Universal sample preparation system and use in an integrated analysis system

• US 9,012,236 B2
• Filed: 08/15/2013
• Issued: 04/21/2015
• Est. Priority Date: 06/05/2009
• Status: Active Grant

• Current Assignee: IntegenX Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: IntegenX Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Jovanovich, Stevan B., Nielsen, William D., Cohen, David S., Recknor, Michael, Vangbo, Mattias, Van Gelder, Ezra, El-Sissi, Omar
• Primary Examiner(s): Sines, Brian J
• Application Number:
  US13/967,957
• Publication Number:
  US 20140170645A1
• Time in Patent Office: 614 Days
• Field of Search: 436/43, 436/180, 422/502, 422/503, 422/504, 422/509, 422/512
• US Class Current: 436/180
• 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 2300/0654 Lenses; Optical fibres
• CPC Class Codes: B01L 2300/0672 Integrated piercing tool
• 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 2400/0421 electrophoretic flow
• CPC Class Codes: B01L 2400/0481 squeezing of channels or chambers
• CPC Class Codes: B01L 2400/0487 fluid pressure, pneumatics
• CPC Class Codes: B01L 2400/0655 pinch valves
• CPC Class Codes: B01L 3/502715 characterised by interfacing components, e.g. fluidic, electrical, optical or mechanical interfaces
• 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: C12Q 1/6806 Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay C12Q1/6804 takes precedence
• CPC Class Codes: G01J 3/4406 Fluorescence spectrometry
• CPC Class Codes: G01N 1/31 Apparatus therefor
• CPC Class Codes: G01N 1/405 by adsorption or absorption
• CPC Class Codes: G01N 2035/00148 : Test cards, e.g. Biomerieux or McDonnel multiwell test cards
• CPC Class Codes: G01N 2035/00247 : Microvalves
• CPC Class Codes: G01N 21/64 : Fluorescence; Phosphorescence
• CPC Class Codes: G01N 2201/06113 : Coherent sources; lasers
• CPC Class Codes: G01N 2201/062 : LED's
• CPC Class Codes: G01N 27/44704 : Details; Accessories
• CPC Class Codes: G01N 27/44721 : by optical means
• CPC Class Codes: G01N 27/44791 : Microapparatus sample containers with integrated microfluidic structures B01L3/5027
• CPC Class Codes: G01N 27/745 : for detecting magnetic beads used in biochemical assays concerning the assays G01N33/54326; sensors therefor G01R33/1269; automatic analysers therefor G01N35/0098
• CPC Class Codes: G01N 35/00029 : provided with flat sample substrates, e.g. slides G01N35/028 takes precedence
• CPC Class Codes: Y10T 436/11 : Automated chemical analysis
• CPC Class Codes: Y10T 436/143333 : Saccharide [e.g., DNA, etc.]
• CPC Class Codes: Y10T 436/25 : including sample preparation
• CPC Class Codes: Y10T 436/2575 : Volumetric liquid transfer

Abstract

The invention provides a system that can process a raw biological sample, perform a biochemical reaction and provide an analysis readout. For example, the system can extract DNA from a swab, amplify STR loci from the DNA, and analyze the amplified loci and STR markers in the sample. The system integrates these functions by using microfluidic components to connect what can be macrofluidic functions. In one embodiment the system includes a sample purification module, a reaction module, a post-reaction clean-up module, a capillary electrophoresis module and a computer. In certain embodiments, the system includes a disposable cartridge for performing analyte capture. The cartridge can comprise a fluidic manifold having macrofluidic chambers mated with microfluidic chips that route the liquids between chambers. The system fits within an enclosure of no more than 10 ft³. and can be a closed, portable, and/or a battery operated system. The system can be used to go from raw sample to analysis in less than 4 hours.

Claims

1. A method comprising:

a) providing at least one sealed reagent chamber comprising a first seal and a second seal, and a reagent;

b) breaking the first and second seals on the reagent chamber to put the reagent chamber in fluidic communication with a microfluidic channel in a microfluidic chip; and

c) exerting positive pressure on the reagent in the reagent chamber to move the reagent from the reagent chamber into the microfluidic channel.

2. The method of claim 1 wherein breaking the first and second seals on the reagent chamber further puts the reagent chamber in fluidic communication with a source of pneumatic pressure.

3. The method of claim 1 wherein the reagent chamber has a non-microfluidic volume of at least 500 microliters.

4. The method of claim 3 wherein the reagent chamber has a volume of about 2 ml.

5. The method of claim 1 wherein the reagent comprises primers for amplifying a plurality of short tandem repeats.

6. The method of claim 1 wherein the reagent comprises a diluent to lower the salt concentration of a PCR reaction product.

7. The method of claim 1 wherein the reagent comprises a nucleic acid size standard having nucleic acid fragments.

8. The method of claim 1 wherein the reagent comprises a wash solution.

9. The method of claim 1 wherein the reagent comprises lysis buffer.

10. The method of claim 1 wherein the reagent comprises an allelic ladder.

11. The method of claim 1 wherein the reagent comprises nucleic acid capture particles.

12. The method of claim 11 wherein the nucleic acid capture particles are magnetically responsive.

13. The method of claim 1 wherein the reagent comprises electrophoresis run buffer.

14. The method of claim 1 wherein the reagent comprises enzymes for performing PCR.

15. The method of claim 1 wherein breaking the first and second seals comprises puncturing each seal with a cannula.

16. The method of claim 1 wherein the first and second seals are plastic seals or a rubber seals.

17. The method of claim 1 wherein the positive pressure is exerted by pressurized air transmitted through a pneumatic manifold.

18. The method of claim 1 comprising moving the reagent through the microfluidic channel into a chamber in a fluidic manifold.

19. The method of claim 1 further comprising moving waste from the microfluidic channel into the reagent chamber.