Systems and methods for genetic and biological analysis

• US 10,260,095 B2
• Filed: 06/13/2018
• Issued: 04/16/2019
• Est. Priority Date: 05/27/2011
• Status: Active Grant

• Current Assignee: Sequencing Health Incorporated
• Original Assignee: GenapSys, Inc.
• Inventors: Esfandyarpour, Hesaam, Parizi, Kosar Baghbani, Oldham, Mark F., Nordman, Eric S., Reel, Richard T., Baumhueter, Susanne, Heiner, Cheryl, Lee, Frank
• Primary Examiner(s): Thomas, David C
• Application Number:
  US16/007,829
• Publication Number:
  US 20180282805A1
• Time in Patent Office: 307 Days
• CPC Class Codes: B01L 2300/06 Auxiliary integrated devices, integrated components
• CPC Class Codes: B01L 2300/0627 Sensor or part of a sensor is integrated
• CPC Class Codes: B01L 3/502715 characterised by interfacing components, e.g. fluidic, electrical, optical or mechanical interfaces
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 2527/119 pH
• CPC Class Codes: C12Q 2549/126 using oligonucleotides as clamps
• CPC Class Codes: C12Q 2563/116 electrical properties of nucleic acids, e.g. impedance, conductivity or resistance
• CPC Class Codes: C12Q 2565/607 being a sensor, e.g. electrode
• CPC Class Codes: G01N 27/327 Biochemical electrodes , e.g. electrical or mechanical details for in vitro measurements
• CPC Class Codes: G01N 33/54313 the carrier being characterised by its particulate form
• CPC Class Codes: G01N 33/5438 Electrodes

Abstract

The invention relate to systems and methods for sequencing polynucleotides, as well as detecting reactions and binding events involving other biological molecules. The systems and methods may employ chamber-free devices and nanosensors to detect or characterize such reactions in high-throughput. Because the system in many embodiments is reusable, the system can be subject to more sophisticated and improved engineering, as compared to single use devices.

Claims

1. A method for nucleic acid sequencing, comprising:

(a) providing an array comprising a plurality of features in optical communication with a plurality of optical sensors, wherein said array is integrated with said plurality of optical sensors, wherein a feature of said plurality of features retains or immobilizes a plurality of nucleic acid molecules having sequences that are substantially identical to a nucleic acid sequence of a template nucleic acid molecule, and wherein an optical sensor of said plurality of optical sensors is in optical communication with said feature;

(b) contacting said plurality of nucleic acid molecules with nucleic acid bases in the presence of polymerizing enzymes under conditions sufficient to incorporate said nucleic acid bases into growing strands complementary to said plurality of nucleic acid molecules, wherein said plurality of nucleic acid molecules is brought in contact with said nucleic acid bases without applying an electric field to confine or isolate said nucleic acid bases within said feature;

(c) using said optical sensor to detect one or more signals from said plurality of nucleic acid molecules indicative of said nucleic acid bases incorporated into said growing strands; and

(d) using said one or more signals detected in (c) to identify said nucleic acid bases, thereby generating a sequence corresponding to said nucleic acid sequence of said template nucleic acid molecule.

2. The method of claim 1, wherein said plurality of features is a plurality of wells.

3. The method of claim 1, wherein said optical sensor is used to detect said one or more signals after said nucleic acid bases are incorporated into said growing strands.

4. The method of claim 1, wherein, in (a), said plurality of nucleic acid molecules is hybridized to a plurality of primers, and wherein in (b) said growing strands complementary to said plurality of nucleic acid molecules are generated as extension products of said plurality of primers.

5. The method of claim 1, wherein said plurality of optical sensors are complementary metal-oxide semiconductor (CMOS) sensors.

6. The method of claim 5, wherein each sensor of said plurality of sensors is individually addressable.

7. The method of claim 5, wherein said CMOS sensor comprises a plurality of rows and columns, and wherein each row or column is individually addressable.

8. The method of claim 1, wherein said plurality of features includes capture sequences that immobilize said plurality of nucleic acid molecules.

9. The method of claim 1, further comprising, prior to (b), amplifying said template nucleic acid molecule to generate said plurality of nucleic acid molecules having sequences that are substantially identical to said nucleic acid sequence of said template nucleic acid molecule.

10. The method of claim 9, wherein said template nucleic acid molecule is amplified by isothermal amplification.

11. The method of claim 1, wherein said nucleic acid bases comprise optical labels, and wherein one or more of said optical labels generate said one or more signals detected in (c).

12. The method of claim 1, wherein said one or more signals are fluorescence signals.

13. The method of claim 1, wherein said feature comprises a polymer that reduces a migration rate of said nucleic acid bases or said plurality of nucleic acid molecules.

14. The method of claim 1, wherein said plurality of features is in fluid communication with a flow cell, which flow cell directs said nucleic acid bases to said feature comprising said plurality of nucleic acid molecules.

15. The method of claim 1, wherein said polymerizing enzymes are strand displacing polymerases.

16. The method of claim 1, wherein at least a portion of said plurality of nucleic acid molecules is within a Debye layer of a surface of said feature.

17. The method of claim 16, wherein said one or more signals are indicative of a change in charge or conductivity within said Debye layer.

18. The method of claim 1, wherein said array and said plurality of optical sensors are part of a chip.

19. The method of claim 1, further comprising repeating (b)-(c) with additional nucleic acid bases to generate said sequence corresponding to said nucleic acid sequence of said template nucleic acid molecule.

20. The method of claim 19, wherein said additional nucleic acid bases are of a different type than said nucleic acid bases.

21. The method of claim 1, wherein said nucleic acid bases are of a same type.

29. The method of claim 1, wherein said optical sensor detects said one or more signals from said nucleic acid bases incorporated into said growing strands.

32. The method of claim 1, wherein said nucleic acid molecule is contacted with more than one type of nucleic acid base simultaneously.

33. The method of claim 1, wherein said nucleic acid molecule is contacted with four types of nucleic acid bases simultaneously.

22. A method for nucleic acid sequencing, comprising:

(a) providing an array comprising a plurality of features in optical communication with a plurality of optical sensors, wherein said array is integrated with said plurality of optical sensors, wherein said plurality of features retains or immobilizes a plurality of nucleic acid molecules, wherein a feature of said plurality of features comprises a nucleic acid molecule of said plurality of nucleic acid molecules, and wherein an optical sensor of said plurality of optical sensors is in optical communication with said feature;

(b) contacting said nucleic acid molecule with nucleic acid bases in the presence of a polymerizing enzyme under conditions sufficient to incorporate at least one of said nucleic acid bases into a growing strand complementary to said nucleic acid molecule;

(c) using said optical sensor to detect one or more signals indicative of said at least one of said nucleic acid bases incorporated into said growing strand;

(d) using said one or more signals detected in (c) to identify said at least one of said nucleic acid bases; and

(e) monitoring and correcting for phase error introduced during incorporation of said at least one of said nucleic acid bases into said growing strand, thereby generating a sequence of said nucleic acid molecule.

23. The method of claim 22, wherein said plurality of features is a plurality of wells.

24. The method of claim 22, wherein said plurality of optical sensors are complementary metal-oxide semiconductor (CMOS) sensors.

25. The method of claim 22, wherein said plurality of features includes capture sequences that immobilize said plurality of nucleic acid molecules.

26. The method of claim 22, wherein said nucleic acid molecule is within a Debye layer of a surface of said feature.

27. The method of claim 26, wherein said one or more signals are indicative of a change in charge or conductivity within said Debye layer.

28. The method of claim 22, wherein said array and plurality of optical sensors are part of a chip.

30. The method of claim 22, wherein said optical sensor detects said one or more signals from said nucleic acid bases incorporated into said growing strands.

31. The method of claim 22, wherein said phase error is monitored and corrected at a position along said growing strand during incorporation of said at least one of said nucleic acid bases into said growing strand.

34. The method of claim 22, wherein said nucleic acid molecule is contacted with more than one type of nucleic acid base simultaneously.

35. The method of claim 22, wherein said nucleic acid molecule is contacted with four types of nucleic acid bases simultaneously.