Over the past several decades, many factors have led to higher rates of patient and graft survival in organ transplantation. These include enhanced immunosuppression, infectious disease prophylaxis, advances in surgical technique, better patient selection criteria, optimal timing of transplantation, and better options for treating complications (Hariharan et al., 2000; Adam and Del Gaudio, 2003). As a result of these advanced immunosuppressive treatments, graft loss due to acute rejection is now rare among solid-organ transplants. The optimal strategy for immunosuppressive treatment in the future will tailor low-dose immunosuppression to the patient's needs with avoidance (or early withdrawal) of corticosteroid and lower doses of calcineurin inhibitors. Drugs aimed at tolerance induction and inhibition of adhesion molecule expression might also lead to better outcomes for many recipients in the near future (Ortiz et al., 2003; Heeger, 2003). However, these substantial gains have not prevented graft loss so much as they have delayed it. To improve transplant outcomes, we need a better understanding of predisposing immunologic and non-immunologic factors. With more sensitive analytical methods, it is becoming increasingly clear that efforts to prevent chronic rejection and avoid inappropriate immunosuppression must include and effective means to proximally diagnose acute cellular rejection (ACR), including sub-clinical forms of injury. The role of concomitant viral infection is also being recognized as increasing germane, and these methods may also assist in more precisely identifying the origin and the 'intent' of immune cell infiltrates. Molecular techniques have become a mainstay for most biomedical research. In particular, sensitive methods for gene transcript detection have played an important role in our understanding of the basic mechanisms promoting allosensitization and adaptive immune regulation. It is becoming increasingly clear that these techniques will aid to better understand human transplant biology, and, more importantly, guide clinical decision making with mechanistically based information. By allowing for critical analysis of the blood and graft microenvironment, these assays are providing early mechanistic data aiding in the correlation of basic and clinical scientific concepts. This chapter will discuss the use of real-time polymerase chain reaction in gene transcript quantification, gene polymorphism analysis, viral load detection and quantification. Clinical correlations will be presented as examples of how these techniques may have clinical relevance.

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