System and method for capturing and analyzing cells

A method for capturing and analyzing a set of cells, comprising:

• capturing the set of cells, including a subpopulation of cells, at a set of parallel pores of a substrate, each pore in the set of parallel pores including a chamber comprising:
• an inlet and an outlet, and a set of walls defining a chamber volume directly corresponding to the volume of a single cell of the set of cells and thereby configured to hold the single cell of the set of cells;
• transmitting a reagent volume to the set of parallel pores at an inlet channel fluidly coupled to the set of parallel pores, wherein the reagent volume is configured to distinguish the subpopulation of cells from the set of cells;
• transmitting excitation wavelengths of light into each pore of the set of parallel pores, thereby enabling identification of at least one cell of the subpopulation of cells;
• guiding a cell removal tool into the inlet channel and to a pore of the set of parallel pores containing a cell of the subpopulation of cells;
• transmitting a force configured to drive the cell of the subpopulation of cells from the pore and into the cell removal tool;
• and
• performing reverse transcription polymerase chain reaction (RT-PCR) for the cell of the subpopulation of cells, wherein the cell comprises a circulating stem cell (CSC), and wherein performing RT-PCR includes determining threshold cycle values for a group of target genes selected from a group consisting of Her2, ALDH1, and TWIST1.