BIOARRAY CHIP REACTION APPARATUS AND ITS MANUFACTURE

• US 20100298165A1
• Filed: 07/23/2010
• Published: 11/25/2010
• Est. Priority Date: 06/08/1994
• Status: Abandoned Application

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Goss, Virginia W., Besemer, Donald M., Winkler, James L.
• Application Number:
  US12/842,977
• Publication Number:
  US 20100298165A1
• Time in Patent Office: Days
• US Class Current: 506/9
• CPC Class Codes: B01F 33/30 Micromixers
• CPC Class Codes: B01F 33/40 Mixers using gas or liquid agitation, e.g. with air supply tubes
• CPC Class Codes: B01F 33/45 Magnetic mixers; Mixers with magnetically driven stirrers
• CPC Class Codes: B01J 19/0046 Sequential or parallel reactions, e.g. for the synthesis of polypeptides or polynucleotides; Apparatus and devices for combinatorial chemistry or for making molecular arrays synthesis methods per se C40B50/00
• CPC Class Codes: B01J 2219/00371 comprising electrodes
• CPC Class Codes: B01J 2219/00432 Photolithographic masks
• CPC Class Codes: B01J 2219/00527 Sheets
• CPC Class Codes: B01J 2219/00529 DNA chips
• CPC Class Codes: B01J 2219/00531 essentially square
• CPC Class Codes: B01J 2219/00536 in the shape of disks
• CPC Class Codes: B01J 2219/0054 Means for coding or tagging the apparatus or the reagents
• CPC Class Codes: B01J 2219/00547 Bar codes
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/0059 Sequential processes
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00605 the compounds being directly bound or immobilised to solid supports
• CPC Class Codes: B01J 2219/00608 DNA chips
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00626 Covalent
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00662 : Two-dimensional arrays within two-dimensional arrays
• CPC Class Codes: B01J 2219/00689 : using computers
• CPC Class Codes: B01J 2219/00695 : Synthesis control routines, e.g. using computer programs
• CPC Class Codes: B01J 2219/00711 : Light-directed synthesis
• CPC Class Codes: B01J 2219/00722 : Nucleotides
• CPC Class Codes: B01J 2219/00725 : Peptides
• CPC Class Codes: B01J 2219/00731 : Saccharides
• CPC Class Codes: B01L 2200/025 : Align devices or objects to ensure defined positions relative to each other
• CPC Class Codes: B01L 2200/027 : for microfluidic devices
• CPC Class Codes: B01L 2200/0689 : Sealing
• CPC Class Codes: B01L 2200/12 : Specific details about manufacturing devices
• CPC Class Codes: B01L 2300/0636 : Integrated biosensor, microarrays
• CPC Class Codes: B01L 2300/0816 : Cards, e.g. flat sample carriers usually with flow in two horizontal directions
• CPC Class Codes: B01L 2300/0825 : Test strips
• CPC Class Codes: B01L 2300/0877 : Flow chambers
• CPC Class Codes: B01L 2400/0487 : fluid pressure, pneumatics
• 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 3/502707 : characterised by the manufacture of the container or its components by shaping or joining plastic parts B29C59/00, B29C65/00; by laminating B32B37/00; manufacture of microstructural devices in general B81C
• CPC Class Codes: B01L 3/502715 : characterised by interfacing components, e.g. fluidic, electrical, optical or mechanical interfaces
• CPC Class Codes: B01L 9/527 : for microfluidic devices, e.g. used for lab-on-a-chip
• CPC Class Codes: B82Y 30/00 : Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: C07H 21/00 : Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
• CPC Class Codes: C12Q 1/6874 : involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C40B 40/06 : Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 40/10 : Libraries containing peptides or polypeptides, or derivatives thereof
• CPC Class Codes: C40B 40/12 : Libraries containing saccharides or polysaccharides, or derivatives thereof
• CPC Class Codes: C40B 60/14 : for creating libraries
• CPC Class Codes: C40B 70/00 : Tags or labels specially adapted for combinatorial chemistry or libraries, e.g. fluorescent tags or bar codes
• CPC Class Codes: G01N 2035/00158 : Elements containing microarrays, i.e. "biochip"
• CPC Class Codes: G01N 33/543 : with an insoluble carrier for immobilising immunochemicals
• CPC Class Codes: G01N 33/54366 : Apparatus specially adapted for solid-phase testing
• CPC Class Codes: Y10S 435/97 : Test strip or test slide
• CPC Class Codes: Y10S 435/973 : Simultaneous determination of more than one analyte
• CPC Class Codes: Y10S 436/809 : Multifield plates or multicontainer arrays
• CPC Class Codes: Y10T 436/112499 : with sample on test slide

Abstract

A body 300 having a cavity 310 for mounting a substrate 120 fabricated with probe sequences at known locations according to the methods disclosed in U.S. Pat. No. 5,143,854 and PCT WO 92/10092 or others, is provided. The cavity includes inlets 350 and 360 for introducing selected fluids into the cavity to contact the probes. Accordingly, a commercially feasible device for use in high throughput assay systems is provided.

Claims

1. An apparatus for detecting an analyte in a test sample comprising:

at least one probe array, wherein the at least one probe array comprises;

a plurality of particles having biological polymers immobilized on the plurality of particles thereon;

a slide, wherein the plurality of particles are attached to a surface of the slide; and

a barcode for identifying the at least one probe array on the slide.

2. The apparatus according to claim 1, wherein the different particles in the plurality of particles have different biological polymers immobilized thereon.

3. The apparatus according to claim 1, wherein the plurality of particles are spheres.

4. The apparatus according to claim 1, wherein the slide is silica.

5. The apparatus according to claim 1, wherein the slide is glass.

6. The apparatus according to claim 1, wherein the biological polymers are immobilized on the slide at a density exceeding 400 different biological polymers per cm².

7. The apparatus according to claim 6, wherein the biological polymers are immobilized on the slide at a density exceeding 100 different biological polymers per cm².

8. The apparatus according to claim 1, wherein the plurality of particles forms an ordered arrangement on the surface of the slide.

9. The apparatus according to claim 8, wherein the ordered arrangement on the surface is circular.

10. The apparatus according to claim 8, wherein the ordered arrangement on the surface is rectangular.

11. The apparatus according to claim 1, wherein the at least one probe array is less than 9 probe arrays.

12. The apparatus according to claim 11, wherein the at least one probe array is 1 probe array.

13. A package for supporting a probe array, comprising:

a plurality of particles having biological polymers immobilized on the plurality of particles thereon;

a slide, wherein the plurality of particles are attached to a surface of the slide; and

a top piece and a bottom piece, wherein the top bottom pieces house the first wafer, creating at least one cavity such that at least one probe array is in fluid communication with the reaction chamber.

14. The package according to claim 13, further comprising a bar code associated with the at least one probe array.

15. The package according to claim 14, further comprising at least one aligning pin and holes to assist in assembling the top piece and the bottom piece together.

16. The package according to claim 13, further comprising screws to assemble the top piece, bottom piece and the at least one probe array together.

17. The package according to claim 13, further comprising clamps to assemble the top piece, bottom piece and the at least one probe array together.

18. The package according to claim 13, further comprising at least one inlet port to introduce a fluid into the cavity.

19. The package according to claim 18, further comprising a septum to seal the at least one inlet ports.

20. The package according to claim 18, further comprising at least one channel for fluid transfer between the at least one inlet port and the cavity.

21. The package according to claim 14, further comprising at least one gasket to form a liquid tight seal around the cavity between the top piece and the at least one probe array.

22. The package according to claim 23, wherein the gaskets are O-rings.

23. The package according to claim 14, wherein the bottom piece comprises a depression to position the at least one probe array.

24. A method of using a probe array, comprising:

providing at least one probe array, wherein the at least one probe array comprises;

a plurality of particles having biological polymers immobilized on the plurality of particles thereon and a slide, wherein the plurality of particles are attached to a surface of the slide;

providing a housing, wherein the housing comprises a cavity to accommodate a fluid to be in contact with the slide;

placing the slide into the housing;

sealably mounting the slide within the housing comprising a mounting surface and a fluid cavity, wherein the fluid cavity comprises at least one inlet port constructed to permit fluid flow into the cavity through the at least one inlet port, wherein the sealably mounting act provides the at least one probe array located inside the cavity;

introducing the fluid inside the cavity to hybridize the at least one probe array on the slide;

performing hybridization, wherein at least some of the polymers hybridizes to a target;

aligning the at least one probe array, wherein the at least one probe array comprises at least one alignment feature; and

detecting a signal from the at least one probe array using a scanner.

25. The method according to claim 24, further comprising reading a bar code associated with the probe array, wherein the slide comprises a bar code.

26. The method according to claim 24, wherein the inlet port comprises of a septum sealed port which uses one or more needles to permit fluid flow into the cavity.

27. The method according to claim 24, further comprising a fluid mixing step, wherein the cavity is at least partially filled with the fluid during mixing.

28. The method according to claim 27 wherein the fluid mixing occurs using the motion of gas relative to fluid in the cavity.

29. The method according to claim 27 wherein said fluid mixing uses agitation.

30. The method according to claim 27 wherein said agitation uses vortexing.

31. An apparatus for mixing a fluid, the apparatus comprising:

a pump, wherein a first housing comprises the pump;

a probe array;

a substrate, wherein the substrate and the probe array create at least one cavity for a fluid;

at least one bubble disposed within said chamber, wherein the at least one bubble is moved by using the pump to move the bubble relative to the fluid to effect mixing the fluid.

32. The apparatus as in claim 31 wherein the at least one bubble is formed using a nitrogen gas.

33. The apparatus as in claim 31, wherein, the pump transfers the fluid from a first container through the cavity and into a second container.

34. The apparatus as in claim 31, wherein, the means for moving the fluid is through agitation.

35. A fluidic station comprising:

a base that is adapted to provide a framework for the fluidics station;

a mounting system coupled to the base, wherein the mounting system is movable between a loading position and a closed position, the mounting system comprising;

a bottom piece adapted to receive a wafer, wherein a wafer comprises at least one probe array, wherein the bottom piece is adapted to receive a top piece positioned above the wafer forming at least one cavity for fluid to be in contact with the wafer and forming a package comprising at least an inlet port and an outlet port for fluid transfer and connecting with at least one cavity;

at least one needle coupled to the base frame, wherein the needle includes a distal end and side ports above the distal ends; and

at least one fluid source in communication with the at least one needle, wherein the wafer is insertable into the mounting system when in the loading position, and wherein the at least one needle is adapted to transfer liquid into the package through the liquid channels when in the closed position.