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Genetic variants at CD28, PRDM1, and CD2/CD58 are associated with rheumatoid arthritis risk
To discover novel RA risk loci, we systematically examined 370 SNPs from 179 independent loci with p<0.001 in a published meta-analysis of RA GWAS of 3,393 cases and 12,462 controls(1). We used GRAIL(2), a computational method that applies statistical text mining to PubMed abstracts, to score the...
| Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Formato: | Online Artículo Texto |
| Lenguaje: | English |
| Publicado: |
2009
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| Materias: | |
| Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3142887/ https://www.ncbi.nlm.nih.gov/pubmed/19898481 http://dx.doi.org/10.1038/ng.479 |
| _version_ | 1782208871869186048 |
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| author | 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 J. 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 Wordsworth, Paul Altshuler, David Karlson, Elizabeth W. Toes, Rene E. M. de Vries, Niek Begovich, Ann B. Siminovitch, Katherine A. Worthington, Jane Klareskog, Lars Gregersen, Peter K. Daly, Mark J. Plenge, Robert M. |
| author_facet | 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 J. 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 Wordsworth, Paul Altshuler, David Karlson, Elizabeth W. Toes, Rene E. M. de Vries, Niek Begovich, Ann B. Siminovitch, Katherine A. Worthington, Jane Klareskog, Lars Gregersen, Peter K. Daly, Mark J. Plenge, Robert M. |
| author_sort | Raychaudhuri, Soumya |
| collection | PubMed |
| description | To discover novel RA risk loci, we systematically examined 370 SNPs from 179 independent loci with p<0.001 in a published meta-analysis of RA GWAS of 3,393 cases and 12,462 controls(1). We used 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 validate convincingly: CD2/CD58 (rs11586238, p=1×10(−6) replication, p=1×10(−9) overall), and CD28 (rs1980422, p=5×10(−6) replication, p=1×10(−9) overall), PRDM1 (rs548234, p=1×10(−5) replication, p=2×10(−8) overall). An additional four replicate (p<0.0023): TAGAP (rs394581, p=0.0002 replication, p=4×10(−7) overall), PTPRC (rs10919563, p=0.0003 replication, p=7×10(−7) overall), TRAF6/RAG1 (rs540386, p=0.0008 replication, p=4×10(−6) overall), and FCGR2A (rs12746613, p=0.0022 replication, p=2×10(−5) overall). Many of these loci are also associated to other immunologic diseases. |
| format | Online Article Text |
| id | pubmed-3142887 |
| institution | National Center for Biotechnology Information |
| language | English |
| publishDate | 2009 |
| record_format | MEDLINE/PubMed |
| spelling | pubmed-31428872011-07-25 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 J. 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 Wordsworth, Paul Altshuler, David Karlson, Elizabeth W. Toes, Rene E. M. de Vries, Niek Begovich, Ann B. Siminovitch, Katherine A. Worthington, Jane Klareskog, Lars Gregersen, Peter K. Daly, Mark J. Plenge, Robert M. Nat Genet Article To discover novel RA risk loci, we systematically examined 370 SNPs from 179 independent loci with p<0.001 in a published meta-analysis of RA GWAS of 3,393 cases and 12,462 controls(1). We used 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 validate convincingly: CD2/CD58 (rs11586238, p=1×10(−6) replication, p=1×10(−9) overall), and CD28 (rs1980422, p=5×10(−6) replication, p=1×10(−9) overall), PRDM1 (rs548234, p=1×10(−5) replication, p=2×10(−8) overall). An additional four replicate (p<0.0023): TAGAP (rs394581, p=0.0002 replication, p=4×10(−7) overall), PTPRC (rs10919563, p=0.0003 replication, p=7×10(−7) overall), TRAF6/RAG1 (rs540386, p=0.0008 replication, p=4×10(−6) overall), and FCGR2A (rs12746613, p=0.0022 replication, p=2×10(−5) overall). Many of these loci are also associated to other immunologic diseases. 2009-11-08 2009-12 /pmc/articles/PMC3142887/ /pubmed/19898481 http://dx.doi.org/10.1038/ng.479 Text en http://www.nature.com/authors/editorial_policies/license.html#terms Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:http://www.nature.com/authors/editorial_policies/license.html#terms |
| spellingShingle | Article 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 J. 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 Wordsworth, Paul Altshuler, David Karlson, Elizabeth W. Toes, Rene E. M. de Vries, Niek Begovich, Ann B. Siminovitch, Katherine A. Worthington, Jane Klareskog, Lars Gregersen, Peter K. Daly, Mark J. Plenge, Robert M. Genetic variants at CD28, PRDM1, and CD2/CD58 are associated with rheumatoid arthritis risk |
| title | Genetic variants at CD28, PRDM1, and CD2/CD58 are associated with rheumatoid arthritis risk |
| title_full | Genetic variants at CD28, PRDM1, and CD2/CD58 are associated with rheumatoid arthritis risk |
| title_fullStr | Genetic variants at CD28, PRDM1, and CD2/CD58 are associated with rheumatoid arthritis risk |
| title_full_unstemmed | Genetic variants at CD28, PRDM1, and CD2/CD58 are associated with rheumatoid arthritis risk |
| title_short | Genetic variants at CD28, PRDM1, and CD2/CD58 are associated with rheumatoid arthritis risk |
| title_sort | genetic variants at cd28, prdm1, and cd2/cd58 are associated with rheumatoid arthritis risk |
| topic | Article |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3142887/ https://www.ncbi.nlm.nih.gov/pubmed/19898481 http://dx.doi.org/10.1038/ng.479 |
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