SCANNING REAL-TIME MICROFLUIDIC THERMOCYCLER AND METHODS FOR SYNCHRONIZED THERMOCYCLING AND SCANNING OPTICAL DETECTION
First Claim
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1. A apparatus for performing real-time nucleic acid amplification and detection, comprising:
- a detector head comprising a plurality of photodetector and light source pairs, said detector head being mounted on a rail, wherein the detector and light source pairs are aligned into a first row and a second row;
a receptacle for a microfluidic cartridge comprising a plurality of independent reaction chambers aligned in adjacent columns of a first row and a second row; and
an aperture plate, the aperture plate configured to be positioned over the microfluidic cartridge when the cartridge is present in the receptacle, the detector head located over the aperture plate,wherein the aperture plate comprises a plurality of apertures that are each aligned over each of the plurality of reaction chambers when the receptacle is holding the microfluidic cartridge,wherein the detector head is moveable along the rail, such that each of the plurality of photodetector and light source pairs in the first row can be positioned over each aperture in the first row of the aperture plate, and each of the plurality of photodetector and light source pairs in the second row can be positioned over each aperture in the second row of the aperture plate.
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Abstract
Systems and methods for performing simultaneous nucleic acid amplification and detection. The systems and methods comprise methods for managing a plurality of protocols in conjunction with directing a sensor array across each of a plurality of reaction chambers. In certain embodiments, the protocols comprise thermocycling profiles and the methods may introduce offsets and duration extensions into the thermocycling profiles to achieve more efficient detection behavior.
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Citations
41 Claims
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1. A apparatus for performing real-time nucleic acid amplification and detection, comprising:
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a detector head comprising a plurality of photodetector and light source pairs, said detector head being mounted on a rail, wherein the detector and light source pairs are aligned into a first row and a second row; a receptacle for a microfluidic cartridge comprising a plurality of independent reaction chambers aligned in adjacent columns of a first row and a second row; and an aperture plate, the aperture plate configured to be positioned over the microfluidic cartridge when the cartridge is present in the receptacle, the detector head located over the aperture plate, wherein the aperture plate comprises a plurality of apertures that are each aligned over each of the plurality of reaction chambers when the receptacle is holding the microfluidic cartridge, wherein the detector head is moveable along the rail, such that each of the plurality of photodetector and light source pairs in the first row can be positioned over each aperture in the first row of the aperture plate, and each of the plurality of photodetector and light source pairs in the second row can be positioned over each aperture in the second row of the aperture plate. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14)
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15. A method implemented on one or more computer processors for optimizing protocols for simultaneously performing a plurality of thermal cycling reactions, wherein each thermal cycling reaction comprises one or more detection steps, and wherein said thermal cycling reactions are performed in a plurality of reactors, the method comprising:
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determining or providing or accessing a detection cycle time for each of said plurality of reactors; receiving or accessing a protocol step, the step associated with a step duration, the step comprising a time for detection; and determining a first adjustment to the step such that the step duration is a multiple of the detection cycle time. - View Dependent Claims (16, 17, 18, 19, 20, 21)
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22. A non-transitory computer-readable medium comprising instructions, the instructions configured to cause one or more processors to perform the following method:
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determining or providing or accessing a detection cycle time; receiving or accessing a protocol step, the step associated with a step duration, the step comprising a time for detection; determining a first adjustment to the step such that the step duration is a multiple of the detection cycle time. - View Dependent Claims (23, 24, 25, 26, 27, 28, 29)
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30. A system for optimizing protocols for a plurality of reaction chambers, the system comprising:
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a processor configured to perform the following; determining or providing or accessing a detection cycle time; receiving or accessing a protocol step, the step associated with a step duration, the step comprising a time for detection; and determining a first adjustment to the step such that the step duration is a multiple of the detection cycle time. - View Dependent Claims (31, 32, 33, 34, 35, 36, 37)
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38. A method for simultaneously performing real-time PCR in a plurality of PCR reaction chambers, comprising:
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(a) providing a scan time sufficient for a detector assembly to perform a scan cycle during which it can scan each of the plurality of PCR reaction chambers for at least one detectable signal and become ready to repeat the scan; (b) providing a reaction protocol for each of the PCR reaction chambers that includes multiple cycles, each cycle comprising a cycle time that includes at least one heating step, at least one cooling step, and at least one temperature plateau that includes a reading cycle period during which the detector assembly is to scan the reaction chamber for at least one detectable signal; (c) determining, using a processor, whether the cycle time for that reaction chamber is the same as or an integer multiple of the scan time, and if not, adjusting the scan time or the cycle time so that the cycle time is the same as or an integer multiple of the scan time; (d) performing at least steps (b) and (c) for the reaction protocol for each of the plurality of PCR reaction chambers so that the cycle time for each reaction protocol is the same as or an integer multiple of the scan time; and (e) under direction of a processor, performing real time PCR on each of the reaction chambers using the reaction protocol for each of the reaction chambers, including performing multiple scan cycles with the detector assembly, wherein each PCR reaction chamber is scanned by the detector assembly during each reading cycle period for that reaction chamber. - View Dependent Claims (39, 40, 41)
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Specification