Method for high throughput screening of nucleic acids

• US 10,017,815 B2
• Filed: 08/28/2015
• Issued: 07/10/2018
• 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:
  US14/839,400
• Publication Number:
  US 20150368711A1
• Time in Patent Office: 1,047 Days
• Field of Search: None
• 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 method of nucleic acid sequencing, comprising the following steps:

placing several flow cells on a reaction platform, each of the flow cells comprising a plurality of distinguishable reaction sites with a plurality of nucleic acid samples attached thereto;

introducing a processing reagent into the flow cells;

reacting the processing reagent with the plurality of nucleic acid samples in the flow cells for a processing period to perform sequencing reactions that produce fluorescent sequencing products;

transferring each of the flow cells from the reaction platform using a carrying device to a position within a viewing area of a detection subsystem configured for capturing optical images of the flow cells;

illuminating each of the flow cells in the viewing area of the detection subsystem; and

capturing an image of the fluorescent sequencing products in each of the flow cells that is illuminated in the viewing area, to determine nucleic acid sequences in the plurality of nucleic acid samples;

wherein sample preparation on the reaction platform and data extraction by the detection subsystem occur at different rates.

2. The method of claim 1, wherein the capturing includes collecting pixel data across four or more emission spectra.

3. The method of claim 1, wherein flow cells on two or more reaction platforms are serviced by a single detection subsystem.

4. The method of claim 1, performed on a system that comprises shock isolators that are positioned within the system so as to decrease effects that vibrations caused by moving parts in the system could have on image capture by the detection subsystem.

5. The method of claim 1, comprising placing the flow cells on multiple reaction platforms, and transferring each of the flow cells from the multiple reaction platforms to the detection subsystem.

6. The method of claim 1, further comprising returning each of the flow cells to its original reaction platform after the image has been captured.

7. The method of claim 6, wherein the returning comprises reconnecting fluid reservoirs in a reaction subsystem to a fluid inlet of each of the flow cells.

8. The method of claim 1, wherein the transferring is performed by a carrying tool that comprises a gripping mechanism controlled by a computer.

9. The method of claim 8, wherein the carrying tool comprises a control and sensing mechanism and the detection subsystem comprises a position registration mechanism.

10. The method of claim 1, wherein each of the flow cells contains a sealed chamber that has a volume of about 50 to 300 μ

L.

11. The method of claim 1, comprising capturing an image from a plurality of different fluorescent sequencing products in each of the flow cells in about 300 milliseconds.

12. The method of claim 1, wherein the image of the fluorescent sequencing products is obtained by an imager that is capable of acquiring 200,000 images per day.

13. The method of claim 1, conducted in a system that comprises a computer programmed to coordinate different activities in different functional subsystems.

14. An automated method of nucleic acid sequencing, comprising iteratively performing the following steps:

processing a plurality of flow cells on a reaction platform such that nucleic acids immobilized in each of the plurality of flow cells are subject to biochemical sequencing reactions that produce fluorescent sequencing products; and

carrying each of the flow cells individually from the reaction platform to a viewing area in a detection subsystem to capture an image of the fluorescent sequencing products; and

returning the flow cells from the detection subsystem back to the reaction platform for further processing.

15. The method of claim 14, wherein the plurality of flow cells is at least four flow cells.

16. The method of claim 14, wherein the plurality of flow cells is at least sixteen flow cells.

17. The method of claim 14, performed on a system that comprises shock isolators that are positioned within the system so as to decrease effects that vibrations caused by moving parts in the system could have on image capture by the detection subsystem.

18. The method of claim 14, wherein the carrying of each of the flow cells is performed by a carrying tool that comprises a gripping mechanism controlled by a computer.

19. The method of claim 14, wherein the image of the fluorescent sequencing products is obtained by an imager that is capable of acquiring 200,000 images per day.

20. The method of claim 18, wherein the carrying tool comprises a control and sensing mechanism and the detection subsystem comprises a position registration mechanism.