO, Murtha, MT, Regueiro, MD, Rotter, JI, Schumm, LP, Steinhart, AH, Targan, SR, Xavier, RJ, Libioulle, C, Sandor, C, Lathrop, M, Belaiche, J, Dewit, O, Gut, I, Heath, S, Laukens, D, Mni, M, Rutgeerts, P, Van Gossum, A, Zelenika, D, Franchimont, D, Hugot, JP, de Vos, M, Vermeire, S, Louis, E, Cardon, LR, Anderson, CA, Drummond, H, Nimmo, E, Ahmad, T, Prescott, NJ, Onnie, CM, Fisher, SA, Marchini, J, Ghori, J, Bumpstead, S, Gwilliam, R, Tremelling, M, Deloukas, P, Mansfield, J, Jewell, D, Satsangi, J, Mathew, CG, Parkes, M, Georges, M, Daly, MJ. Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease. Nat Genet. 2008; 40: 955-962 [OpenAIRE] [PubMed] [DOI]

van Heel, DA, Franke, L, Hunt, KA, Gwilliam, R, Zhernakova, A, Inouye, M, Wapenaar, MC, Barnardo, MC, Bethel, G, Holmes, GK, Feighery, C, Jewell, D, Kelleher, D, Kumar, P, Travis, S, Walters, JR, Sanders, DS, Howdle, P, Swift, J, Playford, RJ, McLaren, WM, Mearin, ML, Mulder, CJ, McManus, R, McGinnis, R, Cardon, LR, Deloukas, P, Wijmenga, C. A genome-wide association study for celiac disease identifies risk variants in the region harboring IL2 and IL21. Nat Genet. 2007; 39: 827-829 [OpenAIRE] [PubMed] [DOI]

Hafler, DA, Compston, A, Sawcer, S, Lander, ES, Daly, MJ, De Jager, PL, de Bakker, PI, Gabriel, SB, Mirel, DB, Ivinson, AJ, Pericak-Vance, MA, Gregory, SG, Rioux, JD, McCauley, JL, Haines, JL, Barcellos, LF, Cree, B, Oksenberg, JR, Hauser, SL. Risk alleles for multiple sclerosis identified by a genomewide study. N Engl J Med. 2007; 357: 851-862 [PubMed] [DOI]

Gregory, SG, Schmidt, S, Seth, P, Oksenberg, JR, Hart, J, Prokop, A, Caillier, SJ, Ban, M, Goris, A, Barcellos, LF, Lincoln, R, McCauley, JL, Sawcer, SJ, Compston, DA, Dubois, B, Hauser, SL, Garcia-Blanco, MA, Pericak-Vance, MA, Haines, JL. Interleukin 7 receptor alpha chain (IL7R) shows allelic and functional association with multiple sclerosis. Nat Genet. 2007; 39: 1083-1091 [OpenAIRE] [PubMed] [DOI]

38 references, page 1 of 3
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