Assays Based on Liquid Flow over Arrays
First Claim
1. A method of storing desiccated biological molecules or similar reagent on a flow-dividing material filling the transverse cross-section and a substantial length of a storage passage within a cassette, including so selecting and sizing the material in the passage that in the presence of a liquefying agent that can form reagent liquid with the desiccated reagent, a displacing flow of a viscosity different from that of the reagent liquid, due to the flow-dividing effect of the material, produces plug-like flow of the reagent liquid.
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Accused Products
Abstract
Flow-through assay reaction chamber (6) of cassette has back and forth liquid mixing in narrow gap (G) over array of capture agent (S), with net flow advance to waste confinement (19), produced by reversible pumps (3 or 12), operable with rolling diaphragm action with at least limited elastic recovery that advance sample or buffer liquids through conditioning paths (4A, 8, 8′, 9, 14, 15, 15′) before reaching the reaction chamber (6). A single pump produces accurate flow control, liquid conditioning, e.g., liquefying dry reagent from internal surfaces of flow-dividing material (14a, 15A, 15A′, e.g. open cell foam or frit), heating (4A), and air bubble removal (8, 8′, 9), as well as replenishment of reagent while accomplishing mixing within the flow-through reaction chamber (6). Lower viscosity buffer liquid is arranged to propel higher viscosity reagent, the flow-dividing storage material preserving reagent concentration. A blister pack (11) acts as a reversible pump (12) in producing accurate forward and backward flows with the net flow advance. Cascaded bubble traps (8, 9) on the cassette render the system tolerant of minor pumping error during cassette priming.
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Citations
110 Claims
- 1. A method of storing desiccated biological molecules or similar reagent on a flow-dividing material filling the transverse cross-section and a substantial length of a storage passage within a cassette, including so selecting and sizing the material in the passage that in the presence of a liquefying agent that can form reagent liquid with the desiccated reagent, a displacing flow of a viscosity different from that of the reagent liquid, due to the flow-dividing effect of the material, produces plug-like flow of the reagent liquid.
- 7. A cassette having a reaction chamber constructed to conduct a reaction related to an assay, the cassette including buffer liquid storage, a buffer liquid displacement pump for displacing liquids at Reynolds number less than 1 through a passage system, the passage system including a buffer delivery passage for buffer liquid displaced by the pump, a reagent storage passage having extended length in the direction of flow relative to the maximum dimension of its transverse cross-section and capable of storing a liquid reagent of viscosity relatively higher than the viscosity of the buffer liquid, and a relatively small flow cross-section reagent delivery passage leading from the reagent storage passage to the reaction chamber, the buffer delivery passage arranged to deliver displaced buffer liquid into the reagent storage passage, wherein a substantial majority of the length of the reagent storage passage is filled with flow-dividing porous material, or is defined by a multiplicity of substantially parallel flow sub-channels, the porous material or sub-channels providing a multiplicity of paths along the reagent storage passage of transverse cross sections that are small relative to the over-all transverse cross section of the reagent storage passage and distributed across its cross-section and along its length to establish, in response to the pump'"'"'s displacement of buffer liquid, plug-like flow of the relatively higher viscosity reagent liquid from the reagent storage passage into the reagent delivery passage.
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34. A cassette having a liquid storage, pumping and passage system and a reaction chamber, the cassette constructed to conduct a reaction related to an assay by flow of liquids with Reynolds number less than 1 through the system and over a capture surface within the reaction chamber, and constructed to exclude air from reaching the reaction chamber until completion of reactions of the assay, the storage, pumping and passage system including:
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an analyte chamber constructed to receive an analyte-containing liquid, an analyte displacement pump for displacing analyte-containing liquid through the system and reaction chamber, a first buoyancy bubble trap arranged to be filled by displaced analyte-containing liquid, and a passage leading from the first bubble trap to the reaction chamber;
the storage, pumping and passage system also including;pre-filled buffer liquid storage, a buffer liquid displacement pump for displacing liquids through the system and the reaction chamber, a buffer delivery passage for buffer liquid displaced by the buffer liquid displacement pump, a reagent storage passage containing a dried reagent and capable of storing the reagent in liquid form when it is liquefied, a reagent delivery passage leading from the reagent storage passage for flow to the reaction chamber, the buffer delivery passage arranged to deliver displaced buffer liquid into the reagent passage and, alternatively, through a wash passage for flow to the reaction chamber, and a second buoyancy bubble trap arranged to be filled by displaced buffer liquid and arranged for flow from the reagent store passage to flow through it the discharge of the second bubble trap connected to flow through the first bubble trap (9) and thence to the reaction chamber. - View Dependent Claims (35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 52)
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44. A method of conducting an assay with a cassette having the components indicated below and operated substantially according to the following protocol:
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1. Insert analyte liquid in analyte chamber 2 via septum 1 2. Close valves 18 &
17 (wash passage 37 and tag reagent chamber 15)3. Open valve 16 (detection reagent chamber 14) 4. Operate buffer pump 12 (rotating stepper motor, depressing piston of buffer pump) to 5. Impale pouch 11 on pyramid 30 to release buffer liquid 6. Continue operation of buffer pump 12, (depressing piston and compressing pouch 11) to fill detection reagent passage 14 until 7. Opto-sensor 13 triggers 8. Close valve 16 9. Open valve 17 10. Operate buffer pump 12 a predetermined number of stepper motor steps to fill tag reagent chamber 15 and slightly beyond within error tolerance. Stop. 11. Close valve 17 12. Open valve 18 13. Operate buffer pump 12 a predetermined number of stepper motor steps to fill wash passage 37 and bubble trap 8 and slightly beyond within error tolerance. Stop 14. Close valve 18 15. Operate analyte pump 3 to fill bubble trap 9 until Opto-sensor 5 triggers 16. Continue operation of analyte pump 3 to flow analyte liquid through reaction chamber 6 per protocol. 17. Open valve 18 and operate buffer pump 12 to wash reaction chamber 6 with buffer liquid per protocol 18. Close valve 18 19. Open valve 16 and operate buffer pump 12 to flow detection reagent through reaction chamber 6 per protocol 20. Close valve 16 21. Open valve 18 and operate buffer pump 12 to wash reaction chamber 6 with buffer liquid per protocol 22. Close valve 18 23. Open valve 17 and operate buffer pump 12 to flow tag reagent through reaction chamber 6 per protocol 24. Close valve 17 25. Open valve 18 and operate buffer pump 12 to wash reaction chamber 6 per protocol 26. Prepare chip for imaging. 27. Image the biochip through the window of the reaction chamber 6 and send data to computer for analysis 28. THE END.
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51. A method of pumping liquid within a cassette employing a deformable metal blister pack including progressively compressing and permanently deforming a body of the blister pack with an actuator (P) to displace liquid forward, and periodically reversing the movement of the actuator and allowing limited elastic recovery of the permanently deformed blister body to maintain contact with the rearward moving actuator, the increase in volume of the deformed blister pack drawing liquid back into the blister pack.
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53. A system for conducting an assay employing a cassette having a liquid displacement pump actuated by an external actuator (P) according to a predetermined automatic pumping protocol, the cassette having a liquid passage system and a reaction chamber having inlet and discharge ends associated respectively with inlet and discharge passages, the cassette constructed to conduct a reaction related to an assay by pumped flow of liquids with Reynolds number less than 1 through the passage system and over a capture surface within the reaction chamber, through the discharge passage to a waste receptacle from which there is no return, wherein;
- a control system responsive to the pumping protocol drives the pump in a cyclic operation with forward pumping and backward pumping phases in repeating cycles, the forward pumping phase arranged to produce flow through the reaction chamber out the discharge end, through the discharge passage to the waste receptacle and the backward pumping phase arranged to produce backward flow withdrawing liquid from the inlet end of the reaction chamber and the discharge passage, the net flow per cycle according to the predetermined protocol being in the forward direction out of the discharge end for substantial discharge of liquid to the waste receptacle, and replenishing flow of the liquid to which the capture surface is exposed.
- View Dependent Claims (54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90)
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64. A pumping control system for causing flow of liquid at Reynolds number less that 1 through a reaction chamber to progressively expose an assay capture surface to the liquid, wherein the control system is responsive to a predetermined pumping protocol to drive a pump in a cyclic operation with forward and backward pumping phases in repeating cycles, the forward pumping phase arranged to produce flow through the reaction chamber and out a discharge end, through a discharge passage to waste confinement and the backward pumping phase arranged to produce backward flow withdrawing liquid from an inlet end of the reaction chamber and from the discharge passage, the net flow per cycle according to the predetermined protocol being in the forward direction out of the discharge end for discharge of liquid to the waste confinement, and replenishing fresh liquid to the reaction chamber, preferably the pump located on a cassette that encloses the reaction chamber and preferably the waste confinement is a waste receptacle enclosed within the cassette.
- 91. An assay cassette having flows limited to Reynolds number NRe less than 1, comprising a flow mixing channel extending in a general direction and connected to supply reagent to a reaction chamber, the channel filled for a substantial length with a three-dimensional mass of open cell foam or frit to cause fluid flowing in the channel to split into a multiplicity of relatively small flows along differing interlaced flow paths, the paths having flow components transverse to the general direction of the channel along with flow components in the direction of the flow channel, the individual flow paths varying in direction relative to one another and being open to interchange with each other effective to produce a substantially chaotic mixing effect upon liquid flowing into and through the open cell foam or frit material, the output of the channel arranged to supply flow of the thus-mixed liquid to the reaction chamber.
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99. A cassette having a flow-through assay reaction chamber constructed for back and forth liquid mixing in a narrow gap (G) over an array of capture agent (S), with net flow advance to waste confinement produced by a reversible pump, preferably operable with rolling diaphragm action with at least limited elastic recovery, that advances sample or buffer liquids through conditioning paths before reaching the reaction chamber, the pump producing accurate flow control, liquid conditioning, e.g. liquefying dry reagent from internal surfaces of flow-dividing material, heating, and air bubble removal, as well as replenishment of reagent while accomplishing mixing within the flow-through reaction chamber;
- in the case of the pumping of buffer liquid;
preferably lower viscosity buffer liquid is arranged to propel higher viscosity reagent liquid, the flow-dividing storage material preserving the concentration of the reagent;
a blister pack on the cassette containing buffer liquid acts as the reversible pump in producing accurate forward and backward flows with the net flow advance; and
cascaded bubble traps on the cassette render the system tolerant of minor pumping error during cassette priming.
- in the case of the pumping of buffer liquid;
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100. A cassette having a liquid storage, pumping and passage system and a reaction chamber, the cassette constructed to conduct a reaction related to an assay by flow of liquids with Reynolds number less than 1 through the system and over a capture surface within the reaction chamber, the cassette constructed to be stored with air-filled passages prior to use, but, after initial entry of analyte-containing liquid into the reaction chamber, constructed to exclude air from reaching the reaction chamber until completion of reactions of the assay, the storage, pumping and passage system including:
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an analyte chamber constructed to receive an analyte-containing liquid, an analyte displacement pump for displacing analyte-containing liquid through the system and reaction chamber, a first buoyancy bubble trap arranged to be filled by displaced analyte-containing liquid, and a passage leading from the first bubble trap to the reaction chamber;
the storage, pumping and passage system also including;pre-filled buffer liquid storage, a buffer liquid displacement pump for displacing liquids through the system and the reaction chamber, the buffer liquid displacement pump having a predetermined range of flow volume error, a buffer delivery passage for buffer liquid displaced by the buffer liquid displacement pump, a reagent storage passage containing a dried reagent and capable of storing the reagent in liquid form when it is liquified, a reagent delivery passage leading from the reagent storage passage for flow to the reaction chamber, the buffer delivery passage arranged to deliver displaced buffer liquid into the reagent passage and, alternatively, through a wash passage for flow to the reaction chamber, and a second buoyancy bubble trap arranged to be filled by displaced buffer liquid; the reagent storage passage adapted to be filled by the buffer pump by activation for a predetermined pumping volume that results in leaving an indeterminate volume of un-displaced air in the buffer delivery passage of volume within a range determined by the predetermined range of flow volume error of the buffer displacement pump, the second buoyancy bubble trap sized to hold the maximum volume of air that can remain in the reagent storage passage due to the buffer pump operating for the predetermined pumping volume at the lowest flow volume within its predetermined range of flow volume error together with air released by liquid flowing through the second bubble trap, the discharge of the second bubble trap connected to flow through the first bubble trap and thence to the reaction chamber, the first bubble trap sized to hold residual air residing between the first and second bubble traps together with air released from the flow of liquids through it.
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101. A cassette, system or method in which a reagent storage channel, defined by surfaces, through which liquid flows is filled over a predetermined length with flow-dividing material, the material defining surfaces throughout the material on which dried reagent is deposited, the surfaces throughout this material in aggregate having surface area at least 10 fold greater than the aggregate surface area of the surfaces defining the portion of the channel that is filled by the material.
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102. A cassette, system or method in which flow-dividing storage material has internal surfaces carrying a deposit of dried reagent.
- 103. A cassette, system or method in which the flow-dividing material has length in the direction of flow at least 10 times the width of the material and a width that is at least twice the thickness of the material.
- 105. A method of priming a cassette passage of known volume with liquid comprising providing in the cassette a pump in the form of a blister pack capable of rolling diaphragm action and containing buffer liquid, and with a linear actuator, displacing the back of the blister pack a predetermined distance inward to displace buffer liquid to fill the known volume.
- 107. A method of conducting a flow assay by advancing liquid through a narrow flow gap (G) reaction chamber including the step of providing a storage channel containing open cell foam or frit on the internal surfaces of which reside a predetermined layer of dried reagent, introducing liquid to the storage chamber to liquefy the reagent to a known reagent concentration and advancing the liquid of known reagent concentration through the flow gap (G).
Specification