Spatially encoded biological assays

• US 10,662,467 B2
• Filed: 02/14/2019
• Issued: 05/26/2020
• Est. Priority Date: 04/05/2010
• Status: Active Grant

• Current Assignee: Prognosys Biosciences Inc.
• Original Assignee: Prognosys Biosciences Inc.
• Inventors: Chee, Mark S.
• Primary Examiner(s): Martinell, James
• Application Number:
  US16/276,260
• Publication Number:
  US 20190177778A1
• Time in Patent Office: 467 Days
• Field of Search: None
• CPC Class Codes: B01L 3/502715 characterised by interfacing components, e.g. fluidic, electrical, optical or mechanical interfaces
• CPC Class Codes: C12Q 1/6804 Nucleic acid analysis using immunogens immunoassay G01N33/53
• CPC Class Codes: C12Q 1/6809 Methods for determination or identification of nucleic acids involving differential detection
• CPC Class Codes: C12Q 1/6834 Enzymatic or biochemical coupling of nucleic acids to a solid phase
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 1/6841 In situ hybridisation
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 2535/122 Massive parallel sequencing
• CPC Class Codes: C12Q 2543/10 the purpose being "in situ" analysis
• CPC Class Codes: C12Q 2563/179 the label being a nucleic acid
• CPC Class Codes: C12Q 2565/515 characterised by the interaction between or sequential use of two or more arrays
• CPC Class Codes: C40B 30/04 by measuring the ability to specifically bind a target molecule, e.g. antibody-antigen binding, receptor-ligand binding
• CPC Class Codes: C40B 60/04 Integrated apparatus specially adapted for both screening libraries and identifying library members
• CPC Class Codes: G01N 2458/10 Oligonucleotides as tagging agents for labelling antibodies
• CPC Class Codes: G01N 33/5308 for analytes not provided for elsewhere, e.g. nucleic acids, uric acid, worms, mites
• CPC Class Codes: G01N 33/543 with an insoluble carrier for immobilising immunochemicals
• CPC Class Codes: G01N 33/6845 Methods of identifying protein-protein interactions in protein mixtures

Abstract

The present invention provides assays and assay systems for use in spatially encoded biological assays. The invention provides an assay system comprising an assay capable of high levels of multiplexing where reagents are provided to a biological sample in defined spatial patterns; instrumentation capable of controlled delivery of reagents according to the spatial patterns; and a decoding scheme providing a readout that is digital in nature.

Claims

1. A method of associating presence or abundance of a target biological molecule with a location of a tissue sample, comprising:

delivering a plurality of probes to a tissue sample affixed to a support, wherein a probe of the plurality of probes comprises a protein that specifically binds a target biological molecule of the tissue sample, wherein the protein is conjugated to an oligonucleotide having a sequence, and

separating the probe specifically bound to the target biological molecule at the location of the tissue sample from the plurality of probes not specifically bound to the target biological molecule at the location of the tissue sample; and

sequencing all or a portion of the sequence of the oligonucleotide or a complement thereof, from the specifically bound probe, and using the determined sequence to associate presence or abundance of the target biological molecule with the location of the tissue sample.

2. The method of claim 1, wherein two or more probes of the plurality of probes specifically bind to unique target biological molecules of the tissue sample.

3. The method of claim 2, wherein the sequences of the oligonucleotides of the two or more probes are determined in parallel.

4. The method of claim 2, wherein the determined sequences of the two or more probes are used to associate the presence of greater than 75 unique target biological molecules with the location of the tissue sample.

5. The method of claim 2, wherein the determined sequences of the two or more probes are used to associate the presence or abundance or both, of the unique target biological molecules with the location of the tissue sample sequentially.

6. The method of claim 5, wherein the unique target biological molecules comprise at least one protein and at least one nucleic acid.

7. The method of claim 2, wherein the determined sequences of the two or more probes are used to associate the presence or abundance or both, of the unique target biological molecules with the location of the tissue sample in parallel.

8. The method of claim 2, wherein the sequences of the oligonucleotides of the two or more probes are determined sequentially.

9. The method of claim 2, wherein the determined sequences of the two or more probes are used to associate the presence of greater than 100 unique target biological molecules with the location of the tissue sample.

10. The method of claim 2, wherein the determined sequences of the two or more probes are used to associate the presence of greater than 150 unique target biological molecules with the location of the tissue sample.

11. The method of claim 2, wherein the determined sequences of the two or more probes are used to associate the presence of greater than 500 unique target biological molecules with the location of the tissue sample.

12. The method of claim 1, wherein the target biological molecule comprises a nucleic acid.

13. The method of claim 1, wherein the target biological molecule comprises a protein.

14. The method of claim 1, wherein the target biological molecule is present in a subcellular target.

15. The method of claim 14, wherein the subcellular target comprises a mitochondrion or a nucleus.

16. The method of claim 1, wherein the plurality of probes is delivered to multiple sites of the tissue sample.

17. The method of claim 16, wherein the multiple sites are determined by histological features of the tissue sample.

18. The method of claim 16, wherein the method further comprises detecting differential expression of the target biological molecule in the multiple sites of the tissue sample.

19. The method of claim 18, wherein the differential expression of the target biological molecule is associated with a biological structure or cell type in the multiple sites of the tissue sample.

20. The method of claim 1, wherein the separating step comprises washing.

21. The method of claim 1, wherein the tissue sample comprises a fresh-frozen or formalin fixed paraffin embedded (FFPE) tissue sample.

22. The method of claim 1, wherein the determined sequence is used to associate abundance of the target biological molecule with the location of the tissue sample.

23. The method of claim 1, further comprising identifying a location of the target biological molecule in one or more serial sections of the tissue sample.

24. The method of claim 23, further comprising generating a 3-dimensional map of the target biological molecule in the tissue sample.

25. The method of claim 1, wherein the determined sequence is used to associate the presence of the target biological molecule with the location of the tissue sample.

26. The method of claim 1, further comprising determining activity of the target biological molecule at the location of the tissue sample.

27. The method of claim 1, wherein the determined sequence is used to associate the presence and abundance of the target biological molecule with the location of the tissue sample.

28. The method of claim 1, wherein the probe comprises an antibody that specifically binds a target biological molecule of the tissue sample.

29. The method of claim 1, wherein the tissue sample is at least one tissue section.

30. The method of claim 29, wherein the location of the target biological molecule is within the at least one tissue section.