Sample processing methods

• US 8,936,933 B2
• Filed: 05/18/2010
• Issued: 01/20/2015
• Est. Priority Date: 02/05/2003
• Status: Active Grant

• Current Assignee: Roche Molecular Systems (Roche Holding AG)
• Original Assignee: Iqumm Incorporated
• Inventors: Chen, Shuqi, Chen, Lingjun
• Primary Examiner(s): BROWN, MELANIE YU
• Application Number:
  US12/782,354
• Publication Number:
  US 20100218621A1
• Time in Patent Office: 1,708 Days
• Field of Search: 435/288.5, 435/286.7, 435/288.7, 436/518, 436/536, 436/538
• US Class Current: 435/288.5
• CPC Class Codes: B01F 31/55 the materials to be mixed being contained in a flexible bag submitted to periodical deformation
• CPC Class Codes: B01L 2200/0621 Control of the sequence of chambers filled or emptied
• 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 2300/042 Caps; Plugs
• CPC Class Codes: B01L 2300/046 Function or devices integrated in the closure
• CPC Class Codes: B01L 2300/047 Additional chamber, reservoir
• CPC Class Codes: B01L 2300/0681 Filter
• CPC Class Codes: B01L 2300/069 Absorbents; Gels to retain a fluid
• CPC Class Codes: B01L 2300/087 Multiple sequential chambers
• CPC Class Codes: B01L 2300/10 Means to control humidity and/or other gases
• CPC Class Codes: B01L 2400/0481 squeezing of channels or chambers
• CPC Class Codes: B01L 2400/0677 phase change valves; Meltable, freezing, dissolvable plugs; Destructible barriers
• 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 3/505 flexible containers not provided for above
• CPC Class Codes: C12N 15/1003 Extracting or separating nucleic acids from biological samples, e.g. pure separation or isolation methods; Conditions, buffers or apparatuses therefor
• CPC Class Codes: G01N 1/10 in the liquid or fluent state burettes, pipettes B01L3/02; sampling of ground water E02D1/06; metering by volume of fluids or fluent solid material G01F11/00, G01F13/00
• CPC Class Codes: G01N 33/543 with an insoluble carrier for immobilising immunochemicals
• CPC Class Codes: Y02A 50/30 Against vector-borne diseases, e.g. mosquito-borne, fly-borne, tick-borne or waterborne diseases whose impact is exacerbated by climate change
• CPC Class Codes: Y10S 435/81 Packaged device or kit
• CPC Class Codes: Y10T 436/25 including sample preparation

Abstract

A method of processing a sample may include introducing a sample into a vessel, the vessel having proximal and distal ends, the sample being introduced into the proximal end of the vessel; incubating the sample in the vessel with a substance capable of specific binding to a preselected component of the sample; propelling components of the incubated sample, other than the preselected component, toward the proximal end of the vessel by clamping the vessel distal to the incubated sample and compressing the vessel where the incubated sample is contained; propelling the preselected component toward a distal segment of the vessel by clamping the vessel proximal to the preselected component and compressing the vessel where the preselected component is contained; and mixing the preselected component with a reagent in the distal segment of the vessel.

Claims

1. A method of processing a sample, comprising:

introducing a sample into a vessel, the vessel having proximal and distal ends, the sample being introduced into the proximal end of the vessel;

incubating the sample in the vessel with a substance capable of specific binding to a preselected component of the sample;

propelling components of the incubated sample, other than the preselected component, toward the proximal end of the vessel by clamping the vessel distal to the incubated sample and compressing the vessel where the incubated sample is contained;

propelling the preselected component toward a distal segment of the vessel by clamping the vessel proximal to the preselected component and compressing the vessel where the preselected component is contained; and

mixing the preselected component with a reagent in the distal segment of the vessel.

2. The method of claim 1, wherein the vessel comprises a plurality of fluidly isolated segments initially separated from one another by breakable seals, the distal segment being among the plurality.

3. The method of claim 2, further comprising moving a fluid from a first segment to an adjacent second segment by clamping the vessel adjacent to the first segment at an end opposite to the second segment, and compressing the first segment.

4. The method of claim 2, further comprising opening a first breakable seal by compressing a segment adjacent to the first breakable seal to open the first breakable seal.

5. The method of claim 4, wherein a fluid is released from a segment by opening a breakable seal adjacent to the segment where the fluid is contained.

6. The method of claim 4, wherein the first breakable seal is opened, while not opening a second breakable seal, by physically protecting a second breakable seal region with an actuator or a clamp to prevent the second breakable seal from breaking while compressing the segment to break the first breakable seal.

7. The method of claim 2, further comprising mixing a fluid by alternately compressing adjoining segments containing the fluid.

8. The method of claim 2, further comprising forming a thin-layer flow channel in the vessel by so compressing the vessel as to leave a gap.

9. The method of claim 8, further comprising driving flow through the thin-layer flow channel by compressing the vessel on one side of the flow channel.

10. The method of claim 1, wherein the vessel further comprises a cap having a waste reservoir and being capable of closing the proximal end of the vessel, and the method further comprises capping the vessel after introducing the sample and propelling waste into the waste reservoir.

11. The method of claim 1, further comprising propelling a reagent within the vessel to contact content within the vessel by clamping the vessel distal to the reagent and compressing the vessel where the reagent is contained.

12. The method of claim 1, further comprising at least one of heating and cooling content within the vessel.

13. The method of claim 1, further comprising ramping a temperature of a fluid within the vessel.

14. The method of claim 13, wherein ramping is performed by moving the fluid from a first vessel segment set at a first temperature to a second vessel segment set at a second temperature.

15. The method of claim 1, further comprising agitating a fluid in a segment by repeatedly compressing and relaxing the segment.

16. The method of claim 1, further comprising adjusting a fluid volume by compressing a segment to set a specific volume within the vessel segment, and closing a clamp to define the volume within the segment and isolate excess volume in an adjacent segment.

17. The method of claim 1, further comprising removing an air bubble by agitating a segment containing a liquid and adjusting a volume of the segment to section the air to an adjacent segment.

18. The method of claim 1, further comprising reconstituting a dry reagent by clamping the vessel adjacent to a segment containing a reconstitution fluid and compressing that segment, thereby propelling a reconstitution fluid into an adjacent segment containing the dry reagent.

19. The method of claim 1, further comprising grinding the sample within the vessel by repeatedly compressing and relaxing the vessel.

20. The method of claim 1, wherein the vessel further comprises a filter, and the method further comprises urging a fluid through a filter by compressing the vessel where the fluid is contained to generate flow of the fluid through the filter.

21. The method of claim 1, further comprising immobilizing the preselected component of the incubated sample.

22. The method of claim 21, wherein the preselected component is immobilized by capturing the substance while the preselected component is bound to it.

23. The method of claim 21, wherein the preselected component is being immobilized during the propelling of components other than the preselected component.

24. The method of claim 1, wherein the substance is coupled to magnetic beads, and the method further comprises capturing the magnetic beads by applying a magnetic field.

25. The method of claim 24, wherein capturing further comprises at least one of forming a flow channel and agitating the magnetic bead mixture.

26. The method of claim 1, further comprising washing the substance bound to the preselected component by propelling a wash reagent into contact with the substance within the vessel, and propelling the resulting wash liquid towards the proximal end of the vessel by clamping the vessel distal to the substance and compressing the vessel where the substance is contained.

27. The method of claim 26, wherein the substance is coupled to magnetic beads, and the method further comprises resuspending the magnetic beads in the wash reagent and capturing the resuspended magnetic beads before propelling resulting wash liquid towards the proximal end.

28. The method of claim 26, further comprising forming a flow channel over the immobilized substance and driving flow of the wash reagent through the flow channel.

29. The method of claim 1, further comprising lysing the sample by at least one of releasing a lysis reagent to mix with the sample, and heating the sample.

30. The method of claim 1, further comprising diluting the sample by releasing a quantity of dilution reagent to mix with the sample.

31. The method of claim 1, further comprising eluting the preselected component from the substance by releasing an elution reagent to mix with the substance.

32. The method of claim 31, wherein the substance is coupled to magnetic beads, and the method further comprises resuspending the magnetic beads in the released elution reagent.

33. The method of claim 32, further comprising capturing the resuspended magnetic beads.

34. The method of claim 1, wherein the sample comprises spores and the method further comprises incubating the sample with a germination solution, whereby the spores are induced to germinate.

35. The method of claim 1, wherein the preselected component comprises a nucleic acid, and the method further comprises amplifying the nucleic acid by at least one of polymerase chain reaction, reverse transcription polymerase chain reaction, rolling circle amplification, ligase chain reaction, nucleic acid based amplification, transcription mediated amplification, and strand displacement amplification reaction.

36. The method of claim 35, further comprising detecting the amplification product.

37. The method of claim 35, wherein amplifying comprises compressing the vessel to move a reaction mixture within the vessel from a first vessel segment to a second vessel segment;

transferring energy to the reaction mixture at the second vessel segment;

compressing the second vessel segment to move the reaction mixture to the first vessel segment; and

transferring energy to the reaction mixture at the first tube segment.

38. The method of claim 1, wherein all steps are performed within the vessel without opening the vessel after the sample is introduced.

39. The method of claim 1, wherein the substance is coupled to magnetic beads, and wherein the method further comprises:

capturing the magnetic beads by applying a magnetic field;

washing the substance bound to the preselected component by propelling a wash reagent into contact with the substance within the vessel;

propelling the resulting wash liquid towards the proximal end of the vessel by clamping the vessel distal to the substance and compressing the vessel where the substance is contained; and

eluting the preselected component from the substance by releasing an elution reagent to mix with the substance.

40. A method of processing a sample, comprising:

introducing a sample into a vessel, the vessel having proximal and distal ends and comprising a plurality of fluidly isolated segments, the sample being introduced into the proximal end of the vessel;

incubating the sample in the vessel with magnetic beads capable of specific binding to nucleic acid within the sample, so that nucleic acids become bound to the magnetic beads;

capturing the incubated magnetic beads;

propelling components of the incubated sample, other than the captured magnetic beads, toward the proximal end of the vessel by clamping the vessel distal to the incubated sample and compressing the vessel where the incubated sample is contained;

washing the captured magnetic beads by propelling a wash reagent from a distal segment to be in contact with the magnetic beads within the vessel, and propelling the wash liquid towards the proximal end of the vessel by clamping the vessel distal to the magnetic beads and compressing the vessel where the magnetic beads are contained,

eluting the nucleic acid from the washed magnetic beads by propelling an elution reagent from a distal segment to mix with the magnetic beads, and resuspending the magnetic beads in the elution reagent;

propelling the eluted nucleic acid mixture toward a distal segment of the vessel by clamping the vessel proximal to the preselected component and compressing the vessel where the preselected component is contained; and

mixing the preselected component with a detection reagent in the distal segment of the vessel.

41. A method of processing a sample, comprising:

introducing a sample into a vessel, the vessel having proximal and distal ends and comprising a plurality of fluidly isolated segments, the sample being introduced into the proximal end of the vessel;

isolating nucleic acid from the sample by incubating the sample in the vessel with at least one reagent contained within a vessel segment and propelling components of the incubated sample, other than the nucleic acid, toward the proximal end of the vessel by clamping the vessel distal to the incubated sample and compressing the vessel where the incubated sample is contained;

propelling the isolated nucleic acid toward a distal segment of the vessel by clamping the vessel proximal to the preselected component and compressing the vessel where the preselected component is contained; and

mixing the preselected component with a detection reagent in the distal segment of the vessel; and

detecting a signal from within the vessel;

wherein all steps are performed within the vessel without opening the vessel after the sample is introduced.