System and method for isolating and analyzing cells

Abstract

A system and method for isolating cells, comprising: a substrate having a broad surface; an array comprising a set of wells defined at the broad surface of the substrate, each well including: a base surface, an open surface directly opposing the base surface, defined at the broad surface of the substrate, and configured to receive one of a single cell and a single cluster of cells from a direction perpendicular to the broad surface of the substrate, and a set of channels that fluidly couple each well to at least one adjacent well; wherein the set of wells includes an interior subset and an exterior subset fluidly coupled to and surrounding the interior subset by way of the set of channels; and a fluid delivery module surrounding the array and fluidly coupled to each well in the set of wells.

We claim: 
     
         1 . A method comprising:
 providing a substrate having a broad surface and an inlet, and a set of wells recessed below the broad surface of the substrate and in fluid communication with the inlet, the set of wells coupled in series by a set of channels;   receiving a biological sample into the set of wells, through the inlet;   delivering a process reagent for polymerase chain reaction (PCR) to the substrate and into the set of wells;   providing a plate over the substrate, the plate sealed against the substrate;   transmitting heat, through the substrate to the set of wells, thereby performing PCR for nucleic acid content of the biological sample within the set of wells; and   performing a quantitative analysis of said nucleic acid content by fluorescent detection.   
     
     
         2 . The method of  claim 1 , wherein the set of wells comprises an initial well coupled to the inlet, a subset of intermediate wells, and a terminal well, wherein each of the subset of intermediate wells is coupled to only two adjacent wells by the set of channels. 
     
     
         3 . The method of  claim 2 , wherein each of the set of channels has an identical length. 
     
     
         4 . The method of  claim 1 , wherein the set of fluid channels is positioned toward a base of the substrate. 
     
     
         5 . The method of  claim 1 , wherein the set of wells is arranged in a rectangular array. 
     
     
         6 . The method of  claim 1 , wherein the set of wells comprises at least 250,000 individual wells. 
     
     
         7 . The method of  claim 1 , wherein each well has a characteristic dimension from 0.5 microns to 50 microns. 
     
     
         8 . The method of  claim 1 , wherein the plate is sealed against the substrate by a compressive force in coordination with fluid delivery to the set of wells by a fluid delivery module during sample processing. 
     
     
         9 . The method of  claim 1 , further comprising performing an in-situ hybridization assay for a least one of DNA and RNA nucleic acid content of the set of wells. 
     
     
         10 . The method of  claim 1 , wherein performing the quantitative analysis comprises performing a multiplexed analysis of a set of biomarkers using a set of fluorophores, upon imaging the substrate. 
     
     
         11 . The method of  claim 1 , wherein performing the quantitative analysis comprises identifying a cancer cell phenotype of the biological sample based upon characterizing mRNA expression according to the quantitative analysis. 
     
     
         12 . The method of  claim 1 , wherein transmitting heat comprises contacting the substrate with a heating element, thereby uniformly transmitting heat to contents of the set of wells through the substrate. 
     
     
         13 . A system comprising:
 a substrate having a broad surface and an inlet;   a set of wells recessed below the broad surface of the substrate and in fluid communication with the inlet,
 wherein the set of wells coupled in series by a set of channels, 
 wherein the set of wells comprises an initial well coupled to the inlet, a subset of intermediate wells, and a terminal well, 
 wherein each of the subset of intermediate wells is coupled to only two adjacent wells by the set of channels, and each of the set of channels has an identical length, and 
 wherein the set of wells comprises at least 250,000 individual wells; and 
   a plate coupled to the substrate and sealed against the substrate, wherein coupling of the plate to the substrate defines a flow path across the set of wells.   
     
     
         14 . The system of  claim 13 , wherein the set of fluid channels is positioned toward a base of the substrate. 
     
     
         15 . The system of  claim 13 , wherein the set of wells is arranged in a rectangular array. 
     
     
         16 . The system of  claim 13 , wherein each well has a characteristic dimension from 0.5 microns to 50 microns. 
     
     
         17 . The system of  claim 13 , further comprising a perimeter channel fluidly coupled to an exterior subset of the set of wells, the exterior subset of the set of wells positioned at an outermost edge of the array. 
     
     
         18 . A method comprising:
 providing a substrate having a broad surface and an inlet, and a set of wells recessed below the broad surface of the substrate and in fluid communication with the inlet, the set of wells coupled in series by a set of channels;   receiving a biological sample into the inlet, and delivering the biological sample into the set of wells under positive pressure;   delivering a process reagent for polymerase chain reaction (PCR) to the substrate and into the set of wells;   providing a plate over the substrate, the plate sealed against the substrate under a compressive force in coordination with fluid delivery to the set of wells by a fluid delivery module;   transmitting heat, through the substrate to the set of wells, thereby performing PCR for nucleic acid content of the biological sample within the set of wells; and   performing a quantitative analysis of said nucleic acid content by fluorescent detection of signals from the set of wells of the substrate.   
     
     
         19 . The method of  claim 18 , wherein performing the quantitative analysis comprises performing a multiplexed analysis of a set of biomarkers, comprising at least one of DNA and RNA, using a set of fluorophores. 
     
     
         20 . The method of  claim 18 , wherein performing the quantitative analysis comprises identifying a cancer cell phenotype of the biological sample based upon characterizing mRNA expression for the biological sample.