Apparatus for high throughput sequencing of nucleic acids

• US 9,382,585 B2
• Filed: 10/30/2008
• Issued: 07/05/2016
• Est. Priority Date: 10/30/2007
• Status: Active Grant

• Current Assignee: Complete Genomics Incorporated (BGI Genomics Co., Ltd.)
• Original Assignee: Complete Genomics Incorporated (BGI Genomics Co., Ltd.)
• Inventors: Oliphant, Arnold
• Primary Examiner(s): CROW, ROBERT THOMAS
• Application Number:
  US12/261,548
• Publication Number:
  US 20090155793A1
• Time in Patent Office: 2,805 Days
• Field of Search: None
• US Class Current: 1/1
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: G01N 2035/00158 Elements containing microarrays, i.e. "biochip"
• CPC Class Codes: G01N 21/6486 Measuring fluorescence of biological material, e.g. DNA, RNA, cells G01N21/6428 takes precedence
• CPC Class Codes: G01N 2201/0461 Simultaneous, e.g. video imaging
• CPC Class Codes: G01N 35/0099 comprising robots or similar manipulators robots per se B25J

Abstract

A scalable reaction and detection system for automated high throughput sequencing of nucleic acids involving a combination of chemical processes and observation processes independent of the chemistry processes. Discrete functional units may be configured in a manner that allows the system to interchangeably utilize different sequencing reaction components in conjunction with discrete apparatus components for optical image collection and/or analysis.

Claims

1. An automated assembly for sequencing nucleic acids, comprising:

a reaction subsystem comprising one or more flow cells on a reaction platform, the one or more flow cells being configured for carrying out biochemical sequencing reactions on nucleic acid samples;

an imaging subsystem configured for capturing optical images of a flow cell from said one or more flow cells when present in the imaging subsystem;

a carrying device configured for transferring any of the one or more flow cells on the reaction platform to and from the imaging subsystem;

wherein the reaction subsystem and the imaging subsystem are configured to operate independently at different rates, and

wherein the assembly further comprises shock isolators that are constructed and arranged so as to sufficiently isolate the imaging subsystem from vibrations from the carrying device.

2. The assembly of claim 1, wherein more than one flow cells are situated on the reaction platform.

3. The assembly of claim 1, wherein the reaction subsystem comprises two or more reaction platforms.

4. The assembly of claim 1, wherein the imaging subsystem comprises a CCD (charged coupled device).

5. The assembly of claim 1, wherein the imaging subsystem is configured to detect 6 to 8 different colors.

6. The assembly of claim 1, wherein the imaging subsystem is configured so that the number of pixels per nucleic acid molecule can be adjusted by increasing or decreasing the field of view of an objective lens from 10 pixels per nucleic acid molecule to 2.5 pixels per nucleic acid molecule.

7. The assembly of claim 1, wherein the carrying device comprises a control and sensing mechanism and the imaging subsystem comprises a position registration mechanism.

8. The assembly of claim 1, wherein the imaging subsystem includes a camera having a resolution of 10 to 16 megapixels.

9. The assembly of claim 8, wherein the camera includes a CCD detector having an exposure time of about 300 milliseconds.

10. The assembly of claim 1, wherein each of the one or more flow cells comprises a sealed chamber with a volume of between 50 μ

L and 300 μ

L.

11. The assembly of claim 1, wherein the one or more flow cells on the reaction platform each contains an array of fluorescently labeled nucleic acids.

12. The assembly of claim 1, further comprising a computer programmed to coordinately control operation of the reaction subsystem, the detection subsystem, and the carrying device.

13. An automated assembly for sequencing nucleic acids, comprising:

a reaction subsystem that is configured to support and operate a plurality of flow cells that each carry out biochemical sequencing reactions on an array of nucleic acids;

an imaging subsystem configured for capturing optical images of the flow cells when present in the imaging subsystem;

a carrying device configured for transferring a flow cell between the reaction subsystem and the detection subsystem; and

shock isolators that are constructed and arranged so as to sufficiently isolate the imaging subsystem from vibrations from the reaction subsystem and from the carrying device, so that the vibrations do not disrupt image capture by the imaging subsystem.

14. The assembly of claim 13, further comprising a computer programmed to coordinately control operation of the reaction subsystem, the detection subsystem, and the carrying device.

15. The assembly of claim 13, wherein the carrying device comprises a motorized gripping mechanism.

16. The assembly of claim 13, wherein the carrying device comprises a control and sensing mechanism that regulates transfer of flow cells by the carrying device so as to prevent vibrations during transfer.

17. The assembly of claim 16, wherein the imaging subsystem comprises a position registration mechanism.

18. The assembly of claim 13, wherein the reaction subsystem comprises a number of reservoirs of processing fluids attached to a pumping mechanism.

19. The assembly of claim 13, with a plurality of flow cells on a reaction platform in the reaction subsystem, each flow cell comprising a plurality of distinguishable reaction sites.

20. The assembly of claim 19, with nucleic acids or primers attached to surface regions in the flow cells.

21. The assembly of claim 19, wherein each of the flow cells contains a sealed chamber with a volume of between 50 μ

L and 300 μ

L.