Methods and systems for determining spatial patterns of biological targets in a sample

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.

1 - 56 . (canceled) 
     
     
         57 . A method of determining a spatial pattern of abundance, expression, and/or activity of one or more biological targets across multiple sites in a sample, comprising:
 delivering a probe for each of one or more biological targets to multiple sites in a sample, wherein each probe comprises a target-binding moiety capable of binding to the probe's corresponding biological target;   allowing each probe to bind to its corresponding biological target in the sample;   delivering at least one adaptor to the multiple sites in the sample, wherein the at least one adaptor specifically binds to the probe and comprises an address tag that identifies each of the multiple sites to which the at least one adaptor is delivered, wherein the probe and/or the adaptor comprises an identity tag that identifies the probe's and/or adaptor's corresponding biological target or target-binding moiety;   analyzing the at least one adaptor and the probe bound to the one or more biological targets, the analysis comprising: (1) determining abundance, expression, and/or activity of each of the one or more biological targets by assessing the amount of at least one adaptor bound to the probe bound to the biological target; and (2) determining the identities of the identity tag, and the address tag of the at least one adaptor; and   determining a spatial pattern of abundance and/or activity of the one or more biological targets across the multiple sites in the sample based on the analysis,   wherein the method does not depend on an imaging technique for determining spatial information of the one or more biological targets in the sample.   
     
     
         58 . A method of determining a spatial pattern of abundance, expression, and/or activity of one or more biological targets across multiple sites in a sample, comprising:
 delivering a probe for each of one or more biological targets to multiple sites in a sample, wherein each probe comprises a target-binding moiety capable of binding to the probe's corresponding biological target;   allowing each probe to bind to its corresponding biological target in the sample;   delivering at least one adaptor to the multiple sites in the sample, wherein the at least one adaptor specifically binds to the probe and comprises an address tag that identifies each of the multiple sites to which the at least one adaptor is delivered, wherein the probe and/or the adaptor comprises an identity tag that identifies the probe's and/or adaptor's corresponding biological target or target-binding moiety;   analyzing the at least one adaptor and the probe bound to the one or more biological targets by sequencing, wherein the amount of a sequencing product indicates abundance, expression, and/or activity of each of the one or more biological targets, the sequencing product comprising all or a portion of the address tag sequence and all or a portion of the identity tag sequence; and   determining a spatial pattern of abundance, expression, and/or activity of the one or more biological targets across the multiple sites in the sample based on the analysis,   wherein the method does not depend on an imaging technique for determining spatial information of the one or more biological targets in the sample.   
     
     
         59 . A method of determining a spatial pattern of abundance, expression, and/or activity of one or more biological targets across multiple sites in a sample, comprising:
 delivering a probe for each of one or more biological targets to multiple sites in a sample, wherein each probe comprises a target-binding moiety capable of binding to the probe's corresponding biological target;   allowing each probe to bind to its corresponding biological target in the sample;   delivering at least one adaptor to the multiple sites in the sample, wherein the at least one adaptor specifically binds to the probe, wherein the probe and/or the adaptor comprises an identity tag that identifies the probe's and/or adaptor's corresponding biological target or target-binding moiety;   delivering an address tag to each of the multiple sites in the sample, wherein the address tag is to be coupled to the at least one adaptor bound to the probe bound to the biological target and identifies the site to which the address tag is delivered;   analyzing the adaptor/address tag conjugate, the analysis comprising: (1) determining abundance, expression, and/or activity of each of the one or more biological targets by assessing the amount of the adaptor/address tag conjugate bound to the probe bound to the biological target; and (2) determining the identities of the identity tag, and the address tag of the adaptor/address tag conjugate; and   determining a spatial pattern of abundance, expression, and/or activity of the one or more biological targets across the multiple sites in the sample based on the analysis,   wherein the method does not depend on an imaging technique for determining spatial information of the one or more biological targets in the sample.   
     
     
         60 . A method of determining a spatial pattern of abundance, expression, and/or activity of one or more biological targets across multiple sites in a sample, comprising:
 delivering a probe for each of one or more biological targets to multiple sites in a sample, wherein each probe comprises a target-binding moiety capable of binding to the probe's corresponding biological target;   allowing each probe to bind to its corresponding biological target in the sample;   delivering at least one adaptor to the multiple sites in the sample, wherein the at least one adaptor specifically binds to the probe, wherein the probe and/or the adaptor comprises an identity tag that identifies the probe's and/or adaptor's corresponding biological target or target-binding moiety;   delivering an address tag to each of the multiple sites in the sample, wherein the address tag is to be coupled to the at least one adaptor bound to the probe bound to the biological target and identifies the site to which the address tag is delivered;   analyzing the adaptor/address tag conjugate by sequencing, wherein the amount of a sequencing product indicates abundance, expression, and/or activity of each of the one or more biological targets, the sequencing product comprising all or a portion of the address tag sequence and all or a portion of the identity tag sequence; and   determining a spatial pattern of abundance, expression, and/or activity of the one or more biological targets across the multiple sites in the sample based on the analysis.   
     
     
         61 . The method of  claim 57 , wherein at least two adaptors are delivered to each of the multiple sites in the sample, wherein the at least two adaptors each specifically binds to one probe that specifically binds to the biological target. 
     
     
         62 . The method of  claim 61 , wherein the at least two adaptors are joined. 
     
     
         63 . The method of  claim 62 , wherein the at least two adaptors are ligated by using a portion of the probe sequence as a splint. 
     
     
         64 . The method of  claim 57 , wherein the probe for each of the one or more biological targets comprises an affinity agent for the biological target and an oligonucleotide, and the adaptor comprises an oligonucleotide. 
     
     
         65 . The method of  claim 58 , wherein at least two adaptors are delivered to each of the multiple sites in the sample, wherein the at least two adaptors each specifically binds to one probe that specifically binds to the biological target. 
     
     
         66 . The method of  claim 65 , wherein the at least two adaptors are joined. 
     
     
         67 . The method of  claim 66 , wherein the at least two adaptors are ligated by using a portion of the probe sequence as a splint. 
     
     
         68 . The method of  claim 58 , wherein the probe for each of the one or more biological targets comprises an affinity agent for the biological target and an oligonucleotide, and the adaptor comprises an oligonucleotide. 
     
     
         69 . The method of  claim 59 , wherein at least two adaptors are delivered to each of the multiple sites in the sample, wherein the at least two adaptors each specifically binds to one probe that specifically binds to the biological target. 
     
     
         70 . The method of  claim 69 , wherein the at least two adaptors are joined. 
     
     
         71 . The method of  claim 70 , wherein the at least two adaptors are ligated by using a portion of the probe sequence as a splint. 
     
     
         72 . The method of  claim 59 , wherein the probe for each of the one or more biological targets comprises an affinity agent for the biological target and an oligonucleotide, and the adaptor comprises an oligonucleotide. 
     
     
         73 . The method of  claim 60 , wherein at least two adaptors are delivered to each of the multiple sites in the sample, wherein the at least two adaptors each specifically binds to one probe that specifically binds to the biological target. 
     
     
         74 . The method of  claim 73 , wherein the at least two adaptors are joined. 
     
     
         75 . The method of  claim 74 , wherein the at least two adaptors are ligated by using a portion of the probe sequence as a splint. 
     
     
         76 . The method of  claim 60 , wherein the probe for each of the one or more biological targets comprises an affinity agent for the biological target and an oligonucleotide, and the adaptor comprises an oligonucleotide.