System and method for isolating and analyzing cells

Abstract

A system and method for isolating and analyzing single cells, comprising: a substrate having a broad surface; a set of wells defined at the broad surface of the substrate, and a set of channels, defined by the wall, that fluidly couple each well to at least one adjacent well in the set of wells; and fluid delivery module defining an inlet and comprising a plate, removably coupled to the substrate, the plate defining a recessed region fluidly connected to the inlet and facing the broad surface of the substrate, the fluid delivery module comprising a cell capture mode.

What is claimed is: 
     
         1 . A method comprising:
 providing a substrate having a broad surface, an inlet, an outlet, and a set of wells recessed below the broad surface of the substrate and in fluid communication with the inlet and the outlet, the set of wells coupled in series by a set of channels;   delivering a sample into the inlet and into the set of wells;   delivering a process reagent for polymerase chain reaction (PCR) to the inlet and into the set of wells;   sealing the set of wells with a plate, under a compressive force applied to the plate and the substrate; and   transmitting heat, through the substrate, thereby performing an assay with nucleic acid content within the set of wells, the assay comprising at least one of an on-chip mRNA assay and an on-chip DNA assay.   
     
     
         2 . The method of  claim 1 , wherein delivering the sample into the inlet and into the set of wells comprises capturing nucleic acid material of the sample within the set of wells. 
     
     
         3 . The method of  claim 1 , wherein each well has a characteristic diameter from 0.5 microns to 50 microns. 
     
     
         4 . The method of  claim 1 , wherein delivering the sample comprises delivering the sample into the inlet and toward the outlet of the substrate, with a pressure differential between the inlet and the outlet. 
     
     
         5 . The method of  claim 1 , wherein the substrate defines the set of wells at a region having a total surface area of at least 144 square millimeters, and wherein the set of wells comprises at least 250,000 individual wells within the total surface area. 
     
     
         6 . The method of  claim 1 , wherein sealing the set of wells with the plate provides a cavity between the plate and the set of wells, the cavity providing a boundary of a fluid layer adjacent to the set of wells. 
     
     
         7 . The method of  claim 1 , wherein the set of wells is coupled in series from the inlet to the outlet, and wherein the set of channels comprises channels having identical lengths between adjacent wells of the set of wells. 
     
     
         8 . The method of  claim 1 , wherein performing the assay comprises performing an in-situ hybridization assay for nucleic acid contents captured within the set of wells. 
     
     
         9 . The method of  claim 1 , wherein transmitting heat through the substrate comprises providing a thermal control module comprising a heating plate arranged near a surface of the substrate. 
     
     
         10 . The method of  claim 9 , wherein transmitting heat comprises transmitting heat for at least one of PCR and an immunoassay with nucleic acid content captured within the set of wells. 
     
     
         11 . The method of  claim 1 , wherein the on-chip assay comprises a multiplexed mRNA assay of multiple biomarkers using a set of fluorophores provided in the process reagent. 
     
     
         12 . The method of  claim 1 , further comprising imaging contents of the set of wells, thereby enabling identification and assessment of contents of the set of wells during performance of the assay. 
     
     
         13 . The method of  claim 1 , further comprising returning a result characterizing a cancer cell phenotype represented in the sample. 
     
     
         14 . The method of  claim 1 , wherein the process reagent comprises PCR primers, polymerase, one or more probes, and a set of fluorophores for detection of biomarkers of the sample. 
     
     
         15 . A method comprising:
 providing a substrate having a broad surface, an inlet, an outlet, and a set of wells recessed below the broad surface of the substrate and in fluid communication with the inlet and the outlet, the set of wells coupled in series by a set of channels, wherein each of the set of channels has an identical length;   delivering a sample into the inlet and into the set of wells under positive pressure;   delivering a process reagent for polymerase chain reaction (PCR) to the inlet and into the set of wells;   sealing the set of wells with a plate, under a compressive force applied to the plate and the substrate; and   transmitting heat, through the substrate, thereby performing an assay with nucleic acid content within the set of wells, the assay comprising an on-chip nucleic acid processing assay.   
     
     
         16 . The method of  claim 15 , wherein performing the assay comprises performing a quantitative analysis of nucleic acid content captured within the set of wells, by fluorescent detection. 
     
     
         17 . The method of  claim 15 , wherein the process reagent comprises PCR primers, polymerase, one or more probes, and a set of fluorophores for multiplexed detection of a set of biomarkers of the sample. 
     
     
         18 . The method of  claim 15 , wherein performing the assay comprises performing an in-situ hybridization assay for nucleic acid contents captured within the set of wells. 
     
     
         19 . The method of  claim 15 , wherein the set of wells comprises an initial well coupled to the inlet, a subset of intermediate wells, and a terminal well coupled to the outlet, wherein each of the subset of intermediate wells is coupled to only two adjacent wells by the set of channels. 
     
     
         20 . The method of  claim 19 , wherein sealing the set of wells with the plate provides a cavity between the plate and the set of wells, the cavity providing a boundary of a fluid layer adjacent to the set of wells.