System and method for processing and detecting nucleic acids

• US 10,010,888 B2
• Filed: 01/24/2017
• Issued: 07/03/2018
• Est. Priority Date: 02/13/2012
• Status: Active Grant

• Current Assignee: Neumodx Molecular, Inc. (Qiagen NV)
• Original Assignee: Neumodx Molecular, Inc. (Qiagen NV)
• Inventors: Williams, Jeffrey, Brahmasandra, Sundaresh, Kusner, Michael T.
• Primary Examiner(s): Bowers, Nathan A
• Assistant Examiner(s): Edwards, Lydia
• Application Number:
  US15/413,735
• Publication Number:
  US 20170128946A1
• Time in Patent Office: 525 Days
• CPC Class Codes: B01L 2200/0668 Trapping microscopic beads
• CPC Class Codes: B01L 2200/0684 Venting, avoiding backpressure, avoid gas bubbles
• CPC Class Codes: B01L 2200/0689 Sealing
• CPC Class Codes: B01L 2200/10 Integrating sample preparation and analysis in single entity, e.g. lab-on-a-chip concept
• CPC Class Codes: B01L 2300/044 pierceable, e.g. films, membranes
• CPC Class Codes: B01L 2300/0627 Sensor or part of a sensor is integrated
• CPC Class Codes: B01L 2300/0681 Filter
• CPC Class Codes: B01L 2300/0816 Cards, e.g. flat sample carriers usually with flow in two horizontal directions
• CPC Class Codes: B01L 2300/0867 Multiple inlets and one sample wells, e.g. mixing, dilution
• CPC Class Codes: B01L 2300/087 Multiple sequential chambers
• CPC Class Codes: B01L 2300/0887 Laminated structure
• CPC Class Codes: B01L 2300/168 Specific optical properties, e.g. reflective coatings
• CPC Class Codes: B01L 2300/1822 using Peltier elements
• CPC Class Codes: B01L 2300/1827 using resistive heater
• CPC Class Codes: B01L 2400/0406 capillary forces
• CPC Class Codes: B01L 2400/043 magnetic forces
• CPC Class Codes: B01L 2400/0481 squeezing of channels or chambers
• CPC Class Codes: B01L 2400/0487 fluid pressure, pneumatics
• CPC Class Codes: B01L 2400/0622 distribution valves, valves having multiple inlets and/or outlets, e.g. metering valves, multi-way valves
• CPC Class Codes: B01L 2400/0633 with moving parts
• CPC Class Codes: B01L 2400/0655 : pinch valves
• CPC Class Codes: B01L 2400/0694 : vents used to stop and induce flow, backpressure valves
• CPC Class Codes: B01L 3/502738 : characterised by integrated valves microvalves F16K99/0001
• CPC Class Codes: B01L 3/502761 : specially adapted for handling suspended solids or molecules independently from the bulk fluid flow, e.g. for trapping or sorting beads, for physically stretching molecules investigating characteristics of particles G01N15/00
• CPC Class Codes: B01L 3/50851 : specially adapted for heating or cooling samples laboratory heating apparatus B01L7/00; incubators C12M
• CPC Class Codes: B01L 3/50855 : using modular assemblies of strips or of individual wells
• CPC Class Codes: B01L 7/52 : with provision for submitting samples to a predetermined sequence of different temperatures, e.g. for treating nucleic acid samples amplification or hybridisation processes per se C12Q1/68; controlling sequential reactions for synthesis B01J19/0046
• CPC Class Codes: B01L 7/525 : with physical movement of samples between temperature zones
• CPC Class Codes: C12Q 1/686 : Polymerase chain reaction [PCR]
• CPC Class Codes: G01N 35/0098 : involving analyte bound to insoluble magnetic carrier, e.g. using magnetic separation magnetic particles used in immunoassays G01N33/54326; magnetic separation in general B03C

Abstract

A system and method for processing and detecting nucleic acids from a set of biological samples, comprising: a capture plate and a capture plate module configured to facilitate binding of nucleic acids within the set of biological samples to magnetic beads; a molecular diagnostic module configured to receive nucleic acids bound to magnetic beads, isolate nucleic acids, and analyze nucleic acids, comprising a cartridge receiving module, a heating/cooling subsystem and a magnet configured to facilitate isolation of nucleic acids, a valve actuation subsystem configured to control fluid flow through a microfluidic cartridge for processing nucleic acids, and an optical subsystem for analysis of nucleic acids; a fluid handling system configured to deliver samples and reagents to components of the system to facilitate molecular diagnostic protocols; and an assay strip configured to combine nucleic acid samples with molecular diagnostic reagents for analysis of nucleic acids.

Claims

1. A system for processing nucleic acid content of a sample in cooperation with a cartridge comprising a heating region defined at a first surface, and a magnet housing region defined by a second surface in thermal communication with the first surface, the system comprising:

a molecular diagnostic module comprising;

a cartridge platform comprising a magnet receiving slot and operable to receive the cartridge and align the second surface of the cartridge with the magnet receiving slot,

a heater operable to transmit heat to the heating region of the cartridge at the first surface, and

a magnet coupled to a magnet heating element that heats the magnet, the magnet operable to pass through the magnet receiving slot into the magnet housing region, thereby facilitating separation of a nucleic acid volume from the sample and heating the sample in cooperation with the heater.

2. The system of claim 1, wherein the magnet is one of a set of magnets, each magnet in the set of magnets coupled to and separated from an adjacent magnet by one of a set of magnet heating elements, the set of magnet heating elements comprising the magnet heating element.

3. The system of claim 1, wherein the molecular diagnostic module further comprises an actuator coupled to the heater and operable to displace the cartridge platform to pass the magnet through the magnet receiving slot into the magnet housing region and to position the heater at the heating region.

4. The system of claim 3, wherein in an extended configuration of the actuator, the magnet is passed through the magnet receiving slot, and wherein in a retracted configuration of the actuator the magnet is retracted from the magnet receiving slot.

5. The system of claim 3, wherein the actuator of the molecular diagnostic module is a linear actuator, configured to vertically displace the cartridge platform, and wherein the cartridge platform of the molecular diagnostic module is coupled to a set of springs configured to counteract a force provided by the linear actuator.

6. The system of claim 3, wherein the heater is configured to heat a capture segment, configured between the first and the second surfaces of the cartridge, through the heating region from a first direction.

7. The system of claim 6, wherein the magnet is configured to apply a field to the capture segment through the magnet housing region, from a second direction substantially opposed to the first direction, wherein a first projection of the heating region onto a plane at least partially overlaps with a second projection of the magnet housing region onto the plane.

8. The system of claim 6, wherein the capture segment is an s-shaped capture segment, and wherein in an operation mode of the system the magnet is configured to cross a portion of the capture segment in a direction perpendicular to a flow direction through the capture segment thereby providing a magnetic field at the portion of the capture segment.

9. The system of claim 1, further comprising a liquid handling system configured to transfer the sample into the cartridge at the molecular diagnostic module, and to aspirate a nucleic acid volume from the cartridge at the molecular diagnostic module.

10. The system of claim 1, wherein the magnet heating element is physically coupled to a surface of the magnet.

11. The system of claim 1, wherein the molecular diagnostic module further comprises a valve actuation subsystem situated inferior to the cartridge platform comprising:

an actuation substrate having an array of active regions and an array of inactive regions, wherein each of the array of active regions is configured to provide a force in a displacement direction normal to a surface of the actuation substrate, thereby manipulating portions of the cartridge during operation.

12. The system of claim 11, the molecular diagnostic module further comprising a set of detection chamber heaters, wherein at least one of the set of detection chamber heaters includes a coating configured to mitigate reflection of light from the set of detection chamber heaters toward photodetectors of the optical subsystem.

13. The system of claim 11, wherein the valve actuation subsystem further comprises a set of pins, each pin in the set of pins including a distal end and a displacement region and operable in:

a retracted configuration and an extended configuration, wherein in the retracted configuration an active region of the actuation substrate is aligned with the displacement region of the pin and the distal end of the pin is displaced in the displacement direction, and wherein in the extended configuration an inactive region of the actuation substrate is aligned with the displacement region of the pin and the distal end of the pin is displaced in a direction opposing the displacement direction and occludes a portion of a fluidic pathway within the cartridge.

14. A method for processing and detecting nucleic acids from a sample with a cartridge including a fluidic pathway passing between a heating region of the cartridge and a magnet housing region of the cartridge, wherein the method comprises:

with a liquid handling system, combining the sample with a quantity of magnetic beads to produce a nucleic acid-magnetic bead sample;

with the liquid handling system, transferring the nucleic acid-magnetic bead sample to the fluidic pathway of the cartridge; and

contemporaneously transmitting heat through the heating region, by way of a heater, and transmitting heat through the magnet housing region, by way of a magnet heating element coupled to a magnet, thereby facilitating capture of nucleic acids of the sample at the fluidic pathway of the cartridge.

15. The method of claim 14, further comprising:

within the liquid handling system, combining the sample with a buffer solution prior to transferring the nucleic acid-magnetic bead sample to the fluidic pathway of the cartridge.

16. The method of claim 14, wherein transferring the nucleic acid-magnetic bead sample to the fluidic pathway of the cartridge comprises transferring the nucleic acid-magnetic bead sample into an s-shaped capture segment passing between the heating region and the magnet housing region of the cartridge.

17. The method of claim 14, further comprising delivering a release solution into the fluidic pathway, thereby producing a nucleic acid volume from the nucleic acid-magnetic bead sample.

18. The method of claim 17, further comprising combining the nucleic acid volume with a molecular diagnostic reagent external to the cartridge, thereby producing a nucleic acid-reagent mixture, prior to detecting nucleic acids using a detection chamber of the cartridge.

19. The method of claim 14, further comprising providing a supernatant component of the sample with the nucleic acid-magnetic bead sample prior upon transferring the nucleic acid-magnetic bead sample into the fluidic pathway.

20. The method of claim 14, further comprising transmitting light through an excitation filter toward the nucleic acid-reagent mixture within the cartridge, and receiving light, at a photodetector, from the nucleic acid-reagent mixture through a set of emission filters, in coordination with a second heater comprising a non-reflective coating that prevents reflection of light from the cartridge.