Methods and systems for determining spatial patterns of biological targets in a sample
First Claim
1. A method, comprising:
- delivering a probe for a target protein to multiple sites in a sample, wherein the probe comprises;
(1) a target-binding moiety capable of binding to the target protein;
(2) a first address tag that identifies each of the multiple sites to which the probe is delivered; and
(3) an identity tag that identifies the target protein or the target-binding moiety;
allowing the probe to bind to the target protein in the sample;
analyzing the probe bound to the target protein, the analysis comprising;
(1) determining abundance, expression, and/or activity of the target protein by assessing the amount of the probe bound to the target protein; and
(2) determining the identities of the identity tag and the first address tag of the probe for the target protein; and
determining a spatial pattern of abundance, expression, and/or activity of the target protein across the multiple sites in the sample based on the analysis,the method further comprising;
delivering a probe for a target polynucleotide to each of the multiple sites in the sample, wherein the probe for the target polynucleotide comprises;
(1) a sequence that hybridizes to and identifies the target polynucleotide;
(2) a second address tag that identifies each of the multiple sites to which the probe for the target polynucleotide is delivered;
allowing the probe for the target polynucleotide to bind to the target polynucleotide in the sample;
analyzing the probe bound to the target polynucleotide, the analysis comprising;
(1) determining abundance, expression, and/or activity of the target polynucleotide by assessing the amount of the probe bound to the target polynucleotide; and
(2) determining the identities of the sequence that hybridizes to and identifies the target polynucleotide and the second address tag of the probe for the target polynucleotide; and
determining a spatial pattern of abundance, expression, and/or activity of the target polynucleotide across the multiple sites in the sample based on the analysis of the probe bound to the target polynucleotide at each of the multiple sites in the sample.
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Abstract
The present disclosure provides methods and assay systems for use in spatially encoded biological assays, including assays to determine a spatial pattern of abundance, expression, and/or activity of one or more biological targets across multiple sites in a sample. In particular, the biological targets comprise proteins, and the methods and assay systems do not depend on imaging techniques for the spatial information of the targets. The present disclosure provides methods and assay systems capable of high levels of multiplexing where reagents are provided to a biological sample in order to address tag the sites to which reagents are delivered; instrumentation capable of controlled delivery of reagents; and a decoding scheme providing a readout that is digital in nature.
222 Citations
30 Claims
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1. A method, comprising:
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delivering a probe for a target protein to multiple sites in a sample, wherein the probe comprises;
(1) a target-binding moiety capable of binding to the target protein;
(2) a first address tag that identifies each of the multiple sites to which the probe is delivered; and
(3) an identity tag that identifies the target protein or the target-binding moiety;allowing the probe to bind to the target protein in the sample; analyzing the probe bound to the target protein, the analysis comprising;
(1) determining abundance, expression, and/or activity of the target protein by assessing the amount of the probe bound to the target protein; and
(2) determining the identities of the identity tag and the first address tag of the probe for the target protein; anddetermining a spatial pattern of abundance, expression, and/or activity of the target protein across the multiple sites in the sample based on the analysis, the method further comprising; delivering a probe for a target polynucleotide to each of the multiple sites in the sample, wherein the probe for the target polynucleotide comprises;
(1) a sequence that hybridizes to and identifies the target polynucleotide;
(2) a second address tag that identifies each of the multiple sites to which the probe for the target polynucleotide is delivered;allowing the probe for the target polynucleotide to bind to the target polynucleotide in the sample; analyzing the probe bound to the target polynucleotide, the analysis comprising;
(1) determining abundance, expression, and/or activity of the target polynucleotide by assessing the amount of the probe bound to the target polynucleotide; and
(2) determining the identities of the sequence that hybridizes to and identifies the target polynucleotide and the second address tag of the probe for the target polynucleotide; anddetermining a spatial pattern of abundance, expression, and/or activity of the target polynucleotide across the multiple sites in the sample based on the analysis of the probe bound to the target polynucleotide at each of the multiple sites in the sample. - View Dependent Claims (2)
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3. A method, comprising:
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delivering a probe for a target protein to multiple sites in a sample, wherein the probe comprises;
(1) a target-binding moiety capable of binding to the target protein; and
(2) an identity tag that identifies the target protein or the protein-binding moiety;allowing the probe to bind to the target protein in the sample; delivering a first address tag to each of the multiple sites in the sample, wherein the first address tag is to be coupled to the probe bound to the target protein and identifies the site to which it is delivered; analyzing the probe/first address tag conjugate bound to the target protein, the analysis comprising;
(1) determining abundance, expression, and/or activity of the target protein by assessing the amount of the probe/first address tag conjugate bound to the target protein; and
(2) determining the identities of the identity tag and the first address tag of the probe/first address tag conjugate; anddetermining a spatial pattern of abundance, expression, and/or activity of the target protein across the multiple sites in the sample based on the analysis, the method further comprising; delivering a probe for a target polynucleotide to each of the multiple sites in the sample, wherein the probe for the target polynucleotide comprises a sequence that hybridizes to and identifies the target polynucleotide; allowing the probe for the target polynucleotide to bind to the target polynucleotide in the sample; delivering a second address tag to each of the multiple sites in the sample, wherein the second address tag is to be coupled to the probe bound to the target polynucleotide and identifies the site to which it is delivered; analyzing the probe/second address tag conjugate bound to the target polynucleotide, the analysis comprising;
(1) determining abundance, expression, and/or activity of the target polynucleotide by assessing the amount of the probe/second address tag conjugate bound to the target polynucleotide; and
(2) determining the identities of the sequence that hybridizes to and identifies the target polynucleotide and the second address tag of the probe/second address tag conjugate; anddetermining a spatial pattern of abundance, expression, and/or activity of the target polynucleotide across the multiple sites in the sample based on the analysis of the probe/second address tag conjugate bound to the target polynucleotide at each of the multiple sites in the sample. - View Dependent Claims (4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30)
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Specification