System and method for capturing and analyzing cells

Abstract

A system and method for capturing and analyzing a set of cells, comprising: an array including a set of parallel pores, each pore including a chamber including a chamber inlet and a chamber outlet, and configured to hold a single cell, and a pore channel fluidly connected to the chamber outlet; an inlet channel fluidly connected to each chamber inlet of the set of parallel pores; an outlet channel fluidly connected to each pore channel of the set of parallel pores; a set of electrophoresis channels fluidly coupled to the outlet channel, configured to receive a sieving matrix for electrophoretic separation; and a set of electrodes including a first electrode and a second electrode, wherein the set of electrodes is configured to provide an electric field that facilitates electrophoretic analysis of the set of cells.

We claim: 
     
         1 . A method comprising:
 providing a substrate comprising:
 an inlet port, 
 an inlet channel coupled to the inlet port, 
 a set of chambers coupled to the inlet channel along a length of the inlet channel, and 
 an outlet channel downstream of the set of chambers and coupled to chamber outlets of the set of chambers; 
   delivering a biological sample to the set of chambers upon receiving a biological sample into the inlet channel through the inlet port;   retaining nucleic acids of the biological sample within the set of chambers;   receiving reagents at the set of chambers, said reagents comprising reagents for polymerase chain reaction (PCR);   amplifying said nucleic acids of the biological sample at the set of chambers with said reagents; and   analyzing contents of the set of chambers upon imaging the set of chambers with fluorescent detection of said contents.   
     
     
         2 . The method of  claim 1 , wherein the set of chambers comprises 100,000 chambers. 
     
     
         3 . The method of  claim 1 , wherein the set of chambers comprises a set of parallel chambers arranged between the inlet channel and the outlet channel. 
     
     
         4 . The method of  claim 1 , wherein nucleic acids of the biological sample comprise RNA molecules. 
     
     
         5 . The method of  claim 1 , wherein nucleic acids of the biological sample comprise DNA molecules. 
     
     
         6 . The method of  claim 1 , wherein said reagents comprise affinity molecules for binding oligonucleotide sequences. 
     
     
         7 . The method of  claim 1 , further comprising performing allele specific polymerase chain reaction (AS-PCR) in coordination with amplifying said nucleic acids. 
     
     
         8 . The method of  claim 1 , wherein amplifying said nucleic acids comprises performing whole genome amplification (WGA). 
     
     
         9 . The method of  claim 1 , further comprising transmitting heat to the substrate according to a set of thermocycling parameters in coordination with amplifying said nucleic acids. 
     
     
         10 . The method of  claim 1 , wherein said reagents comprise two allele specific forward primers and a common reverse primer for each of a set of single nucleotide polymorphisms (SNPs). 
     
     
         11 . The method of  claim 10 , further comprising detecting single nucleotide polymorphism (SNP) mutations upon analyzing contents of the set of chambers. 
     
     
         12 . The method of  claim 1 , wherein delivering the biological sample comprises delivering the biological sample into the inlet port and toward the outlet channel with a pressure differential. 
     
     
         13 . The method of  claim 1 , further comprising sealing the substrate with a laminate. 
     
     
         14 . The method of  claim 1 , wherein analyzing contents of the set of chambers comprises identifying occupied chambers upon imaging the set of chambers. 
     
     
         15 . The method of  claim 1 , wherein each of the set of chambers has a depth from 5-200 microns. 
     
     
         16 . A method comprising:
 providing a substrate comprising:
 an inlet port, 
 an inlet channel coupled to the inlet port, 
 a set of chambers coupled to the inlet channel along a length of the inlet channel, the set of chambers arranged in array from the inlet channel to the outlet channel, and 
 an outlet channel downstream of the set of chambers and coupled to chamber outlets of the set of chambers; 
   delivering a biological sample to the set of chambers upon receiving a biological sample into the inlet channel through the inlet port under pressure;   retaining targets of the biological sample within the set of chambers;   receiving reagents at the set of chambers;   transmitting heat to the substrate with a variable temperature profile, thereby amplifying processing said targets of the biological sample at the set of chambers with said reagents; and   analyzing contents of the set of chambers upon imaging the set of chambers with fluorescent detection of said contents.   
     
     
         17 . The method of  claim 16 , wherein the set of chambers comprises loo,cloo chambers, and wherein each of the set of chambers has a depth from 5-200 microns. 
     
     
         18 . The method of  claim 16 , wherein said targets comprise a set of single nucleotide polymorphisms, wherein said reagents comprise two allele specific forward primers and a common reverse primer for each of the set of single nucleotide polymorphisms (SNPs), and wherein the method further comprises detecting single nucleotide polymorphism (SNP) mutations upon analyzing contents of the set of chambers. 
     
     
         19 . The method of  claim 16 , further comprising sealing the substrate with a laminate. 
     
     
         20 . The method of  claim 16 , wherein targets of the biological sample comprise target genes, and wherein analyzing contents of the set of chambers comprises performing quantitation of gene expression of said target genes.