System and method for processing and detecting nucleic acids

• US 9,604,213 B2
• Filed: 02/04/2015
• Issued: 03/28/2017
• 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
• Assistant Examiner(s): Edwards, Lydia
• Application Number:
  US14/613,616
• Publication Number:
  US 20150151300A1
• Time in Patent Office: 783 Days
• US Class Current: 1/1
• 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 and detecting nucleic acids in cooperation with a cartridge comprising a heating region defined at a first surface, and a magnet housing region defined at a second surface in thermal communication with the first surface, the system comprising:

a capture plate configured to facilitate combination of a set of magnetic beads with a biological sample, thus producing a magnetic bead-sample; and

a molecular diagnostic module, configured to process the magnetic bead-sample from the capture plate and separate nucleic acids from the set of magnetic beads, comprising;

a cartridge platform configured to receive the cartridge and comprising a magnet receiving slot aligned with the second surface during operation,

a heater configured to transmit heat to the heating region at the first surface during operation, and

a magnet coupled to a magnet heating element that heats the magnet during operation with the magnet proximal the second surface, the magnet configured to pass through the magnet receiving slot into the magnet housing region during operation, thereby facilitating separation of a nucleic acid volume from the magnetic bead-sample and heating of the magnetic bead-sample in cooperation with the heater.

2. The system of claim 1, wherein the molecular diagnostic module further comprises an actuator configured 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, wherein the actuator is coupled to the heater.

3. The system of claim 2, wherein the heater is configured to heat a capture segment of the cartridge through the heating region from a first direction, and wherein the magnet is configured to apply a field to the capture segment between the first and second surfaces while heating the capture segment at the second surface during operation, 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.

4. The system of claim 3, 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 subset of the capture segment in a direction perpendicular to a flow direction through the capture segment thereby providing a magnetic field at the subset of the capture segment to capture the magnetic bead-sample within the capture segment.

5. 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.

6. The system of claim 2, 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.

7. 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.

8. The system of claim 1, further comprising a liquid handling system configured to transfer the magnetic bead-sample from the capture plate to the molecular diagnostic module, and to aspirate the nucleic acid volume from the molecular diagnostic module.

9. The system of claim 8, wherein the liquid handling system is further configured to automatically combine the biological sample with a buffer solution, couple to a filter, and deliver the biological sample with the buffer solution through the filter and into the capture plate.

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

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,

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 the fluidic pathway at an occlusion position and

a valve actuator configured to provide relative displacement in a direction tangential to the displacement direction between the array of active regions and the set of pins.

11. The system of claim 1, wherein the molecular diagnostic module further comprises an optical subsystem comprising a first unit and a second unit, wherein each of the first unit and the second unit includes a set of excitation filters, a set of emission filters, a set of photodetectors aligned with the set of emission filters, and a set of dichroic mirrors configured to reflect light from the set of excitation filters toward one of a set of nucleic acid-reagent mixtures at the cartridge, and to transmit emitted light from one of the set of nucleic acid-reagent mixtures, through at least one of the set of emission filters, and toward at least one of the set of photodetectors.

12. The system of claim 11, wherein the molecular diagnostic module further includes a set of detection chamber heaters configured to heat a set of detection chambers through the second surface of the cartridge, and wherein the optical subsystem is configured to receive light, emitted from the set of nucleic acid-reagent mixtures at the set of detection chambers, from the first surface of the cartridge.

13. The system of claim 12, 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.

14. The system of claim 1, wherein the molecular diagnostic module is configured to receive and align a microfluidic cartridge comprising a set of sample port-reagent port pairs, a fluid port, a set of detection chambers, a waste chamber, an elastomeric layer, and a set of fluidic pathways, wherein each fluidic pathway of the set of fluidic pathways is coupled to a sample port-reagent port pair, the fluid port, and a detection chamber, comprises a capture segment configured to cross the magnet, and is configured to transfer a waste fluid to the waste chamber, and to be occluded upon deformation of the elastomeric layer.