Systems and methods for processing fluids

Abstract

Systems and methods for processing fluid samples are disclosed. Fluid sample processing is accomplished using a series of microfluidic bump arrays include an automated and integrated system for sorting particles from a biological sample, lysing those particles to expose total RNA or DNA, purifying the RNA or DNA, processing the RNA or DNA by chemical or enzymatic modification, to select RNA or DNA molecules by size, or to generate, optionally, a sequencing library. The sequencing library is suitable for use in next generation sequencing (“NGS”).

1 . A method for processing of a biological fluid, comprising:
 separating at least one first cell from the biological fluid;   applying at least one first treatment to the at least one separated cell to produce a first treated solution;   applying at least one second treatment to the first treated solution to produce a second treated solution; and   processing at least one of the first treated solution and the second treated solution using a deterministic lateral displacement to generate an output solution.   
     
     
         2 . The method according to  claim 1 , wherein the biological fluid includes at least one of the following: whole blood, urine, spinal fluid, saliva, buccal swabs, sputum, bronchial lavage, gastric lavage fluid, microbial culture media, feces, buffy coat, serum, plasma, platelet concentrate, water samples, and/or any other biological, chemical, and/or biochemical fluids and/or any combination thereof. 
     
     
         3 . The method according to  claim 1 , wherein the deterministic lateral displacement uses at least one bump array to process at least one of the first treated solution and the second treated solution. 
     
     
         4 . The method according to  claim 1 , wherein the deterministic lateral displacement uses a sequential arrangement of a plurality of bump arrays to process at least one of the first treated solution and the second treated solution. 
     
     
         5 . The method according to  claim 1 , wherein
 the biological fluid is whole blood;   the applying at least one first treatment includes lysing cells separated from the whole blood to generate a purified deoxyribonucleic acid (“DNA”); and   the applying at least one second treatment includes combining the purified DNA with a transposase complex and at least one sequencing adaptor.   
     
     
         6 . The method according to  claim 1 , further comprising fractionating the output solutions based on a size of at least one cell contained within the output solution. 
     
     
         7 . A system for processing of a biological fluid, comprising:
 at least one input reservoir for receiving the biological fluid and separating at least one first cell from the biological fluid;   at least bump array mechanism coupled to the at least one input reservoir for
 applying at least one first treatment to the at least one separated cell to produce a first treated solution; 
 applying at least one second treatment to the first treated solution to produce a second treated solution; and 
 processing at least one of the first treated solution and the second treated solution using a deterministic lateral displacement to generate an output solution; and 
   an output reservoir for receiving the output solution.   
     
     
         8 . The system according to  claim 7 , wherein the biological fluid includes at least one of the following: whole blood, urine, spinal fluid, saliva, buccal swabs, sputum, bronchial lavage, gastric lavage fluid, microbial culture media, feces, buffy coat, serum, plasma, platelet concentrate, water samples, and/or any other biological, chemical, and/or biochemical fluids and/or any combination thereof. 
     
     
         9 . The system according to  claim 7 , wherein the at least one bump array uses a deterministic lateral displacement to process at least one of the first treated solution and the second treated solution. 
     
     
         10 . The system according to  claim 7 , further comprising a sequential arrangement of a plurality of bump arrays to process at least one of the first treated solution and the second treated solution. 
     
     
         11 . The system according to  claim 7 , wherein
 the biological fluid is whole blood;   the applying at least one first treatment includes lysing cells separated from the whole blood to generate a purified deoxyribonucleic acid (“DNA”); and   the applying at least one second treatment includes combining the purified DNA with a transposase complex and at least one sequencing adaptor.   
     
     
         12 . The system according to  claim 7 , wherein the output reservoir fractionates the output solutions based on a size of at least one cell contained within the output solution. 
     
     
         13 . A method for processing a whole blood sample using a sequential and continuous arrangement of bump arrays integrated in a continuous flow operation, comprising:
 receiving the whole blood sample at a first bump array in the arrangement of bump arrays;   purifying the hole blood sample to produce white blood cells;   isolating nuclei from the white blood cells;   isolating deoxyribonucleic acid (“DNA”) from the nuclei;   purifying DNA from the nuclei; and   treating the purified DNA using at least one chemical and/or enzymatic DNA treatment.   
     
     
         14 . method for processing of a fluid sample using at least one bump array, comprising
 receiving the fluid sample at the at least one bump array;   isolating, using the at least one bump array, at least one nucleic acid-containing cell and/or particle of interest from the fluid sample on the basis of a size of the cell and/or particle;   contacting using the at least one bump array, the isolated cell and/or particle with at least one reagent stream for releasing at least one nucleic acid from the cell and/or particles in substantially pure form;   moving, using the at least one bump array, the at least one purified nucleic acid out of the reagent stream; and   removing the at least one purified nucleic acid from the at least one bump array.   
     
     
         15 . The method according  claim 14 , wherein a plurality of bump arrays processes the nucleic acid, wherein individual bump arrays in the plurality of bump arrays are connected in series, wherein an output of one bump array is provided to an input of a subsequent individual bump array. 
     
     
         16 . The method according to  claim 14 , wherein a single bump array is used for the receiving, the isolating, the contacting and the moving. 
     
     
         17 . The method according to  claim 14 , wherein the fluid sample includes at least one of following: an avian whole blood and a mammalian whole blood; and
 wherein the nucleic acid-containing cells and/or particles are white blood cells.   
     
     
         18 . The method according to  claim 14 , wherein the fluid sample includes at least one of the following: an avian whole blood and a mammalian whole blood; and
 wherein the nucleic acid-containing cells and/or particles are circulating tumor cells.   
     
     
         19 . The method according to  claim 14 , wherein the fluid sample includes at least one of the following: an avian whole blood and a mammalian whole blood; and
 wherein the nucleic acid-containing cells and/or particles include at least one of the following: white blood cells, bacteria, viruses, fungi, and parasitic protozoans.   
     
     
         20 . The method according to  claim 19 , wherein the biological fluid includes at least one of the following: whole blood, urine, spinal fluid, saliva, buccal swabs, sputum, bronchial lavage, gastric lavage fluid, microbial culture media, feces, buffy coat, serum, plasma, platelet concentrate, water samples, and/or any other biological, chemical, and/or biochemical fluids and/or any combination thereof. 
     
     
         21 . A method for serially processing of a high molecular weight (“HMW”) nucleic acid using at least one chemical and/or enzymatic reagent stream using at least one bump array, wherein HMW nucleic acid has an effective hydrodynamic radius that is greater than a critical size of the at least one bump array, comprising:
 receiving the HMW nucleic acid at the at least one bump array; and 
 contacting the HMW nucleic acid with the at least one chemical and/or enzymatic reagent stream, wherein the at least one chemical and/or enzymatic reagent stream flows in a direction of the flow of the HMW nucleic acid through the bump array; 
 wherein the HMW nucleic acid reacts with the at least one chemical and/or enzymatic reagent stream. 
 
     
     
         22 . A method for serial processing of a nucleic acid using at least one chemical and/or enzymatic reagent stream using at least one bump array, comprising:
 receiving the nucleic acid;   flowing the nucleic acid into the at least one bump array,   contacting, using the at least one bump array, the nucleic acid with at least one chemical and/or enzymatic reagent stream;   modifying, using at least one chemical and/or enzymatic reagent stream, the nucleic acid; and   removing, using the at least one bump array, the purified nucleic acid from the at least one chemical and/or enzymatic reagent stream.   
     
     
         23 . The method according to  claim 23 , wherein a plurality of bump arrays serially process the nucleic acid, wherein individual bump arrays in the plurality of bump arrays are connected in series, wherein an output of one bump array in the plurality of bump arrays is input to the subsequent individual bump array in the plurality of bump arrays. 
     
     
         24 . The method according to  claim 23 , wherein a single bump array performs the flowing, the contacting, the modifying, and the removing. 
     
     
         25 . The method according to  claim 23 , wherein the nucleic acid is high molecular weight (“HMW”) nucleic acid. 
     
     
         26 . The method according to  claim 23 , wherein the nucleic acid is a deoxyribonucleic acid (“DNA”), wherein the DNA is bound to at least one microparticle for carrying the DNA through the bump array. 
     
     
         27 . The method according to  claim 26 , wherein the is bound using at least one of the following: covalent binding and non-covalent binding. 
     
     
         28 . A method for processing of a fluid sample using at least one bump array, comprising
 receiving the fluid sample at the at least one bump array;   isolating, using the at least one bump array, at least one nucleic acid-containing cell and/or particle of interest from the fluid sample on the basis of a size of the cell and/or particle;   contacting, using the at least one bump array, the isolated cell and/or particle with at least one reagent stream for releasing at least one nucleic acid from the cell and/or particles in substantially pure form;   modifying the nucleic acid;   moving, using the at least one bump array, the at least one purified nucleic acid out of the reagent stream; and   removing the at least one purified nucleic acid from the at least one bump array.   
     
     
         29 . The method according to  claim 28 , wherein the nucleic acid is high molecular weight (“HMW”) nucleic acid. 
     
     
         30 . The method according to  claim 28 , wherein the nucleic acid is a deoxyribonucleic acid (“DNA”), wherein the DNA is bound to at least one microparticle for carrying the DNA through the bump array. 
     
     
         31 . The method according to  claim 28 , wherein the DNA is bound using at least one of the following: covalent binding and non-covalent binding. 
     
     
         32 . The method according to  claim 28 , wherein the fluid sample is serially processed using at least one chemical and/or enzymatic reagent stream using the at least one bump array. 
     
     
         33 . The method according to  claim 32 , wherein the nucleic acid is modified using at least one chemical and/or enzymatic reagent stream. 
     
     
         34 . The method according to  claim 33 , wherein the modified nucleic acid includes at least one of the following: a deoxyribonucleic acid (“DNA”) sequencing library and a recombinant DNA library. 
     
     
         35 . A reagent system for generating DNA sequencing libraries, comprising:
 a transposase reagent complexed with a linear DNA reagent, the DNA reagent having transposase recognition sequences and sequencing adapter sequences at each end of the DNA reagent, whereby on reaction with a DNA molecule targeted for sequencing, the transposase inserts the adapter-bearing linear DNA reagent into the sequencing target to form a cointegrate structure, wherein the sequencing target is cleaved at a single position, and the ends of the cleaved target are joined to the ends of the adapter-bearing linear DNA reagent.