Methods and devices for sequencing nucleic acids in smaller batches

• US 9,791,409 B2
• Filed: 05/11/2015
• Issued: 10/17/2017
• Est. Priority Date: 02/05/2007
• Status: Active Grant

• Current Assignee: IsoPlexis Corporation (Bruker Corporation)
• Original Assignee: Intelligent Bio-Systems Incorporated. (Qiagen NV)
• Inventors: Gordon, Steven, Hagerott, Thomas, Golaski, Edmund, Olejnik, Jerzy
• Primary Examiner(s): THOMAS, DAVID C
• Application Number:
  US14/708,675
• Publication Number:
  US 20150316505A1
• Time in Patent Office: 890 Days
• Field of Search: None
• CPC Class Codes: B01L 2200/0668 Trapping microscopic beads
• CPC Class Codes: B01L 2300/0877 Flow chambers
• CPC Class Codes: B01L 2400/0487 fluid pressure, pneumatics
• CPC Class Codes: B01L 3/502715 characterised by interfacing components, e.g. fluidic, electrical, optical or mechanical interfaces
• CPC Class Codes: B01L 3/502761 specially adapted for handling suspended solids or molecules independently from the bulk fluid flow, e.g. for trapping or sorting beads, for physically stretching molecules investigating characteristics of particles G01N15/00
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: G01N 27/44726 using specific dyes, markers or binding molecules
• CPC Class Codes: G01N 27/44791 Microapparatus sample containers with integrated microfluidic structures B01L3/5027

Abstract

The invention provides methods and compositions, including, without limitation, algorithms, computer readable media, computer programs, apparatus, and systems for determining the identity of nucleic acids in nucleotide sequences using, for example, data obtained from sequencing by synthesis methods. A plurality of smaller flow cells is employed, each with a relatively small area to be imaged, in order to provide greater flexibility and efficiency.

Claims

1. A method for carrying out steps of a nucleic acid sequencing protocol, said method comprising:

a) providing;

i) a flow cell comprising nucleic acids to be sequenced, said flow cell mounted on ii) a moveable support, said support configured to move said flow cell to iii) a detection station, said station comprising iv) a vertical actuator fitted with v) a gripper configured to grasp the flow cell and lift it off the moveable support;

b) moving said moveable support to said detection station;

c) grasping the flow cell with said gripper; and

d) lifting said flow cell off of the moveable support with said vertical actuator, so as to create a lifted flow cell.

2. The method of claim 1, wherein prior to step b), sequence reagents are introduced into said flow cell under conditions such that said reagent contacts said nucleic acids.

3. The method of claim 2, wherein said nucleic acid sequencing reagents comprise dye-labeled nucleotide analogues.

4. The method of claim 3, wherein one or more dye-labeled nucleotide analogues are incorporated into an extension strand complementary to said nucleic acids in said flow cell.

5. The method of claim 4, further comprising e) depositing said lifted flow cell on a programmable surface so as to create a deposited flow cell.

6. The method of claim 5, further comprising f) positioning at least a part of said deposited flow cell under a detector.

7. The method of claim 6, further comprising g) generating high-magnification data across an area of said deposited flow cell so as to create an analyzed flow cell.

8. The method of claim 7, further comprising h) grasping said analyzed flow cell with said gripper and i) repositioning said analyzed flow cell on said moveable surface with said vertical actuator.

9. The method of claim 1, wherein said nucleic acids are on a chip in said flow cell.

10. The method of claim 1, further comprising adding a second flow cell comprising nucleic acids to said moveable support.

11. The method of claim 10, wherein said second flow cell was not present on said moveable support prior to step b).

12. The method of claim 10, wherein at least a portion of said flow cells is transparent.

13. The method of claim 1, wherein said moveable support is a carousel.

14. The method of claim 13, wherein said carousel is under the control of a processor.

15. The method of claim 14, wherein said processor can be programmed to change the movement of said carousel.

16. The method of claim 1, wherein said nucleic acids are immobilized on a plurality of beads in said flow cell.

17. The method of claim 1, wherein said nucleic acids are on an interior surface of said flow cell.

18. A system comprising:

i) a flow cell comprising nucleic acids to be sequenced, said flow cell mounted on ii) a moveable support, said support configured to move said flow cell to iii) a detection station, said station comprising iv) a vertical actuator fitted with v) a gripper configured to grasp the flow cell and lift it off the moveable support.

19. The system of claim 18, further comprising a programmable surface and a detector, wherein said programmable surface is positioned such that a flow cell lifted off the moveable support can be deposited on the programmable surface, wherein said programmable surface is configured to bring a flow cell deposited on said programmable surface to said detector.

20. The system of claim 19, wherein said detector comprises a camera for imaging said flow cell.

21. The system of claim 19, wherein said programmable surface is capable of x/y movement.