A cartridge for being disposed in an instrument for manipulating, actuating and/or interacting with the cartridge to perform a nucleic acid isolation, transcription and/or amplification on a test sample contained within the cartridge, the cartridge comprising at least: - a sample preparation (or isolation) module including a first housing and a second housing, wherein ∘ the first housing includes a first (or top) portion and a second (or bottom) portion, ∘ the second housing is coupled to and/or at least partially within the first housing and defines a series of holding chambers (7163a - 7163d) that contain reagents and/or substances for being used in the isolation process, ∘ each of the holding chambers (7163a - 7163d) includes an actuator movably disposed therein, said actuator being configured to function as a transfer mechanism (7166a - 7166d) to convey substances from a chamber (7163a-7163d) into another portion of the isolation module when moved towards said another portion of the isolation module, ∘ the internal portions of the second housing, a puncturable member and the actuators (7166a - 7166d) collectively define the holding chambers (7163a - 7163d) as fluidically isolated holding chambers (7163a - 7163d) within which reagents and/or substances are stored, ∘ the second housing includes a mixing pump, which can be actuated to agitate, mix and/or produce a turbulent motion within the sample, reagents and/or other substances contained with a portion of the isolation module, ∘ the isolation module includes a cap that is removably coupled to the housing, characterized in that - the sample preparation module and an amplification module are coupled together to form an integrated cartridge, - a cover is disposed about a portion of the isolation module and the amplification module, - the amplification module includes a substrate that is constructed to from a first layer and a second layer, a PCR vial coupled to the second layer, a transfer mechanism, a first reagent module and a second reagent module, wherein the PCR vial is coupled to the first end portion of the housing and defines a volume within which a sample can be disposed to facilitate a reaction associated with the sample. - a sample preparation (or isolation) module including a first housing and a second housing, wherein ∘ the first housing includes a first (or top) portion and a second (or bottom) portion, ∘ the second housing is coupled to and/or at least partially within the first housing and defines a series of holding chambers (7163a - 7163d) that contain reagents and/or substances for being used in the isolation process, ∘ each of the holding chambers (7163a - 7163d) includes an actuator movably disposed therein, said actuator being configured to function as a transfer mechanism (7166a - 7166d) to convey substances from a chamber (7163a-7163d) into another portion of the isolation module when moved towards said another portion of the isolation module, ∘ the internal portions of the second housing, a puncturable member and the actuators (7166a - 7166d) collectively define the holding chambers (7163a - 7163d) as fluidically isolated holding chambers (7163a - 7163d) within which reagents and/or substances are stored, ∘ the second housing includes a mixing pump, which can be actuated to agitate, mix and/or produce a turbulent motion within the sample, reagents and/or other substances contained with a portion of the isolation module, ∘ the isolation module includes a cap that is removably coupled to the housing, ∘ the first housing includes a first (or top) portion and a second (or bottom) portion, ∘ the second housing is coupled to and/or at least partially within the first housing and defines a series of holding chambers (7163a - 7163d) that contain reagents and/or substances for being used in the isolation process, ∘ each of the holding chambers (7163a - 7163d) includes an actuator movably disposed therein, said actuator being configured to function as a transfer mechanism (7166a - 7166d) to convey substances from a chamber (7163a-7163d) into another portion of the isolation module when moved towards said another portion of the isolation module, ∘ the internal portions of the second housing, a puncturable member and the actuators (7166a - 7166d) collectively define the holding chambers (7163a - 7163d) as fluidically isolated holding chambers (7163a - 7163d) within which reagents and/or substances are stored, ∘ the second housing includes a mixing pump, which can be actuated to agitate, mix and/or produce a turbulent motion within the sample, reagents and/or other substances contained with a portion of the isolation module, ∘ the isolation module includes a cap that is removably coupled to the housing, - the sample preparation module and an amplification module are coupled together to form an integrated cartridge, - a cover is disposed about a portion of the isolation module and the amplification module, - the amplification module includes a substrate that is constructed to from a first layer and a second layer, a PCR vial coupled to the second layer, a transfer mechanism, a first reagent module and a second reagent module, wherein the PCR vial is coupled to the first end portion of the housing and defines a volume within which a sample can be disposed to facilitate a reaction associated with the sample.