Methods and systems for extraction, processing, and detection of nucleic acids

A method for extracting and detecting nucleic acids with a cartridge comprising:

• a plurality of reservoirs defining at least a first wash buffer reservoir for holding a first wash buffer;
• a microfluidic assembly configured to attach to the plurality of reservoirs comprising:
• at least one sample reservoir positioned in a first input defined by the microfluidic assembly;
• a nucleic acid extraction matrix positioned in the microfluidic assembly and in fluid communication to an automated sample preparation (ASP) reservoir through a first flow channel defined by the microfluidic assembly,
• a waste reservoir defined within the microfluidic assembly;
• a fluid switching assembly configured to provide a first setting that permits flow from the first wash buffer reservoir through the nucleic acid extraction matrix and then to the waste reservoir and a second setting that permits collection of a nucleic acid-containing sample;
• an assay chamber in fluid communication with a third flow channel and with the waste reservoir through a fourth flow channel such that a labeled nucleic acid-containing sample flows through the assay chamber and then to the waste reservoir, wherein vibration-driven mixing agitates fluids while present in the assay chamber, wherein the labeled nucleic acid sample is mixed with a vibration motor that is proximate to a first side of the assay chamber, and air-filled cavities inside the assay chamber are in contact with an inner portion of the first side of the assay chamber, the vibration motor and the air-filled cavities configured to promote microfluidic mixing of fluid in the assay chamber.;
• and
• a nucleic acid-detecting microarray module positioned in the assay chamber, the method comprising:
• a) introducing a nucleic acid-containing sample into the ASP reservoir;
• b) flowing the nucleic acid-containing sample to the nucleic acid extraction matrix such that at least a portion of the nucleic acid sample adheres the nucleic acid extraction matrix;
• c) flowing the first wash buffer through the nucleic acid extraction matrix and then to the waste reservoir;
• d) flowing an elution buffer through the nucleic acid extraction matrix and then to an output collection vessel to collect a purified nucleic acid sample;
• e) removing or pumping purified nucleic acid sample from collection vessel to labeling apparatus;
• f) labeling the purified nucleic acid sample with a label to form a labeled nucleic acid sample;
• g) placing a vessel holding the labeled nucleic acid sample into the microfluidic assembly or pumping the labeled nucleic acid sample into the microfluidic assembly;
• h) flowing the labeled sample from the vessel holding the labeled nucleic acid sample through the assay chamber and then to the waste reservoir, wherein vibration-driven mixing agitates the labeled sample while present in the assay chamber and closed-loop thermal control maintains steady temperature in the assay chamber;
• and
• i) collecting data from the nucleic acid-detecting microarray module.

A mixing chamber comprising:

• an assay chamber having a predetermined thickness and a first side having an outer surface and an inner surface, the assay chamber configured to receive a fluid therein;
• a vibration motor affixed to or proximate to the outer surface of the assay chamber;
• and
• a plurality of air-filled cavities in inside the assay chamber contacting the inner surface of the first side of the assay chamber, the vibration motor and the air-filled cavities configured to promote microfluidic mixing of fluid in the assay.