Fluid-tight flow system to isolate biomarkers from a liquid sample

Abstract

The presently disclosed subject matter provides a fluid-tight flow system; a method of isolating biomarker cells from a liquid sample; a method of extracting cfDNA, ctDNA, or exosomes from plasma; a method of extracting cfDNA, ctDNA, or exosomes from blood; a method of capturing DNA or RNA released from biomarker cells; a method of amplifying a nucleotide sequence; a method of sequencing a nucleotide sequence; a method of detecting a chromosomal abnormality; and a method of analyzing a protein.

What is claimed: 
     
         1 . A fluid-tight flow system comprising:
 a microfluidic chip comprising an inlet port in fluid communication with an outlet port;   a first automated pipetting channel comprising a first pump, and a first pipette tip containing a liquid sample and coupled to the inlet port;   a second automated pipetting channel comprising a second pump, and a second pipette tip coupled to the outlet port; and   a non-transitory computer readable medium in communication with the first pump and the second pump, and programmed to command the first pump of the first automated pipetting channel and the second pump of the second automated pipetting channel to control flow of the liquid sample through the microfluidic chip.   
     
     
         2 . The fluid-tight flow system of  claim 1 , wherein the first pump or the second pump comprises a plunger and a pipetting drive motor. 
     
     
         3 . The fluid-tight flow system of  claim 1 , wherein the first pump or the second pump comprises a piston contained within the first pipette tip and a pipetting drive motor. 
     
     
         4 . The fluid-tight flow system of  claim 1 , wherein the system further comprises closed-loop feedback control wherein:
 the first automated pipetting channel further comprises a first pressure sensor;   the second automated pipetting channel further comprises a second pressure sensor; and   the non-transitory computer readable medium is further in communication with the first pressure sensor and second pressure sensor; wherein said non-transitory computer readable medium is further programmed to receive data from the first pressure sensor in real-time and data from the second pressure sensor in real-time, and adjust command of at least the first pump of the first automated pipetting channel or the second pump of the second automated pipetting channel to adjust flow through the microfluidic chip using real-time feedback based on said data from the first pressure sensor and the second pressure sensor.   
     
     
         5 . The fluid-tight flow system of  claim 4 , wherein the real-time feedback based on said data from the first pressure sensor and the second pressure sensor comprises detection at, above or below a pressure threshold or a flow rate threshold. 
     
     
         6 . The fluid-tight flow system of  claim 1 , wherein the liquid sample is a bodily fluid. 
     
     
         7 . The fluid-tight flow system of  claim 6 , wherein the bodily fluid is blood, saliva, lymphatic fluid, cells suspended in fluid, synovial fluid, semen, urine, cerebrospinal fluid, or amniotic fluid. 
     
     
         8 . The fluid-tight flow system of  claim 1 , wherein the microfluidic chip further comprises a cell selection module, a plasma isolation module, or a solid-phase extraction module in fluid communication with the inlet and the outlet port. 
     
     
         9 . The fluid-tight flow system of  claim 8 , wherein the microfluidic chip comprises a cell selection module and said cell selection module comprises a capture bed in fluid communication with the inlet port and the outlet port. 
     
     
         10 . The fluid-tight flow system of  claim 9 , wherein the capture bed comprises a plurality of isolation channels configured to isolate biomarker cells from the liquid sample, solid supports configured to bind to biomarker cells, or a filter substrate configured as a size-based separator for biomarker cells. 
     
     
         11 . The fluid-tight flow system of  claim 10 , wherein the filter substrate is a microcavity array. 
     
     
         12 . The fluid-tight flow system of  claim 10 , wherein the solid supports are pillars, beads, or resins. 
     
     
         13 . The fluid-tight flow system of  claim 10 , wherein the plurality of isolation channels are configured to isolate circulating tumor cells or circulating leukemic cells. 
     
     
         14 . A method of isolating biomarker cells from a liquid sample comprising:
 providing the system of  claim 10 , wherein the non-transitory computer readable medium programmed to command the first pump of the first automated pipetting channel and the second pump of the second automated pipetting channel to control flow of the liquid sample through the microfluidic chip comprises programming to control flow of the liquid sample through the cell selection module;   controlling flow of the liquid sample through the cell selection module; and   isolating biomarker cells from the liquid sample.   
     
     
         15 . The method of  claim 14 , wherein the biomarker cells are circulating tumor cells.