Integrated nucleic acid diagnostic device

• US 6,830,936 B2
• Filed: 12/31/2000
• Issued: 12/14/2004
• Est. Priority Date: 06/29/1995
• Status: Expired due to Fees

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Lipshutz, Robert J., Anderson, Rolfe C., Rava, Richard P., Fodor, Stephen P. A.
• Primary Examiner(s): Beisner, William H.
• Application Number:
  US09/751,658
• Publication Number:
  US 20010036672A1
• Time in Patent Office: 1,444 Days
• Field of Search: 435/4, 435/6, 435/287.2, 435/286.5, 435/286.6, 435/288.5, 436/180, 436/52, 436/53, 422/56, 422/58, 422/81, 422/82, 422/100, 422/102, 204/453, 204/604
• US Class Current: 436/180
• CPC Class Codes: B01F 2101/23 Mixing of laboratory samples e.g. in preparation of analysing or testing properties of materials
• CPC Class Codes: B01F 2101/44 Mixing of ingredients for microbiology, enzymology, in vitro culture or genetic manipulation
• CPC Class Codes: B01F 31/65 the materials to be mixed being directly submitted to a pulsating movement, e.g. by means of an oscillating piston or air column
• CPC Class Codes: B01F 31/86 with vibration of the receptacle or part of it
• CPC Class Codes: B01F 33/25 Mixers with loose mixing elements, e.g. loose balls in a receptacle
• CPC Class Codes: B01F 33/30 Micromixers
• CPC Class Codes: B01F 33/45 Magnetic mixers; Mixers with magnetically driven stirrers
• CPC Class Codes: B01F 35/71 Feed mechanisms with proportioning B01F35/80
• CPC Class Codes: B01F 35/712 for feeding fluids
• CPC Class Codes: B01F 35/71745 using pneumatic pressure, overpressure, gas or air pressure in a closed receptacle or circuit system
• CPC Class Codes: B01F 35/71761 Membrane pumps
• CPC Class Codes: B01F 35/718 using vacuum, under pressure in a closed receptacle or circuit system
• CPC Class Codes: B01F 35/71805 using valves, gates, orifices or openings
• CPC Class Codes: B01L 2200/0621 Control of the sequence of chambers filled or emptied
• CPC Class Codes: B01L 2200/0684 Venting, avoiding backpressure, avoid gas bubbles
• 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 2300/087 Multiple sequential chambers
• CPC Class Codes: B01L 2300/0883 Serpentine channels
• CPC Class Codes: B01L 2300/16 Surface properties and coatings
• CPC Class Codes: B01L 2400/0415 electrical forces, e.g. electrokinetic
• CPC Class Codes: B01L 2400/0421 : electrophoretic flow
• CPC Class Codes: B01L 2400/0487 : fluid pressure, pneumatics
• CPC Class Codes: B01L 2400/049 : vacuum
• CPC Class Codes: B01L 2400/084 : Passive control of flow resistance
• CPC Class Codes: B01L 2400/086 : using baffles or other fixed flow obstructions
• 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 3/502715 : 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 3/502753 : characterised by bulk separation arrangements on lab-on-a-chip devices, e.g. for filtration or centrifugation separation in general B01D; microapparatus for analysis using electrophoresis G01N27/44791; sample preparation G01N1/28
• CPC Class Codes: B01L 3/502784 : specially adapted for droplet or plug flow, e.g. digital microfluidics automatic analysis using a stream of discrete samples in a tube system G01N35/08
• 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 9/527 : for microfluidic devices, e.g. used for lab-on-a-chip
• CPC Class Codes: G01N 2035/00158 : Elements containing microarrays, i.e. "biochip"
• CPC Class Codes: G01N 35/1095 : for supplying the samples to flow-through analysers for a specific analyser see relevant groups, e.g. under G01N15/00, G01N21/00, G01N27/00, G01N30/00, H01J49/00
• CPC Class Codes: Y10T 436/11 : Automated chemical analysis
• CPC Class Codes: Y10T 436/118339 : with formation of a segmented stream
• CPC Class Codes: Y10T 436/25 : including sample preparation
• CPC Class Codes: Y10T 436/25375 : Liberation or purification of sample or separation of material from a sample [e.g., filtering, centrifuging, etc.]
• CPC Class Codes: Y10T 436/2575 : Volumetric liquid transfer

Abstract

The present invention provides a miniaturized integrated nucleic acid diagnostic device and system. The or more sample acquisition and preparation operations, in combination with one or more sample analysis operations. For example, the device can integrate several or all of the operations involved in sample acquisition and storage, sample preparation and sample analysis, within a single integrated unit. The device is useful in a variety of applications, and most notably, nucleic acid based diagnostic applications and de novo sequencing applications.

Claims

1. A method of repeatedly measuring a known volume of a fluid in a miniature fluidic system, comprising:

providing a microfabricated device having at least first and second chambers connected by at least one common channel disposed therein, wherein said first and second chambers are in fluid connection with at least one vent port and at least one pressure inlet, and wherein at least one of said chambers is a volumetric chamber having a known volume;

providing a diaphragm valve constructed in communication with said at least one chamber and constructed to create a pressure differential in said device for displacing fluid;

filling said volumetric chamber with said fluid to create a first aliquot of said fluid by actuating said diaphragm valve using an external source to generate said pressure differential in said device;

transporting said first aliquot of said fluid to said at least second chamber by actuating said diaphragm; and

repeating said filling and transporting steps by applying said pressure differential from said diaphragm valve using said external source and by employing said at least one vent port.

2. The method of claim 1, wherein each of said chambers of said device provided in said providing step has a cross sectional dimension of from about 0.05 to about 20 mm, and a depth dimension of from about 0.05 to about 5 mm.

3. The method of claim 1 including applying a positive pressure with respect to said volumetric chamber, whereby said positive pressure forces said fluid from said volumetric chamber.

4. The method of claim 1 including applying a negative pressure with respect to said volumetric chamber, whereby said negative pressure forces said fluid from said volumetric chamber.

5. A method of measuring and processing a known volume of a fluid in a miniature fluidic system for integrated nucleic acid analysis, comprising the acts of:

providing a microfabricated device having at least first and second chambers each including a fluid port connected by a common channel disposed therein, said at least first and second chambers being in communication with at least one vent port, and at least one of said chambers being a volumetric chamber having a known volume;

providing a sealable closure inlet to said microfabricated device constructed and arranged to introduce fluid to be delivered to said chambers;

providing at least one valve controllable by an external pressure source constructed for displacing fluid inside said device;

filling said volumetric chamber with said fluid to create a first aliquot of said fluid by opening said controllable valve and by using said vent port;

creating a pressure differential in said device acting on said fluid in said volumetric chamber; and

transporting said first aliquot of said fluid to said at least second chamber by applying said pressure differential from said external source.

6. The method of claim 5 including applying a positive pressure with respect to said volumetric chamber, whereby said positive pressure forces said fluid from said volumetric chamber during said opening of said controllable valve.

7. The method of claim 5 or 6 including venting said volumetric chamber using said vent port.

8. The method of claim 5 or 6 including venting said volumetric chamber using a hydrophobic membrane sealably disposed across said vent port.

9. The method of claim 6 wherein said applying said positive pressure includes using a pneumatic system cooperatively arranged with said external source.

10. The method of claim 9 wherein said using said pneumatic system includes using a differential pressure delivery system capable of applying a first pressure to said volumetric chamber and a second pressure to said second chamber.

11. The method of claim 5 including applying a negative pressure with respect to said volumetric chamber, whereby said negative pressure forces said fluid into said volumetric chamber during said opening of said controllable valve.

12. The method of claim 11 wherein said applying said negative pressure includes using a pneumatic system cooperatively arranged with said external source.

13. The method of claim 12 wherein said using said pneumatic system includes using a differential pressure delivery system capable of applying a first pressure to said volumetric chamber and a second pressure to said second chamber.

14. The method of claim 5 including measuring temperature of said fluid.

15. The method of claim 5 including heating said fluid.

16. The method of claim 5 including performing microcapillary electrophoresis.

17. The method of claim 5 including performing transcription.

18. The method of claim 5 including performing labeling.

19. The method of claim 5 including performing fragmentation.

20. The method of claim 5 including performing amplification.

21. The method of claim 20 wherein said performing amplification includes performing polymerase chain reaction (PCR).

22. The method of claim 20 wherein said performing amplification includes performing ligase chain reaction (LCR).

23. The method of claim 20 wherein said performing amplification includes performing self substained sequence replication.

24. The method of claim 20 wherein said performing amplification includes performing nucleic acid based sequence amplification (NASBA).

25. The method of claim 5 wherein said fluid includes a reagent.

26. The method of claim 5 wherein said fluid includes a buffer.

27. The method of claim 5 wherein said fluid includes a biological polymer.

28. The method of claim 5 including reconstituting a reagent kept in a lyophilized form.

29. The method of claim 28, wherein said reconstituting includes transporting said first aliquot of said fluid to said second chamber wherein said reagent is located.

30. The method of claim 5 includes introducing a liquid including a sample through said sealable closure inlet formed by a septum.

31. A miniature fluidic system for measuring and processing a known volume of a fluid controlled by an external pressure source, comprising:

a microfabricated device having at least first and second chambers in communication with a common channel disposed therein, each said at least first and second chambers including at least one vent port and at least one of said chambers being a volumetric chamber having a known volume;

a sealable closure inlet to said microfabricated device constructed to enable introduction of a liquid to be delivered to said chambers;

at least one valve controlled by an external pressure source;

means for creating pressure differential in said device for filling said volumetric chamber with said fluid to create a first aliquot of said fluid;

means for opening said controllable valve and thereby applying said pressure differential to said first aliquot of said fluid; and

means for enabling transport of said first aliquot of said fluid to said at least second chamber using said pressure differential.

32. The system of claim 31 including means for measuring temperature of said fluid.

33. The system of claim 31 including means for heating said fluid.

34. The system of claim 31 including means for performing microcapillary electrophoresis.

35. The system of claim 31 including means for performing transcription.

36. The system of claim 31 including means for performing labeling.

37. The system of claim 31 including means for performing fragmentation.

38. The system of claim 31 including means for performing amplification.

39. The system of claim 38 wherein said means for performing amplification includes means for performing polymerase chain reaction (PCR).

40. The system of claim 38 wherein said means for performing amplification includes means for performing ligase chain reaction (LCR).

41. The system of claim 31 wherein said sealable closure inlet is constructed for introduction of a reagent.

42. The system of claim 31 wherein said sealable closure inlet is constructed for introduction of a buffer.

43. The system of claim 31 wherein said sealable closure inlet is constructed for introduction of a biological polymer.

44. The system of claim 31 including means for reconstituting a reagent kept in a lyophilized form.

45. The system of claim 44, wherein said means for reconstituting includes means for transporting said first aliquot of said fluid to said second chamber wherein said reagent is located.

46. The system of claim 31 wherein said sealable closure inlet includes a septum.