Spatially Encoded Biological Assays

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.

1 . (canceled) 
     
     
         2 . A system for analyzing target biological molecules of a tissue sample, the system comprising:
 an imaging apparatus configured to obtain at least one image of a tissue sample and comprising a plurality of probes, wherein a probe of the plurality of probes comprises a protein that specifically binds a target biological molecule of the tissue sample, and wherein the protein is conjugated to an oligonucleotide having a sequence;   a processing circuit comprising instructions that, when executed, cause the processing circuit to obtain information about one or more locations of interest of the tissue sample; and   an analysis apparatus configured so that for at least one of the one or more locations of interest of the tissue sample, the analysis apparatus separates all or a portion of the oligonucleotide from the tissue sample at the at least one location of interest.   
     
     
         3 . The system of  claim 2 , wherein the analysis apparatus is configured so that the analysis apparatus collects the all or a portion of the oligonucleotide for detection from the at least one location of interest. 
     
     
         4 . The system of  claim 2 , wherein the analysis apparatus comprises a radiation source configured to illuminate the at least one location of interest of the tissue sample to separate the all or a portion of the oligonucleotide from the tissue sample. 
     
     
         5 . The system of  claim 2 , wherein the processing circuit comprises instructions that, when executed, cause the processing circuit to obtain the information about the one or more locations of interest of the tissue sample from the at least one image. 
     
     
         6 . The system of  claim 2 , wherein the processing circuit comprises instructions that, when executed, cause the processing circuit to receive the information about the one or more locations of interest of the tissue sample from a user of the system. 
     
     
         7 . The system of  claim 2 , wherein the plurality of probes comprises two or more probes, each comprising protein that specifically binds a unique target biological molecule of the tissue sample and is conjugated to an oligonucleotide having a different sequence. 
     
     
         8 . The system of  claim 2 , wherein the target biological molecule comprises a protein. 
     
     
         9 . The system of  claim 2 , wherein the tissue sample comprises a fresh-frozen or formalin-fixed paraffin embedded (FFPE) tissue sample. 
     
     
         10 . The system of  claim 2 , wherein the probe comprises an antibody that specifically binds the target biological molecule. 
     
     
         11 . The system of  claim 2 , further comprising a reagent delivery apparatus configured to deliver one or more reagents to the tissue sample. 
     
     
         12 . The system of  claim 11 , wherein the one or more reagents comprise at least some of the plurality of probes. 
     
     
         13 . The system of  claim 12 , wherein the at least some of the plurality of probes comprises the probe that specifically binds the target biological molecule of the tissue sample. 
     
     
         14 . The system of  claim 13 , wherein the probe that specifically binds the target biological molecule is cleavable. 
     
     
         15 . The system of  claim 11 , further comprising a gasket, wherein the system is configured to position the gasket atop the tissue sample. 
     
     
         16 . The system of  claim 15 , wherein the reagent delivery apparatus is configured to deliver the one or more reagents into the gasket. 
     
     
         17 . The system of  claim 3 , wherein the detection apparatus comprises a fluid conduit for collecting the all or a portion of the oligonucleotide. 
     
     
         18 . The system of  claim 2 , wherein each of the one or more locations of interest corresponds to a different group of one or more cells in the tissue sample. 
     
     
         19 . The system of  claim 2 , wherein each of the one or more locations of interest corresponds to a different cell type in the tissue sample. 
     
     
         20 . The system of  claim 2 , wherein each of the one or more locations of interest corresponds to a different cell in the sample. 
     
     
         21 . The system of  claim 5 , wherein the processing circuit obtains the information about the one or more locations of interest of the tissue sample based on differentiated immunohistochemistry of the tissue sample identified in the at least one image by the processing circuit. 
     
     
         22 . The system of  claim 5 , wherein the processing circuit obtains the information about the one or more locations of interest of the tissue sample based on differentiated chemical staining of the tissue sample identified in the at least one image by the processing circuit.