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. Criswell; J. Bart A. Crusius; Jing Cui; Phillip L. de Jager; Bo Ding; Paul Emery; Edward Flynn; Pille Harrison; Lynne J. 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; Paul Wordsworth; David Altshuler; Elizabeth W. Karlson; Rene E. M. Toes; Niek de Vries; Ann B. Begovich; Katherine A. Siminovitch; Jane Worthington; Lars Klareskog; Peter K. Gregersen; Mark J. Daly; Robert M. Plenge

doi:10.1038/ng.479

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. Criswell

J. Bart A. Crusius, Jing Cui, Phillip L. de Jager, Bo Ding, Paul Emery, Edward Flynn, Pille Harrison, Lynne J. 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, Paul Wordsworth, David Altshuler, Elizabeth W. Karlson, Rene E. M. Toes, Niek de Vries, Ann B. Begovich, Katherine A. Siminovitch, Jane Worthington, Lars Klareskog, Peter K. Gregersen, Mark J. Daly, Robert M. Plenge

Research output: Contribution to journal › Article › Academic › peer-review

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(1). We used Gene Relationships Across Implicated Loci (GRAIL)(2), 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(1,3-11). 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 language	English
Pages (from-to)	1313-U76
Journal	Nature genetics
Volume	41
Issue number	12
DOIs	https://doi.org/10.1038/ng.479
Publication status	Published - 2009

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Raychaudhuri, S., Thomson, B. P., Remmers, E. F., Eyre, S., Hinks, A., Guiducci, C., Catanese, J. J., Xie, G., Stahl, E. A., Chen, R., Alfredsson, L., Amos, C. I., Ardlie, K. G., Barton, A., Bowes, J., Burtt, N. P., Chang, M., Coblyn, J., Costenbader, K. H., ... Plenge, R. M. (2009). Genetic variants at CD28, PRDM1 and CD2/CD58 are associated with rheumatoid arthritis risk. Nature genetics, 41(12), 1313-U76. https://doi.org/10.1038/ng.479

@article{221b095ed7d6458fa7bfb10790f04e6c,

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

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(1). We used Gene Relationships Across Implicated Loci (GRAIL)(2), 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(1,3-11). 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",

author = "Soumya Raychaudhuri and Thomson, \{Brian P.\} and Remmers, \{Elaine F.\} and Stephen Eyre and Anne Hinks and Candace Guiducci and Catanese, \{Joseph J.\} and Gang Xie and Stahl, \{Eli A.\} and Robert Chen and Lars Alfredsson and Amos, \{Christopher I.\} and Ardlie, \{Kristin G.\} and Anne Barton and John Bowes and Burtt, \{Noel P.\} and Monica Chang and Jonathan Coblyn and Costenbader, \{Karen H.\} and Criswell, \{Lindsey A.\} and Crusius, \{J. Bart A.\} and Jing Cui and \{de Jager\}, \{Phillip L.\} and Bo Ding and Paul Emery and Edward Flynn and Pille Harrison and Hocking, \{Lynne J.\} and Huizinga, \{Tom W. J.\} and Kastner, \{Daniel L.\} and Xiayi Ke and Kurreeman, \{Fina A. S.\} and Lee, \{Annette T.\} and Xiangdong Liu and Yonghong Li and Paul Martin and Morgan, \{Ann W.\} and Leonid Padyukov and Reid, \{David M.\} and Mark Seielstad and Seldin, \{Michael F.\} and Shadick, \{Nancy A.\} and Sophia Steer and Tak, \{Paul P.\} and Wendy Thomson and \{van der Helm-van Mil\}, \{Annette H. M.\} and \{van der Horst-Bruinsma\}, \{Irene E.\} and Weinblatt, \{Michael E.\} and Wilson, \{Anthony G.\} and Wolbink, \{Gert Jan\} and Paul Wordsworth and David Altshuler and Karlson, \{Elizabeth W.\} and Toes, \{Rene E. M.\} and \{de Vries\}, Niek and Begovich, \{Ann B.\} and Siminovitch, \{Katherine A.\} and Jane Worthington and Lars Klareskog and Gregersen, \{Peter K.\} and Daly, \{Mark J.\} and Plenge, \{Robert M.\}",

year = "2009",

doi = "10.1038/ng.479",

language = "English",

volume = "41",

pages = "1313--U76",

journal = "Nature genetics",

issn = "1061-4036",

publisher = "Nature Publishing Group",

number = "12",

}

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, LJ, 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, Wordsworth, P, Altshuler, D, Karlson, EW, Toes, REM, de Vries, N, Begovich, AB, Siminovitch, KA, Worthington, J, Klareskog, L, Gregersen, PK, Daly, MJ & Plenge, RM 2009, 'Genetic variants at CD28, PRDM1 and CD2/CD58 are associated with rheumatoid arthritis risk', Nature genetics, vol. 41, no. 12, pp. 1313-U76. https://doi.org/10.1038/ng.479

TY - JOUR

T1 - Genetic variants at CD28, PRDM1 and CD2/CD58 are associated with rheumatoid arthritis risk

AU - Raychaudhuri, Soumya

AU - Thomson, Brian P.

AU - Remmers, Elaine F.

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

AU - Costenbader, Karen H.

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 J.

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 - Wordsworth, Paul

AU - Altshuler, David

AU - Karlson, Elizabeth W.

AU - Toes, Rene E. M.

AU - de Vries, Niek

AU - Begovich, Ann B.

AU - Siminovitch, Katherine A.

AU - Worthington, Jane

AU - Klareskog, Lars

AU - Gregersen, Peter K.

AU - Daly, Mark J.

AU - Plenge, Robert M.

PY - 2009

Y1 - 2009

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(1). We used Gene Relationships Across Implicated Loci (GRAIL)(2), 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(1,3-11). 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

AB - 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(1). We used Gene Relationships Across Implicated Loci (GRAIL)(2), 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(1,3-11). 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

U2 - 10.1038/ng.479

DO - 10.1038/ng.479

M3 - Article

C2 - 19898481

SN - 1061-4036

VL - 41

SP - 1313-U76

JO - Nature genetics

JF - Nature genetics

IS - 12

ER -

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

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