Case-control collections are listed in
Table 1 and described in detail in our previous studies
6 (link),7 (link),11 (link),13 (link),19 (link). Collections were composed entirely of individuals of selfdescribed European ancestry, and all cases either met the 1987 American College of Rheumatology (ACR) criteria for diagnosis of RA
50 (link) or were diagnosed by board-certified rheumatologists. All RA cases were further limited to anti-CCP+ patients, or RF+ patients if anti-CCP status data were missing. The BRASS RA samples have been used in our previous 100K GWAS
6 (link), but here are presented for the first time genotyped with the Affymetrix 6.0 array. In the current study, controls were matched to BRASS RA cases using principal components analysis from GWAS data from three separate studies: controls from a multiple sclerosis GWAS
31 (link), controls from an age-related macular degeneration GWAS
51 , and controls from a myocardial infarction GWAS
52 (link). WTCCC collection controls included the 1958 birth and National Blood Service cohorts as well as non-autoimmune disease cases (bipolar disorder, cardiovascular disease, hypertension and type 2 diabetes)
15 (link). All GWAS collections except WTCCC were restricted to control subjects matching cases using principal components analysis of GWAS data. All replication sample collections were composed of epidemiologically and/or geographically matched cases and controls, except NARAC II collection, which was case-control matched based on genotypes at a set of ancestry-informative markers as previously described
11 (link). The eight replication samples included: (1) CCP positive cases and controls from Halifax and Toronto (CANADA-II)
13 (link); (2) RF positive Dutch cases from Groningen and Nijmegen, together with geographically matched controls
53 (link); (3) CCP positive Dutch cases and controls collected from the greater Amsterdam region (GENRA)
54 (link); (4) North American RF positive cases and controls matched on gender, age, and grandparental country of origin from the Genomics Collaborative Initiative (GCI)
4 (link); (5) CCP or RF positive Dutch cases and controls from Leiden University Medical Center (LUMC)
5 (link); (6) CCP positive cases drawn from North American clinics and controls from the New York Cancer Project (together this collection is called NARAC-II)
7 (link); (7) CCP or RF positive cases recruited at multiple sites in the United Kingdom by the United Kingdom Rheumatoid Arthritis Genetics (UKRAG) collaboration
9 (link); and (8) CCP or RF positive cases identified by chart review from the Nurses Health Study (NHS) and matched controls based on age, gender, menopausal status, and hormone use
55 (link). We used available SNP data from this and previous studies to identify genetically identical samples from the same country
13 (link); we assumed these represented duplicated individuals and removed them. Institutional review boards at each collection site approved the study, and all individuals gave their informed consent.
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