System and method for processing and detecting nucleic acids

• US 9,050,594 B2
• Filed: 02/13/2013
• Issued: 06/09/2015
• 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 E
• Application Number:
  US13/766,359
• Publication Number:
  US 20130210127A1
• Time in Patent Office: 846 Days
• Field of Search: 4352831-3094
• US Class Current: 1/1
• CPC Class Codes: B01L 2200/025 Align devices or objects to ensure defined positions relative to each other
• CPC Class Codes: B01L 2200/027 for microfluidic devices
• CPC Class Codes: B01L 2200/0605 Metering of fluids
• CPC Class Codes: B01L 2200/0615 Loss of fluid by dripping
• 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 2200/12 Specific details about manufacturing devices
• CPC Class Codes: B01L 2200/142 Preventing evaporation
• CPC Class Codes: B01L 2300/021 Identification, e.g. bar codes
• CPC Class Codes: B01L 2300/022 Transponder chips
• CPC Class Codes: B01L 2300/044 pierceable, e.g. films, membranes
• CPC Class Codes: B01L 2300/06 Auxiliary integrated devices, integrated components
• CPC Class Codes: B01L 2300/0609 Holders integrated in container to position an object
• CPC Class Codes: B01L 2300/0627 Sensor or part of a sensor is integrated
• CPC Class Codes: B01L 2300/0636 Integrated biosensor, microarrays
• CPC Class Codes: B01L 2300/0672 Integrated piercing tool
• CPC Class Codes: B01L 2300/0681 Filter
• CPC Class Codes: B01L 2300/0809 rectangular shaped
• CPC Class Codes: B01L 2300/0816 : Cards, e.g. flat sample carriers usually with flow in two horizontal directions
• CPC Class Codes: B01L 2300/0861 : Configuration of multiple channels and/or chambers in a single devices
• CPC Class Codes: B01L 2300/0864 : comprising only one inlet and multiple receiving wells, e.g. for separation, splitting
• 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 2300/0883 : Serpentine channels
• CPC Class Codes: B01L 2300/0887 : Laminated structure
• CPC Class Codes: B01L 2300/0893 : having a very large number of wells, microfabricated wells
• CPC Class Codes: B01L 2300/123 : Flexible; Elastomeric
• CPC Class Codes: B01L 2300/14 : Means for pressure control
• CPC Class Codes: B01L 2300/16 : Surface properties and coatings
• CPC Class Codes: B01L 2300/1805 : Conductive heating, heat from thermostatted solids is conducted to receptacles, e.g. heating plates, blocks
• 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 2400/0478 : pistons
• 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 2400/065 : sliding valves
• 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 2400/086 : using baffles or other fixed flow obstructions
• CPC Class Codes: B01L 3/502 : with fluid transport, e.g. in multi-compartment structures centrifugal-type cuvettes G01N21/07; analysis by separation into components G01N30/00; automatic analysers G01N35/00
• CPC Class Codes: B01L 3/5025 : for parallel transport of multiple samples
• CPC Class Codes: B01L 3/5027 : by integrated microfluidic structures, i.e. dimensions of channels and chambers are such that surface tension forces are important, e.g. lab-on-a-chip B01L3/5023 takes precedence; micromixers B01F33/30; microreactors for synthesis B01J19/0093; microcapillary devices in general B81B1/00
• CPC Class Codes: B01L 3/502707 : characterised by the manufacture of the container or its components by shaping or joining plastic parts B29C59/00, B29C65/00; by laminating B32B37/00; manufacture of microstructural devices in general B81C
• CPC Class Codes: B01L 3/502715 : characterised by interfacing components, e.g. fluidic, electrical, optical or mechanical interfaces
• CPC Class Codes: B01L 3/502723 : characterised by venting arrangements
• CPC Class Codes: B01L 3/50273 : characterised by the means or forces applied to move the fluids micropumps F04B19/006, of the membrane type F04B43/043
• CPC Class Codes: B01L 3/502738 : characterised by integrated valves microvalves F16K99/0001
• CPC Class Codes: B01L 3/502746 : characterised by the means for controlling flow resistance, e.g. flow controllers, baffles B01L3/502738 takes precedence
• 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 3/508 : rigid containers not provided for above
• CPC Class Codes: B01L 3/527 : for a plurality of reagents
• CPC Class Codes: B01L 3/567 : Valves, taps or stop-cocks in combination with burettes B01L3/0203; in general F16K
• 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: B29C 65/08 : using ultrasonic vibrations non-plastics element to plastics elements B29C65/645
• CPC Class Codes: B29C 65/484 : Moisture curing adhesives
• CPC Class Codes: B29C 65/606 : the rivets being integral with one of the parts to be joined, i.e. staking
• CPC Class Codes: B29C 66/71 : characterised by the composition of the plastics material of the parts to be joined welding bar compositions B29C65/125
• CPC Class Codes: B29C 66/81423 : being concave
• CPC Class Codes: B29C 66/8322 : Joining or pressing tools reciprocating along one axis
• CPC Class Codes: B29K 2021/00 : Use of unspecified rubbers as moulding material
• CPC Class Codes: B29L 2031/756 : Microarticles, nanoarticles
• CPC Class Codes: C12M 23/42 : Integrated assemblies, e.g. cassettes or cartridges
• CPC Class Codes: C12N 13/00 : Treatment of microorganisms or enzymes with electrical or wave energy, e.g. magnetism, sonic waves
• CPC Class Codes: C12N 15/1013 : by using magnetic beads
• CPC Class Codes: C12Q 1/68 : involving nucleic acids
• CPC Class Codes: C12Q 1/6806 : Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6813 : Hybridisation assays
• CPC Class Codes: C12Q 1/686 : Polymerase chain reaction [PCR]

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, comprising:

a capture plate comprising at least one well configured to facilitate a 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 at least one magnetic bead-sample obtained from the capture plate, and separate nucleic acids from magnetic beads, wherein the molecular diagnostic module comprises;

a cartridge platform comprising a magnet receiving slot,

an actuator configured to displace the cartridge platform,

a magnet, wherein an extended configuration of the actuator allows the magnet to pass through the magnet receiving slot to facilitate separation of the at least one nucleic acid volume, and

a cam card contacting a set of pins, wherein the extended configuration of the actuator combined with movement of the cam card displaces a subset of the set of pins through a set of slots of the cartridge platform, to define at least one distinct pathway configured to receive at least one magnetic bead-sample.

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

3. The system of claim 2, wherein the system is not configured to remove a supernatant from the capture plate prior to transfer of at least one magnetic bead-sample from the capture plate to the molecular diagnostic module.

4. The system of claim 1, wherein the capture plate comprises a set of wells and a foil seal configured to seal each well of the set of wells, wherein each well in the set of wells contain a set of magnetic beads, a set of lysing reagents, and a sample process control.

5. The system of claim 1, further comprising a capture plate module comprising a thermally conducting substrate configured to cradle at least one well of the capture plate, and a heater coupled to the thermally conducting substrate.

6. The system of claim 1, 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 a retracted configuration of the actuator allows the magnet to retract from the magnet receiving slot.

8. The system of claim 1, wherein the magnet is configured to provide a magnetic field spanning at least three fluidic pathways configured to facilitate isolation and extraction of three nucleic acid volumes.

9. The system of claim 1, wherein the magnet is at least one of an electromagnet and a permanent magnet.

10. The system of claim 1, further comprising an assay strip comprising at least one reagent well, each containing a molecular diagnostic reagent configured to be combined with a nucleic acid volume.

11. The system of claim 9, wherein the molecular diagnostic module further comprises an optical subsystem comprising at least one unit, wherein each unit includes an excitation filter, an emission filter, a photodetector aligned with the emission filter, and a dichroic mirror configured to reflect light from the excitation filter toward one of three nucleic acid-reagent mixtures, and to transmit emitted light from one of the three nucleic acid-reagent mixtures, through the emission filter, and toward the photodetector.

12. The system of claim 1, wherein the molecular diagnostic module further comprises a molecular diagnostic module heater configured to heat at least one magnetic bead-sample.

13. The system of claim 1, wherein the molecular diagnostic module is configured 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 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.

14. The system of claim 1, wherein the liquid handling system comprises a multichannel pipette head and a syringe pump.

15. The system of claim 14, wherein the syringe pump is coupled to a nozzle coupled to the actuator of the molecular diagnostic module.

16. A system for processing and detecting nucleic acids, comprising:

a capture plate comprising at least one well containing a set of magnetic beads configured to be combined with a biological sample to produce a magnetic bead-sample;

an assay strip comprising at least one well containing a molecular diagnostic reagent configured to be combined with a nucleic acid volume to produce a nucleic acid-reagent mixture;

a molecular diagnostic module, configured to process the magnetic bead-sample from the capture plate, separate the nucleic acid volume from the magnetic bead-sample, and analyze the nucleic acid-reagent mixture from the assay strip,

wherein the molecular diagnostic module comprises a cartridge platform including a set of parallel slots, a cam card, and a set of pins contacting the cam card, wherein movement of the cam card displaces a subset of the set of pins through a subset of the set of parallel slots to define at least one pathway configured to receive the magnetic bead-sample; and

a liquid handling system configured to transfer the magnetic bead-sample from the capture plate to the molecular diagnostic module, transfer the nucleic acid volume from the molecular diagnostic module to the assay strip, and transfer the nucleic acid-reagent mixture from the assay strip to the molecular diagnostic module.

17. The system of claim 16, wherein the capture plate comprises a first foil seal configured to seal each well of the set of wells, and wherein the assay strip comprises a second foil seal, configured to seal each reagent well of the set of reagent wells.

18. The system of claim 16, wherein the molecular diagnostic module comprises an optical subsystem comprising at least one unit, wherein each unit includes an excitation filter, an emission filter, a photodetector aligned with the emission filter, and a dichroic mirror configured to reflect light from the excitation filter toward the nucleic acid-reagent mixture, and to transmit light from the nucleic acid reagent mixture, through the emission filter, and toward the photodetector wherein each unit of the optical subsystem further comprises an LED aligned with the excitation filter, wherein the LED provides multiple wavelengths of light corresponding to at least one of the excitation filter, the dichroic mirror, and the emission filter.

19. The system of claim 16, wherein the molecular diagnostic module further comprises a heater and a detection chamber heater, wherein the heater is configured to heat the magnetic bead-sample, and wherein the detection chamber heater is configured to individually heat the nucleic acid-reagent mixture, and wherein at least one of the heater and the detection chamber heater is a Peltier heater.

20. The system of claim 18, wherein the molecular diagnostic module further comprises a linear actuator coupled to the optical subsystem, such that an extended configuration of the linear actuator vertically displaces the optical subsystem.

21. The system of claim 16, wherein the liquid handling system comprises a multichannel pipette head and a syringe pump.

22. The system of claim 21, wherein the syringe pump is coupled to a nozzle coupled to the actuator of the molecular diagnostic module.

23. A system for processing and detecting nucleic acids, comprising:

a molecular diagnostic module, configured to process a set of biological samples combined with magnetic beads and separate a set of nucleic acid volumes from the set of biological samples combined with magnetic beads, wherein the molecular diagnostic module comprises an actuator configured to displace a cartridge, a set of pins, and at least one cam contacting the set of pins, wherein an extension or retraction of the actuator moves the cartridge, and a displacement of a subset of the set of pins defines a set of pathways in the cartridge, each configured to receive a biological sample combined with magnetic beads of the set of biological samples combined with magnetic beads.

24. The system of claim 23, further comprising:

a capture plate comprising at least one well containing a set of magnetic beads configured to be combined with a biological sample, a lysing reagent, and a sample process control, wherein the capture plate facilitates production of at least one biological sample combined with magnetic beads;

an assay strip comprising at least one reagent well containing a molecular diagnostic reagent volume configured to be combined with a nucleic acid volume of the set of nucleic acid volumes to produce at least one nucleic acid-reagent mixture; and

a liquid handling system configured to transfer at least one biological sample combined with magnetic beads from the capture plate to the molecular diagnostic module, transfer at least one nucleic acid volume from the molecular diagnostic module to the assay strip, and transfer at least one nucleic acid-reagent mixture from the assay strip back to the molecular diagnostic module.

25. The system of claim 23, wherein the actuator of the molecular diagnostic module is a linear actuator, configured to vertically displace the cartridge.

26. The system of claim 23, wherein the cartridge of the molecular diagnostic module contacts a cartridge platform coupled to a set of springs configured to counteract a force provided by the linear actuator.

27. The system of claim 26, further comprising a pin housing configured to house the set of pins and to guide the set of pins through a set of slots of the cartridge platform.

28. The system of claim 27, wherein at least one pin in the set of pins has a first diameter and a second diameter, different from the first diameter, such that the first diameter and the second diameter are configured to limit motion of the at least one pin through the pin housing.

29. The system of claim 28, wherein at least one pin in the set of pins includes a spring configured to counteract a force provided by the cam.

30. The system of claim 23, wherein the cam is a cam card is coupled to a cam card actuator configured to linearly displace the cam card under the set of pins.

31. The system of claim 30, wherein the cam card comprises a fixed set of hills and valleys, such that a pin of the set of pins is raised when a hill of the cam card passes under the pin, and a pin of the set of pins is lowered when a valley of the cam card passes under the pin.

32. The system of claim 24, wherein the liquid handling system comprises a multichannel pipette head and a syringe pump.