Methods for biological sample processing and analysis

Patent metadata

Field	Value
Publication number	US-11732298-B2
Application number	US-201916416856-A
Country	US
Kind code	B2
Filing date	May 20, 2019
Priority date	Nov 17, 2017
Publication date	Aug 22, 2023
Grant date	Aug 22, 2023

Abstract

Provided are methods for biological sample processing and analysis. A method can comprise providing a substrate configured to rotate. The substrate can comprise an array having immobilized thereto a biological analyte. A solution comprising a plurality of probes may be directed, via centrifugal force, across the substrate during rotation of the substrate, to couple at least one of the plurality of probes with the biological analyte. A detector can be configured to detect a signal from the at least one probe coupled to the biological analyte, thereby analyzing the biological analyte.

First claim

What is claimed is:

1. A method for processing a biological analyte, comprising:
(a) directing a solution comprising a plurality of probes from a first location of a substrate to a second location of said substrate, wherein said first location is different than said second location, wherein said biological analyte is immobilized adjacent to said substrate at said first location or said second location, and wherein said directing is performed in absence of flowing said solution through a flow cell channel;
(b) coupling at least one probe of said plurality of probes to said biological analyte; and
(c) detecting, by providing an excitation light down to said substrate and using a detector comprising an optical imaging objective disposed above said substrate, wherein said optical imaging objective is at least partially immersed in a fluid in contact with said substrate, one or more signals or signal changes from said biological analyte having said at least one probe coupled thereto.

2. The method of claim 1 , further comprising, prior to (a), using a dispensing unit comprising one or more fluid channels to dispense said solution comprising said plurality of probes to said substrate.

3. The method of claim 1 , wherein said solution is exposed to air when in contact with said substrate.

4. The method of claim 1 , wherein said directing in (a) comprises subjecting said substrate to movement.

5. The method of claim 1 , wherein said substrate is substantially planar.

6. The method of claim 1 , wherein said substrate is textured or patterned.

7. The method of claim 1 , wherein said substrate comprises an array of individually addressable locations, wherein said biological analyte is immobilized to an individually addressable location of said array, and wherein said array has immobilized thereto one or more additional biological analytes at different individually addressable locations.

8. The method of claim 1 , wherein said biological analyte is coupled to a bead, which bead is immobilized to said substrate.

9. The method of claim 8 , wherein said bead comprises a plurality of biological analytes, including said biological analyte, attached thereto, and wherein said plurality of biological analytes have sequence homology to one another.

10. The method of claim 1 , wherein said biological analyte is a nucleic acid molecule.

11. The method of claim 10 , further comprising, based at least in part on said one or more signals or signal changes, determining a sequence of at least a portion of said nucleic acid molecule.

12. The method of claim 10 , wherein said plurality of probes comprises a plurality of nucleotides or nucleotide analogs, and wherein said at least one probe comprises a nucleotide or nucleotide analog from said plurality of nucleotides or nucleotide analogs.

13. The method of claim 10 , wherein said plurality of probes comprises a plurality of oligonucleotide molecules, and wherein said at least one probe comprises an oligonucleotide molecule from said plurality of oligonucleotide molecules.

14. The method of claim 1 , wherein said detecting in (c) comprises continuously scanning said substrate during relative movement of said substrate with respect to a detection system configured to perform said detecting.

15. The method of claim 1 , wherein prior to (c), a substantially even layer of said solution is adjacent to said substrate.

16. A method for processing a biological analyte, comprising:
(a) directing a solution comprising a plurality of probes along one or more flow paths from a first location of a substrate to a second location of said substrate, wherein said first location is different than said second location, wherein said biological analyte is immobilized adjacent to said substrate at said first location or said second location, and wherein said one or more flow paths are not part of a flow cell channel;
(b) coupling at least one probe of said plurality of probes to said biological analyte; and
(c) detecting, by providing an excitation light down to said substrate and using a detector comprising an optical imaging objective disposed above said substrate, wherein said optical imaging objective is at least partially immersed in a fluid in contact with said substrate, one or more signals or signal changes from said biological analyte having said at least one probe coupled thereto.

17. The method of claim 16 , further comprising, prior to (a), using a dispensing unit comprising one or more fluid channels to dispense said solution comprising said plurality of probes to said substrate.

18. The method of claim 16 , wherein said solution is exposed to air when in contact with said substrate.

19. The method of claim 16 , wherein said directing in (a) comprises subjecting said substrate to movement.

20. The method of claim 16 , wherein said substrate is substantially planar.

21. The method of claim 16 , wherein said substrate is textured or patterned.

22. The method of claim 16 , wherein said substrate comprises an array of individually addressable locations, wherein said biological analyte is immobilized to an individually addressable location of said array, and wherein said array has immobilized thereto one or more additional biological analytes at different individually addressable locations.

23. The method of claim 16 , wherein said biological analyte is coupled to a bead, which bead is immobilized to said substrate.

24. The method of claim 23 , wherein said bead comprises a plurality of biological analytes, including said biological analyte, attached thereto, and wherein said plurality of biological analytes have sequence homology to one another.

25. The method of claim 16 , wherein said biological analyte is a nucleic acid molecule.

26. The method of claim 25 , further comprising, based at least in part on said one or more signals or signal changes, determining a sequence of at least a portion of said nucleic acid molecule.

27. The method of claim 25 , wherein said plurality of probes comprises a plurality of nucleotides or nucleotide analogs, and wherein said at least one probe comprises a nucleotide or nucleotide analog from said plurality of nucleotides or nucleotide analogs.

28. The method of claim 25 , wherein said plurality of probes comprises a plurality of oligonucleotide molecules, and wherein said at least one probe comprises an oligonucleotide molecule from said plurality of oligonucleotide molecules.

29. The method of claim 16 , wherein said detecting in (c) comprises continuously scanning said substrate during relative movement of said substrate with respect to a detection system configured to perform said detecting.

30. The method of claim 16 , wherein prior to (c), a substantially even layer of said solution is adjacent to said substrate.

Assignees

• Ultima Genomics Inc

Inventors

• Almogy Gilad
• Barbee Kristopher
• Beckett Nathan

Classifications

• G01N33/54366

  Apparatus specially adapted for solid-phase testing · CPC title

• C12Q1/6874 Primary

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

• C12Q1/6837 Primary

  using probe arrays or probe chips (C12Q1/6874 takes precedence) · CPC title

• C12Q2565/60

  Detection means characterised by use of a special device · CPC title

• C12Q2563/149

  Particles, e.g. beads · CPC title