publication . Article . 2009

Data for Genetic Analysis Workshop 16 Problem 1, association analysis of rheumatoid arthritis data

Amos Christopher I; Chen Wei Vivien; Seldin Michael F; Remmers Elaine F; Taylor Kimberly E; Criswell Lindsey A; Lee Annette T; Plenge Robert M; Kastner Daniel L; Gregersen Peter K;
Open Access English
  • Published: 01 Dec 2009 Journal: BMC Proceedings, volume 3, issue Suppl 7, pages S2-S2 (eissn: 1753-6561, Copyright policy)
  • Publisher: BioMed Central
  • Country: United States
Abstract
<p>Abstract</p> <p>For Genetic Analysis Workshop 16 Problem 1, we provided data for genome-wide association analysis of rheumatoid arthritis. Single-nucleotide polymorphism (SNP) genotype data were provided for 868 cases and 1194 controls that had been assayed using an Illumina 550 k platform. In addition, phenotypic data were provided from genotyping DRB1 alleles, which were classified according to the rheumatoid arthritis shared epitope, levels of anti-cyclic citrullinated peptide, and levels of rheumatoid factor IgM. Several questions could be addressed using the data, including analysis of genetic associations using single SNPs or haplotypes, as well as gene...
Subjects
Medical Subject Headings: musculoskeletal diseases
free text keywords: Proceedings, Medicine, R, Science, Q, General Biochemistry, Genetics and Molecular Biology, General Medicine, Rheumatoid arthritis, medicine.disease, Single-nucleotide polymorphism, Haplotype, Bioinformatics, Allele, Genetic association, Genetics, business.industry, business, Genotyping, Genotype, SNP
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| NARAC The Genetics of Rheumatoid Arthritis
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01AR044422-10
  • Funding stream: NATIONAL INSTITUTE OF ARTHRITIS AND MUSCULOSKELETAL AND SKIN DISEASES
22 references, page 1 of 2

Seldin, MF, Amos, CI, Ward, R, Gregersen, PK. The genetics revolution and the assault on rheumatoid arthritis. Arthritis Rheum. 1999; 42: 1071-1079 [PubMed] [DOI]

Gregersen, PK, Silver, J, Winchester, RJ. The shared epitope hypothesis. An approach to understanding the molecular genetics of susceptibility to rheumatoid arthritis. Arthritis Rheum. 1987; 30: 1205-1213 [OpenAIRE] [PubMed] [DOI]

Newton, JL, Harney, SM, Wordsworth, BP, Brown, MA. A review of the MHC genetics of rheumatoid arthritis. Genes Immun. 2004; 5: 151-157 [OpenAIRE] [PubMed] [DOI]

du Montcel, ST, Michou, L, Petit-Teixeira, E, Osorio, J, Lemaire, I, Lasbleiz, S, Pierlot, C, Quillet, P, Bardin, T, Prum, B, Cornelis, F, Clerget-Darpoux, F. New classification of HLA-DRB1 alleles supports the shared epitope hypothesis of rheumatoid arthritis susceptibility. Arthritis Rheum. 2005; 52: 1063-1068 [OpenAIRE] [PubMed] [DOI]

Morgan, AW, Haroon-Rashid, L, Martin, SG, Gooi, HC, Worthington, J, Thomson, W, Barrett, JH, Emery, P. The shared epitope hypothesis in rheumatoid arthritis: evaluation of alternative classification criteria in a large UK Caucasian cohort. Arthritis Rheum. 2008; 58: 1275-1283 [OpenAIRE] [PubMed] [DOI]

Lee, HS, Korman, BD, Le, JM, Kastner, DL, Remmers, EF, Gregersen, PK, Bae, SC. Genetic risk factors for rheumatoid arthritis differ in Caucasian and Korean populations. Arthritis Rheum. 2009; 60: 364-371 [OpenAIRE] [PubMed] [DOI]

Jawaheer, D, Li, W, Graham, RR, Chen, W, Damle, A, Xiao, X, Monteiro, J, Khalili, H, Lee, A, Lundsten, R, Begovich, A, Bugawan, T, Erlich, H, Elder, JT, Criswell, LA, Seldin, MF, Amos, CI, Behrens, TW, Gregersen, PK. Dissecting the genetic complexity of the association between human leukocyte antigens and rheumatoid arthritis. Am J Hum Genet. 2002; 71: 585-594 [OpenAIRE] [PubMed] [DOI]

Irigoyen, P, Lee, AT, Wener, MH, Li, W, Kern, M, Batliwalla, F, Lum, RF, Massarotti, E, Weisman, M, Bombardier, C, Remmers, EF, Kastner, DL, Seldin, MF, Criswell, LA, Gregersen, PK. Regulation of anti-cyclic citrullinated peptide antibodies in rheumatoid arthritis: contrasting effects of HLA-DR3 and the shared epitope alleles. Arthritis Rheum. 2005; 52: 3813-3818 [OpenAIRE] [PubMed] [DOI]

Huizinga, TW, Amos, CI, Helm-van Mil, AH van der, Chen, W, van Gaalen, FA, Jawaheer, D, Schreuder, GM, Wener, M, Breedveld, FC, Ahmad, N, Lum, RF, de Vries, RR, Gregersen, PK, Toes, RE, Criswell, LA. Refining the complex rheumatoid arthritis phenotype based on specificity of the HLA-DRB1 shared epitope for antibodies to citrullinated proteins. Arthritis Rheum. 2005; 52: 3433-3438 [OpenAIRE] [PubMed] [DOI]

Kroot, EJ, de Jong, BA, van Leeuwen, MA, Swinkels, H, Hoogen, FH van den, van't Hof, M, Putte, LB van de, van Rijswijk, MH, van Venrooij, WJ, van Riel, PL. The prognostic value of anti-cyclic citrullinated peptide antibody in patients with recent-onset rheumatoid arthritis. Arthritis Rheum. 2000; 43: 1831-1835 [OpenAIRE] [PubMed] [DOI]

Begovich, AB, Carlton, VE, Honigberg, LA, Schrodi, SJ, Chokkalingam, AP, Alexander, HC, Ardlie, KG, Huang, Q, Smith, AM, Spoerke, JM, Conn, MT, Chang, M, Chang, SY, Saiki, RK, Catanese, JJ, Leong, DU, Garcia, VE, McAllister, LB, Jeffery, DA, Lee, AT, Batliwalla, F, Remmers, E, Criswell, LA, Seldin, MF, Kastner, DL, Amos, CI, Sninsky, JJ, Gregersen, PK. A missense single-nucleotide polymorphism in a gene encoding a protein tyrosine phosphatase (PTPN22) is associated with rheumatoid arthritis. Am J Hum Genet. 2004; 75: 330-337 [OpenAIRE] [PubMed] [DOI]

Michou, L, Lasbleiz, S, Rat, AC, Migliorini, P, Balsa, A, Westhovens, R, Barrera, P, Alves, H, Pierlot, C, Glikmans, E, Garnier, S, Dausset, J, Vaz, C, Fernandes, M, Petit-Teixeira, E, Lemaire, I, Pascual-Salcedo, D, Bombardieri, S, Dequeker, J, Radstake, TR, Van Riel, P, Putte, L van de, Lopes-Vaz, A, Prum, B, Bardin, T, Dieudé, P, Cornélis, F. Linkage proof for PTPN22, a rheumatoid arthritis susceptibility gene and a human autoimmunity gene. Proc Natl Acad Sci USA. 2007; 104: 1649-1654 [OpenAIRE] [PubMed] [DOI]

Carlton, VE, Hu, X, Chokkalingam, AP, Schrodi, SJ, Brandon, R, Alexander, HC, Chang, M, Catanese, JJ, Leong, DU, Ardlie, KG, Kastner, DL, Seldin, MF, Criswell, LA, Gregersen, PK, Beasley, E, Thomson, G, Amos, CI, Begovich, AB. PTPN22 genetic variation: evidence for multiple variants associated with rheumatoid arthritis. Am J Hum Genet. 2005; 77: 567-581 [OpenAIRE] [PubMed] [DOI]

Plenge, RM, Padyukov, L, Remmers, EF, Purcell, S, Lee, AT, Karlson, EW, Wolfe, F, Kastner, DL, Alfredsson, L, Altshuler, D, Gregersen, PK, Klareskog, L, Rioux, JD. 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. Am J Hum Genet. 2005; 77: 1044-1060 [OpenAIRE] [PubMed] [DOI]

Plenge, RM, Seielstad, M, Padyukov, L, Lee, AT, Remmers, EF, Ding, B, Liew, A, Khalili, H, Chandrasekaran, A, Davies, LR, Li, W, Tan, AK, Bonnard, C, Ong, RT, Thalamuthu, A, Pettersson, S, Liu, C, Tian, C, Chen, WV, Carulli, JP, Beckman, EM, Altshuler, D, Alfredsson, L, Criswell, LA, Amos, CI, Seldin, MF, Kastner, DL, Klareskog, L, Gregersen, PK. TRAF1-C5 as a risk locus for rheumatoid arthritis--a genomewide study. N Engl J Med. 2007; 357: 1199-1209 [OpenAIRE] [PubMed] [DOI]

22 references, page 1 of 2
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publication . Article . 2009

Data for Genetic Analysis Workshop 16 Problem 1, association analysis of rheumatoid arthritis data

Amos Christopher I; Chen Wei Vivien; Seldin Michael F; Remmers Elaine F; Taylor Kimberly E; Criswell Lindsey A; Lee Annette T; Plenge Robert M; Kastner Daniel L; Gregersen Peter K;