publication . Article . Conference object . 2009

identification of novel putative rheumatoid arthritis susceptibility genes via analysis of rare variants

Morris, Andrew P; Zeggini, Eleftheria; Lindgren, Cecilia M;
Open Access
  • Published: 01 Dec 2009 Journal: BMC Proceedings, volume 3 (eissn: 1753-6561, Copyright policy)
  • Publisher: Springer Nature
  • Country: United Kingdom
Abstract
<p>Abstract</p> <p>Established loci for rheumatoid arthritis (RA), including <it>HLA-DRB1 </it>and <it>PTPN22</it>, do not fully account for the genetic component of susceptibility to the disease. One possible source of as yet undiscovered susceptibility genes are those mediated through effects of rare variants. We present a novel method for gene-based genome-wide scans of whole-genome association (WGA) data to identify accumulations of rare variants associated with disease. We apply our method to WGA SNP genotype data obtained from 868 RA cases and 1194 controls. Our results highlight novel putative RA susceptibility genes that have not previously been identifi...
Subjects
free text keywords: General Biochemistry, Genetics and Molecular Biology, General Medicine, Genetics, Bioinformatics, PTPN22, Rheumatoid arthritis, medicine.disease, medicine, Gene, Disease, SNP, Genotype, business.industry, business, Locus (genetics), R, Science, Q, Proceedings
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)

Wordsworth, P, Bell, J. Polygenic susceptibility in rheumatoid arthritis. Ann Rheum Dis. 1991; 50: 343-346 [OpenAIRE] [PubMed] [DOI]

Brennan, P, Silman, A. Why the gender difference in susceptibility to rheumatoid arthritis. Ann Rheum Dis. 1995; 54: 694-695 [OpenAIRE] [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]

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]

Hinks, A, Eyre, S, Barton, A, Thomson, W, Worthington, J. Investigation of genetic variation across PTPN22 in UK rheumatoid arthritis (RA) patients. Ann Rheum Dis. 2006; 66: 683-686 [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]

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]

Plenge, RM, Cotsapas, C, Davies, L, Price, AL, de Bakker, PI, Maller, J, Pe'er, I, Burtt, NP, Blumenstiel, B, De Felice, M, Parkin, M, Barry, R, Winslow, W, Healy, C, Graham, RR, Neale, BM, Izmailova, E, Roubenoff, R, Parker, AN, Glass, R, Karlson, EW, Maher, N, Hafler, DA, Lee, DM, Seldin, MF, Remmers, EF, Lee, AT, Padyukov, L, Alfredsson, L, Coblyn, J, Weinblatt, ME, Gabriel, SB, Purcell, S, Klareskog, L, Gregersen, PK, Shadick, NA, Daly, MJ, Altshuler, D. Two independent alleles at 6q23 associated with risk of rheumatoid arthritis. Nat Genet. 2007; 39: 1477-1482 [OpenAIRE] [PubMed] [DOI]

Anderson, CA, Pettersson, FH, Barrett, JC, Zhuang, JJ, Ragoussis, J, Cardon, LR, Morris, AP. Evaluating the effects of imputation on the power, coverage, and cost-efficiency of genome-wide SNP platforms. Am J Hum Genet. 2008; 83: 112-119 [OpenAIRE] [PubMed] [DOI]

A Deep Catalog of Human Genetic Variation.

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