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Approaches to autoimmune antibody profiling using protein arrays Multiplexing technology holds the potential to become the standard for laboratory analyses. Craig S. Hixson and Steven R. Binder Autoimmune diseases are chronic degenerative or inflammatory conditions that result from abnormal immune reactions. Different autoimmune diseases affect the body in different ways. For example, in multiple sclerosis the autoimmune reaction is directed against the central nervous system, while the intestinal tract is afflicted in Crohn’s disease. Further, the tissues and organs affected may vary among individuals with the same disease. The severity of an autoimmune disease depends on the suffering individual’s immune system. Such diseases occur in at least 3% of the population, with women and the elderly affected disproportionately. Inflammation is a common symptom with many of these diseases, as is dizziness, fatigue, malaise, and low-grade fever. Organ-specific autoimmune diseases are destructive toward the targeted organ or tissue, leading to impaired function. Autoimmune diseases can be difficult to diagnose, particularly early in their development. Testing of healthy individuals for specific autoantibodies indicates that the prevalence of a positive result ranges from near 0% to more than 10%, depending on the disease. Most of the antibodies found in healthy people are of low titer and of no consequence to their health. Autoantibodies are not always specific for a single rheumatic condition. As an example, antibodies reactive with native double-stranded DNA (dsDNA) are often associated with a diagnosis of systemic lupus erythematosus (SLE). However, anti-dsDNA antibodies are also found in some individuals with rheumatoid arthritis, Sjögren’s syndrome, scleroderma, drug-induced lupus, chronic active hepatitis, Graves’ disease, and other conditions. Anti-dsDNA antibodies appear in people with these conditions with a frequency of less than 5% typically. The presence of anti-dsDNA alone therefore is not diagnostic of SLE. In a few cases, autoantibodies are quite disease specific.