Sample preparation, processing and analysis systems

• US 10,525,467 B2
• Filed: 11/03/2016
• Issued: 01/07/2020
• Est. Priority Date: 10/21/2011
• Status: Active Grant

• Current Assignee: IntegenX Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: IntegenX Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Nielsen, William D., Belcinski, Richard J., Bogdan, Gregory, Eberhart, David, EL-Sissi, Omar, Jovanovich, Stevan B., Recknor, Michael, Van Gelder, Ezra, Wyrick, David W.
• Primary Examiner(s): Wright, Kathryn
• Application Number:
  US15/342,914
• Publication Number:
  US 20170197213A1
• Time in Patent Office: 1,160 Days
• Field of Search: None
• CPC Class Codes: B01F 33/30 Micromixers
• CPC Class Codes: B01F 33/452 using independent floating stirring elements
• CPC Class Codes: B01L 2200/025 Align devices or objects to ensure defined positions relative to each other
• CPC Class Codes: B01L 2200/028 Modular arrangements
• CPC Class Codes: B01L 2200/04 Exchange or ejection of cartridges, containers or reservoirs
• CPC Class Codes: B01L 2200/0647 Handling flowable solids, e.g. microscopic beads, cells, particles
• CPC Class Codes: B01L 2200/143 Quality control, feedback systems
• CPC Class Codes: B01L 2300/023 Sending and receiving of information, e.g. using bluetooth
• CPC Class Codes: B01L 2300/027 Digital display, e.g. LCD, LED
• CPC Class Codes: B01L 2300/0672 Integrated piercing tool
• CPC Class Codes: B01L 2300/123 Flexible; Elastomeric
• CPC Class Codes: B01L 2400/0421 electrophoretic flow
• CPC Class Codes: B01L 2400/043 magnetic forces
• CPC Class Codes: B01L 2400/0478 pistons
• CPC Class Codes: B01L 2400/0487 fluid pressure, pneumatics
• CPC Class Codes: B01L 2400/0616 Ball valves
• CPC Class Codes: B01L 2400/0638 membrane valves, flap valves
• CPC Class Codes: B01L 3/502715 characterised by interfacing components, e.g. fluidic, electrical, optical or mechanical interfaces
• CPC Class Codes: B01L 3/5029 using swabs
• CPC Class Codes: B01L 3/527 for a plurality of reagents
• 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: G01N 2035/00158 : Elements containing microarrays, i.e. "biochip"
• CPC Class Codes: G01N 2035/0091 : GUI [graphical user interfaces]
• CPC Class Codes: G01N 27/44743 : Introducing samples
• CPC Class Codes: G01N 27/44791 : Microapparatus sample containers with integrated microfluidic structures B01L3/5027

Abstract

This disclosure provides an integrated and automated sample-to-answer system that, starting from a sample comprising biological material, generates a genetic profile in less than two hours. In certain embodiments, the biological material is DNA and the genetic profile involves determining alleles at one or a plurality of loci (e.g., genetic loci) of a subject, for example, an STR (short tandem repeat) profile, for example as used in the CODIS system. The system can perform several operations, including (a) extraction and isolation of nucleic acid; (b) amplification of nucleotide sequences at selected loci (e.g., genetic loci); and (c) detection and analysis of amplification product. These operations can be carried out in a system that comprises several integrated modules, including an analyte preparation module; a detection and analysis module and a control module.

Claims

1. A cartridge, comprising:

(a) a container comprising a plurality of closed and fluidically isolated chambers, wherein each of the plurality of chambers comprises a friable seal; and

(b) a microfluidic device engageably connected to the container, the microfluidic device comprising a fluidics layer, the fluidics layer comprising;

(i) a plurality of microfluidic channels; and

(ii) a plurality of puncturing elements, each of the plurality of puncturing elements protruding from the microfluidic device and disposed opposite the friable seal of one of the plurality of chambers and configured to puncture said friable seal, wherein each of the plurality of puncturing elements has an opening in fluidic communication with a microfluidic channel,

wherein, upon engaging the microfluidic device with the container, the plurality of puncturing elements puncture the respective friable seals of the plurality of chambers and bring the plurality of microfluidic channels into fluidic communication with the plurality of chambers by means of the respective openings of the plurality of puncturing elements, thereby (1) creating a fluid flow path between a pair of chambers of said plurality of chambers of the container through a microfluidic channel of the microfluidic device and/or (2) creating a fluid flow path between a pair of microfluidic channels of the microfluidic device through one of said plurality of chambers of the container, and

wherein, for each of the plurality of chambers, the microfluidic device has a corresponding first puncturing element disposed opposite a first portion of said chamber and a corresponding second puncturing element disposed opposite a second portion of said chamber such that, upon engaging the microfluidic device with the container, each first puncturing element punctures the friable seal at the first portion of said chamber and each second puncturing element punctures the friable seal at the second portion of said chamber and brings at least one of the plurality of microfluidic channels into fluidic communication with said chamber by means of the opening of the first puncturing element and the opening of the second puncturing element.

2. The cartridge of claim 1, wherein the friable seal comprises a metallic material.

3. The cartridge of claim 1, wherein each friable seal covers two holes in a fluidically isolated chamber.

4. The cartridge of claim 1, wherein the container comprises a top side sealed by a sealing member.

5. The cartridge of claim 1, wherein each chamber comprises a fluid.

6. The cartridge of claim 1, wherein the plurality of closed and fluidically isolated chambers comprises a first fluidically isolated chamber comprising a wash solution, a second fluidically isolated chamber comprising a bead suspension and a third fluidically isolated chamber comprising a lysis reagent.

7. The cartridge of claim 1, further comprising at least one inlet and at least one outlet communicating with the microfluidic channels.

8. The cartridge of claim 1, wherein the microfluidic device comprises at least one valve controlling flow along a microfluidic channel.

9. The cartridge of claim 8, wherein at least one of the valves is a diaphragm valve.

10. The cartridge of claim 1, wherein the microfluidic device comprises at least one pump for pumping liquid through a microfluidic channel.

11. The cartridge of claim 10, wherein at least one of the pumps is a diaphragm pump.

12. The cartridge of claim 1, wherein the microfluidic device further comprises;

a pneumatic layer comprising pneumatic channels and an elastomeric layer disposed between the fluidic layer and the pneumatic layer.

13. The cartridge of claim 12, wherein the fluidic layer and the pneumatic layer comprise a polymeric material.

14. The cartridge of claim 1, further comprising one or more gaskets between the container and microfluidic device.

15. The cartridge of claim 1, further comprising a frame, wherein the frame is attached to the microfluidic device and comprises at least one sample chamber communicating with a microfluidic channel through ports in the frame and in the microfluidic device.

16. The cartridge of claim 15, wherein the sample chamber is configured to accommodate a cotton swab.

17. The cartridge of claim 15, wherein the frame comprises a slot to hold the container.

18. The cartridge of claim 15, wherein the frame comprises a slot to hold a thermocycler assembly.

19. The cartridge of claim 1, further comprising a thermocycler assembly comprising at least one reaction chamber having an inlet and an outlet, said inlet and outlet in fluidic communication through ports with at least one microfluidic channel in the microfluidic device.

20. The cartridge of claim 19, wherein the at least one reaction chamber comprises a thermal conductor.

21. The cartridge of claim 20, wherein the thermal conductor comprises graphite.

22. The cartridge of claim 19, wherein the thermocycler assembly comprises a premix chamber comprising reagents for performing nucleic acid amplification.

23. The cartridge of claim 22, wherein the premix chamber is configured to be actuated with a plunger to deliver reagents to the reaction chamber.

24. The cartridge of claim 1, further comprising a plurality of lanes, each lane comprising a fluidic circuit, each fluidic circuit comprising a sample chamber comprising an inlet, one or more fluidically isolated chambers, a premix chamber, a reaction chamber and an outlet, wherein, when the container is engaged with the microfluidic device, the chambers communicate through microfluidic channels.