Clinical data for the ACR classification criteria [36] for each participant was obtained through medical record review. ANA, anti-dsDNA, anti-Sm, anti-cardiolipin were determined in the CAP-certified OMRF Clinical Immunology Laboratory by an immunofluorescence (ANA, anti-dsDNA), immunodiffusion (anti-SM), or enzyme linked immunosorbent assay (aCL) at the enrollment time point [46]. Individual ACR criterion, or sub-criterion, including autoantibody status, were coded as positive, negative, or missing. SLE patients were grouped by the presence or absence of individual ACR criterion. Logistic regression and Pearson χ2 tests were used to assess statistical significance with associated SNPs in both case-only (all cases positive for given criteria versus all cases negative for the same criterion) and case-control (all cases positive for given criterion versus all healthy controls) analyses.
