Abstract: A method for determining an unknown starting quantity of a target nucleic acid sequence in a test sample comprises the steps of amplifying the unknown starting quantity of the target nucleic acid sequence in the test sample and known starting quantities of a calibration nucleic acid sequence in respective calibration samples; and determining a respective threshold value for each of the nucleic acid sequences using a derivative of a growth curve derived for the sequence. The starting quantity of the target nucleic acid sequence in the test sample is determined using the threshold value determined for the target sequence and a calibration curve derived from the threshold values determined for the known starting quantities of the calibration nucleic acid sequences. The invention also provides methods for determining a starting quantity of a nucleic acid sequence in a sample using quantitative internal controls or using internal standards.

Abstract: An apparatus for determining a threshold value (e.g., a threshold cycle number or a time value) in a nucleic acid amplification reaction comprises a detection mechanism for measuring, at a plurality of different times during the amplification reaction, at least one signal whose intensity is related to the quantity of a nucleic acid sequence being amplified in the reaction. A controller in communication with the detection mechanism is programmed to store signal values defining a growth curve for the nucleic acid sequence, determine a derivative of the growth curve, and calculate a cycle number or time value associated with a characteristic of the derivative.

Abstract: An analyte is separated from a fluid sample by introducing the sample into a cartridge having a sample port and a first flow path extending from the sample port. The first flow path includes an extraction chamber containing a solid support for capturing the analyte from the sample. The cartridge has a second flow path for eluting the captured analyte from the extraction chamber, the second flow diverging from the first flow path after passing through the extraction chamber. The sample is forced to flow through the extraction chamber and into a waste chamber, thereby capturing the analyte with the solid support as the sample flows through the extraction chamber. The captured analyte is then eluted from the extraction chamber by forcing an elution fluid to flow through the extraction chamber and along the second flow path.

Abstract: An apparatus for thermally controlling and optically interrogating a reaction mixture includes a vessel [2] having a chamber [10] for holding the mixture. The apparatus also includes a heat-exchanging module [37] having a pair of opposing thermal plates [34A, 34B] for receiving the vessel [2] between them and for heating/and or cooling the mixture contained in the vessel. The module [37] also includes optical excitation and detection assemblies [46,48] positioned to optically interrogate the mixture. The excitation assembly [46] includes multiple light sources [100] and a set of filters for sequentially illuminating labeled analytes in the mixture with excitation beams in multiple excitation wavelength ranges. The detection assembly [48] includes multiple detectors [102] and a second set of filters for detecting light emitted from the chamber [10] in multiple emission wavelength ranges.

Abstract: A method for determining an unknown starting quantity of a target nucleic acid sequence in a test sample comprises amplifying the unknown starting quantity of the target nucleic acid sequence in the test sample and known starting quantities of a calibration nucleic acid sequence in respective calibration samples; and determining a respective threshold value for each of the nucleic acid sequences using a derivative of a growth curve derived for the sequence. The starting quantity of the target nucleic acid sequence in the test sample is determined using the threshold value determined for the target sequence and a calibration curve derived from the threshold values determined for the known starting quantities of the calibration nucleic acid sequences.

Abstract: An analyte is separated from a fluid sample by introducing the sample into a cartridge having an extraction chamber containing capture material for capturing the analyte. The sample is forced to flow through the extraction chamber to capture the analyte with the capture material in the extraction chamber. The captured analyte is then eluted from the extraction chamber by forcing an elution fluid to flow through the extraction chamber. The cartridge may optionally include a lysing region for lysing sample components (e.g., cells spores, or microorganisms), a waste chamber for storing waste fluid, and reaction or detection chambers for chemically reacting or detecting the eluted analyte.

Abstract: A device for lysing components (e.g., cells, spores, or microorganisms) of a fluid sample comprises a cartridge having a lysing chamber for receiving the sample and having at least one solid phase in the lysing chamber for capturing the sample components to be lysed. An ultrasonic transducer is coupled to a wall of the lysing chamber to transfer ultrasonic energy to the captured sample components.

Abstract: A method for determining a threshold cycle number or time value in a nucleic acid amplification reaction comprising the steps of amplifying a nucleic acid sequence in a reaction mixture; at a plurality of different times during the amplification reaction, measuring at least one signal whose intensity is related to the quantity of the nucleic acid sequence in the reaction mixture; and storing signal values defining a growth curve for the nucleic acid sequence. A derivative of the growth curve is determined and the threshold cycle number or time value is calculated as a cycle number or time value corresponding to a characteristic (e.g., maximum, minimum, or zero-crossing) of the derivative.

Abstract: A system for controlling the temperature of a reaction mixture comprises at least one heating device for heating the mixture and a power regulator for regulating the amount of power supplied to the heating device. A controller in communication with the power regulator includes program instructions for heating the reaction mixture by setting a variable target temperature that initially exceeds a desired setpoint temperature for the mixture. When the heating device reaches a threshold temperature, the variable target temperature is decreased to the desired setpoint temperature. In another embodiment, the controller includes an adaptive control program for dynamically adjusting the duration or intensity of power pulses provided to the heating device.

Abstract: A computer program product for determining a threshold value (e.g., a threshold cycle number or time value) in a nucleic acid amplification reaction tangibly embodies instructions readable by a machine to perform the steps of deriving a growth curve from measurements of a signal whose intensity is related to a quantity of nucleic acid sequence being amplified in the reaction, calculating a derivative of the growth curve, identifying a characteristic of the derivative, and determining a threshold value associated with the characteristic of the derivative. The method provides for highly reproducible threshold values that are independent of noise or background signal in the amplification reaction. Embodiments of a computer program product for determining a starting quantity of a nucleic acid sequence in a test sample are also provided.

Abstract: An apparatus for determining a threshold value (e.g., a threshold cycle number or a time value) in a nucleic acid amplification reaction comprises a detection mechanism for measuring, at a plurality of different times during the amplification reaction, at least one signal whose intensity is related to the quantity of a nucleic acid sequence being amplified in the reaction. The apparatus also includes a controller in communication with the detection mechanism. The controller is programmed to perform the steps of deriving a growth curve from the measurements of the signal; calculating a derivative of the growth curve; identifying a characteristic of the derivative; and determining a threshold value associated with the characteristic of the derivative. Embodiments of an apparatus for determining a starting quantity of a nucleic acid sequence in a test sample are also provided.

Abstract: A device for separating an analyte from a fluid sample comprises a cartridge incorporating a flow-through microfluidic chip. The microfluidic chip includes an extraction chamber having an array of microstructures for capturing the analyte and for subsequently releasing the captured analyte into an elution fluid. Each of the microstructures has an aspect ratio of at least 2:1. The cartridge also includes channels and at least one low controller (e.g., one or more valves) for directing the flow of the sample and elution fluid through the microfluidic chip. The cartridge may optionally include a lysing region for lysing sample components (e.g., cells spores, or microorganisms), a waste chamber for storing waste fluid, and reaction or detection chambers for amplifying or detecting the analyte.

Abstract: The present invention provides an apparatus for performing heat-exchanging chemical reactions, such as nucleic acid amplification. The apparatus includes a reaction vessel having a chamber for holding a sample for chemical reaction and optical detection. The vessel has a rigid frame defining the side walls of the chamber, and flexible sheets attached to opposite sides of the frame to form opposing major walls of the chamber. The frame further includes a port and a channel connecting the port to the chamber. The temperature of the sample is controlled by opposing plates positioned to receive the chamber of the vessel between them. The apparatus also includes a plunger which is inserted into the channel of the vessel to seal the port and increase pressure in the chamber. The increased pressure forces the flexible major walls of the chamber to contact and conform to the surfaces of the plates, thus ensuring optimal thermal conductance between the plates and the chamber.

Abstract: This invention provides an apparatus for rapidly heating and/or cooling a sample in a reaction vessel. In some embodiments, the apparatus includes optics for the efficient detection of a reaction product in the vessel. The invention also provides a reaction vessel having a reaction chamber designed for optimal thermal conductance and for efficient optical viewing of reaction products in the chamber.

Abstract: The present invention provides a reaction vessel and apparatus for performing heat-exchanging reactions. The vessel has a chamber for holding a sample, the chamber being defined by a plurality of walls, at least two of the walls being light transmissive to provide optical windows to the chamber. The apparatus comprises at least one heating surface for contacting at least one of the plurality of walls, a heat source for heating the surface, and optics positioned to optically interrogate the chamber while the heating surface is in contact with at least one of the plurality of walls. The optics include at least one light source for transmitting light to the chamber through a first one of the light transmissive walls and at least one detector for detecting light exiting the chamber through a second one of the light transmissive walls.

Abstract: The invention provides a device and method for the manipulation of materials (e.g., particles, cells, macromolecules, such as proteins, nucleic acids or other moieties) in a fluid sample. The device comprises a substrate having a plurality of microstructures and an insulator film on the structures. Application of a voltage to the structures induces separation of materials in the sample. The device and method are useful for a wide variety of applications such as dielectrophoresis (DEP) or the separation of a target material from other material in a fluid sample.

Abstract: A reaction vessel has a reaction chamber, a loading reservoir connected to the reaction chamber via a first channel, and an aspiration port connected to the chamber via a second channel. To load the sample into the reaction chamber, the sample is dispensed into the loading reservoir and then drawn into the chamber by application of a vacuum to the aspiration port. A system for controlling the temperature of the sample in the reaction vessel includes one or more thermal elements for heating or cooling the sample and optionally optics for detecting one or more analytes in the sample.

Abstract: A cartridge (101) for separating a desired analyte from a fluid sample includes a sample port (103) and a sample flow path extending from the port through the body of the cartridge. The sample flow path includes at least one flow-through component (122), e.g., filter paper or a microfabricated chip, for capturing the desired analyte from the sample as the sample flows through the cartridge. The cartridge also includes an elution flow path for carrying elution fluid through the component (122) to release captured analyte from the component into the elution fluid. The elution flow path diverges from the sample flow path after passing through the component (122). Flow controllers (41A) and (41B) direct the remaining fluid sample into a waste chamber (139) after the sample flows through the component (122) and direct the elution fluid and eluted analyte into a reagent chamber (141) and reaction chamber (143).

Abstract: An apparatus for thermally controlling and optically interrogating a reaction mixture includes a vessel [2] having a chamber [10] for holding the mixture. The apparatus also includes a heat-exchanging module [37] having a pair of opposing thermal plates [34A, 34B] for receiving the vessel [2] between them and for heating/and or cooling the mixture contained in the vessel. The module [37] also includes optical excitation and detection assemblies [46,48] positioned to optically interrogate the mixture. The excitation assembly [46] includes multiple light sources [100] and a set of filters for sequentially illuminating labeled analytes in the mixture with excitation beams in multiple excitation wavelength ranges. The detection assembly [48] includes multiple detectors [102] and a second set of filters for detecting light emitted from the chamber [10] in multiple emission wavelength ranges.

Abstract: The invention provides a reaction vessel and temperature control system for performing heat-exchanging chemical reactions, such as nucleic acid amplification. The vessel has a body defining a reaction chamber, and a loading structure extending from the body for loading a sample into the chamber. The loading structure has a loading reservoir, an aspiration port, and respective fluid channels connecting the loading reservoir and aspiration port to the chamber. To load the sample into the vessel, the sample is first dispensed into the loading reservoir and then drawn into the chamber by application of a vacuum to the aspiration port. The vessel also includes a seal aperture extending over the outer ends of the loading reservoir and aspiration port. A plug is inserted into the aperture after loading the sample into the chamber to simultaneously seal the chamber, loading reservoir, and aspiration port from the external environment.