Table 1.
Patient collections.
| Case Collection | Control Collection | Geographical Origin | Case Antibody Status | Cases | Controls | Genotyping Platform | Case-Control Stratification Correction | |
|---|---|---|---|---|---|---|---|---|
| Brigham Rheumatoid Arthritis Sequential Study (BRASS) | Shared controls | Boston, USA | 100% CCP+ | 483 | 1449 | Affymetrix 6.0 | GWAS data PC matching | |
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| Meta-analysis | CANADA | CANADA and Shared controls | Toronto, Canada | 100% CCP+ | 589 | 1472 | Illumina 370K | GWAS data PC matching |
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| Epidemiological Investigation of Rheumatoid Arthritis (EIRA) | EIRA | Sweden | 100% CCP+ | 1173 | 1089 | Illumina 317K | Epidemiologically matched & GWAS data PC matching | |
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| 5,539 Cases; 20,169 Controls | North American Rheumatoid Arthritis Consortium (NARAC) I | Shared controls | North America | 100% CCP+ | 867 | 1041 | Illumina 550K | GWAS data PC matching |
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| NARAC III | Shared controls | North America | 100% CCP+ | 902 | 4510 | Illumina 317K | GWAS data PC matching | |
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| Wellcome Trust Case Control Consortium (WTCCC) | Shared controls from WTCCC | United Kingdom | 100% RF+ or CCP+ | 1525 | 10608 | Affymetrix 500K | Geographically matched | |
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| CANADA II | CANADA II | Toronto & Halifax, Canada | 100% CCP+ | 1076 | 1269 | Sequenom iPlex | Geographically matched | |
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| Replication | Dutch | Dutch | The Netherlands | 100% RF+ | 718 | 697 | Sequenom iPlex | Geographically matched |
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| Genetics Network Rheumatology Amsterdam (GENRA) | GENRA | Amsterdam, The Netherlands | 100% CCP+ | 519 | 1155 | Sequenom iPlex | Geographically matched | |
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| 6,768 Cases; 8,806 Controls | Genomics Collaborative Initiative (GCI) | GCI | North America | 100% RF+ | 461 | 460 | Kinetic PCR | Epidemiologically matched |
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| Leiden University Medical Center (LUMC) | LUMC | Leiden, The Netherlands | 100% RF+ or CCP+ | 310 | 544 | Kinetic PCR | Geographically matched | |
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| NARAC II | Shared controls | North America | 100% CCP+ | 462 | 693 | Sequenom iPlex | Ancestry informative marker data matching | |
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| United Kingdom Rheumatoid Arthritis Genetics (UKRAG) | UKRAG | United Kingdom | 100% RF+ or CCP+ | 2906 | 3494 | Sequenom iPlex | Geographically matched | |
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| Nurses Health Study (NHS) | NHS | North America | 100% RF+ or CCP+ | 316 | 494 | Biotrove OpenArray | Epidemiologically matched | |
Meta-analysis of GWAS results for six collections (top panel) was used to identify SNPs for replication in eight collections (bottom panel). For each collection, we list the source of controls, geographic origin, autoantibody status of cases, numbers of cases and controls, genotyping platform (GWAS collection microarray platform, and replication and validation/prediction collection direct-genotyping technology), and the strategy used to correct for casecontrol population stratification. See Methods and Supplementary Note for details.