System and method for processing large number of biological microarrays

• US 8,796,186 B2
• Filed: 06/10/2009
• Issued: 08/05/2014
• Est. Priority Date: 04/06/2005
• Status: Active Grant

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Shirazi, Mohsen
• Primary Examiner(s): FORMAN, BETTY J
• Application Number:
  US12/481,852
• Publication Number:
  US 20100069265A1
• Time in Patent Office: 1,882 Days
• Field of Search: None
• US Class Current: 506/39
• CPC Class Codes: B01L 9/52 Supports specially adapted for flat sample carriers, e.g. for plates, slides, chips
• CPC Class Codes: B01L 9/523 for multisample carriers, e.g. used for microtitration plates
• CPC Class Codes: G01N 1/312 for samples mounted on planar substrates
• CPC Class Codes: G01N 2035/00158 Elements containing microarrays, i.e. "biochip"
• CPC Class Codes: G01N 2035/00356 Holding samples at elevated temperature (incubation)
• CPC Class Codes: G01N 2035/0425 Stacks, magazines or elevators for plates
• CPC Class Codes: G01N 2035/0498 Drawers used as storage or dispensing means for vessels or cuvettes
• CPC Class Codes: G01N 2035/1048 using the transfer device for another function
• CPC Class Codes: G01N 35/0099 comprising robots or similar manipulators robots per se B25J
• CPC Class Codes: G01N 35/028 having reaction cells in the form of microtitration plates

Abstract

A system and method for processing biological sensors. The system includes a support component configured to support a fluidic component. The fluidic component includes at least a first container and a second container. The first container is capable of holding a first volume of a first fluid, and the second container is capable of holding a second volume of a second fluid. Additionally, the system includes a hybridization component configured to perform a hybridization process on a first sensor and a second sensor. Moreover, the system includes a transport component configured to move the first sensor, directly or indirectly, from the hybridization component into the first container and in contact with the first volume of the first fluid.

Claims

1. A device for hybridizing, processing, and scanning a plurality of microarrays, the device comprising:

a fluidic component comprising;

a plurality of well plates, wherein each well plate comprises a plurality of wells arranged in a plurality of columns and a plurality of rows, wherein each well plate is configured to mate with a peg plate comprising a base, a plurality of pegs arranged in rows and columns on the base, and a plurality of microarrays, each microarray individually attached to one of the plurality of pegs, and wherein each well of the well plate is configured to receive one of the plurality of microarrays when the well plate is mated with a peg plate;

a first fluidic container; and

a second fluidic container;

a support component comprising a plurality of drawer assemblies, wherein each drawer assembly comprises a drawer panel, and wherein each drawer panel is configured to support one or more well plates;

a hybridization component comprising a hybridization oven, wherein the hybridization oven is configured to hybridize a nucleic acid sample to a microarray, and wherein the hybridization component is fixed to the support component;

a scanning component fixed to the support component, wherein the scanning component is configured to scan the plurality of microarrays after hybridization and processing;

a transport component configured to grip, move and release a peg plate, wherein the transport component comprises a gripper assembly having a closed position suitable for gripping a peg plate and an open position suitable for releasing the peg plate, wherein the gripper assembly comprises a base plate, sensors, a motor, a cam, rack and pinion, a spring, two arms, and finger assemblies, wherein the arms extend outward from the base plate substantially parallel to one another with a finger assembly attached to an interior surface of each arm such that the finger assemblies are oppositely facing one another and capable of contacting opposing sides of the support component of a peg plate, wherein the arms are movably joined to one another through the cam, rack and pinion, and the spring, and wherein the motor increases or decreases the distance between the arms by applying force to the cam, thereby moving the gripper between the open and closed positions, and wherein the transport component moves the peg plate within and between the components; and

a processing system, wherein the processing system comprises a computer, and wherein the computer is configured to direct the movements of the transport component.

2. The device of claim 1, additionally comprising:

a barcode reader configured to read one or more barcodes on the well plates.

3. The device of claim 1, additionally comprising:

an unclamping station configured to separate a peg plate from a hybridization tray after the plurality of microarrays have been hybridized to nucleic acid samples.

4. The device of claim 3, wherein the hybridization tray comprises a plurality of handles, and wherein the handles are configured to facilitate clamping of the hybridization tray with the peg plate.

5. The device of claim 4, wherein the unclamping station comprises a plurality of fingers, and wherein the fingers are configured to unclamp the peg plate from the hybridization tray.

6. The device of claim 1, wherein the first fluidic container is configured to hold a first washing fluid, and wherein the first fluidic container and the transport component are configured to wash the plurality of microarrays a plurality of times.

7. The device of claim 6, wherein the second fluidic container is configured to hold and heat a second washing fluid, and wherein the second fluidic container and the transport component are configured to wash the plurality of microarrays with the heated second washing fluid.

8. The device of claim 1, wherein each drawer panel is configured to support two well plates in a side-by-side configuration.

9. The device of claim 1, wherein each drawer panel is configured to slide horizontally.

10. The device of claim 1, wherein each drawer panel comprises one or more biasing features configured to align and fix a well plate to the drawer panel.

11. The device of claim 1, wherein each drawer panel (i) is configured to support two well plates in a side-by-side configuration, (ii) is configured to slide horizontally, and (iii) comprises one or more biasing features configured to align and fix two well plates to the drawer panel.

12. The device of claim 11, wherein each drawer assembly additionally comprises a splash guard.

13. The device of claim 1, wherein the plurality of drawer assemblies includes a handoff drawer assembly, wherein the handoff drawer assembly comprises a handoff drawer panel, wherein the transport component is configured to place the peg plate on the handoff drawer panel after hybridization and processing, and wherein the handoff drawer assembly and the transport component are configured to transfer the peg plate from the handoff drawer assembly to the scanning component.

14. The device of claim 1, wherein the scanning component comprises a CCD camera and an XYZ table and a tip-tilt assembly, wherein the XYZ table and tip-tilt assembly are configured to manipulate the peg plate.

15. The device of claim 1, wherein the finger assemblies fit into recesses located on opposing sides of the base of the peg plate.

16. The device of claim 1, wherein the arms of the gripper assembly extend beyond the section used for attaching the finger assemblies.

17. The device of claim 16, wherein the distal end of at least one arm of the gripper assembly comprises a notched flange configured to latch onto a drawer assembly, thereby enabling the transport component to move the drawer assembly between open and closed positions by moving the gripper assembly.

18. The device of claim 1, further comprising a peg plate comprising a base, a plurality of pegs arranged in rows and columns on the base, and a plurality of microarrays, each microarray individually attached to one of the plurality of pegs.

19. The device of claim 18, wherein the peg plate comprises 96 pegs.

20. The device of claim 18, wherein each of the plurality of microarrays has a substantially square shape with a length equal to or less than 10 mm, a width equal to or less than 10 mm, and a thickness equal to or less than 1000 μ

m.

21. A device for hybridizing, processing, and scanning a plurality of microarrays, the device comprising:

a fluidic component comprising;

a plurality of well plates, wherein each well plate comprises a plurality of wells arranged in a plurality of columns and a plurality of rows, wherein each well plate is configured to mate with a peg plate comprising a base, a plurality of pegs arranged in rows and columns on the base, and a plurality of microarrays, each microarray individually attached to one of the plurality of pegs, and wherein each well of the well plate is configured to receive one of the plurality of microarrays when the well plate is mated with a peg plate;

a first fluidic container configured to wash the plurality of microarrays a plurality of times with a first washing fluid; and

a second fluidic container configured to wash the plurality of microarrays with a second washing fluid, wherein the second fluidic container is additionally configured to heat the second washing fluid;

a barcode reader configured to read one or more barcodes on the well plates;

a support component comprising a plurality of drawer assemblies, wherein each drawer assembly comprises a drawer panel, wherein each drawer panel is configured to support two well plates in a side-by-side configuration and slide horizontally, wherein each drawer panel comprises one or more biasing features configured to align and fix two well plates to the drawer panel, and wherein the drawer assemblies includes a handoff drawer assembly comprising a handoff drawer panel;

a hybridization component comprising a hybridization oven, wherein the hybridization oven is configured to hybridize a nucleic acid sample to a microarray, and wherein the hybridization component is fixed to the support component;

a scanning component fixed to the support component, wherein the scanning component is configured to scan the plurality of microarrays after hybridization and processing;

a transport component configured to grip, move and release a peg plate, wherein the transport component comprises a gripper assembly having a closed position suitable for gripping a peg plate and an open position suitable for releasing the peg plate, wherein the gripper assembly comprises a base plate, sensors, a motor, a cam, rack and pinion, a spring, two arms, and finger assemblies, wherein the arms extend outward from the base plate substantially parallel to one another with a finger assembly attached to an interior surface of each arm such that the finger assemblies are oppositely facing one another and capable of contacting opposing sides of the support component of a peg plate, wherein the arms are movably joined to one another through the cam, rack and pinion, and the spring, and wherein the motor increases or decreases the distance between the arms by applying force to the cam, thereby moving the gripper between the open and closed positions, wherein the transport component moves the peg plate within and between the components, and wherein the transport component and handoff drawer assembly are configured to transfer the peg plate from the handoff drawer assembly to the scanning component;

an unclamping station configured to separate a peg plate from a hybridization tray after the plurality of microarrays have been hybridized to the nucleic acid sample in the hybridization component; and

a processing system, wherein the processing system comprises a computer, and wherein the computer is configured to direct the movements of the transport component.

22. The device of claim 21, wherein the finger assemblies fit into recesses located on opposing sides of the base of the peg plate.

23. The device of claim 21, wherein the arms of the gripper assembly extend beyond the section used for attaching the finger assemblies.

24. The device of claim 23, wherein the distal end of at least one arm of the gripper assembly comprises a notched flange configured to latch onto a drawer assembly, thereby enabling the transport component to move the drawer assembly between open and closed positions by moving the gripper assembly.

25. The device of claim 21, further comprising a peg plate comprising a base, a plurality of pegs arranged in rows and columns on the base, and a plurality of microarrays, each microarray individually attached to one of the plurality of pegs.

26. The device of claim 25, wherein the peg plate comprises 96 pegs.

27. The device of claim 25, wherein each of the plurality of microarrays has a substantially square shape with a length equal to or less than 10 mm, a width equal to or less than 10 mm, and a thickness equal to or less than 1000 μ

m.