Methods for biological sample processing and analysis

Patent metadata

Field	Value
Publication number	US-11512350-B2
Application number	US-202017089781-A
Country	US
Kind code	B2
Filing date	Nov 5, 2020
Priority date	Nov 17, 2017
Publication date	Nov 29, 2022
Grant date	Nov 29, 2022

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 or analyzing a biological analyte, comprising:
(a) subjecting a substrate to movement to direct a solution dispensed at a first location of said substrate to a second location of said substrate, wherein said first location is different from said second location, wherein said solution comprises a plurality of probes, wherein said biological analyte is immobilized adjacent to said substrate at said first location or said second location, wherein at least one probe of said plurality of probes couples to said biological analyte, and wherein said substrate is an open substrate; and
(b) detecting 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 , wherein said movement comprises non-rotational motion of said substrate.

3. The method of claim 1 , wherein said movement comprises rotational motion of said substrate with respect to an axis of said substrate.

4. The method of claim 1 , wherein said first location and said second location are disposed at different radial distances from a central axis of said substrate.

5. The method of claim 1 , wherein said solution is dispensed to said first location of said substrate during said movement.

6. The method of claim 1 , wherein said solution is dispensed to said first location of said substrate prior to said movement.

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

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

9. The method of claim 1 , wherein said substrate comprises an array of individually addressable locations, and wherein said biological analyte is immobilized to an individually addressable location of said array of individually addressable locations.

10. The method of claim 9 , wherein said array of individually addressable locations has immobilized thereto one or more additional biological analytes at different individually addressable locations.

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

12. The method of claim 11 , wherein said bead comprises a plurality of biological analytes, including said biological analyte, attached thereto.

13. The method of claim 12 , wherein said plurality of biological analytes has sequence homology to one another.

14. The method of claim 1 , wherein said biological analyte is immobilized adjacent to said substrate through one or more binders.

15. The method of claim 14 , wherein said substrate comprises at least 100,000 binders, wherein a binder of said at least 100,000 binders immobilizes said biological analyte to said substrate.

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

17. The method of claim 16 , 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.

18. The method of claim 16 , further comprising, based at least in part on said one or more signals or signal changes, identifying a presence of a homopolymer sequence in said nucleic acid molecule.

19. The method of claim 16 , wherein said plurality of probes comprises a plurality of nucleotides or nucleotide analogs, and wherein said at least one probe is at least one nucleotide or nucleotide analog from said plurality of nucleotides or nucleotide analogs.

20. The method of claim 19 , wherein (a) comprises incorporating said at least one nucleotide or nucleotide analog into a growing strand that is complementary to said nucleic acid molecule.

21. The method of claim 16 , wherein said plurality of probes comprises a plurality of oligonucleotide molecules, and wherein said at least one probe is at least one oligonucleotide molecule of said plurality of oligonucleotide molecules.

22. The method of claim 21 , wherein (a) comprises hybridizing said at least one oligonucleotide molecule to said nucleic acid molecule.

23. The method of claim 1 , further comprising terminating said movement prior to said detecting in (b).

24. The method of claim 1 , further comprising altering a velocity of said movement prior to said detecting in (b).

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

26. The method of claim 1 , wherein said one or more signals or signal changes comprise one or more optical signals or optical signal changes.

27. The method of claim 1 , further comprising, subsequent to (b), (i) dispensing an additional solution comprising an additional plurality of probes to said substrate, wherein said additional plurality of probes is different from said plurality of probes, wherein at least one additional probe of said additional plurality of probes couples to said biological analyte, and (ii) detecting one or more additional signals or additional signal changes from said biological analyte having said at least one additional probe coupled thereto, to analyze said biological analyte.

28. The method of claim 27 , wherein said plurality of probes comprises a first plurality of nucleotides or nucleotide analogs of a first canonical base type and wherein said additional plurality of probes comprises a second plurality of nucleotides or nucleotide analogs of a second canonical base type different than said first canonical base type.

29. The method of claim 1 , wherein said plurality of probes comprises a first plurality of nucleotides or nucleotide analogs of a first canonical base type and a second plurality of nucleotides or nucleotide analogs of a second canonical base type different than said first canonical base type.

30. The method of claim 1 , wherein prior to (b), 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

• B01L2200/0647

  Handling flowable solids, e.g. microscopic beads, cells, particles · CPC title

• B01J2219/00722

  Nucleotides · CPC title

• C12Q1/6834

  Enzymatic or biochemical coupling of nucleic acids to a solid phase · CPC title

• B01J2219/00605

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