Genetic variants at CD28, PRDM1 and CD2/CD58 are associated with rheumatoid arthritis risk

Soumya Raychaudhuri, Brian P Thomson, Elaine F Remmers, Stephen Eyre, Anne Hinks, Candace Guiducci, Joseph J Catanese, Gang Xie, Eli A Stahl, Robert Chen, Lars Alfredsson, Christopher I Amos, Kristin G Ardlie, Anne Barton, John Bowes, Noel P Burtt, Monica Chang, Jonathan Coblyn, Karen H Costenbader, Lindsey A CriswellJ Bart A Crusius, Jing Cui, Phillip L De Jager, Bo Ding, Paul Emery, Edward Flynn, Pille Harrison, Lynne Hocking, Tom W J Huizinga, Daniel L Kastner, Xiayi Ke, Fina A S Kurreeman, Annette T Lee, Xiangdong Liu, Yonghong Li, Paul Martin, Ann W Morgan, Leonid Padyukov, David M Reid, Mark Seielstad, Michael F Seldin, Nancy A Shadick, Sophia Steer, Paul P Tak, Wendy Thomson, Annette H M van der Helm-van Mil, Irene E van der Horst-Bruinsma, Michael E Weinblatt, Anthony G Wilson, Gert Jan Wolbink, BIRAC consortium

Research output: Contribution to journalLetter

237 Citations (Scopus)

Abstract

To discover new rheumatoid arthritis (RA) risk loci, we systematically examined 370 SNPs from 179 independent loci with P <0.001 in a published meta-analysis of RA genome-wide association studies (GWAS) of 3,393 cases and 12,462 controls. We used Gene Relationships Across Implicated Loci (GRAIL), a computational method that applies statistical text mining to PubMed abstracts, to score these 179 loci for functional relationships to genes in 16 established RA disease loci. We identified 22 loci with a significant degree of functional connectivity. We genotyped 22 representative SNPs in an independent set of 7,957 cases and 11,958 matched controls. Three were convincingly validated: CD2-CD58 (rs11586238, P = 1 x 10(-6) replication, P = 1 x 10(-9) overall), CD28 (rs1980422, P = 5 x 10(-6) replication, P = 1 x 10(-9) overall) and PRDM1 (rs548234, P = 1 x 10(-5) replication, P = 2 x 10(-8) overall). An additional four were replicated (P <0.0023): TAGAP (rs394581, P = 0.0002 replication, P = 4 x 10(-7) overall), PTPRC (rs10919563, P = 0.0003 replication, P = 7 x 10(-7) overall), TRAF6-RAG1 (rs540386, P = 0.0008 replication, P = 4 x 10(-6) overall) and FCGR2A (rs12746613, P = 0.0022 replication, P = 2 x 10(-5) overall). Many of these loci are also associated to other immunologic diseases.
Original languageEnglish
Pages (from-to)1313-1318
Number of pages6
JournalNature Genetics
Volume41
Issue number12
Early online date8 Nov 2009
DOIs
Publication statusPublished - Dec 2009

Fingerprint

Rheumatoid Arthritis
Single Nucleotide Polymorphism
TNF Receptor-Associated Factor 6
Data Mining
Genome-Wide Association Study
Immune System Diseases
PubMed
Genes
Meta-Analysis

Keywords

  • antigens, CD2
  • antigens, CD28
  • antigens, CD58
  • arthritis, rheumatoid
  • case-control studies
  • genetic predisposition to disease
  • genetic Variation
  • genotype
  • humans
  • polymorphism, single nucleotide
  • repressor proteins
  • risk factors

Cite this

Raychaudhuri, S., Thomson, B. P., Remmers, E. F., Eyre, S., Hinks, A., Guiducci, C., ... BIRAC consortium (2009). Genetic variants at CD28, PRDM1 and CD2/CD58 are associated with rheumatoid arthritis risk. Nature Genetics, 41(12), 1313-1318. https://doi.org/10.1038/ng.479

Genetic variants at CD28, PRDM1 and CD2/CD58 are associated with rheumatoid arthritis risk. / Raychaudhuri, Soumya; Thomson, Brian P; Remmers, Elaine F; Eyre, Stephen; Hinks, Anne; Guiducci, Candace; Catanese, Joseph J; Xie, Gang; Stahl, Eli A; Chen, Robert; Alfredsson, Lars; Amos, Christopher I; Ardlie, Kristin G; Barton, Anne; Bowes, John; Burtt, Noel P; Chang, Monica; Coblyn, Jonathan; Costenbader, Karen H; Criswell, Lindsey A; Crusius, J Bart A; Cui, Jing; De Jager, Phillip L; Ding, Bo; Emery, Paul; Flynn, Edward; Harrison, Pille; Hocking, Lynne; Huizinga, Tom W J; Kastner, Daniel L; Ke, Xiayi; Kurreeman, Fina A S; Lee, Annette T; Liu, Xiangdong; Li, Yonghong; Martin, Paul; Morgan, Ann W; Padyukov, Leonid; Reid, David M; Seielstad, Mark; Seldin, Michael F; Shadick, Nancy A; Steer, Sophia; Tak, Paul P; Thomson, Wendy; van der Helm-van Mil, Annette H M; van der Horst-Bruinsma, Irene E; Weinblatt, Michael E; Wilson, Anthony G; Wolbink, Gert Jan; BIRAC consortium.

In: Nature Genetics, Vol. 41, No. 12, 12.2009, p. 1313-1318.

Research output: Contribution to journalLetter

Raychaudhuri, S, Thomson, BP, Remmers, EF, Eyre, S, Hinks, A, Guiducci, C, Catanese, JJ, Xie, G, Stahl, EA, Chen, R, Alfredsson, L, Amos, CI, Ardlie, KG, Barton, A, Bowes, J, Burtt, NP, Chang, M, Coblyn, J, Costenbader, KH, Criswell, LA, Crusius, JBA, Cui, J, De Jager, PL, Ding, B, Emery, P, Flynn, E, Harrison, P, Hocking, L, Huizinga, TWJ, Kastner, DL, Ke, X, Kurreeman, FAS, Lee, AT, Liu, X, Li, Y, Martin, P, Morgan, AW, Padyukov, L, Reid, DM, Seielstad, M, Seldin, MF, Shadick, NA, Steer, S, Tak, PP, Thomson, W, van der Helm-van Mil, AHM, van der Horst-Bruinsma, IE, Weinblatt, ME, Wilson, AG, Wolbink, GJ & BIRAC consortium 2009, 'Genetic variants at CD28, PRDM1 and CD2/CD58 are associated with rheumatoid arthritis risk', Nature Genetics, vol. 41, no. 12, pp. 1313-1318. https://doi.org/10.1038/ng.479
Raychaudhuri S, Thomson BP, Remmers EF, Eyre S, Hinks A, Guiducci C et al. Genetic variants at CD28, PRDM1 and CD2/CD58 are associated with rheumatoid arthritis risk. Nature Genetics. 2009 Dec;41(12):1313-1318. https://doi.org/10.1038/ng.479
Raychaudhuri, Soumya ; Thomson, Brian P ; Remmers, Elaine F ; Eyre, Stephen ; Hinks, Anne ; Guiducci, Candace ; Catanese, Joseph J ; Xie, Gang ; Stahl, Eli A ; Chen, Robert ; Alfredsson, Lars ; Amos, Christopher I ; Ardlie, Kristin G ; Barton, Anne ; Bowes, John ; Burtt, Noel P ; Chang, Monica ; Coblyn, Jonathan ; Costenbader, Karen H ; Criswell, Lindsey A ; Crusius, J Bart A ; Cui, Jing ; De Jager, Phillip L ; Ding, Bo ; Emery, Paul ; Flynn, Edward ; Harrison, Pille ; Hocking, Lynne ; Huizinga, Tom W J ; Kastner, Daniel L ; Ke, Xiayi ; Kurreeman, Fina A S ; Lee, Annette T ; Liu, Xiangdong ; Li, Yonghong ; Martin, Paul ; Morgan, Ann W ; Padyukov, Leonid ; Reid, David M ; Seielstad, Mark ; Seldin, Michael F ; Shadick, Nancy A ; Steer, Sophia ; Tak, Paul P ; Thomson, Wendy ; van der Helm-van Mil, Annette H M ; van der Horst-Bruinsma, Irene E ; Weinblatt, Michael E ; Wilson, Anthony G ; Wolbink, Gert Jan ; BIRAC consortium. / Genetic variants at CD28, PRDM1 and CD2/CD58 are associated with rheumatoid arthritis risk. In: Nature Genetics. 2009 ; Vol. 41, No. 12. pp. 1313-1318.
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abstract = "To discover new rheumatoid arthritis (RA) risk loci, we systematically examined 370 SNPs from 179 independent loci with P <0.001 in a published meta-analysis of RA genome-wide association studies (GWAS) of 3,393 cases and 12,462 controls. We used Gene Relationships Across Implicated Loci (GRAIL), a computational method that applies statistical text mining to PubMed abstracts, to score these 179 loci for functional relationships to genes in 16 established RA disease loci. We identified 22 loci with a significant degree of functional connectivity. We genotyped 22 representative SNPs in an independent set of 7,957 cases and 11,958 matched controls. Three were convincingly validated: CD2-CD58 (rs11586238, P = 1 x 10(-6) replication, P = 1 x 10(-9) overall), CD28 (rs1980422, P = 5 x 10(-6) replication, P = 1 x 10(-9) overall) and PRDM1 (rs548234, P = 1 x 10(-5) replication, P = 2 x 10(-8) overall). An additional four were replicated (P <0.0023): TAGAP (rs394581, P = 0.0002 replication, P = 4 x 10(-7) overall), PTPRC (rs10919563, P = 0.0003 replication, P = 7 x 10(-7) overall), TRAF6-RAG1 (rs540386, P = 0.0008 replication, P = 4 x 10(-6) overall) and FCGR2A (rs12746613, P = 0.0022 replication, P = 2 x 10(-5) overall). Many of these loci are also associated to other immunologic diseases.",
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AU - Raychaudhuri, Soumya

AU - Thomson, Brian P

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AU - Eyre, Stephen

AU - Hinks, Anne

AU - Guiducci, Candace

AU - Catanese, Joseph J

AU - Xie, Gang

AU - Stahl, Eli A

AU - Chen, Robert

AU - Alfredsson, Lars

AU - Amos, Christopher I

AU - Ardlie, Kristin G

AU - Barton, Anne

AU - Bowes, John

AU - Burtt, Noel P

AU - Chang, Monica

AU - Coblyn, Jonathan

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AU - Criswell, Lindsey A

AU - Crusius, J Bart A

AU - Cui, Jing

AU - De Jager, Phillip L

AU - Ding, Bo

AU - Emery, Paul

AU - Flynn, Edward

AU - Harrison, Pille

AU - Hocking, Lynne

AU - Huizinga, Tom W J

AU - Kastner, Daniel L

AU - Ke, Xiayi

AU - Kurreeman, Fina A S

AU - Lee, Annette T

AU - Liu, Xiangdong

AU - Li, Yonghong

AU - Martin, Paul

AU - Morgan, Ann W

AU - Padyukov, Leonid

AU - Reid, David M

AU - Seielstad, Mark

AU - Seldin, Michael F

AU - Shadick, Nancy A

AU - Steer, Sophia

AU - Tak, Paul P

AU - Thomson, Wendy

AU - van der Helm-van Mil, Annette H M

AU - van der Horst-Bruinsma, Irene E

AU - Weinblatt, Michael E

AU - Wilson, Anthony G

AU - Wolbink, Gert Jan

AU - BIRAC consortium

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N2 - To discover new rheumatoid arthritis (RA) risk loci, we systematically examined 370 SNPs from 179 independent loci with P <0.001 in a published meta-analysis of RA genome-wide association studies (GWAS) of 3,393 cases and 12,462 controls. We used Gene Relationships Across Implicated Loci (GRAIL), a computational method that applies statistical text mining to PubMed abstracts, to score these 179 loci for functional relationships to genes in 16 established RA disease loci. We identified 22 loci with a significant degree of functional connectivity. We genotyped 22 representative SNPs in an independent set of 7,957 cases and 11,958 matched controls. Three were convincingly validated: CD2-CD58 (rs11586238, P = 1 x 10(-6) replication, P = 1 x 10(-9) overall), CD28 (rs1980422, P = 5 x 10(-6) replication, P = 1 x 10(-9) overall) and PRDM1 (rs548234, P = 1 x 10(-5) replication, P = 2 x 10(-8) overall). An additional four were replicated (P <0.0023): TAGAP (rs394581, P = 0.0002 replication, P = 4 x 10(-7) overall), PTPRC (rs10919563, P = 0.0003 replication, P = 7 x 10(-7) overall), TRAF6-RAG1 (rs540386, P = 0.0008 replication, P = 4 x 10(-6) overall) and FCGR2A (rs12746613, P = 0.0022 replication, P = 2 x 10(-5) overall). Many of these loci are also associated to other immunologic diseases.

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KW - antigens, CD2

KW - antigens, CD28

KW - antigens, CD58

KW - arthritis, rheumatoid

KW - case-control studies

KW - genetic predisposition to disease

KW - genetic Variation

KW - genotype

KW - humans

KW - polymorphism, single nucleotide

KW - repressor proteins

KW - risk factors

U2 - 10.1038/ng.479

DO - 10.1038/ng.479

M3 - Letter

C2 - 19898481

VL - 41

SP - 1313

EP - 1318

JO - Nature Genetics

JF - Nature Genetics

SN - 1061-4036

IS - 12

ER -