Spatially Encoded Biological Assays
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 a target biological molecule of a tissue sample, the system comprising:
an imaging apparatus configured to obtain at least one image of a tissue sample comprising a plurality of probes, wherein at least one 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 a location of interest in the tissue sample; and
a detection apparatus configured to:
receive all or a portion of the oligonucleotide and a fluorescent label after liberation of the oligonucleotide or a portion thereof, from the location of interest in the tissue sample;
measure fluorescence emission from the fluorescent label;
determine a relative abundance of the oligonucleotide or a portion thereof at the location of interest based on the measured fluorescence emission.
3 . The system of claim 2 , wherein the detection apparatus is configured to receive the oligonucleotide or a portion thereof hybridized to a microarray.
4 . The system of claim 2 , wherein the plurality of probes comprises at least two probes each comprising a protein that specifically binds a unique target biological molecule of the tissue sample, each probe of the at least two probes being conjugated to an oligonucleotide having a sequence.
5 . The system of claim 4 , wherein each probe of the at least two probes comprises a protein conjugated to an oligonucleotide having a different sequence, and wherein the detection apparatus is configured to receive at least two chemical moieties, each of the chemical moieties comprising at least a portion of the different oligonucleotides and a different fluorescent label.
6 . The system of claim 5 , wherein the detection apparatus is configured to measure and resolve fluorescence emission signals from each of the different fluorescent labels.
7 . The system of claim 2 , wherein the processing circuit is configured to obtain information about multiple locations of interest in the tissue sample, and the detection apparatus is configured to determine a relative abundance of the oligonucleotide or a portion thereof at different locations in the tissue sample corresponding to the multiple locations of interest.
8 . The system of claim 2 , wherein the processing circuit comprises instructions that, when executed, cause the processing circuit to obtain the information about the location of interest in the tissue sample from the at least one image.
9 . The system of claim 2 , wherein the processing circuit comprises instructions that, when executed, cause the processing circuit to receive the information about the location of interest in the tissue sample from a user of the system.
10 . The system of claim 2 , wherein the target biological molecule comprises a protein.
11 . The system of claim 2 , wherein the tissue sample comprises a fresh-frozen or formalin-fixed paraffin embedded (FFPE) tissue sample.
12 . The system of claim 2 , wherein the probe comprises an antibody that specifically binds the target biological molecule.
13 . The system of claim 2 , further comprising a reagent delivery apparatus configured to deliver one or more reagents to the tissue sample.
14 . The system of claim 13 , wherein the one or more reagents comprise at least some of the plurality of probes.
15 . The system of claim 14 , wherein the at least some of the plurality of probes comprises the probe that specifically binds the target biological molecule of the tissue sample.
16 . The system of claim 13 , further comprising a gasket, wherein the system is configured to position the gasket atop the tissue sample.
17 . The system of claim 16 , wherein the reagent delivery apparatus is configured to deliver the one or more reagents into the gasket.
18 . The system of claim 7 , wherein each of the multiple locations of interest corresponds to a different group of one or more cells in the tissue sample.
19 . The system of claim 7 , wherein each of the multiple locations of interest corresponds to a different cell type in the tissue sample.
20 . The system of claim 7 , wherein each of the multiple locations of interest corresponds to a different cell in the tissue sample.
21 . The system of claim 8 , wherein the processing circuit obtains the information about the location of interest in 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 8 , wherein the processing circuit obtains the information about the location of interest in the tissue sample based on differentiated staining of the tissue sample identified in the at least one image by the processing circuit.
23 . A system for analyzing a target biological molecule of a tissue sample, the system comprising:
an imaging apparatus configured to obtain at least one image of a tissue sample that comprises a plurality of probes, wherein at least one 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 a location of interest in the tissue sample; and
a detection apparatus configured to:
receive all or a portion of the oligonucleotide and a fluorescent label after liberation of the oligonucleotide or a portion thereof, from the location of interest in the tissue sample; and
measure fluorescence emission from the fluorescent label to detect the oligonucleotide or a portion thereof at the location of interest.
24 . The system of claim 23 , wherein the detection apparatus is further configured to determine a relative abundance of the oligonucleotide or a portion thereof at the location of interest based on the measured fluorescence emission.