Validating affymetrix chip results with real time pcr
Differentially expressed genes were involved in processes such as chemotaxis, immune function, signal transduction and inflammatory responses.
The value of tissue biopsies is still under debate, and biopsies repeated in quick succession are not feasible.
RNA was extracted from peripheral blood mononuclear cells of 19 rheumatoid arthritis patients before the first application of the TNFα blocker etanercept as well as after 72 hours.
Clinical response was assessed over 3 months using the 28-joint-count Disease Activity Score and X-ray scans.
Using supervised learning methods, pairs and triplets derived from these genes were found to have a high prognostic value – reflected by prediction accuracies of over 89% for seven gene pairs and of 95% for 10 specific gene triplets.
Nineteen patients (15 females, four males; mean age, 50.8 ± 11.0 years; mean duration of disease, 15.8 ± 9.4 years; all Caucasian) who met the American College of Rheumatology criteria for RA  were studied; for details, refer to Table 1.
More than three different disease-modifying antirheumatic drugs had failed to control disease activity before etanercept was administered.
The study was approved by the ethics committee of the University of Magdeburg (71/99) and all patients were asked for written consent. Patients were assessed for overall disease activity using the 28-joint-count Disease Activity Score (DAS28) as described elsewhere .
Rheumatoid arthritis (RA) is an autoimmune disease of unknown aetiology that is characterized by recruitment and activation of inflammatory cells, synovial hyperplasia, and destruction of cartilage and bone.
About 30% of rheumatoid arthritis patients fail to respond adequately to TNFα-blocking therapy.
There is a medical and socioeconomic need to identify molecular markers for an early prediction of responders and nonresponders.
The proinflammatory cytokine TNFα is a key mediator in the pathogenesis of RA .
Etanercept (Enbrel; Wyeth, Cambridge, MA, USA), a soluble TNFα receptor immunoglobulin fusion protein, has been recognized as a potent biological that neutralizes TNFα [2–4].
Clara, CA, USA) to monitor changes in the expression levels of mononuclear cells from peripheral blood during etanercept treatment.