Microfluidic system for amplifying and detecting polynucleotides in parallel

• US 7,998,708 B2
• Filed: 11/14/2007
• Issued: 08/16/2011
• Est. Priority Date: 03/24/2006
• Status: Active Grant

• Current Assignee: HandyLab Incorporated (Becton, Dickinson & Co)
• Original Assignee: HandyLab Incorporated (Becton, Dickinson & Co)
• Inventors: Williams, Jeff, Handique, Kalyan, Ganesan, Karthik, Brahmasandra, Sundaresh N.
• Primary Examiner(s): Kim; Young J
• Application Number:
  US11/985,577
• Publication Number:
  US 20080182301A1
• Time in Patent Office: 1,371 Days
• Field of Search: None
• US Class Current: 435/91.2
• CPC Class Codes: B01L 2200/027 for microfluidic devices
• 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 2200/147 Employing temperature sensors
• CPC Class Codes: B01L 2200/148 Specific details about calibrations
• CPC Class Codes: B01L 2200/16 Reagents, handling or storing thereof
• CPC Class Codes: B01L 2300/021 Identification, e.g. bar codes
• CPC Class Codes: B01L 2300/045 whereby the whole cover is slidable
• 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 2300/1822 using Peltier elements
• CPC Class Codes: B01L 2300/1827 using resistive heater
• CPC Class Codes: B01L 2300/1861 using radiation
• CPC Class Codes: B01L 2400/0442 thermal energy, e.g. vaporisation, bubble jet
• CPC Class Codes: B01L 2400/0481 squeezing of channels or chambers
• CPC Class Codes: B01L 2400/0487 fluid pressure, pneumatics
• CPC Class Codes: B01L 2400/0611 duck bill valves
• CPC Class Codes: B01L 2400/0677 phase change valves; Meltable, freezing, dissolvable plugs; Destructible barriers
• CPC Class Codes: B01L 2400/0683 : mechanically breaking a wall or membrane within a channel or chamber
• 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 3/502738 : characterised by integrated valves microvalves F16K99/0001
• 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: C12Q 1/6806 : Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/686 : Polymerase chain reaction [PCR]
• CPC Class Codes: F16K 2099/0084 : Chemistry or biology, e.g. "lab-on-a-chip" technology
• CPC Class Codes: F16K 99/0001 : Microvalves microdevices B81B1/00; manufacture or treatment of devices or systems in or on a substrate B81C1/00; microfluidic structures B01L3/5027; micropumps F04B19/006
• CPC Class Codes: F16K 99/003 : Valves for single use only
• CPC Class Codes: F16K 99/0032 : using phase transition or influencing viscosity
• CPC Class Codes: F16K 99/0044 : using thermo-electric means
• CPC Class Codes: F16K 99/0061 : actuated by an expanding gas or liquid volume
• CPC Class Codes: G01N 2021/6419 : Excitation at two or more wavelengths
• CPC Class Codes: G01N 2021/6421 : Measuring at two or more wavelengths
• CPC Class Codes: G01N 2021/6441 : with two or more labels
• CPC Class Codes: G01N 2035/00881 : network configurations
• CPC Class Codes: G01N 21/6428 : Measuring fluorescence of fluorescent products of reactions or of fluorochrome labelled reactive substances, e.g. measuring quenching effects, using measuring "optrodes" in vivo A61B5/00; immunoassay G01N33/53

Abstract

The present technology provides for an apparatus for detecting polynucleotides in samples, particularly from biological samples. The technology more particularly relates to microfluidic systems that carry out PCR on nucleotides of interest within microfluidic channels, and detect those nucleotides. The apparatus includes a microfluidic cartridge that is configured to accept a plurality of samples, and which can carry out PCR on each sample individually, or a group of, or all of the plurality of samples simultaneously.

Claims

1. An apparatus, comprising:

a multi-lane microfluidic cartridge, each lane comprising a PCR reaction zone;

a receiving bay configured to receive the microfluidic cartridge;

each PCR reaction zone comprising a separately controllable heat source thermally coupled thereto, wherein the heat source maintains a substantially uniform temperature throughout the PCR reaction zone and thermal cycles the PCR reaction zone to carry out PCR on a polynucleotide-containing sample in the PCR reaction zone;

a detector configured to detect the presence of an amplification product in the respective PCR reaction zone; and

a processor coupled to the detector and the heat source, configured to control heating of one or more PCR reaction zones by the heat sources.

2. The apparatus of claim 1, further comprising a registration member that is complementary to the microfluidic cartridge, whereby the receiving bay receives the microfluidic cartridge in a single orientation.

3. The apparatus of claim 1, wherein the processor is programmable to operate the detector to detect a polynucleotide or a probe thereof in a microfluidic cartridge located in the receiving bay.

4. The apparatus of claim 3, wherein the detector is an optical detector.

5. The apparatus of claim 4, wherein the optical detector comprises a light source that selectively emits light in an absorption band of a fluorescent dye and a light detector that selectively detects light in an emission band of the fluorescent dye, wherein the fluorescent dye corresponds to a fluorescent polynucleotide probe or a fragment thereof.

6. The apparatus of claim 5, wherein the optical detector comprises a bandpass-filtered diode that selectively emits light in the absorption band of the fluorescent dye and a bandpass filtered photodiode that selectively detects light in the emission band of the fluorescent dye.

7. The apparatus of claim 6, wherein the optical detector is configured to independently detect a plurality of fluorescent dyes having different fluorescent emission spectra, wherein each fluorescent dye corresponds to a fluorescent polynucleotide probe or a fragment thereof.

8. The apparatus of claim 6, wherein the optical detector is configured to independently detect a plurality of fluorescent dyes at a plurality of different locations, wherein each fluorescent dye corresponds to a fluorescent polynucleotide probe or a fragment thereof.

9. The apparatus of claim 1, wherein the processor is programmable to operate the plurality of heat sources.

10. The apparatus of claim 1, wherein at least one of the plurality of heat sources is a contact heat source selected from a resistive heater, a radiator, a fluidic heat exchanger and a Peltier device.

11. The apparatus of claim 10, wherein the contact heat source is configured at the receiving bay to be thermally coupled to a distinct location in a microfluidic cartridge received in the receiving bay, whereby the distinct location is selectively heated.

12. The apparatus of claim 11, wherein the distinct location has a surface area of between about 1 mm² and about 225 mm².

13. The apparatus of claim 12, wherein the contact heat source is configured to be in direct physical contact with a distinct location of a microfluidic cartridge received in the receiving bay.

14. The apparatus of claim 12, further comprising a compliant layer at the contact heat source configured to thermally couple the contact heat source with at least a portion of a microfluidic cartridge received in the receiving bay.

15. The apparatus of claim 14, wherein the compliant layer at the contact heat source has a thickness of between about 0.05 and about 2 millimeters and a Shore hardness of between about 25 and about 100.

16. The apparatus of claim 11, wherein the distinct location has a surface area of between about 1 mm² and about 100 mm².

17. The apparatus of claim 16, further comprising at least one additional contact heat source, wherein the contact heat sources are each configured at the receiving bay to be independently thermally coupled to a different distinct location in a microfluidic cartridge received in the receiving bay, whereby the distinct locations are independently heated.

18. The apparatus of claim 1, wherein at least one of the plurality of heat sources is a radiative heat source configured to direct heat to a distinct location of a microfluidic cartridge received in the receiving bay.

19. The apparatus of claim 1, further comprising a lid at the receiving bay, the lid being operable to at least partially exclude ambient light from the receiving bay.

20. The apparatus of claim 19, wherein the lid is a sliding lid.

21. The apparatus of claim 19, wherein the lid comprises the optical detector.

22. The apparatus of claim 19, wherein a major face of the lid at the receiving bay varies from planarity by less than about 100 micrometers.

23. The apparatus of claim 19, wherein the lid is configured to be removable from the apparatus.

24. The apparatus of claim 19, wherein the lid comprises a latching member.

25. The apparatus of claim 1, further comprising at least one input device coupled to the processor, the input device being selected from the group consisting of a keyboard, a touch-sensitive surface, a microphone, a hard disk drive, an optical disk drive, a serial connection, a parallel connection, a wireless network connection, a wired network connection and a mouse.

26. The apparatus of claim 1, further comprising at least one sample identifier coupled to the processor, the sample identifier being selected from an optical character reader, a bar code reader and a radio frequency tag reader.

27. The apparatus of claim 26, wherein the sample identifier is a handheld bar code reader.

28. The apparatus of claim 1, further comprising at least one output coupled to the processor, the output being selected from a display, a printer, a speaker, a serial connection, a parallel connection, a wireless network connection and a wired network connection.

29. The apparatus of claim 1, further comprising a heating stage configured to be removable from the apparatus wherein at least one of the plurality of heat sources is located in the heating stage.

30. The apparatus of claim 1, configured to carry out PCR on multiple polynucleotide-containing samples, and to detect presence of an amplification product in each of the samples.

31. The apparatus of claim 1, configured to carry out PCR on 4, 8, 10, 16, 20, 24, 25, 30, 32, 36, 40, or 48 samples.

32. The apparatus of claim 1, wherein the polynucleotide-containing sample is PCR-ready.

33. A method of carrying out PCR on a plurality of samples, the method comprising:

introducing the plurality of samples into a multi-lane microfluidic cartridge, wherein each lane comprises a PCR reaction zone configured to permit thermal cycling of a sample independently of the other samples;

moving the plurality of samples into the respective plurality of PCR reaction zones; and

amplifying polynucleotides contained with the plurality of samples in the PCR reaction zones while thermal cycling the PCR reaction zones, at least one PCR reaction zone separately thermally controllable from another PCR reaction zone.