Methods and systems for analyte detection and analysis

Patent metadata

Field	Value
Publication number	US-10273528-B1
Application number	US-201815974543-A
Country	US
Kind code	B1
Filing date	May 8, 2018
Priority date	Nov 17, 2017
Publication date	Apr 30, 2019
Grant date	Apr 30, 2019

Abstract

Provided are systems and methods for analyte detection and analysis. A system can comprise an open substrate configured to rotate. The open substrate can comprise an array of immobilized analytes. A solution comprising a plurality of probes may be directed, via centrifugal force, across the array during rotation of the substrate, to couple at least one of the plurality of probes with at least one of the analytes to form a bound probe. A detector can be configured to detect a signal from the bound probe via continuous rotational area scanning of the substrate.

First claim

What is claimed is:

1. A method for analyte detection or analysis, comprising:
(a) rotating an open substrate about a central axis, the open substrate having an array of immobilized analytes thereon;
(b) delivering a solution having a plurality of probes to a region proximal to the central axis to introduce the solution to the open substrate;
(c) dispersing the solution across the open substrate at least by centrifugal force such that at least one of the plurality of probes binds to at least one of the immobilized analytes to form a bound probe; and
(d) using a detector to (i) undergo continuous rotational area scanning of the open substrate, which continuous rotational area scanning of the open substrate comprises performing a non-linear scan of the open substrate including a first area of the open substrate and a second area of the open substrate, wherein the first area and the second area comprise subsets of the array of immobilized analytes, wherein the first area and the second area are at different radial positions of the open substrate with respect to the central axis, and wherein the first area and the second area are spatially resolved by the detector, and (ii) detect at least one signal from the bound probe at the second area of the open substrate.

2. The method of claim 1 , wherein the continuous rotational area scanning compensates for velocity differences at different radial positions of the array with respect to the central axis within a scanned area.

3. The method of claim 2 , wherein the continuous rotational area scanning comprises using an optical imaging system having an anamorphic magnification gradient substantially transverse to a scanning direction along the open substrate, and wherein the anamorphic magnification gradient at least partially compensates for tangential velocity differences that are substantially perpendicular to the scanning direction.

4. The method of claim 2 , wherein the continuous rotational area scanning comprises reading two or more regions on the open substrate at two or more scan rates, respectively, to at least partially compensate for tangential velocity differences in the two or more regions.

5. The method of claim 1 , wherein (d) further comprises using an immersion objective lens in optical communication with the detector and the open substrate to detect the at least one signal, which immersion objective lens is in contact with a fluid that is in contact with the open substrate.

6. The method of claim 5 , wherein the fluid is in a container, and wherein an electric field is used to regulate a hydrophobicity of one or more surfaces of the container to retain at least a portion of the fluid contacting the immersion objective lens and the open substrate.

7. The method of claim 1 , wherein the continuous rotational area scanning is performed in a first environment having a first operating condition, and wherein the delivering of the solution is performed in a second environment having a second operating condition different from the first operating condition.

8. The method of claim 1 , wherein the immobilized analytes comprise nucleic acid molecules, wherein the plurality of probes comprises fluorescently labeled nucleotides, and wherein at least one of the fluorescently labeled nucleotides binds to at least one of the nucleic acid molecules via nucleotide complementarity binding.

9. The method of claim 1 , wherein the open substrate is substantially planar.

10. An apparatus for analyte detection or analysis, comprising:
a housing configured to receive an open substrate having an array of immobilized analytes thereon;
one or more dispensers configured to deliver a solution having a plurality of probes to a region proximal to a central axis of the open substrate;
a rotational unit configured to rotate the open substrate about a central axis to thereby disperse the solution across the open substrate at least by centrifugal force, such that at least one of the plurality of probes binds to at least one of the immobilized analytes to form a bound probe; and
a detector programmed to:
(i) undergo continuous rotational area scanning of the open substrate, which continuous rotational area scanning of the open substrate comprises performing a non-linear scan of the open substrate including a first area of the open substrate and a second area of the open substrate, wherein the first area and the second area comprise subsets of the array of immobilized analytes, wherein the first area and the second area are at different radial positions of the open substrate with respect to the central axis, and wherein the first area and the second area are spatially resolved by the detector, and
(ii) detect at least one signal from the bound probe at the second area of the open substrate.

11. The apparatus of claim 10 , further comprising a processor programmed to direct the detector to compensate for velocity differences at different radial positions of the array with respect to the central axis within a scanned area.

12. The apparatus of claim 10 , further comprising one or more optics that are configured to generate an anamorphic magnification gradient substantially transverse to a scanning direction along the open substrate, and wherein the anamorphic magnification gradient at least partially compensates for tangential velocity differences that are substantially perpendicular to the scanning direction.

13. The apparatus of claim 12 , further comprising a processor programmed to adjust the anamorphic magnification gradient to compensate for different imaged radial positions with respect to the central axis.

14. The apparatus of claim 11 , wherein the processor is programmed to direct the detector to scan two or more regions on the open substrate at two or more scan rates, respectively, to at least partially compensate for tangential velocity differences in the two or more regions.

15. The apparatus of claim 10 , wherein the detector comprises a sensor and one or more optics in optical communication with the open substrate.

16. The apparatus of claim 10 , further comprising an immersion objective lens in optical communication with the detector and the open substrate, which immersion objective lens is configured to be in contact with a fluid that is in contact with the open substrate.

17. The apparatus of claim 16 , further comprising a container configured to retain the fluid and an electric field application unit configured to regulate a hydrophobicity of one or more surfaces of the container to retain at least a portion of the fluid contacting the immersion objective lens and the open substrate.

18. The apparatus of claim 16 , wherein the immersion objective lens separates a first environment from a second environment, wherein the first environment and second environment have different operating conditions.

19. The apparatus of claim 18 , wherein the immersion objective lens forms a seal between the first environment and the second environment.

20. The apparatus of claim 10 , further comprising a processor programmed to direct the detector to detect the at least one signal from the bound probe while scanning along a non-linear scanning path across the open substrate.

21. The apparatus of claim 20 , wherein the non-linear scanning path is a substantially spiral scanning path or a substantially ring-like scanning path.

22. A computer-readable medium comprising non-transitory instructions stored thereon, which when executed cause one or more computer processor

Assignees

• Ultima Genomics Inc

Inventors

• Barbee Kristopher
• Beckett Nathan
• Pristinski Denis
• Schulte Derek
• Bartov Avishai
• Sullivan Jamie
• Brinza Dumitru
• Lakdawalla Abizar
• Menchen Steven
• Almogy Gilad
• Pratt Mark

Classifications

• C12Q1/6825 Primary

  Nucleic acid detection involving sensors · CPC title

• B01J19/0046

  Sequential or parallel reactions, e.g. for the synthesis of polypeptides or polynucleotides; Apparatus and devices for combinatorial chemistry or for making molecular arrays (synthesis methods per se C40B50/00) · CPC title

• B01J2219/00605

  the compounds being directly bound or immobilised to solid supports · CPC title

• C12Q1/6874 Primary

  involving nucleic acid arrays, e.g. sequencing by hybridisation · CPC title

• B01L2200/026

  Fluid interfacing between devices or objects, e.g. connectors, inlet details · CPC title