Spatially encoded biological assays
First Claim
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1. A method to determine a spatial pattern of abundance or activity or both of a biological target in a sample, comprising the following steps:
- delivering encoded probes for a biological target to multiple sites in a sample affixed to a support, wherein each encoded probe comprises a probe region capable of interacting with the biological target and a coding tag comprising an oligonucleotide that identifies the location of the site to which the encoded probe is delivered;
allowing the encoded probes to interact with the biological target in the sample;
separating encoded probes that specifically interact with the biological target from encoded probes that do not specifically interact with the biological target;
determining all or a portion of the sequence of the coding tag oligonucleotide of an encoded probe that specifically interacts with the biological target, thereby identifying the location of the site in the sample at which the encoded probe and its specifically interacting biological target are located; and
associating the abundance or activity or both of the biological target to the locations of the multiple sites in the sample.
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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.
231 Citations
43 Claims
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1. A method to determine a spatial pattern of abundance or activity or both of a biological target in a sample, comprising the following steps:
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delivering encoded probes for a biological target to multiple sites in a sample affixed to a support, wherein each encoded probe comprises a probe region capable of interacting with the biological target and a coding tag comprising an oligonucleotide that identifies the location of the site to which the encoded probe is delivered; allowing the encoded probes to interact with the biological target in the sample; separating encoded probes that specifically interact with the biological target from encoded probes that do not specifically interact with the biological target; determining all or a portion of the sequence of the coding tag oligonucleotide of an encoded probe that specifically interacts with the biological target, thereby identifying the location of the site in the sample at which the encoded probe and its specifically interacting biological target are located; and associating the abundance or activity or both of the biological target to the locations of the multiple sites in the sample. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16)
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17. A method to determine a spatial pattern of abundance or activity or both of a nucleic acid target in a sample, comprising the following steps:
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delivering an oligonucleotide probe for a nucleic acid target to multiple sites in a sample affixed to a support; allowing the oligonucleotide probe to hybridize with the nucleic acid target in the sample; washing unhybridized oligonucleotide probe from the sample; delivering one or more encoding agents to the multiple sites in the sample, wherein the one or more encoding agents delivered to each site comprise an oligonucleotide that identifies the location of the site in the sample; coupling the one or more encoding agents and the oligonucleotide probe delivered to each site to form an encoded probe hybridized with the nucleic acid target at the site; determining all or a portion of the sequence of the encoded probe hybridized with the nucleic acid target, thereby identifying the location of the site in the sample at which the encoded probe and its hybridized nucleic acid target are located; and associating the abundance or activity or both of the nucleic acid target to the locations of the multiple sites in the sample. - View Dependent Claims (18, 19, 20, 21, 22, 23)
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24. A method to determine a spatial pattern of abundance or activity or both of a biological target in a sample, comprising the following steps:
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delivering a probe for a biological target to multiple sites in a sample affixed to a support; allowing the probe to interact with the biological target in the sample; delivering an encoding agent to the multiple sites in the sample, wherein the encoding agent delivered to each site comprises an oligonucleotide that identifies the location of the site in the sample; coupling the encoding agent and the probe delivered to each site to form an encoded probe interacting with the biological target at the site; determining all or a portion of the sequence of the encoded probe interacting with the biological target, thereby identifying the location of the site in the sample at which the encoded probe and its interacting biological target are located; associating the abundance or activity or both of the biological target to the locations of the multiple sites in the sample. - View Dependent Claims (25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43)
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Specification