Association between complement C4 copy number and 3 systemic inflammatory autoimmune diseases (SIADs). A Workflow for analysis. Three patient groups with systemic inflammatory autoimmune diseases and 1 reference cohort were analyzed for HLA alleles and copy number of the paralogous C4 genes C4A and C4B, using targeted sequencing data. Association analysis of C4 was performed for clinical subsets of the diseases. Additionally, common and rare variants in the C4 genes were analyzed from the sequencing data. B, Total C4 copy number in healthy controls and patients with systemic lupus erythematous (SLE), primary Sjögren's syndrome (SS), or myositis (n = 3,541). Logistic regression was performed to analyze associations in the combined patient group compared to healthy controls, with adjustment for sex and principal components 1–4 (PC1–PC4). Odds ratios (ORs) represent disease risk in association with each decrease in C4 copy number. C, Copy number of C4A and C4B in each patient group and healthy controls (n = 3,520). Analysis is based on logistic regression with both C4A and C4B included as additive variables and with adjustment for sex and PC1–PC4. ORs represent disease risk in association with each decrease in C4A or C4B copy number. MHC = major histocompatibility complex; CI95% = 95% confidence interval.