As for any clinical molecular test, the choice of controls is critical. Previously positive patient specimens and T-lymphocyte-derived cell lines can serve as positive controls. Sensitivity controls can be made by dilution of a positive control cell line in a polyclonal T-cell population, such as tonsil, to determine the level of detection in a polyclonal background. The sensitivity in a nonlymphoid background will be higher and may lead to inaccurate assessment of sensitivity. In addition to a positive control, and one or more sensitivity controls, PCR tests should always include a normal (negative) sample and a sample containing reagents but no DNA as controls for possible contamination with extraneous DNA. SBA controls include size markers, germline DNA (e.g. from placenta), and a sensitivity control.

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