Table 1.
Sample collections
| Case collection | Control collection | Origin | Antibody status | Cases | Controls | Genotyping platform | Case-control stratification | |
|---|---|---|---|---|---|---|---|---|
| Meta-analysis | North American Rheumatoid Arthritis Consortium (NARAC) | New York Cancer Project, New York City | North America | 100% CCP+ | 873 | 1,196 | Illumina 550K | Identity-by-state clustering |
| 3,393 cases; 12,460 controls | Epidemiological Investigation of Rheumatoid Arthritis (EIRA) | EIRA | Sweden | 100% CCP+ | 660 | 658 | Illumina 317K | Epidemiologically matched, identity- by-state clustering |
| Wellcome Trust Case Control Consortium (WTCCC) | Shared controls, multiple non-autoimmune diseases | United Kingdom | 80% CCP+, 84% RF+ | 1,860 | 10,606 | Affymetrix 500K | Geographically matched | |
| Stage 1 replication | Nurses Health Study (NHS) | NHS | North America | 100% RF+ or CCP+ | 257 | 411 | Sequenom iPlex | Epidemiologically matched |
| Brigham Rheumatoid Arthritis Sequential Study (BRASS) | National Institutes of Mental Health (NIMH) | Boston, USA | 100% CCP+ | 407 | 814 | Sequenom iPlex, Affymetrix 500K | Case-control matching with GWAS data | |
| 1,089 cases; 1,862 controls | NARAC II | New York Cancer Project, New York City | North America | 100% CCP+ | 425 | 637 | Sequenom iPlex | Case-control matching with ancestry informative markers |
| NARAC III | Publicly available Shared controls | North America | 100% CCP+ | 869 | 1,303 | Illumina 317K | Case-control matching with GWAS data | |
| Stage 2 replication | Genomics Collaborative Initiative (GCI) | GCI | North America | 100% RF+ | 457 | 460 | Kinetic PCR | Epidemiologically matched |
| Leiden University Medical Center (LUMC) | LUMC | Leiden, The Netherlands | 100% RF+ or CCP+ | 528 | 540 | Kinetic PCR | Geographically matched | |
| 2,840 cases; 3,945 controls | EIRA-II | EIRA-II | Sweden | 100% CCP+ | 435 | 412 | Sequenom iPlex | Epidemiologically matched |
| Genetics Network Rheumatology Amsterdam (GENRA) | GENRA | Amsterdam, The Netherlands | 100% CCP+ | 551 | 1,230 | Sequenom iPlex | Geographically matched | |
GWA data from three meta-analysis collections were used to identify candidate SNPs for replication. The replication set was divided into two stages: stage 1 replication (three collections) and stage 2 replication (five collections). For each collection we list the geographic origin, the source of the controls, the autoantibody status of cases, and the number of cases and controls. We also list the genotyping technology used to type SNPs of interest. Finally, we specify the strategy used to correct for case-control population stratification.