Fluid Testing Cassette

Abstract

Disposable cassettes for detecting nucleic acids or performing other assays are provided. [Solution] A cassette for detecting target nucleic acids, comprising a plurality of chambers, a plurality of vent pockets connected to the chambers, and a heat-labile material for sealing one or more of the vent pockets, wherein at least one of the vent pockets comprises a protrusion.

Description

[Technical field]

[0001] [CROSS REFERENCE TO RELATED APPLICATIONS] This application claims priority to and the benefit of U.S. Provisional Patent Application No. 62 / 152,724, entitled "Fluidic Test Cassette," filed April 24, 2015, and U.S. Provisional Patent Application No. 62 / 322,738, entitled "Fluidic Test Cassette," filed April 14, 2016, the specifications and claims of which are incorporated herein by reference.

[0002] [Technical field of the invention] FIELD OF THE DISCLOSURE Embodiments of the present invention relate to integrated devices and associated methods for detecting and identifying nucleic acids. The devices may be completely disposable or may include disposable and reusable parts. [Background technology]

[0003] Please note that the following discussion may refer to several publications and references. Discussion of such publications herein is provided for a more complete context of scientific principles and should not be construed as an admission that such publications are prior art for patentability purposes.

[0004] Due to the increasing public health impact and awareness of infectious and emerging diseases, biothreat agents, genetic diseases and environmental reservoirs of pathogens, the need for more informative, sensitive, specific, point-of-use rapid assays is increasing the demand for polymerase chain reaction (PCR) based tools. Nucleic acid based molecular tests through methods such as PCR based amplification are extremely sensitive, specific and informative. Unfortunately, currently available nucleic acid tests require sophisticated and expensive instrumentation, specialized laboratory materials and / or multiple operations dependent on user intervention, making them unsuitable for the field or of limited usefulness. As a result, most samples for molecular testing are shipped to central laboratories, requiring long round trip times to obtain the required information.

[0005] To address the need for rapid point-of-use molecular testing, previous efforts have focused on product designs that use disposable cartridges and relatively expensive associated equipment. The use of external instrumentation to accomplish fluid transfer, amplification temperature control, and detection simplifies many of the technical challenges inherent in integrating the multiple steps required for molecular testing. Unfortunately, the reliance on sophisticated instrumentation imposes significant economic barriers for small clinics, local and state governments, and law enforcement agencies. Furthermore, relying on a small number of instruments to perform testing can cause unnecessary delays during periods of increased need, such as occurs during suspected releases of biological warfare agents or emerging infectious diseases. Indeed, when an outbreak requires surge capacity and increased throughput, the instrument and disposable reagent cartridge model potentially becomes a significant bottleneck. Furthermore, the reliance on instrumentation complicates special distribution of testing devices to deployment sites where logistical constraints prevent the transportation of bulky associated equipment or where infrastructure requirements (e.g., reliable power sources) do not exist.

[0006] Gravity has been described as a means of fluid movement in existing microfluidic devices. However, typical devices do not allow for programmable or electronic control of such fluid movement, nor mixing of three or more fluids. Some devices also use the pressure drop caused by the drop of an inert or pre-fill fluid when oriented vertically to induce a slight vacuum to draw reactants into the processing chamber, which adds storage and transport complexity and ensures the stability of the pre-fill fluid. Existing devices that teach moving fluids in multiple discrete steps require fragile seals or valves between chambers, which complicate operation and manufacturing. These devices do not teach the use of separate vents located remotely for each chamber.

[0007] Typical microfluidic devices utilize smaller reaction volumes than are used in standard laboratory procedures. PCR or other nucleic acid amplification reactions, such as loop-mediated amplification (LAMP), nucleic acid-based sequence amplification (NASBA) and other isothermal and thermal cycling methods, are typically performed in testing and research laboratories using reaction volumes of 5-100 μL. These reaction volumes accommodate sufficient test specimen volume to ensure detection of rare assay targets in dilute specimens. Microfluidic systems, which reduce reaction volumes compared to those used in traditional laboratory molecular testing, also necessarily reduce the volume of specimen that can be added to a reaction. As a result of the smaller reaction volumes, there is a reduced ability to accommodate sufficient specimen volume to ensure the presence of detectable amounts of target in dilute specimens or when assay targets are scarce. [Prior art documents] [Patent documents]

[0008] [Patent Document 1] (None in particular) Summary of the Invention

[0009] The present invention is a cassette for detecting a target nucleic acid, comprising a plurality of chambers, a plurality of vent pockets connected to the chambers, and a heat labile material for sealing one or more of the vent pockets, wherein at least one of the vent pockets includes a protrusion, preferably including a dimple or irregularity, sufficient to prevent the molten heat labile material from adhering to a heat stable material disposed adjacent to the heat labile material, preferably to prevent resealing of the vent pocket after the heat labile material has ruptured.

[0010] The present invention also provides a cassette for detecting a target nucleic acid, comprising a plurality of chambers, a plurality of vent pockets connected to the chambers, a thermolabile material for sealing one or more of the vent pockets, a thermostable material, and a gasket disposed between the thermolabile material and the thermostable material, the gasket comprising an opening that encompasses the plurality of vent pockets. The gasket is preferably thick enough to provide a sufficient air volume to balance pressure and ensure free air movement between the open vent pockets. The cassette preferably comprises a flexible circuit, the flexible circuit comprising a patterned metal electrical component disposed on the thermostable material. The gasket preferably comprises a second opening or is restricted in size such that the flexible circuit is in direct contact with the fluid in at least one of the chambers. The electrical component preferably comprises a resistive heating element or conductive traces. The resistive heating element is preferably aligned with the vent pockets and the chambers. The cassette preferably comprises one or more ambient temperature sensors for regulating the heating temperature, heating time and / or heating rate of one or more of the chambers.

[0011] The invention also relates to a cassette for detecting target nucleic acids, comprising a vertically oriented detection chamber, a lateral flow detection strip disposed within the detection chamber oriented such that the sample receiving end of the detection strip is the lower end of the detection strip, and a space within the detection chamber below the lateral flow detection strip for receiving a fluid containing the amplified target nucleic acid, the space comprising a volume sufficient to accommodate a total volume of fluid with a height that allows the fluid to flow by capillary action to the detection strip without overflowing or bypassing the area of ​​the detection strip. The space preferably comprises detection particles such as dye polystyrene microspheres, latex, colloidal gold, colloidal cellulose, nanogold or semiconductor nanocrystals. The detection particles preferably comprise oligonucleotides complementary to the sequence of the amplified target nucleic acid or ligands capable of binding to the amplified target nucleic acid, such as biotin, streptavidin, haptens or antibodies. The detection particles are preferably present on at least a portion of the interior surface dried, lyophilized or as a dry mixture of detection particles in a carrier such as a polysaccharide, detergent or protein to facilitate resuspension of the detection particles. A capillary pool of fluid is preferably formed within the space to improve mixing and dispersion of the detection particles and promote intermingling of the detection particles with the amplified target nucleic acid. The cassette optionally performs an assay having a volume of less than about 200 μL, preferably less than about 60 μL.

[0012] The present invention also relates to a cassette for detecting a target nucleic acid, comprising one or more recesses for containing at least one lyophilized or dried reagent, wherein at least one recess comprises one or more structures for directing fluid to facilitate rehydration of the at least one dried or lyophilized reagent, the recess being one or more channels connected to the chamber or the cassette disposed within the one or more channels, the structures preferably comprising ridges, grooves, dimples or combinations thereof.

[0013] The invention is also a cassette for detecting target nucleic acids, comprising at least one chamber including a feature that prevents fluids that enter vertically at the top of the chamber from flowing directly into the outlet of the chamber. The feature preferably deflects the fluid to the side of the chamber opposite the outlet. The resulting fluid flow path preferably includes a horizontal component, thereby sufficiently increasing the effective length of the flow path and sufficiently reducing the flow rate of the fluid to limit the amount of fluid exiting the outlet. The feature preferably creates a swirling of the fluid in the chamber, thereby increasing the mixing of reagents in the fluid. The feature is preferably triangular or trapezoidal in shape. The outlet is optionally tapered. The channel located downstream of the outlet optionally includes a turn to increase the effective length of the channel. The feature is preferably located near the chamber or at its bottom or near the center of the chamber.

[0014] The invention is also a method of controlling the vertical flow of a fluid through a chamber in a device, by deflecting the fluid flow entering the top of the chamber, thereby preventing the fluid from flowing directly into the outlet of the chamber. The method preferably includes the step of reducing the flow rate of the fluid, thereby reducing the distance the fluid flows down a channel connected to the outlet before the flow stops. The method preferably includes the step of splitting the fluid flow into the chamber into a first fluid flow that faces upwards in contact with the walls of the chamber, and a second fluid flow that enters the outlet. The first fluid flow preferably swirls within the chamber, thereby increasing the mixing of reagents within the fluid. The second fluid flow preferably forms a meniscus and travels through a channel connected to the outlet, which increases the pressure within the closed space of the channel downstream of the fluid, until the pressure stops the fluid flow in the channel. The outlet is optionally tapered, thereby increasing the compressible air volume at the inlet to the outlet. The method optionally includes the step of providing a turn in the channel connected to the outlet, thereby increasing the effective path length of the channel and reducing the flow rate of the fluid in the channel.

[0015] The objects, advantages, and novel features, as well as further scope of applicability of the present invention, will be set forth in part in the following detailed description taken in conjunction with the accompanying drawings, and in part will become apparent to those skilled in the art upon examination of the following or may be learned by the practice of the invention. The objects and advantages of the present invention may be realized and attained by means of the instrumentalities and combinations particularly pointed out in the appended claims.

[0016] The accompanying drawings, which are incorporated in and form a part of this specification, illustrate embodiments of the invention and, together with the description, serve to explain the principles of the invention. The drawings are only for the purpose of illustrating certain embodiments of the invention and are not to be construed as limiting the invention. [Brief description of the drawings]

[0017] [Figure 1A] FIG. 1 illustrates an embodiment of a test cassette of the present invention. [Figure 1B] FIG. 1 is an exploded view of one embodiment of a test cassette revealing the interior areas of the sliding seal, sample port, sample cup, and expansion chamber. [Figure 2A] FIG. 2 is a diagram of a fluid network in one embodiment of a test cassette of the present invention. [Figure 2B] FIG. 13 is a schematic diagram of how a thermally induced vent can be used to vent an expansion chamber to achieve fluid flow control in the context of a hermetically sealed test cassette, prior to vent opening. [Figure 2C] FIG. 13 is a schematic diagram of how a thermally induced vent can be used to vent an expansion chamber to achieve fluid flow control in the context of a hermetically sealed test cassette, after vent opening. [Figure 2D] FIG. 1 illustrates one embodiment of a disposable test cassette showing the placement of a printed circuit assembly (PCA) including a resistive heating element and a temperature sensor. [Figure 2E] 2B is a photograph of an injection molded plastic test cassette including the features described in FIG. 2A. [Figure 3A] FIG. 1 illustrates the working principle of one embodiment of an expansion chamber. [Figure 3B] FIG. 13 is a cross-sectional view of a piston-based expansion chamber prior to gas expansion within a testing cassette. [Figure 3C] 13 is a cross-sectional view of a piston-based expansion chamber after gas expansion within a testing cassette. FIG. [Figure 4A] FIG. 1 illustrates an approach using an inflatable air bladder to form an expansion chamber that provides an expanded interior volume. [Figure 4B] 1 is a cross-sectional view of a bladder-based expansion chamber prior to gas expansion within a testing cassette. [Figure 4C] 13 is a cross-sectional view of a bladder-based expansion chamber after gas expansion within the testing cassette. FIG. [Figure 5A] FIG. 13 illustrates an approach using an expandable bellows to form an expansion chamber that provides an expanded interior volume. [Figure 5B] FIG. 13 is a cross-sectional view of a bellows-based expansion chamber prior to gas expansion within a testing cassette. [Figure 5C] 13 is a cross-sectional view of a bellows-based expansion chamber after gas expansion within the testing cassette. [Figure 6A] FIG. 1 illustrates the use of a semi-permeable barrier, membrane or material that allows gases to pass freely while retaining particles such as bacteria, viruses or larger molecules (such as DNA or RNA) within the device. [Figure 6B] FIG. 13 is a cross-sectional view of a semi-permeable barrier used in place of an expansion chamber to equalize internal forces with ambient pressure or to reduce internal forces. [Figure 7] FIG. 1 is an exploded view of a test cassette design in which the expansion chamber is formed by a spacer between layers of biaxially oriented polystyrene (BOPS) film. [Figure 8A] FIG. 1 is a diagram of an embodiment of a flexible circuit including resistive heating elements for two fluid chambers, a detection strip chamber, three vents and electrical contact pads. [Figure 8B]FIG. 1 is a diagram of an embodiment of a flexible circuit including resistive heating elements for two fluid chambers, a detection strip chamber, and three vents and electrical contact pads for energizing the resistive heating elements. [Figure 8C] FIG. 2 is an exploded view of one embodiment of a testing cassette. [Figure 8D] FIG. 8D is a diagram of the assembled test cassette of FIG. 8C. [Figure 9] 1 shows a lateral flow strip from a device with and without a capillary pool at the sample receiving end of the strip. When the capillary pool is present, a more uniform distribution of detection particles and a more uniform signal across the strip is observed. [Figure 10] FIG. 1 illustrates a hierarchical approach to sample partitioning. [Figure 11] 1 illustrates a multi-channel fluidic network for multiplexing and sample fractionation showing the fluid flow paths for each test. Additional fluid paths or channels can be incorporated into the network to further increase the number of parallel tests that can be performed simultaneously on a single disposable test cassette. [Figure 12] FIG. 1 illustrates the fluidic network of one embodiment of a test cassette of the present invention in which a sample is introduced into the sample cup via a sample port and then split to allow parallel independent tests on the same input sample. A bifurcated fluidic path from the sample cup allows the sample solution to be split into two separate fluidic channels or passages in the test cassette for parallel simultaneous tests on the split samples. [Figure 13A] FIG. 1 illustrates the assembled sample preparation subsystem showing internal component placement. [Figure 13B] FIG. 1 is an exploded view of the sample preparation subsystem showing components of a nucleic acid purification device configured for integration with a test cassette. [Figure 14] FIG. 2 is a cross-sectional view of a sample preparation subsystem showing the movement of parts that occur during sample processing. [Figure 15] FIG. 13 is an exploded view showing the hermetically sealed components, the injection molded fluidic subsystem, the corresponding cassette backing and the sample preparation subsystem with PCA. [Figure 16] 1 is a photograph of an embodiment of a test cassette having an integrated sample preparation subsystem. [Figure 17A] FIG. 13 is an exploded view showing the sample preparation subsystem with hermetically sealed components and an injection molded fluidic subsystem design. [Figure 17B] FIG. 1 illustrates an embodiment of a test cassette with an integrated sample preparation subsystem shown interfaced to a PCA. [Figure 17C] 1 is a cutaway view of an embodiment of a test cassette showing the fluid paths, interfaced electronics, and sample preparation components. [Figure 18A] FIG. 1 illustrates one embodiment of a docking unit of the present invention, shown with the lid in an open position and a test cassette inserted. [Figure 18B] FIG. 1 illustrates the docking unit with the lid shown in the closed position. [Figure 19] 1 is a photograph of one embodiment of the docking unit shown with the lid in the open position and a test cassette inserted. The LCD display indicates detection of the insertion of an Influenza A / B test cassette. [Figure 20] FIG. 1 illustrates one embodiment of a cassette sealing mechanism of the present invention. [Figure 21A] FIG. 13 illustrates the cassette seal sensor placement in a docking unit with a cassette inserted with the seal in the open position. [Figure 21B] FIG. 13 is a cutaway view showing the cassette seal sensor placement in a docking unit with a cassette inserted with the seal in the open position. [Figure 21C] FIG. 13 illustrates the cassette seal sensor placement in a docking unit with a cassette inserted with the seal in the closed position. [Figure 21D] FIG. 13 is a cutaway view showing the cassette seal sensor placement in a docking unit with a cassette inserted with the seal in the closed position. [Figure 22] 13A-13C illustrate one embodiment of a cassette sealing mechanism using a driven gear to mediate sealed closure with a rotating valve. [Figure 23A] 1 illustrates an embodiment of a test cassette in which the lid is a hinged lid that includes an O-ring seal and an empty air volume that acts as an expansion chamber, with the lid in the open position. [Figure 23B] FIG. 13 shows the lid in the closed position, with the O-ring forming an airtight seal with the rim of the sample port. [Figure 24A] FIG. 2 is an exploded view of the heater board and test cassette holder components of the docking unit that form the test cassette receiving subassembly. [Figure 24B] 1 illustrates one embodiment of a test cassette receiving subassembly of a docking unit. [Diagram 25] 1A-1C are slide views of the test cassette holder and heater board mounting system in engaged and disengaged positions. [Figure 26] 13A-13C show placement of infrared temperature sensors in one embodiment of a docking unit for monitoring the temperature of the first and second heated fluid chambers. [Figure 27A] FIG. 13 illustrates the placement of an optical sensor within one embodiment of a docking unit that allows for reading of a bar code located near the bottom of a test cassette. [Figure 27B] FIG. 27B is a detailed view of FIG. 27A. [Figure 28A] FIG. 13 is an exploded view of a dual heater board configuration in which a test cassette is sandwiched between two heater board assemblies. [Figure 28B] FIG. 13 is an assembly drawing of a dual heater board configuration in which the test cassette is sandwiched between two heater board assemblies. [Figure 29A] FIG. 1 is a solid line drawing of an embodiment of a docking unit in which a pivoting door is used to receive a test cassette. [Figure 29B] 1 is a perspective view of an embodiment of a docking unit in which a pivoting door is used to receive a test cassette, the closing of the pivoting door causing the rear of the test cassette to contact a heater board mounted within the docking unit. [Figure 30A]FIG. 13 is a front cutaway view of the internal components of the docking unit, including servo motors for actuating sample preparation and an optical system for test result collection. [Figure 30B] FIG. 13 is a side cutaway view of the internal components of the docking unit, including servo motors for actuating sample preparation and an optical system for test result collection. [Figure 31A] 1 is a photograph of a front view of the optical subsystem of one embodiment of a docking unit incorporating a test reader. [Figure 31B] 1 is a side view photograph of the optical subsystem of one embodiment of a docking unit incorporating a test reader. [Figure 32A] 1 is a photograph of an embodiment of a docking unit with a pivoting test cassette receiving door in an open position. [Figure 32B] 1 is a photograph of an embodiment of a docking unit with a pivoting test cassette receiving door in a closed position. [Diagram 33] FIG. 1 illustrates a reusable subassembly for the docking unit of the present invention. [Diagram 34] FIG. 1 shows test results obtained in Example 1 described herein. [Diagram 35] FIG. 1 shows test results obtained in Example 2 described herein. [Diagram 36] FIG. 1 shows test results obtained in Example 3 described herein. [Figure 37A] FIG. 1 is a perspective view of a cassette containing three chambers. [Figure 37B] FIG. 37B is an exploded view of the cassette of FIG. 37A. [Figure 38] FIG. 37B is a see-through view of the cassette of FIG. 37A showing the fluidic characteristics. [Figure 39] FIG. 1 illustrates one embodiment of a chamber of the present invention including a triangular protruding flow feature and a tapered outlet. [Diagram 40] FIG. 1 illustrates one embodiment of a chamber of the present invention including triangular protruding flow features and parallel outlets. [Diagram 41]FIG. 1 illustrates one embodiment of a chamber of the present invention including trapezoidal protruding flow features and parallel outlets. [Diagram 42] FIG. 1 illustrates one embodiment of a chamber of the present invention including stacked triangular flow features and parallel outlets. [Diagram 43] FIG. 1 illustrates an embodiment of a chamber of the present invention that includes a protruding flow feature approximately in the center of the chamber. [Diagram 44] FIG. 13 illustrates a reagent well including internal features for directing fluid flow. [Diagram 45] FIG. 1 illustrates one embodiment of a vent pocket of the present invention including a dimple structure. DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

[0018] An embodiment of the present invention is preferably a sealable disposable platform for detecting target nucleic acids, comprising a sample chamber for receiving a sample containing a target nucleic acid, an amplification chamber connected to the sample chamber via a first channel and connected to a first vent pocket via a second channel, a labeling chamber connected to the amplification chamber via a third channel and connected to a second vent pocket via a fourth channel, a detection subsystem connected to the labeling chamber via a fifth channel and connected to a third vent pocket via a sixth channel, a plurality of resistive heating elements, and one or more temperature measuring devices, each of the vent pockets being sealed from communication with the air chamber by a suitable form of thermolabile material, such as a membrane, film or plastic sheet located near the one or more resistive heating elements. The disposable platform optionally includes a seal for sealing the platform prior to the start of the detection assay. The disposable platform preferably includes a recess along the channel between the chambers to accommodate the incorporation of dried or lyophilized reagents into the disposable platform. These recesses may include structure on one or more surfaces facing the reagent(s) to help direct the fluid, possibly using capillary or surface tension effects on the enclosed dried reagent to facilitate rehydration of the dried reagent. Such features may include ridges, such as ridge (or ridge) 7001 in FIG. 44, grooves, dimples, or other structures to direct fluid into the interior space of the recess as it passes through the recess, or to aid in fluid flow into the interior space of the recess during fluid flow. Alternatively, the recesses may be located directly within the chamber(s).

[0019] The disposable platform further comprises a sample preparation stage, optionally including an output port in direct fluid connection with the input port of the sample chamber. The dimensions of the substantially flat surface of the amplification chamber are preferably approximately the same as the dimensions of the substantially flat surface of the resistive heating element in thermal contact with the amplification chamber. The amplification chamber optionally contains an amplification solution, and the recess in the channel from the sample chamber to the amplification chamber is recessed in the channel from the amplification chamber to the labeling chamber, which optionally contains a lyophilized amplification reagent mixture, and preferably contains dried or lyophilized detection particles. The amplification chamber and the labeling chamber are preferably heatable using a resistive heating element. The detection subsystem preferably comprises a lateral flow strip containing the detection particles. The chambers, channels and vent pockets are preferably located on a fluid assembly layer, and the electronics of the device are preferably located on a separate layer including a printed circuit board, which is coupled to the fluid assembly layer or contacted by a docking unit with the fluid assembly layer. The detection subsystem is preferably located on the fluid assembly layer, or optionally on a second fluid assembly layer. The volume of at least one of the chambers is preferably about 1 μL to about 150 μL. The disposable platform further includes a docking unit, which preferably maintains the disposable platform in a vertical or tilted orientation and optionally provides electrical contacts, components and / or power sources, and connectors for docking of the disposable platform.

[0020] One embodiment of the present invention is a method for detecting one or more target nucleic acids, preferably comprising the steps of dispensing a sample containing the target nucleic acid in a sample chamber of a disposable platform; orienting the disposable platform vertically or at an angle; opening a first vent pocket connected to the amplification chamber to a sealed air volume, thereby allowing the sample to flow into the amplification chamber; reacting the sample with a pre-lyophilized amplification reagent mixture located in a recess of the channel between the sample chamber and the amplification chamber; amplifying the target nucleic acid in the amplification chamber; opening a second vent pocket connected to the labeling chamber to the closed air volume, thereby allowing the amplified target nucleic acid to flow into the labeling chamber; labeling the amplified target nucleic acid with detection particles in a recess of the channel between the amplification chamber and the labeling chamber; opening a third vent pocket connected to a detection subsystem to the closed air volume, thereby allowing the labeled target nucleic acid to flow into the detection subsystem; and detecting the amplified target nucleic acid. The amplifying step preferably comprises amplifying the target nucleic acid using a resistive heating element located in the disposable platform near the amplification chamber. The method preferably further comprises passively cooling the amplification chamber. The method further comprises heating the labeling chamber during the labeling step using a resistive heating element preferably located within the disposable platform near the labeling chamber. The method further comprises controlling operation of the disposable platform by using a docking unit, which is preferably not an external device.

[0021] Embodiments of the present invention include disposable platforms that integrate an external equipment-independent means of performing all the essential steps of a nucleic acid molecular assay and complement current immuno-lateral flow rapid assays with next generation nucleic acid tests that provide more informative and sensitive analysis. Embodiments of the present invention promote the more widespread use of rapid nucleic acid tests in small clinics and austere or remote settings where infectious disease, biothreat agents, agricultural and environmental testing may have the greatest impact. Certain embodiments of the present invention are fully self-contained and disposable, allowing for "surge capacity" when demand increases by allowing parallel tests to be performed without the bottlenecks imposed by external equipment. Furthermore, in application areas where a low-cost disposable cartridge coupled with an inexpensive battery- or AC-adapter-powered docking unit is preferred, embodiments of the present invention where a simple docking unit is used further reduces the cost of testing by placing the reusable components on a reusable but inexpensive base. The platform technology disclosed herein offers similar sensitivity to laboratory nucleic acid amplification-based methods, minimal user intervention and training requirements, sequence specificity afforded by both amplification and detection, multiplexing capabilities, stable reagents, compatibility with low-cost large-scale manufacturing, battery- or solar-powered operation allowing for use in simple settings, and a flexible platform technology allowing the incorporation of additional or alternative biomarkers without instrumentation design.

[0022] The present invention provides a system and method for low-cost, point-of-use detection and identification of nucleic acids suitable for performing the analysis away from the laboratory environment where the test is typically performed. Advantageously, the nucleic acid amplification reaction volume can be in the same volume range (e.g., 5-150 μL) as is commonly used in traditional laboratory testing. Thus, the reactions performed in the present invention are directly comparable to accepted laboratory assays and allow for the accommodation of the same specimen volumes as are typically used in traditional molecular testing. Furthermore, the amplification of nucleic acids is preferably performed in a hermetically sealed test cassette that is preferably permanently sealed prior to the start of amplification. By keeping the amplified nucleic acid in a sealed system, the test environment and surrounding areas are prevented from being contaminated with the amplification products, thereby reducing the likelihood that subsequent tests will produce false positive results. Incorporating a sealing system into the test cassette allows for the formation of a seal at the start of the assay using a corresponding seal engagement system in the docking unit. In one embodiment of the present invention, a rack and pinion mechanism is used to slide the test cassette integrated seal mechanism into place to ensure pre-amplification sealed closure. A sensor located within the docking unit interrogates the test cassette to ensure that a seal has been formed before initiating the test reaction.

[0023] Embodiments of the invention can be manufactured using injection molding methods and ultrasonic welding to achieve high throughput manufacturing and low cost disposable parts. In some embodiments, one or more recesses are provided in the fluidic parts to accommodate dry reagent pellets, respectively. The recesses allow for the use of freeze-dried or otherwise dried materials present in the fluidic parts during final assembly, where ultrasonic welding can be used, without destroying the pellets by the energy introduced into the system during welding.

[0024] The embodiments of the present invention can be used to detect the presence of a target nucleic acid sequence(s) in a sample. The target sequence can be DNA, such as chromosomal or extrachromosomal DNA (e.g., mitochondrial DNA, chloroplast DNA, plasmid DNA, etc.), or RNA (e.g., rRNA, mRNA, small RNA, or viral RNA). Similarly, embodiments of the present invention can be used to identify nucleic acid polymorphisms, including single nucleotide polymorphisms, deletions, insertions, inversions, and sequence duplications. Additionally, embodiments of the present invention can be used to detect gene regulatory events, such as gene up- and down-regulation at the transcriptional level. Thus, embodiments of the present invention can be used for applications such as: 1) detection and identification of pathogen nucleic acids in agricultural, clinical, food, environmental, and veterinary samples; 2) detection of genetic biomarkers of disease; and 3) diagnosis of the presence of a disease or metabolic condition through detection of associated biomarkers of the disease or metabolic condition, such as gene regulatory events (mRNA up- or down-regulation, or induction of small RNAs or other nucleic acid molecules that are generated or suppressed during a disease or metabolic condition) that occur in response to the presence of a pathogen, toxin, other etiologic agent, environmental stimulus, or metabolic condition.

[0025] The embodiments of the present invention include means for target nucleic acid sample preparation, amplification and detection upon addition of the nucleic acid sample, including all aspects of fluid control, temperature control and reagent mixing. In some embodiments of the present invention, the device provides means for nucleic acid testing using a portable power source such as a battery and is completely disposable. In other embodiments of the present invention, a disposable nucleic acid testing cartridge works in conjunction with simple reusable electronics that can perform all of the functions of laboratory instrumentation, such as external equipment, typically required for nucleic acid testing without the need for the use of such laboratory instrumentation or external equipment.

[0026] The embodiments of the present invention provide a nucleic acid amplification and detection device that includes, but is not limited to, a housing, a circuit board, and a fluidic or microfluidic component. In certain embodiments, the circuit board can contain various surface mount components such as resistors, thermistors, light emitting diodes (LEDs), photodiodes, and microcontrollers. In certain (certain) embodiments, the circuit board can include a flexible circuit board that includes a thermally stable substrate such as polyimide. The flexible circuit can include a copper or other conductive coating or layer deposited on or bonded to the thermally stable substrate in some embodiments. These coatings can be etched or patterned to include resistive heating elements used for biochemical reaction temperature control and / or conductive traces to accommodate such heating elements and / or surface mount components (such as resistors, thermistors, light emitting diodes (LEDs), photodiodes, and microcontrollers). The fluidic or microfluidic components are the device parts that receive, contain, and move aqueous samples, and can be manufactured from various plastics and by various manufacturing techniques including ultrasonic welding, gluing, fusing or lamination, laser cutting, water jet cutting, and / or injection molding. The fluidic and circuit board components are held together reversibly or irreversibly, and their thermal coupling may be enhanced by a thermally conductive material or compound. The housing preferably serves in part as a cosmetic and protective sheath, hiding the delicate components of the microfluidic and circuit board layers, and may also serve to facilitate sample input, buffer release, nucleic acid elution, seal formation, and initiation of steps necessary for device functionality. For example, the housing may incorporate a sample input port, a mechanical system for forming or engaging a seal, a button, or similar mechanical features that allow user activation, buffer release, initiation of sample flow, nucleic acid elution, and thermal or other physical interface formation between the electronic and fluidic components.

[0027] In some embodiments of the invention, the fluidic or microfluidic component comprises a series of chambers in controlled fluid communication, where the chambers are optionally temperature controlled, thereby subjecting the fluids contained therein to a programmable temperature regime. In some embodiments of the invention, the fluidic or microfluidic component preferably comprises five chambers, including an expansion chamber, a sample input chamber, a reverse transcription chamber, an amplification chamber and a detection chamber. The sample input chamber preferably comprises a conduit to the expansion chamber, a sample input orifice to which a nucleic acid-containing sample can be added, a first recess in which a dry material can be placed during production to mix with the input sample, and an outlet conduit to a second recess in which a dry material can be placed during production, and a conduit from there to the reverse transcription chamber. In other embodiments, two or more functions of the chambers are integrated into a single chamber, allowing the use of fewer chambers.

[0028] The first and second recesses may also contain lyophilized reagents, which may include, for example, appropriate buffers, salts, deoxyribonucleotides, ribonucleotides, oligonucleotide primers, and enzymes (such as DNA polymerase and reverse transcriptase). Such lyophilized reagents are preferably solubilized upon entry of the nucleic acid sample into the recesses. In some embodiments of the invention, the first recess contains salts, chemicals, and buffers useful for lysis of the biological sample and / or stabilization of nucleic acids present in the input sample. In some embodiments of the invention, the input sample is heated in the sample input chamber to achieve lysis of cells or viruses present in the sample. In some embodiments of the invention, the second recess contains lyophilized reagents and enzymes, such as reverse transcriptase, useful for synthesis of cDNA from RNA. In one embodiment of the invention, the second recess is sufficiently isolated from the sample input chamber to allow the material in the second recess to maintain a lower temperature than the temperature of the sample input chamber during heating. In some embodiments of the invention, the reverse transcription chamber includes a conduit that includes a third recess containing lyophilized reagents for amplification of nucleic acids. The sample input chamber, reverse transcription chamber, amplification chamber and detection chamber are preferably positioned in alignment or sufficient proximity to the heating elements on the heater circuit board to provide thermal conduction when attached to the heater board, either directly or through insertion of a fluidic or microfluidic component or cassette into a docking unit. Similarly, the electronic components present on the heater circuit board are preferably positioned in physical contact or proximity to vent pockets in the fluidic components to allow electronic control by opening of the vents. The physical layout of the heater circuit board is designed to provide alignment with the elements of the fluidic or microfluidic components, such that the resistive heating elements of the heater circuit board for lysis, reverse transcription, amplification, hybridization and / or fluid flow control are positioned to form a thermal interface with the elements of the fluidic components with which they interact.

[0029] In some embodiments of the invention, the fluidic or microfluidic component preferably comprises five chambers including a sample input chamber, a lysis chamber, a reverse transcription chamber, an amplification chamber and a detection chamber, and recesses for dried or lyophilized reagents located along the channel between each chamber. In this embodiment, reverse transcription of RNA to cDNA and amplification of cDNA occur in separate chambers. In this embodiment, a first recess located along the conduit leading from the sample input cup to the lysis chamber contains salts, chemicals (e.g., dithiothreitol) and buffers (e.g., stabilizing, increasing or decreasing pH) useful for lysis of biological material and / or stabilizing nucleic acids present in the input sample. In some embodiments of the invention, the input sample is first heated in a thermal lysis chamber flowing from the sample input cup through the first recess, where the sample optionally mixes with the material that constitutes the first recess. In other embodiments of the invention, lysis is achieved by a chemical process resulting from the mixing of the sample with chemicals in the first recess and incubation of the sample in the presence of these chemicals in the lysis chamber.

[0030] After the process in the lysis chamber is substantially completed, the sample solution is released by electronic control of a heater that non-mechanically bursts the vent, allowing the sample solution to flow through the second recess into the reverse transcription chamber. The second recess may contain lyophilized reagents that may optionally contain suitable buffers, salts, deoxyribonucleotides, ribonucleotides, oligonucleotide primers and enzymes (such as DNA polymerase and / or reverse transcriptase required to achieve reverse transcription of RNA in the sample into cDNA). After the reverse transcription reaction is substantially completed, the second vent is opened, releasing the sample solution to flow through a channel composed of lyophilized reagents that may contain reagents necessary for nucleic acid amplification, such as suitable buffers, salts, deoxyribonucleotides, ribonucleotides, oligonucleotide primers and enzymes (such as DNA polymerase) and the third recess into the amplification chamber.

[0031] After the nucleic acid amplification in the amplification chamber is substantially complete, the third vent is opened to release the sample solution into the channel leading to the detection chamber. The channel optionally but preferably includes a fourth recess containing a dried or lyophilized detection reagent, such as a chemical and / or a detection particle conjugate useful for the detection of the nucleic acid in the detection chamber. The detection chamber preferably includes a capillary pool, a reagent for detecting the amplified nucleic acid, and a lateral flow detection strip. The capillary pool preferably provides a space of sufficient volume to accommodate the entire volume of fluid in the detection chamber, with a height designed to receive the fluid for correct capillary migration to the detection strip, allowing the fluid to flow by capillary action to the detection strip without overflowing or bypassing the area of ​​the detection strip. In some embodiments of the invention, the detection reagent is a lyophilized reagent. In some embodiments of the invention, the detection reagent includes dyed polystyrene microspheres, colloidal gold, semiconductor nanocrystals, or cellulose nanoparticles. The sample solution mixes with the detection reagent in the detection chamber and flows by capillary action to the detection strip. A microheater aligned with the detection chamber can optionally be used to control the temperature of the solution as it travels to the detection strip.

[0032] In some embodiments of the present invention, the amplification reaction is an asymmetric amplification reaction, in which one primer of each primer pair in the reaction is present at a different concentration from the other primer of a given pair.Asymmetric reactions can be useful for making single-stranded nucleic acid to facilitate detection by hybridization.Asymmetric reactions can also be useful for generating amplicons in linear amplification reactions, which allow quantitative or semi-quantitative analysis of target levels in samples.

[0033] Other embodiments of the invention include a nucleic acid reverse transcription, amplification and detection device integrated with a sample preparation device. The embodiments that include a sample preparation device provide a means of fluid communication between an output port or valve of the sample preparation subsystem and an input port(s) of the fluidic or microfluidic component of the device.

[0034] Other embodiments of the invention include a means for splitting an input sample into two or more fluid paths within a fluidic or microfluidic component. The means for splitting the input sample includes a branching conduit for carrying the input fluid to metering chambers of a volume designed to split the fluid across the multiple fluid paths. Each metering chamber includes a channel conduit to a vent pocket and a channel conduit to the next chamber in the fluid path, such as a lysis chamber or a reverse transcription chamber or an amplification chamber.

[0035] Unless otherwise defined, all technical terms, notations and other scientific terms used herein are intended to have the meanings commonly understood by those skilled in the art to which the present invention belongs.The techniques and procedures described or referenced herein are generally well understood and commonly used by those skilled in the art using conventional methodologies, such as the widely used molecular cloning methodologies described in Sambrook et al., Molecular Cloning: A Laboratory Manual, 3rd Edition (2001) Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, and Current Protocols in Molecular Biology (Ausbel et al., editors, John Wiley & Sons, Inc. 2001).Procedures involving the use of commercially available kits and reagents, where necessary, are generally carried out according to manufacturer-defined protocols and / or parameters, unless otherwise specified.

[0036] As used throughout the specification and claims, the term "target nucleic acid" or "template nucleic acid" refers to a fragment or sequence of single- or double-stranded DNA or RNA intended to be detected.

[0037] As used throughout the specification and claims, the term "microparticle" or "detection particle" refers to any compound used to label nucleic acid products generated during an amplification reaction, including fluorescent dyes specific for double-stranded nucleic acids, fluorescently modified oligonucleotides and oligonucleotide-conjugated quantum dots, or solid phase elements such as polystyrene, latex, cellulose or paramagnetic particles or microspheres.

[0038] As used throughout the specification and claims, the term "chamber" refers to a fluid compartment in which a fluid resides for a period of time. For example, a chamber can be a sample chamber, an amplification chamber, a labeling chamber, or a detection chamber.

[0039] As used throughout the specification and claims, the term "cassette" is defined as a disposable or consumable cassette, housing, component, or cartridge used in performing an assay or other chemical or biochemical analysis. Cassettes may be single use or multiple use.

[0040] As used throughout the specification and claims, the term "pocket" refers to a compartment that serves as a venting mechanism. The pocket is preferably adjacent to or overlaid with a resistor or other mechanism for opening the pocket. For example, unlike the fluid chambers described above, a pocket formed in the fluidic component of the cassette can have one open side that aligns with a resistor on the PCA. This open side is preferably covered by a membrane, film or other material to form a sealed cavity that is easily ruptured by applying energy to the underlying resistor.

[0041] As used throughout the specification and claims, the term "channel" typically refers to a narrow conduit in a fluidic assembly that connects two or more chambers and / or pockets or combinations thereof, including, for example, an inlet, outlet or vent channel. In the case of an inlet or outlet channel, the fluid sample travels through the channel. In the case of a vent channel, a conduit is preferably separate from the fluid and connects the fluid chamber to the vent pocket.

[0042] As used throughout the specification and claims, the term "external instrument" means a reusable instrument that has one or more of the following characteristics: performs mechanical actions on the disposable assay or cassette other than sealing the cassette, including but not limited to puncturing and / or pumping buffer packets or actively providing a transport force for fluids, contains moving parts to control valves and other components for fluid flow control in the cassette or disposable assay, controls fluid flow other than by selective heating of the assay, or requires periodic calibration.

[0043] As used throughout the specification and claims, the term "docking unit" means a reusable device that controls an assay but does not have any of the characteristics listed above for the external instrument.

[0044] An embodiment of the present invention is a device for low-cost, point-of-use nucleic acid testing, suitable for performing analysis away from the laboratory environment where the testing is typically performed. Certain devices include fluidic and electronic components or layers, optionally encased by a protective housing. In an embodiment of the present invention, the fluidic components are constructed of plastic and include a series of chambers and pockets connected by narrow channels that are oriented perpendicular to each other during operation. The fluidic components are preferably covered by or placed in physical contact with electronic components controlled via a microcontroller, such as printed circuit boards containing prefabricated surface mount devices (SMDs) and / or flexible circuits containing etched conductive materials to form resistive heating elements and optionally containing SMDs. In some embodiments of the device, the entire assembly is disposable. In other embodiments, the fluidic and physically coupled electronic layers are disposable and the small, inexpensive control unit is reusable. In another embodiment, the fluidic components are disposable and the small control docking unit or docking unit is reusable. For all embodiments, the present invention may be integrated with a nucleic acid sample preparation device such as described in WO 2009 / 137059, entitled "Highly Simplified Lateral Flow-Based Nucleic Acid Sample Preparation and Passive Fluid Flow Control," which is incorporated herein by reference, and / or the methods of use described therein.

[0045] Embodiments of the invention include an integrated nucleic acid testing device that can be inexpensively manufactured with established manufacturing methods. The invention maintains simplicity from the end user's perspective of a widely accepted portable immunoassay, overcomes the challenges of regulating fluid temperatures within the device, and transports small sample volumes with sequential steps of reagent addition, reagent mixing, and nucleic acid detection while providing molecular testing data. In some embodiments of the invention, subsystems for collecting, interpreting, reporting, and / or communicating assay results are incorporated into the invention. Embodiments of the invention are uniquely adapted to utilize off-the-shelf electronic elements that can be constructed by standard assembly techniques and require no or few moving parts. Furthermore, the fluidic layer design allows for the use of readily available plastics and manufacturing techniques. The result is an inexpensive, disposable, reliable device capable of isolating, amplifying, and detecting nucleic acids without the need for dedicated laboratory infrastructure.

[0046] Existing nucleic acid testing devices typically use sophisticated heating elements such as deposited film heaters and Peltier devices that add significant cost and / or require specialized manufacturing methods. In an embodiment of the present invention, heating of the reaction solution is preferably achieved by the use of simple resistive surface mount devices that can be purchased for less than a few pennies and are assembled and tested by common manufacturing standards. By laminating a fluid chamber over these resistive elements and associated sensor elements, the fluid temperature of the reaction solution can be conveniently adjusted. The wide use of SMD resistors and flexible circuits in the electronics industry ensures that the present invention can be subjected to well-established quality control methods. In another embodiment of the present invention, resistive heating is achieved using heating elements formed by patterns assembled on the conductive layer of a flexible circuit board. Many nucleic acid amplification techniques, such as PCR, not only require rapid heating of the reaction solution, but also rapid cooling. The reaction chamber of the present invention is preferably heated on one side, and ambient temperature across the opposite face is used to help reduce the fluid temperature. Additionally, the vertical orientation of device embodiments allows for more rapid cooling by passive convection than if the device were oriented horizontally, thereby reducing thermal cycling periods without the use of expensive devices such as Peltier devices. In some embodiments of the invention, fans are used to facilitate cooling.

[0047] Fluid control is another challenge associated with low-cost nucleic acid testing device design. Devices known in the art generally use electromechanical, electrokinetic or piezoelectric pumping mechanisms to manipulate fluids during device operation. These pumping elements increase both the complexity and cost of the device. Similarly, valves using elaborate micromechanical designs or moving parts can increase fabrication costs and reduce reliability due to complications such as moving part failure or biofouling. Unlike the nucleic acid testing devices described above, embodiments of the present invention utilize hydrostatic pressure under microcontroller control along with capillary forces and surface tension to manipulate fluid volumes. The vertical orientation of some embodiments of the present invention allows reaction solutions to be cascaded from chamber to chamber under microcontroller control to accommodate the required operation of the assay. Fluids can be retained within the individual reaction chambers by balancing channel size, hydrostatic pressure and surface tension, with surface tension and hydrostatic pressure impeding fluid advancement by gas displacement. Samples preferably advance to the lower chamber only after a simple venting mechanism is activated under microcontroller control. Once open, the vent allows fluid to move from a first chamber to a second chamber by providing a passage for displaced air to escape the second chamber as fluid enters. Each chamber (or each channel between chambers) in the fluidic component connects to a sealed vent pocket, preferably through a narrow vent channel. The vent pocket is sealed on one side with a membrane or sheet of thin thermolabile plastic that is easily ruptured by heating a small surface mount resistor, preferably underneath, near or adjacent to the membrane or sheet. Once the lower chamber vent is opened, fluid progression proceeds even under low hydrostatic pressure.

[0048] As described more specifically below, the fluidic or microfluidic venting mechanism used in some embodiments of the invention preferably allows electronic control of fluid movement by venting the low elevation chamber to allow fluid from the high elevation chamber to flow into the lower chamber using heat and (optional) a heating element in physical contact with the thermolabile seal. In one embodiment, a resistor is mounted on a printed circuit board using widely used and well-established electronics manufacturing methods and is in physical contact with the channel seal containing the thermolabile material. When energized, the surface mounted resistor generates enough heat to rupture the seal, resulting in venting of the chamber to allow for pressure equilibration in the area or chamber where the fluid is present prior to venting and the area or chamber where the fluid is moving. The pressure equilibration between the chambers allows for fluid movement from the high elevation chamber to the low elevation chamber. A direct seal between the high elevation chamber and the low elevation chamber is preferably not used. The channel and vent seals may be located away from the fluid chambers, facilitating fluidic device layout in a configuration that is efficient for manufacturing. The sealant can include any material, such as a thin plastic sheet, that is capable of sealing the vent channel and bursting from the heating described. This approach to fluid movement control within the device benefits from low material costs, suitability for manufacturing using established manufacturing techniques, while providing the ability to move fluids through a series of chambers under the control of electronic control circuitry, such as a microprocessor or microcontroller. The use of vents, a thermolabile material that seals the vents (and does not seal either the fluid chambers or the fluidic microchannels themselves), and electronic means of breaking said seals by heat provides a means to control the fluid flow through the device to allow movement of fluids at a predetermined time or after completion of a particular event (e.g., reaching a temperature, a temperature change or series of temperature changes, or completion of an incubation time(s), or other event). In some embodiments, blockages may be introduced into the channels between the chambers if water in the gas phase must be isolated from the chambers connected by said channels.The blockage may be a soluble material that dissolves upon contact with liquid water after the vent is opened, or it may be an easily meltable material such as paraffin that can be removed by introducing heat to the blockage site.

[0049] Furthermore, the vent approach has several advantages over sealing the fluid chambers themselves. The vent pockets can be located anywhere in the fluidics layout and can simply communicate with the regulating chambers via the vent channels. From a manufacturing standpoint, the vent pockets can be localized such that only a single sealing membrane for the entire vent pocket (which may include the vent pocket manifold) is attached to the fluidic components, preferably by well-established methods such as adhesives, thermal lamination, ultrasonics, laser welding, etc. In contrast, directly sealing the fluid chambers requires the sealant to be placed at different locations corresponding to each chamber location, which is more difficult to manufacture. This presents a more challenging scenario during manufacturing compared to a single vent pocket manifold sealed by a single membrane. Furthermore, when sealing the chambers directly, the molten sealing material can remain in the channels between the chambers and occlude the flow. The viscosity of the sealing material can require more pressure in the fluid column than can be obtained with a miniaturized gravity-driven device.

[0050] In embodiments of the present invention, reagent mixing requires less complexity than other systems. Reagents necessary for nucleic acid amplification, such as buffers, salts, deoxyribonucleotides, oligonucleotide primers and enzymes, are preferably stably incorporated by the use of lyophilized pellets or cakes. These lyophilized reagents are sealed in fluid chambers, recesses in fluid chambers or recesses in channels and can be easily solubilized upon contact with aqueous solutions. If additional mixing is required, the vertical orientation of embodiments of the present invention provides the opportunity for novel methods of mixing solutions. By utilizing a heater below the fluid chamber, the gas is heated and bubbles are transferred to the reaction solution in the chamber if the solution contains heat-sensitive components. Alternatively, if the solution does not contain heat-sensitive components, the heater can be used to directly heat the solution to a point where boiling occurs. The generation of bubbles is usually undesirable in previously disclosed fluidic and microfluidic devices, as the bubbles accumulate in the fluid chambers and channels and displace the reaction solution or impede fluid movement within the device. The vertical design of the embodiments of the invention presented herein allows the bubbles to rise to the fluid surface, resulting in only minimal transient fluid displacement, effectively ameliorating the adverse effects of bubbles on the fluid or microfluidic system. Mixing by boiling is also convenient in this vertical design, as the fluid displaced during the process simply returns to the original fluid chamber by gravity after the heating element is turned off.

[0051] In an embodiment of the invention, a colorimetric detection strip is used to detect the amplified nucleic acid. Due to its ease of use, reliability and low cost, lateral flow assays are commonly used for immunoassay testing. The prior art includes descriptions of the use of lateral flow strips to detect nucleic acids using a porous material as a sample receiving zone located at or near a labeling zone also comprised of a porous material and disposed at or near one end of a lateral flow assay device. In these previous inventions, the labeling moiety is in the labeling zone. The use of a porous material as the sample receiving zone and labeling zone results in the retention of some sample solution as well as detection particles in the porous material. Although an embodiment of the invention can use a labeling zone comprising a porous material with reversibly immobilized moieties necessary for detection, an embodiment of the invention preferably utilizes detection particles or moieties that are retained in an area of ​​the device that comprises a non-porous material with low fluid retention properties, unlike the sample receiving zone of the lateral flow strip. This approach allows the nucleic acid target-containing sample to be labeled prior to introduction into the porous component at the sample receiving end of the lateral flow component of the device, thereby eliminating retention and / or loss of sample material and detection particles in the porous labeling zone. The method further allows for the use of various treatments of the sample in the presence of the detection moiety, such as treatment at elevated temperatures, to achieve denaturation of secondary structures within double-stranded or single-stranded targets without concern for the effects of temperature on the porous sample receiving or labeling zone material or the lateral flow detection strip material. Furthermore, by using a labeling zone that is not in lateral flow contact with the sample receiving zone but is subject to the control of a fluidic component such as a vent, the target and label can remain in contact for a time period controlled by the fluid flow control system. Thus, embodiments of the present invention may differ from traditional lateral flow test strips where the interaction time and conditions of the sample and detection particles are determined by the capillary transport properties of the material. By incorporating the detection particles in a temperature regulated chamber, denaturation of double-stranded nucleic acids is possible, allowing for efficient hybridization-based detection. In an alternative embodiment, fluorescence is used to detect nucleic acid amplification using a combination of LEDs, photodiodes and optical filters.These optical detection systems can be used for real-time nucleic acid detection and quantification during amplification, as well as end-point detection after amplification.

[0052] Embodiments of the invention include a low-cost point-of-use system that can selectively amplify and detect nucleic acid samples. Further embodiments include integration with a nucleic acid sample preparation device such as that described in WO 2009 / 137059 entitled "Highly Simplified Lateral Flow-Based Nucleic Acid Sample Preparation and Passive Fluid Flow Control." Device embodiments preferably include both plastic fluidic components and printed circuit assemblies (PCAs) and / or flexible circuits, optionally housed in a housing that protects the active components. Temperature regulation, fluid and reagent mixing are preferably coordinated by a microcontroller. The reaction cassette is preferably oriented and runs vertically such that gravity, hydrostatic pressure, capillary forces and surface tension, in conjunction with vents triggered by the microcontroller, control fluid movement within the device.

[0053] In an embodiment of the invention, a prepared sample fluid or crude sample fluid enters the sample port and fills or partially fills the sample cup. The sample can be held for various times in the sample cup where dried or lyophilized reagents can be mixed with the sample. Reagents such as positive control reagents, control templates or chemical reagents beneficial to the performance of the test can be introduced to the sample solution by including them in dry, liquid or lyophilized form in the sample cup. Other processing such as controlled temperature incubation or thermal lysis of bacterial or viral analytes can optionally be accomplished in the sample cup by an underlying microheater and temperature sensor system interfaced with temperature control electronics.The fluidic network may include subsystems such as: a sample port, where a sample is introduced into the cassette manually by a user or via an automated system, essential for example a docking unit or a sample processing subsystem; a sample cup, which holds the sample to facilitate accumulation while the sample is being introduced and for the addition of reagents, components for performing any required processing (e.g., heat treatment to perform lysis of bacterial cells or viruses) before further movement of the sample to downstream parts of the fluidic network; recirculation vent passages for equilibration of the air, gas or solution pressures of the fluidic channels and / or chambers with the pressures of the expansion chambers of the cassette; a sample port, where a sample is introduced into the cassette by a sample solution or a buffer introduced into the cassette prior to the addition of the sample; The cassette may include: a bead recess that can be opened to rehydrate beads or pellets contained therein and thus mix the material therein with the sample solution; a set of one or more vents that can be opened to control fluid movement within the cassette; a first chamber in which the sample can be subjected to a temperature regime; any barrier in the fluid channel connecting the first chamber with the second chamber to prevent premature entry of liquid and / or gas into the second chamber or to temporarily control the movement of solution or gas into the second chamber; a second chamber in which the sample solution can be subjected to a further temperature regime, optionally after adding reagent from an optional reagent bead recess located between the first and second chambers; and a test strip recess that forms a chamber in which a test strip is mounted to detect an analyte or a reporter molecule or other substance indicative of the presence of an analyte. In some embodiments, the cassette is inserted into a docking unit that performs the functions of sealing, elution, detection and data transfer of the cassette. Preferably, no user intervention is required once the cassette is inserted into the docking unit, the sample is filled and the lid is closed.

[0054] With reference to the representative drawing of the cassette 2500 in Figs. 1-2, a nucleic acid sample is added to the sample cup 10 in the fluidic component 5 through the sample port 20. The sliding seal 91 is moved to a closed position by closing the docking unit lid at the start of the assay. The cover 25 holds the slide 91 in place to seal the expansion chamber 52. The nucleic acid sample may be derived from an online (i.e., integrated nucleic acid preparation subsystem), a separate nucleic acid preparation process (e.g., one of many commercially available methods, e.g., spin column), subsequent addition of purified nucleic acid to the device by pipette, or from an unprocessed nucleic acid-containing sample. Already present in the sample cup, preferably in the recess 13 in or adjacent to the sample cup, is a reagent mixture 16, which may be in liquid or dry form and contains components useful for promoting lysis of cells and viruses and / or stabilizing free nucleic acids. For example, dithiothreitol and / or pH buffering reagents may be used to stabilize nucleic acids and inhibit RNases. Similarly, reagents for achieving acid- or base-mediated lysis may be used. In some embodiments, the reagent mixture is lyophilized to form a lyophilized reagent. In some embodiments, a positive control, such as a virus, bacteria, or nucleic acid, is present in the reagent mixture. Introduction of the sample into the sample cup causes the reagent and sample to mix so that the reagent acts on the sample. An optional bubble mixing step can optionally be performed to further mix the sample with the reagent or to resuspend the reagent. The fluid is then optionally heated in the sample cup 10 to lyse cells and viral particles. The fluid is then directed, preferably through channel 40, to the first chamber 30 that is present below the sample cup when the device is in a vertical orientation. The reagent recess 15 is preferably positioned along the inlet channel such that the fluid passes through the recess and mixes with the dried or lyophilized reagent contained therein before entering the first chamber 30. In embodiments in which the first chamber is a reverse transcription chamber, preferably present in the reagent recess 15 are all components necessary for the reverse transcription reaction, such as buffer reagents in dried or lyophilized form, dNTPs, oligonucleotide primers, and / or enzymes (e.g., reverse transcriptase).The reverse transcription chamber is preferably in contact with a heating element to provide a means for temperature regulation necessary to support reverse transcription of RNA to cDNA. Channel 35 connects chamber 30 to reagent recess 37. After cDNA synthesis in chamber 30, vent 50 is opened to allow the reverse transcription reaction to flow through channel 35 into reagent recess 37. The dried or lyophilized reagents present in reagent recess 37 mix with the fluid as it passes through the recess via inlet 39 to second chamber 90 so that the reagents act on the sample in the second chamber, which is preferably an amplification chamber. Preferably, all components required for an amplification reaction are present in reagent recess 37, such as buffers, salts, dNTPs, rNTPs, oligonucleotide primers and / or enzymes. In some embodiments, the reagent mixture is lyophilized to form lyophilized reagents. To facilitate multiplexed testing generating multiple amplicons, multiplex amplification can be achieved by depositing multiple primer sets in the amplification chamber(s), preferably in the reagent recesses upstream of said amplification chamber(s). Furthermore, the circuit board and fluid design that incorporates multiple amplification and detection chambers into the device supports multiple parallel amplification reactions, which may be single-plex or multiplex reactions. This approach reduces or eliminates the complications known to those skilled in the art that arise from multiplex amplification using multiple primer pairs in the same reaction. Furthermore, the use of multiple amplification reaction chambers allows simultaneous amplification under different temperature regimes to accommodate the requirements for optimal amplification, such as different melting or annealing temperatures required for different targets and / or primer sequences.

[0055] After nucleic acid amplification, vent pocket 150 is opened to allow the amplification reaction products to flow through channel 135 into chamber 230. Detection strip 235 located within chamber 230 allows for detection of target nucleic acids labeled with detection particles located on the region of detection strip 235 or optionally within capillary pool 93.

[0056] Fluid transfer from the sample cup 10 to the first chamber 30 occurs as the chamber 30 is vented to the expansion chamber 52 through the opening 51. Fluid transfer from the first chamber to the second chamber of the device is preferably achieved by the opening of a vent connected to the second chamber. When the fluid enters the first chamber 30, the vent pocket 50 connected to the downstream chamber is sealed, so that the fluid does not pass through the channel 35 connecting the two chambers. Now referring to FIG. 2A, the transfer of fluid from the chamber 30 to the chamber 90 can be achieved by rupturing the seal covering the vent pocket 50, thereby communicating the air in the chamber 90 with the air in the expansion chamber 52. The rupture of the seal in the vent pocket 50 allows communication of the air in the chamber 90 through the vent channel 60 with the air in the expansion chamber 52 connected to the vent pocket 54 through the opening 51. As shown in FIG. 2B, the seal in the vent pocket 54 is preferably open or pre-ruptured. As shown in FIG. 2C, the rupture of the seal of the vent pocket 50 allows the vent pocket 50 (and thus the chamber 90) to communicate with the vent pocket 54 (and thus the expansion chamber 52). This method of fluid transfer is preferably embodied in an airtight sealed space to contain the biohazard sample and the amplified nucleic acid in the test cassette. To enable an airtight sealed cassette, selective heat resistant and heat labile materials are layered in a manner that is represented diagrammatically in the cross-sectional views of FIG. 2B-2C. Referring now to FIG. 2B-2C, a heat source 70, preferably comprising a resistor on a printed circuit board or PCA 75, is positioned in alignment with the vent pockets 50, 54 and in close proximity to a heat labile vent pocket sealant 80. The vent pocket seal may comprise a heat labile material such as polyolefin or polystyrene. A heat stable material (such as polyimide) 72 is preferably positioned between the heat source 70 and the heat labile vent pocket sealant 80 to form an airtight barrier.In some embodiments, the sealed space 55 between or surrounding the vent pockets is augmented by including an optional gasket or spacer 56, preferably including an adhesive layer that bonds the thermally stable material 72 to the thermally labile material 80 and / or the fluidic component 5 and maintains an airtight seal of the test cassette in the area of ​​the vent after opening one or more vents, while also providing an air gap for air communication between the open vents and / or optional expansion chambers. In this embodiment, heat is transferred from the heat source 70 through the thermally stable material 72 and the sealed space 55 to the thermally labile vent pocket sealant 80, rupturing it and opening the vent pocket 50. The microcontroller is preferably responsible for sending an electric current to the heat source 70. The vent pocket 50 preferably opens into a closed space such that the gas within the test cassette remains sealed against the environment outside the test cassette. The sealed space can contain air within the test cassette, optionally including an empty air chamber to allow gas expansion, such as an expansion chamber. As shown in FIG. 2C, the vent pocket 54 has been pre-ruptured by a heat source 71, and the vent pocket 54 is in gas communication with the expansion chamber, so that opening the vent pocket 50 results in communication of the gas in the vented fluid chamber with the gas in the expansion chamber. The resulting reduced pressure in the vented fluid chamber allows fluid to flow by gravity from the upper chamber into the vented chamber. Other embodiments of the vent pocket can include seals other than a heat sensitive membrane and can utilize other methods of disrupting the seal, such as puncturing, rupturing or melting. A photograph of such a cassette is shown in FIG. 2E.

[0057] The surface of the vent pocket opposite the opening surface can optionally include dimples, protrusions, irregularities or other similar structures, such as dimple 7004 in FIG. 45, to facilitate the formation of an opening during rupture of the vent sealant. Such structures also preferably prevent resealing of the vent after rupture of the seal. This can occur in embodiments that include a circuit board with surface mounted components. In such embodiments, a surface mounted resistor can stretch the polyimide film and press it against the opening in the gasket and against the thermally unstable material. Once the seal ruptures, the molten sealant can form a secondary seal with the polyimide, thereby closing the vent. In flexible circuit embodiments that include metal traces that form a heating element, the heater can locally deform the polyimide flexible circuit, often forming protrusions (often including heater material) that extend into the opening in the gasket, possibly blocking the vent opening with the molten sealant. Dimple 7004 can help prevent these occurrences.

[0058] The sealed space 55 optionally provides a conduit to other vents, vent pockets or chambers (such as expansion chamber 52). After vent opening, the fluidic component 5 remains sealed from the external environment 59. The expansion chamber 52 preferably accommodates gas expansion during heating by buffering the air / water vapor volume by providing a volume large enough that gas expansion due to temperature changes does not significantly affect the pressure of the system, or by accommodating gas expansion by displacement of a piston (FIG. 3), flexible air bladder (FIG. 4), bellows (FIG. 5) or hydrophobic barrier (FIG. 6) that allows gas to pass freely across the barrier but not large molecules. In FIG. 3, the expansion chamber utilizes a piston that is displaced by increasing pressure within the sealed fluid system. The expansion chamber serves to reduce or eliminate pressure buildup within the sealed system. The displacement of the piston occurs in response to increased pressure within the hermetically sealed test cassette, reducing the internal pressure within the test cassette resulting from processes such as gas expansion during heating. In Figure 4, deflection of the bladder occurs in response to an increase in pressure within the hermetically sealed test cassette. The displacement of the bladder reduces the internal pressure within the test cassette resulting from processes such as gas expansion during heating. In Figure 5, expansion of the bellows occurs in response to an increase in pressure within the hermetically sealed test cassette. The expansion of the bellows reduces the internal pressure within the test cassette resulting from processes such as gas expansion during heating.

[0059] The expansion chamber can be incorporated as an empty air volume, such as the contained volume shown in the expansion chamber 52 in the top of the test cassette shown in FIG. 1. As shown in FIG. 7, to facilitate the fabrication of a cassette of minimal thickness, the expansion chamber can be incorporated into an air gap 440 formed by a properly designed gasket 420 to form the backing of the fluidic component 400 when sealed to the thermally labile material 410 and the thermally stable material 430. Minimization of the physical dimensions of the test cassette is desirable to reduce shipping costs, reduce thermal mass, and provide an aesthetically pleasing and convenient design. In addition to forming an air volume for gas expansion, the gasket 420 creates a space between the thermally stable material 430 and the thermally labile material 410 to facilitate the free movement of air through the open vent while maintaining a sealed system and preventing exposure to the environment. The gasket 420 is preferably thick enough to provide a sufficient air gap to balance the pressure between the open vents, but thin enough not to substantially affect the interface between the heater and the corresponding vent pocket or the sealing of the cassette by the thermally stable material. In embodiments of the invention that include a flexible circuit, the flexible circuit may include a thermally stable material such as polyimide, in which case a separate sheet of thermally stable material 430 is not required, as shown, for example, in FIG. 8C. The use of an expansion chamber to reduce or balance the pressure within the sealed test cassette ensures that pressure imbalances do not result in undesirable or premature solution movement within the test cassette, and that pressure buildup does not adversely affect desired fluid movement, such as movement between chambers or through channels. This pressure control, i.e., the establishment of a specified pressure distribution throughout the device, allows the system to operate as designed regardless of atmospheric pressure. The expansion chamber therefore allows for controlled fluid movement that relies on a stable pressure within the system used, and also allows for the use of hermetically sealed test cassettes, thereby avoiding the drawbacks of venting the test cassette to atmosphere, such as potential release of amplicons into the atmosphere.Additionally, methods that allow fluid flow by reducing the pressure downstream of the fluid, such as by opening a vent to the expansion chamber, eliminate the need for pumps, such as those that generate positive pressure upstream of the fluid, or other devices with moving parts. A similar advantage is possible by venting the downstream region of the fluid to a relatively large reservoir (such as the expansion chamber) at substantially the same pressure as the downstream region, thereby allowing the fluid to flow under gravity (as long as the device is in the proper orientation). The size of the expansion chamber is preferably large enough to accommodate the reactant vapors generated during the assay without increasing the pressure of the system to the point of overcoming the capillary forces or gravity required for fluid flow.

[0060] In embodiments where the second chamber is an amplification chamber, the chamber is preferably in contact with a heating element to provide a means for temperature regulation necessary to support nucleic acid amplification. In some embodiments of the invention, the amplification chamber may contain oligonucleotides on at least a portion of the interior surface. As shown in FIG. 2D, it may be advantageous to place a thermally conductive material, such as a thermal grease or compound, at the interface between the wall 95 of the chamber 30 and one or more heating elements 100. The microcontroller adjusts the current to the resistive heating element(s), preferably by a metal oxide semiconductor field effect transistor (MOSFET), based on data collected from the temperature sensor 110 on the PCA 75, preferably using a simple on / off or proportional integral derivative (PID) temperature control method or other algorithmic temperature control known to those skilled in the art.

[0061] Placing the heating elements, and in some embodiments the corresponding temperature sensor(s), on the disposable components allows for the fabrication of highly reproducible thermal coupling between the temperature control subsystems and the amplification and detection chambers to which they interface. This approach allows for a reliable means of coupling the fluidic and electronic thermal control subsystems by forming a thermally conductive interface during fabrication. The resulting excellent thermal contact between the electronic temperature control components and the fluidic subsystem results in rapid temperature equilibration and therefore rapid assays. The use of flexible circuits to provide disposable resistive heating elements fused to the rear of the fluidic component backing, either directly or with an intervening gasket, allows for a low-cost means of achieving excellent thermal contact, rapid temperature cycling and reproducible fabrication. Resistive heating elements for reverse transcription, amplification and fluid flow vent control can be formed directly on the flexible circuit by etching the conductive layer of the flexible circuit to form geometries that exhibit the required resistance. This approach eliminates the need for additional electronic components, simplifying fabrication while reducing costs.

[0062] In one embodiment of the present invention, a flexible circuit 799 for resistive heating and vent opening is shown in FIG. 8. The use of a flexible heater as part of the disposable cassette allows the cassette lining to be configured to allow the fluid in the heated fluid chamber to come into direct contact with the material that comprises the flexible heater circuit. For example, as shown in FIG. 8C, a window 806 of a thermally labile material 807 (preferably including BOPS) that forms the rear of the cassette can be placed over the fluid chamber to allow the fluid to come into direct contact with the flexible circuit 799. Direct contact between the flexible circuit layer and the fluid that is temperature controlled by the heater on the flexible circuit provides a low thermal mass system capable of rapid temperature changes. Temperature sensors can optionally be incorporated into the flexible circuit to allow collection of temperature data for use in temperature regulation, and / or non-contact means of temperature monitoring such as infrared sensors can be used. Resistive heating elements such as heating element 800 in the flexible circuit can be utilized for vent bursting when placed in alignment with the vent pocket. Electrical pads 812 provide electrical current to heating element 800. Similarly, the flexible circuit(s) can include resistive heating elements 802 and 803 for heating the fluid chambers and an optional resistive heating element 804 for regulating the temperature of the detection strip.

[0063] In this embodiment, the flexible circuit 799 preferably also functions as a heat stable seal to maintain an airtight sealed cassette, similar to the heat stable material 72 described above. Optionally, an additional heat stable layer (e.g., comprising polyimide) may be disposed between the flexible circuit 799 and the rear housing or panel 805. A spacer or gasket 808 is preferably disposed around the vent resistor 800 between the heat labile material 807 and the flexible circuit 799 to ensure free air movement through the open vent while maintaining a sealed cassette. The rear housing or panel 805 preferably comprises a thin plastic, preferably disposed on its exposed surface to protect the flexible circuit during handling. The rear housing or panel 805 may include a window over the heating element on the flexible circuit 799 to facilitate cooling and temperature monitoring. Electrical contact with the control electronics of the docking unit (described below) may be provided by a set of electrical pads 810, optionally preferably comprising an edge connector or connector pins (such as spring loaded pins).

[0064] Embodiments of the test cassette chamber preferably include materials capable of withstanding repeated heating and cooling to temperatures ranging from about 30°C to about 110°C. Even more preferably, the chamber includes materials capable of withstanding repeated heating and cooling to temperatures ranging from about 30°C to about 110°C at a temperature change rate of about 10°C to about 50°C / sec. The chamber is preferably capable of maintaining solutions therein at temperatures suitable for heat-mediated lysis and biochemical reactions, such as reverse transcription, thermal cycling or isothermal amplification protocols, preferably controlled by microcontroller programming. In some nucleic acid amplification applications, it is desirable to provide an initial incubation at elevated temperatures, e.g., from about 37°C to about 110°C, for 1 second to 5 minutes to denature the target nucleic acid and / or activate a hot start polymerase. The reaction solution is then held at an amplification temperature in an amplification chamber for isothermal amplification, or varied in temperature between at least two temperatures, including, but not limited to, a temperature that results in nucleic acid duplex denaturation and a temperature suitable for primer annealing by hybridization with the target and extension of the primer through polymerase-catalyzed nucleic acid polymerization, for thermocycling-based amplification. The duration of incubation at each required temperature in a thermocycling regimen can vary depending on the sequence composition of the target nucleic acid and the composition of the reaction mixture, but is preferably about 0.1 seconds to about 20 seconds. Repeated heating and cooling is typically performed for about 20 cycles to about 50 cycles. In embodiments involving isothermal amplification, the temperature of the reaction solution is maintained at a constant temperature (in some cases after an initial incubation at a high temperature) for about 3 minutes to about 90 minutes, depending on the amplification technique used. Once the amplification reaction is completed, the amplification reaction solution is transported to the lower chamber by opening a vent that communicates with the chamber below the chamber used for amplification to achieve further manipulation of the amplified nucleic acid. In some embodiments of the invention, the manipulation involves denaturation of the amplified nucleic acid and hybridization with detection oligonucleotides conjugated to detection particles.In some embodiments of the invention, the amplified nucleic acid is hybridized with detection oligonucleotides conjugated to detection particles and capture probes immobilized on a detection strip.

[0065] In some embodiments, additional biochemical reactions can be performed in the amplification chamber before, during or after the amplification reaction. Such processes can include, but are not limited to, reverse transcription, where RNA is transcribed into cDNA, multiplexing, where multiple primer pairs simultaneously amplify multiple target nucleic acids, and real-time amplification, where amplification products are detected during the amplification reaction process. In the latter case, the amplification chamber may not include valves or outlet channels, and the amplification chamber will preferably include an optical window or be configured to allow interrogation of amplicon concentration during the amplification reaction process. In one real-time amplification embodiment, either a fluorescently labeled oligonucleotide complementary to the target nucleic acid or a fluorescent dye specific to double-stranded DNA is monitored for fluorescence intensity by an excitation light source such as an LED or diode laser(s) and a detector such as a photodiode, and appropriate optical components including, but not limited to, optical filters.

[0066] <Detection> The embodiment of the detection chamber 230 preferably provides specific labeling of the amplified target nucleic acid produced in the amplification chamber. As shown in FIG. 2A, the detection chamber 230 preferably includes a capillary pool or space 93 and a detection strip 235. Detection particles including dye polystyrene microspheres, latex, colloidal gold, colloidal cellulose, nanogold, or semiconductor nanocrystals are preferably present in the capillary pool 93. The detection particles can include oligonucleotides complementary to the target analyte, or can include ligands capable of binding to the amplified target nucleic acid, such as biotin, streptavidin, haptens, or antibodies to a label such as a hapten present on the target amplified nucleic acid. The detection chamber 230 may contain detection particles that are dried, lyophilized, or present on at least a portion of the interior surface as a dry mixture of detection particles in a carrier such as a polysaccharide, detergent, protein, or other compound known to those skilled in the art to facilitate resuspension of the detection particles. In some embodiments, the lateral flow detection strip can include the detection particles. In other embodiments, the reagent recess channel 135 leading to the detection chamber my can include the detection particles. The detection chamber can be heated and / or cooled.

[0067] Suitable detection particles include, but are not limited to, fluorescent dyes specific for double-stranded nucleic acids, fluorescently modified oligonucleotides, or oligonucleotide-conjugated dyed microparticles or gold colloids or colloidal cellulose. Detection of amplicons involves "detection oligonucleotides" or other "detection probes" that are complementary to or can otherwise specifically bind to the amplicons to be detected. Conjugation of detection oligonucleotides to microparticles can occur through the use of streptavidin-coated particles and biotinylated oligonucleotides, or through carbodiimide chemistry, where carboxylated particles are activated in the presence of carbodiimides and react specifically with primary amines present on the detection oligonucleotides. Conjugation of detection oligonucleotides to detectable moieties can occur internally or at the 5' or 3' ends. Detection oligonucleotides can be attached directly to the microparticles, or more preferably through a spacer moiety such as ethylene glycol or a polynucleotide. In some embodiments of the invention, detection particles can bind to multiple species of amplified nucleic acids resulting from processes such as multiplex amplification. In these embodiments, specific detection of each species of amplified nucleic acid can be achieved by detection on a detection strip using a method specific for each species to be detected. In such embodiments, tags introduced into the target nucleic acid during amplification can be used to label all amplified species present, while subsequent hybridization of the labeled nucleic acid to species-specific capture probes immobilized on a detection strip is used to determine which specific species of amplified DNA are present.

[0068] For double-stranded DNA amplification products, detection can be facilitated by heating the reaction solution after introduction into the detection chamber. Melting the double-stranded DNA or denaturing the secondary structure of the single-stranded DNA, followed by cooling in the presence of detection oligonucleotides, results in sequence-specific labeling of the amplified target nucleic acid. A heating element below the detection chamber can be used to heat the fluid volume for about 1 to about 120 seconds to initiate double-stranded DNA melting or denaturing the single-stranded DNA secondary structure. As the solution cools to room temperature, the amplified target nucleic acid can specifically hybridize to the detection microparticles. The reaction volume is then directed to the region of the detection chamber below the labeling chamber, preferably by opening the vent of the detection chamber.

[0069] For efficient labeling, the solubilized detection particles are preferably well mixed with the reaction solution. In an embodiment of the present invention, the detection particles can be localized in a capillary pool 93 at the outlet of the channel 135 to facilitate mixing with the solution as it enters the chamber 230. The detection particles in the capillary pool 93 can optionally be lyophilized detection particles. The capillary pool improves particle mixing and dispersion to promote mixing of the detection particles and the nucleic acids to which they bind. The capillary pool also increases the uniformity of particle migration on the detection strip, as shown in FIG. 9. The capillary pool is particularly advantageous for low volume assays, such as those with volumes of less than 200 μL, more specifically less than about 100 μL, even more specifically less than about 60 μL, and even more specifically less than about 40 μL.

[0070] The detection chamber embodiments of the present invention provide specific detection of the amplified target nucleic acid. In certain embodiments of the present invention, this is accomplished by capillary wicking of a solution containing the labeled amplicons through an absorbent strip composed of a porous material (such as cellulose, nitrocellulose, polyethersulfone, polyvinylidine fluoride, nylon, charge-modified nylon or polytetrafluoroethylene) patterned with lines, dots, microarrays or other visually identifiable elements that contain binding moieties that can specifically bind directly or indirectly to the labeled amplicons. In some embodiments, the absorbent strip component of the device includes up to three porous substrates in physical contact: a surfactant pad containing an amphiphilic reagent to enhance wicking, a detection zone comprising a porous material (such as cellulose, nitrocellulose, polyethersulfone, polyvinylidine fluoride, nylon, charge-modified nylon or polytetrafluoroethylene) to which at least one binding moiety that can selectively bind to the labeled amplicons is immobilized, and / or an absorbent pad to provide additional absorption capacity. Detection particles can optionally be incorporated within the lateral flow porous material in the detection chamber, but unlike previously described lateral flow detection devices, the detection particles are preferably instead held upstream of the capillary pool, where substantially enhanced formation of binding complexes between amplicons and detection particles can occur prior to or simultaneously with introduction of the resulting labeled nucleic acid into the porous component of the device.

[0071] "Capture oligonucleotides" or "capture probes" are immobilized on the detection strip element of the device, preferably by any of a variety of means known to those of skill in the art, such as UV irradiation. The capture probes capture the labeled nucleic acids as a solution containing the labeled nucleic acids passes through the capture zone, increasing the concentration of label at the capture probe immobilization site, thus generating a detectable signal indicative of the presence of the labeled nucleic acid amplicon(s). A single detection strip can be patterned with one or more capture probes to allow multiplex detection of multiple amplicons, determination of amplicon sequence, quantification of amplicons by extending the linearity of the detection signal, and quality control of the assay (positive and negative controls).

[0072] <Fluid components> Fluidic component embodiments preferably include plastics, such as acrylic, polycarbonate, PETG, polystyrene, polyester, polypropylene and / or other similar materials. These materials are readily available and can be manufactured by standard methods. Fluidic components include both chambers and channels. A fluid chamber includes a wall, two faces, and connects to one or more channels, such as an inlet, an outlet, a recess, or a vent. A channel can connect two fluid chambers or a fluid chamber and a recess, and includes a wall and two faces. Fluid chamber designs preferably maximize surface area to volume ratios to facilitate heating and cooling. The interior volume of the chamber is preferably about 1 μL to about 200 μL. The area of ​​the chamber face in contact with the solution preferably matches the area to which the heating element is interfaced to ensure uniform fluid temperatures during heating. The shape of the fluid chamber may be selected to mate with the heating element, as well as to provide a favorable geometry for the ingress and egress of the solution. In some embodiments, the volume of the chamber may be larger than the fluid volume to provide space for air bubbles that appear during device operation. The fluid chamber can have an enlarged expansion that leads into the vent channel to ensure that fluid does not wick up the channel by capillary action or to block the venting mechanism.

[0073] In some embodiments, it may be desirable to reduce or eliminate the ingress of liquid or gas phase water into the chamber prior to solution release. The high temperatures used in some embodiment processes generate steam (e.g., gas phase water) that may result in premature ingress of moisture into the channels, chambers or recesses. For example, reducing liquid or gas phase ingress may be desirable to maintain the dryness of dried or lyophilized reagents present in the chambers or recesses. In some embodiments, the channels can be fully or partially temporarily blocked with a material that can be removed by an external force such as heat, moisture and / or pressure. Materials suitable for temporary blocking of channels include, but are not limited to, latex, cellulose, polystyrene, thermal glue, paraffin, wax and oil.

[0074] In some embodiments, the test cassette preferably includes injection molded fluidic components including the sample cup, chamber, channel, vent pocket, and energy director. The injection molded test cassette fluidic components are preferably constructed of a plastic suitable for ultrasonic welding to a backing plastic of similar composition. In one embodiment of the present invention, the test cassette fluidic components include a single injection molded component that is ultrasonically welded to the backing material. The energy director is an optional feature of the fluidic components that directs ultrasonic energy only to areas of the thermally unstable layer that are intended to couple to the fluidic components. The injection molded fluidic components may optionally be contained within a housing. FIG. 7 illustrates a cassette preferably including an injection molded fluidic component 400 (preferably including a polymer such as high impact polystyrene (HIPS), polyethylene, polypropylene or NAS30, a styrene acrylic copolymer, etc.), a thermally labile material 410 (e.g., BOPS having a relatively low melting temperature of about 239° C. and a glass transition temperature of about 100° C. sufficient to withstand high temperatures during denaturation or polycarbonate having a melting temperature of 265° C. and a glass transition temperature of 150° C.), an adhesive spacer 420 (e.g., including a silicone transfer adhesive, preferably without a carrier, an acrylic adhesive with a polyester carrier, or any adhesive that can withstand the high temperatures of the device), and a heat resistant layer 430. The thermally labile material 410 ruptures via heat, which is preferably transmitted through the overlying heat resistant layer 430 (e.g., including polyimide or other polymers with high heat resistance). Melting of the thermally labile material over the vent feature of the cassette opens the vent and vent channel to an expansion chamber, thereby allowing pressure equalization within the cassette. The overlying heat resistant layer 430 preferably remains intact, thereby enabling the cassette to maintain an airtight seal after vent opening.

[0075] In some embodiments, the adhesive spacer includes an empty area 440 that can act as an expansion chamber to buffer the expansion of the gas during heating to reduce the internal pressure of the sealed cassette. The thermally unstable layer 410 is bonded to the fluidic component 400 by a bonding method or process, such as ultrasonic welding or using an adhesive. The resulting part is then bonded with the spacer and the heat-resistant layer. In some embodiments, the heat-resistant layer is configured so that it is not present on the heated chamber. In other embodiments, the heat-resistant layer is present on the heater chamber. In yet other embodiments, the adhesive spacer and the heat-resistant layer are present only on the area that is aligned with the vent pocket feature of the fluidic component. In this embodiment, the heat-resistant layer can be placed directly on top of the thermally unstable material in the area aligned with the optionally heated chamber.

[0076] In some embodiments of the invention, the thickness of the fluid chamber and channel walls is in the range of about 0.025 mm to about 1 mm, preferably in the range of about 0.1 mm to about 0.5 mm. This thickness preferably meets both the requirements of structural integrity of the fluidic component and supports sealing of the sealed chamber under high temperatures and associated pressures. The thickness of the channel walls, especially the vent channel walls, is preferably less than the thickness of the chamber and is in the range of about 0.025 mm to about 0.25 mm. The width of the inlet and outlet channels is preferably selected to enhance capillarity. Shallow vent channels impart improved rigidity to the fluidic component without adversely affecting ventilation. The plastic molded surfaces of the fluidic component are preferably thinner than the surfaces that form the walls to maximize heat transfer. An optional insulating layer cuts through some parts of the fluidic component and surrounds the amplification and detection chambers, contributing to the thermal isolation of the temperature control chamber.

[0077] In some embodiments of the invention, additional components of the test cassette, such as lyophilized reagents 16, detection strip assembly 230 and detection particles, can be incorporated prior to bonding of fluidic components 400 to thermolabile backing material 410. In some embodiments, components can be laminated by applying pressure to ensure good adhesion. In some embodiments, components can be bonded by a combination of methods, such as pressure sensitive adhesives and ultrasonic welding. Adhesives known or found to adversely affect the performance of the nucleic acid amplification reaction must be avoided. Acrylic or silicone adhesives have been used successfully in the present invention. One preferred adhesive film is SI7876, supplied by Advanced Adhesives Research. Other adhesives can be used if they are found to be chemically compatible with the buffers, plastics and reaction chemistries used while providing a robust seal over the temperatures encountered during device operation.

[0078] 2 and 7, the vent pocket is preferably distinct from the other chambers in its configuration. After configuration of the fluidic components above, the vent pocket has an open surface on the side of the fluidic component that meets the PCA 75 directly or in some embodiments indirectly through an intervening air gap 440 or vent pocket 54 and heat resistant material 430. To form the vent pocket, an additional plastic component is bonded to seal the chamber, preferably including a thin thermolabile film 410 adjacent the vent resistor 70 of the PCA. The film 410 comprises a material suitable for ultrasonic welding to injection molded fluidic components such as polystyrene, although other similar materials can be used. The film is suitable to seal the vent pocket while at the same time allowing easy piercing, thus venting the lower pressure chamber when current passes through the vent resistor causing a rapid temperature increase. Preferably, the film is stable enough when heated so that the material can withstand temperatures used for other operations of the test cassette such as thermal lysis, reverse transcription and nucleic acid amplification. The use of a material that is stable in the temperature ranges used for denaturation, labeling, reverse transcription, nucleic acid amplification and detection, but has a melting temperature that is easily achieved by resistor 70, allows a single material used to line the injection molded fluidic component 400 to serve as both the face of the chamber and the face of the vent pocket. In some embodiments, additional temperature stability in the area of ​​the temperature controlled chamber can be achieved by an overlying film of a heat resistant material such as polyimide. In other embodiments of the invention, a window in the heat labile film is aligned with the temperature controlled chamber to allow direct contact between the fluid in the chamber and the substrate of a flexible circuit fused to the rear of the test cassette.

[0079] <Additional parts for fluid components> As mentioned above, some additional components are preferably incorporated into the fluidic components of the present invention before final bonding. Reagents including buffers, salts, dNTPs, NTPs, oligonucleotide primers and enzymes (such as DNA polymerase and reverse transcriptase) can be lyophilized or freeze-dried into pellets, spheres or cakes before device assembly. Lyophilization of reagents is well known in the art and involves dehydration of frozen reagent aliquots by sublimation under an applied vacuum. The activity of enzymes can be protected and the rate of rehydration increased by adding specific blends of lyoprotectants such as sugars (disaccharides and polysaccharides) and polyalcohols to the reagents before freezing. Lyophilized reagent pellets, spheres or cakes are manufactured by standard methods and, once formed, are reasonably durable and can be easily placed into specific chambers of the fluidic components before laminating the final surface. More preferably, recesses are incorporated into the fluidic network to allow pellets, spheres or cakes of lyophilized reagents to be placed into the fluidic components before bonding the fluidic components with the backing material. By selecting the geometry of the fluid network and the location and order of the recesses, the sample can react with the desired lyophilized reagents at the desired time to optimize performance. For example, depositing lyophilized (or dried) reverse transcription (RT) and amplification reagent spheres in two separate recesses in the flow path of the RT reaction chamber and the amplification chamber allows for optimal reverse transcription reaction without interference of the amplification enzyme. Furthermore, to minimize the interference of the RT enzyme with the subsequent amplification reaction, the RT enzyme presented in the RT reaction after the RT reaction could be heat inactivated before introduction into the amplification reagent to minimize interference with the amplification. Optionally, other salts, surfactants and other enhancing chemicals could be added to the different recesses to adjust the performance of the assay. Furthermore, these recesses also help to facilitate the mixing of the lyophilized reagents with the liquid as they pass through the recesses, to isolate the lyophilized material from ultrasonic energy during ultrasonic welding, and to isolate the lyophilized reagents from extreme high and low temperatures during the heating step of the test before solubilization.Additionally, the recesses ensure that the freeze-dried pellets are not compressed or crushed during manufacture, allowing the pellets to remain porous and minimizing rehydration times.

[0080] In some embodiments of the invention, the detection microparticles are another additional part of the fluidic component. In some embodiments, these microparticles can be freeze-dried as described for the reaction reagents above. In other embodiments, the microparticles in a liquid buffer can be applied directly to the inner surface of the fluid chamber and dried before final assembly of the test cassette. The liquid buffer containing the microparticles also preferably contains a sugar or polyalcohol to aid in rehydration. By incorporating the microparticles in an aqueous buffer directly into the fluidic component before drying, the final manufacturing cost can be simplified and reduced, and the complete intermixing of the freeze-dried particles with the reaction solution and the denaturation of the double-stranded nucleic acid or double-stranded regions of the nucleic acid to single-stranded nucleic acid can be promoted by heating or nucleate boiling. In some embodiments, the freeze-dried detection particles are placed in a recess in the fluidic network. In other embodiments, the freeze-dried or desiccated detection particles are placed in the space 93 directly below the detection strip. In other embodiments, the detection particles are dried or freeze-dried in an absorbent substrate in capillary communication with the detection strip or directly on the detection strip. The capillary communication may be a direct physical contact between the absorbent substrate and the detection strip, or it may be indirect (wherein the capillary communication spans an intervening distance consisting of a channel or chamber region through which capillary transport is achieved to transport fluid from the absorbent substrate loaded with detection particles to the detection strip).

[0081] In some embodiments of the invention, a lateral flow detection strip assembly is also incorporated into the fluidic component. The detection strip preferably includes a membrane assembly composed of at least one porous component, and may optionally include an absorbent pad, a detection membrane, a surfactant pad, and a backing film. The detection membrane is preferably made of nitrocellulose, cellulose, polyethersulfone, polyvinylidine fluoride, nylon, charge-modified nylon, or polytetrafluoroethylene, and may be backed with a plastic film. As described above, the capture probes may be deposited and irreversibly immobilized on the detection membrane in lines, spots, microarrays, or any pattern that can be visualized by the naked eye or an automated detection system, such as an imaging system. The deposited oligonucleotides may be permanently immobilized by UV irradiation of the detection membrane after capture probe deposition. The surfactant pad may preferably include a porous substrate with minimal nucleic acid binding and fluid retention properties that allow unhindered movement of the nucleic acid product and detection microparticles. The surfactant pad may include materials such as glass fiber, cellulose, or polyester. In an embodiment of the invention, a formulation including at least one amphiphilic reagent is dried on the surfactant pad to allow uniform movement of the sample through the detection membrane. The absorbent pad may include any absorbent material and serves to guide sample wicking through the detection membrane assembly. Using an adhesive backed film, such as a double-sided adhesive film as a substrate, the detection membrane components are assembled by first placing the detection membrane, followed by any absorbent pad and / or surfactant pad in physical contact with the detection membrane with an overlap of about 1 mm to about 2 mm. In some embodiments of the invention, the detection membrane may be in indirect capillary communication with the surfactant pad, where there is a physical separation between the surfactant pad and the detection pad, with the intervening space being comprised of a capillary space, allowing fluid to traverse the space by capillary action. In some embodiments, the surfactant pad or a region of the surfactant pad may include detection particles, dried detection particles or lyophilized detection particles.

[0082] <Three-chamber cassette> In some embodiments of the invention, additional reaction chambers and / or additional recesses for dried or lyophilized reagents can be incorporated. In some embodiments, such a design facilitates tests in which it is desirable to provide an initial separate lysis reaction prior to reverse transcription and amplification. As shown in Figures 37A, 37B and 38, the cassette 5000 includes a cover 5020 that seals the expansion chamber 5021, a flexible heater circuit 5022 that is preferably placed in intimate contact with the fluidic components 5023, and a rear cover 5024 that hides the circuitry from the user. A sample containing nucleic acid is introduced into the sample cup 5002 through the sample port 5001. The sample flows freely into the recess 5003 where it reconstitutes the first lyophilized beads 5004, which preferably contain a lysis reagent, before flowing down the channel 5005 into the first reaction chamber 5006. This free flow is facilitated by a vent channel 5007 that connects with the top of the sample cup 5002. The vent channel 5007 may further connect with an expansion chamber 5021 via a void 5008. The sealed air space below the first reaction chamber 5006 is slightly pressurized by the fluid flow, causing the flow to stop just below the first reaction chamber 5006. The first reaction chamber 5006 is then preferably heated to a temperature that promotes an appropriate reaction with a lysis reagent to lyse biological particles and / or cells in the sample and expose nucleic acids present therein.

[0083] A vent valve 5009 connected to the top of the second reaction chamber 5011 is then opened to facilitate sample flow into the second recess, where the second lyophilized beads 5010, preferably containing reagents for reverse transcription, are reconstituted. The fluid then enters the second reaction chamber 5011, where the flow stops as a result of the air pressure increase in the closed air volume below the flow. The second reaction chamber 5011 is then preferably heated to an appropriate temperature to facilitate the reverse transcription process.

[0084] Opening a next vent valve 5009 connected to the top of the third reaction chamber 5013 initiates sample flow from the second reaction chamber 5011 through the third recess, where lyophilized beads 5012, preferably containing lyophilized PCR amplification reagents, are reconstituted. The sample then flows into the third reaction chamber 5013, where it undergoes thermal cycling to amplify target analytes present in the sample.

[0085] The final vent valve 5009 connected to the far end of the lateral flow strip 5014 is then opened, allowing the sample containing the amplified analyte to flow into the lateral flow strip 5014 for detection of the analyte as described above.

[0086] Flow Control Features The design of the fluidic components can optionally include flow control features in the reaction chamber or at the outlet of the reaction chamber. These features deflect the flow entering the chamber to the side of the chamber opposite the outlet before the flow enters the outlet. As a result, the flow enters the outlet channel at a slower rate, decreasing the distance the fluid flow travels down the channel before stopping. Furthermore, the horizontal components of the flow path add length to the channel without adding vertical spacing between the chambers, increasing the effective length of the flow path, sufficient to stop the flow at a desired location based on the reduced flow rate. This allows for tighter vertical spacing between the chambers of the cassette since fewer vertical channels are required. Furthermore, the redirection of the flow across the reaction chamber creates a swirling action on the flow within the chamber, improving mixing of the reagents and sample fluids. The flow control features can include any shape.

[0087] In the embodiment shown in FIG. 39, fluid enters reaction chamber 4003 from inlet channel 4002 and flows to the bottom of the reaction chamber where it is redirected by triangular flow control feature 4001 to the side of reaction chamber 4003 opposite the opening to inlet channel 4002. As the flow proceeds to the opposite corner 4004, it splits and some enters outlet 4005 while the rest contacts the wall and is directed upwards, creating a swirling effect that improves mixing. The flow to the outlet preferably forms a meniscus and travels through outlet channel 4006 towards the next reaction chamber or lyophilized bead recess. Because outlet channel 4006 is sealed below reaction chamber 4003, as the fluid travels along outlet channel 4006, the air pressure in the channel below the flow increases until it reaches equilibrium with the fluid pressure head, causing the flow to stop. In this embodiment, the outlet 4005 tapers from the reaction chamber 4003 towards the outlet channel 4006 to effectively form a meniscus that can subsequently increase the pressure in the enclosed space downstream of the flow. This larger opening to the outlet channel preferably increases the compressible air volume to ensure that a meniscus forms at the wider opening.

[0088] In the embodiment shown in FIG. 40, fluid enters reaction chamber 4103 from inlet channel 4102 and flows to the bottom of the reaction chamber where it is redirected by triangular flow control feature 4101 to the side of reaction chamber 4103 opposite the opening to inlet channel 4102. As the flow proceeds to the opposite corner 4104, the flow splits and some enters outlet 4105 while the rest contacts the wall and is directed upwards, creating a swirling effect that improves mixing. The flow to the outlet preferably forms a meniscus and travels through outlet channel 4106 towards the next reaction chamber or lyophilized bead recess. Because outlet channel 4106 is sealed below reaction chamber 4103, as the fluid travels along outlet channel 4106, the air pressure in the channel below the flow increases until it reaches equilibrium with the fluid pressure head, causing the flow to stop. In this embodiment, outlet 4105 and outlet channel 4106 have a uniform width. In this embodiment, the formation of a meniscus in the reaction chamber may be somewhat more reliable as a result of the narrower channel. The meniscus then increases the pressure in the enclosed space downstream of the flow.

[0089] In the embodiment shown in FIG. 41, fluid enters reaction chamber 4203 from inlet channel 4202 and flows to the bottom of the reaction chamber where it is redirected by trapezoidal flow control feature 4201 to the side of reaction chamber 4203 opposite the opening to inlet channel 4202. As the flow proceeds to the opposite corner 4204, the flow splits and some enters outlet 4205 while the rest contacts the wall and is directed upwards, creating a swirling effect that improves mixing. In this embodiment, outlet 4205 is oriented substantially vertically. The flow to the outlet preferably forms a meniscus and travels through outlet channel 4206 towards the next reaction chamber or lyophilized bead recess. Because outlet channel 4206 is sealed below reaction chamber 4203, as the fluid travels along outlet channel 4206, the air pressure in the channel below the flow increases until it reaches equilibrium with the fluid pressure head, causing the flow to stop. In this embodiment, outlet 4205 and outlet channel 4206 have a uniform width. In this embodiment, the formation of a meniscus in the reaction chamber may be somewhat more reliable as a result of the narrower channel. The meniscus then increases the pressure in the enclosed space downstream of the flow.

[0090] In the embodiment shown in FIG. 42, fluid enters reaction chamber 4305 from inlet channel 4304 and flows to the bottom of the reaction chamber where it is redirected by triangular flow control feature 4303 to the side of reaction chamber 4305 opposite the opening to inlet channel 4304. As the flow proceeds to the opposite corner 4306, the flow splits and some enters outlet 4307 while the rest contacts the wall and is directed upwards, creating a swirling effect that improves mixing. The flow to the outlet preferably forms a meniscus and travels through outlet channel 4306 towards the next reaction chamber or lyophilized bead recess. In this embodiment, outlet channel 4306 proceeds through stacked successive flow control features 4303, 4302 and 4301 which provide a tortuous path for the fluid to flow providing increased outlet channel length in a small vertical space.

[0091] In the embodiment shown in Figure 43, fluid enters reaction chamber 4403 from inlet channel 4402 and is redirected to the side of reaction chamber 4403 opposite inlet channel 4402 by flow control feature 4401 located above the bottom of the reaction chamber, preferably about halfway along the length of reaction chamber 4403. In contrast to the previous embodiment, flow control feature 4401 does not form an outlet for reaction chamber 4403. Flow control feature 4401 deflects the flow away from outlet channel 4405 to the opposite corner 4404, thereby slowing the flow rate before exiting the chamber. As with the previous embodiment, redirecting the fluid promotes turbulence and mixing of reagents.

[0092] Assay multiplexing In some embodiments of the invention, multiple independent assays can be performed in parallel by using a fluidic design that allows for the splitting of an input fluid sample into two or more parallel fluidic paths through the device. FIG. 10 is a schematic diagram of splitting an 80 μL fluid volume, for example, first into two separate 40 μL volumes and then into four 20 μL volumes in two successive steps. The illustrated scheme is useful for allowing independent and separate operations, such as biochemical reactions, to be performed on the split volumes. Such a configuration is useful for increasing the number of analytes that can be detected with a single device by facilitating multiplex detection of multiple targets, such as nucleic acid sequences, in multiplexed nucleic acid reverse transcription and / or amplification reactions. Similarly, the use of multiple detection strips at the ends of the independent fluidic paths can increase the readability of the strips for detection of multiple targets or identification of sequence differences or mutations in nucleic acid analytes. Furthermore, providing additional detection strips for independent interrogation of multiple amplification reaction products can enhance specificity by reducing the possibility of false cross-reactions, such as cross-hybridization, during the detection step of the test. FIG. 11 shows a test cassette that includes two fluidic paths within a single test cassette. Each fluid path can be independently controlled with respect to timing, type of reaction, etc. Referring now to FIG. 12, a sample introduced into a sample cup 1000 is split into approximately equal volumes and flows into volume split chambers 1001 and 1002, the flow into which is regulated by vent valves 1003 and 1004. Split chambers 1001 and 1002 control the volume of sample in each test path by passively equilibrating the amount of sample in each chamber. After volume splitting, solutions are allowed to flow through reagent recesses 1007 and 1008 by opening vents 1005 and 1006. Reagents, such as lyophilized reagents, are placed in recesses 1007, 1008 and mix with the sample as it flows through the recesses into a first set of preferably temperature controlled chambers 1009 and 1010. Reactions such as thermal lysis, reverse transcription and / or nucleic acid amplification take place in each of a first set of heating chambers facilitated by reagents provided in reagent recesses 1007,1008.Such reagents include, but are not limited to, lyophilized positive control agents (e.g., nucleic acids, viruses, bacterial cells, etc.), lyophilized reverse transcriptase and associated ancillary reagents required for reverse transcription of RNA to DNA (nucleotides, buffers, DTT, salts, etc.), and / or DNA amplification using lyophilized DNA polymerase or a thermostable lyophilized DNA polymerase and the necessary ancillary reagents (nucleotides, buffers and salts, etc.).

[0093] After completion of a biochemical reaction such as reverse transcription, nucleic acid amplification or concomitant reverse transcription and nucleic acid amplification (e.g. single tube reverse transcription-polymerase chain reaction (RT-PCR) or one-step RT-PCR or one-step RT-Oscar) in the first set of chambers, the seals of the vent pockets 1011 and 1012 are ruptured to allow fluid to flow from the first set of chambers through the second set of reagent recesses 1013 and 1014 to the second set of preferably temperature controlled chambers 1015 and 1016. Reagents such as lyophilized reagents may be placed in the recesses 1013 and 1014 to mix with the sample solution as the fluid flows from the chambers 1009 and 1010 to the chambers 1015 and 1016. Reagents such as lyophilized reagents for nucleic acid amplification or dried or lyophilized detection particles (such as probe-conjugated dyed polystyrene microspheres or probe-conjugated colloidal gold) may optionally be placed in the reagent recesses 1013 and / or 1014. After completion of a reaction or other operation, such as binding or hybridization to the probe-conjugated detection particles in the heated chamber, the solution can flow into the detection strip chambers 1017 and 1018 by opening the vent valves 1019 and 1020. In some embodiments, a third set of reagent recesses can be placed in the fluid path from chambers 1015 and 1016 to allow additional reagents, such as detection reagents containing detection particles, salts and / or surfactants, and other substances useful for facilitating hybridization or other detection modalities, to mix with the solution flowing into the strip chambers 1017 and 1018. The detection strip chambers 1017 and 1018 may be heated and preferably include a detection strip, such as a lateral flow strip for detection of an analyte, such as an amplified nucleic acid.The detection strip may include dried or lyophilized detection reagents such as detection particles (e.g., dyed microsphere conjugates and / or colloidal gold conjugates), capture probes for capturing analytes (such as hybridization capture oligonucleotides for capturing nucleic acid analytes by sequence-specific hybridization), ligands (such as biotin or streptavidin for capturing appropriately modified analytes), and a series of absorbent materials doped or patterned with absorbent materials that provide sufficient absorption capacity to ensure complete movement of the same solution volume through the detection strip by means such as capillary action or wicking.

[0094] <Sample preparation> In some embodiments of the invention, it may be desirable to incorporate a sample preparation system into the cassette. A sample preparation system, such as a nucleic acid purification system, may include an encapsulation solution to accomplish sample preparation and elution of purified molecules (such as purified DNA, RNA or proteins) into the test cassette. FIG. 13 shows a nucleic acid sample preparation subsystem 1300 designed to integrate with a test cassette. The sample preparation subsystem includes a main housing 1302 and a housing lid 1301 for housing the components of the subsystem. The solution compartmentalization component 1303 includes a crude sample reservoir 1312, which is preferably open at the top but sealed below by a lower seal 1305. The solution compartmentalization component 1303 also preferably includes a reservoir 1314 containing a first wash buffer and a reservoir 1315 containing a second wash buffer, both of which are preferably sealed by upper seal 1304 and lower seal 1305. A nucleic acid binding matrix 1306 is disposed within the solution capillary flow path provided by absorbent materials 1307 and 1308. Glass fiber or silica gel, which exhibit nucleic acid binding and wicking properties, are examples of materials suitable for use as the binding matrix 1306. A wide range of absorbent materials, including polyester, glass fiber, nitrocellulose, polysulfone, cellulose, cotton or combinations thereof as well as other wicking materials, may comprise the absorbent materials 1307 and 1308, so long as they provide sufficient capillary action and minimal binding with the molecules to be purified by the subsystem. Any easily ruptured or frangible material that can be sealed to the solution compartmentalization component 1303 and chemically compatible with the encapsulation solution is suitable for use as the sealant 1304 and 1305. The sealant 1305 must contact the sample or sample dissolution solution and further be chemically compatible with the sample or sample dissolution solution. Examples of suitable sealants are heat-sealable metal and plastic films. The sealant 1305 is ruptured in use by displacement of the solution compartmentalization component 1303 such that the sealant 1305 is pierced by the structure 1311 present in the housing 1302.A crude sample or a crude sample mixed with a lysis buffer, such as a buffer comprised of a chaotropic agent, is introduced into the sample reservoir 1312 through the sample port 1309 of the lid 1301 in use. In some embodiments, the lysis buffer can optionally be encapsulated within the reservoir 1312 by extending the seal 1304 over the top orifice of the reservoir 1312. In such embodiments, it may be desirable to include a tab or other means to partially remove an area of ​​the seal 1304 covering the reservoir 1312 to allow addition of the crude sample to the reservoir 1312 so that the crude sample can mingle or mix with the lysis buffer contained within the reservoir 1312. A sample solution or lysis solution containing sample material is introduced into the sample addition port 1309 and is held in the sample reservoir 1312 of the buffer reservoir 1303 until the start of the sample preparation process.

[0095] At the start of sample preparation, the solution compartmentalization component 1303 is pressed onto the sealing perforation structure 1311, resulting in the simultaneous release of the sample solution or lysis solution in reservoir 1312 and the first and second wash buffers in reservoirs 1314 and 1315, respectively. Mechanical displacement of the component 1303 can be achieved manually or by use of an actuator(s) present in the reusable instrument into which the disposable test cassette is placed at the time of use. Actuator access or manual displacement mechanism access to the reservoirs 1303 is preferably provided through an access port 1310 in the housing lid 1301. The sample or lysis solution and the first and second wash buffers migrate through the materials 1307, 1306 and 1308 by capillary action. The physical arrangement of the reservoirs and the geometric configuration of the absorbent material 1307 ensure a continuous flow of the crude lysis solution, the first wash buffer and the second wash buffer through the binding matrix 1306. An absorbent pad 1313 placed in contact with the wick 1308 provides additional absorbent capacity to ensure continued capillary transport of all solution volumes through the system. Upon completion of solution transport through the absorbent material, the spent solution resides on the absorbent pad 1313. After exhaustion of capillary transport of all solution through the system, the purified nucleic acid binds to the binding matrix 1306 (1406) from which the nucleic acid can be eluted into the sample cup 1402 of the integrated test cassette, as shown in FIG.

[0096] The movement of the sample preparation subsystem components that occurs during the sample preparation process is illustrated in FIG. 14, which shows an embodiment of the sample preparation subsystem in cross section before and after sample processing. Prior to elution, there is a displacement of the binding matrix 1306 out of the capillary flow path and through the seal component 1316 by the action of an actuator in the associated reusable testing instrument. The seal component 1316 forms a seal with a portion of an elution buffer conduit 1318 to allow the elution buffer to be injected through the binding matrix 1306 into the sample cup 1402 without solution loss into the capillary flow path of the sample preparation subsystem. The conduit 1318 is attached to or is part of an elution buffer injector component that is comprised of an elution buffer reservoir 1317 and a plunger 1319. The plunger 1319 can optionally include an O-ring to facilitate sealing the elution buffer in the reservoir 1317. During elution of purified nucleic acid, the actuator moves elution reservoir component 1317 such that attached conduit 1318 forms a seal with seal component 1316, displacing binding matrix 1306 into chamber 1321. Mechanical access to depress elution reservoir 1317 is provided through actuator access port 1320. After binding matrix 1306 is disengaged from the main capillary solution flow path of the sample preparation subsystem, it resides in elution chamber 1321. Elution of purified nucleic acid into sample cup 1402 is accomplished by displacing elution buffer from elution buffer reservoir 1317, through reservoir 1317 to plunger 1319 by the actuator acting through actuator port 1322, in a syringe-like action. Elution buffer travels through binding matrix 1306 via conduit 1318, injecting elution buffer containing eluted purified nucleic acid into sample cup 1402.

[0097] 15, the sample preparation subsystem 1300 is preferably coupled to the fluidic components 1403 of the cassette 1500 by commonly used manufacturing methods such as ultrasonic welding to form an integrated single-use sample-to-result test cassette. In some embodiments, it is desirable to hermetically seal the test cassette fluids after introduction of the elution fluid containing the purified nucleic acid to reduce the possibility of the amplified nucleic acid escaping the cassette. A sliding seal 1404 can optionally but preferably be disposed between the sample preparation subsystem and the test cassette fluidic housing 1403 to seal the cassette at the inlet of the sample cup 1402. The sliding seal 1404 is moved to a sealing position by the action of an actuator to form an airtight seal including an O-ring 1405. A cassette liner 1406 is coupled to the fluidic housing after introduction of the dried reagents and test strips. As described above for the linings of other test cassette embodiments, the lining 1406 may include materials for vent functionality, maintaining an airtight seal, thermal interface, expansion chamber(s), and may optionally include a fluid carrying printed circuit board or flexible circuit layer and temperature control electronics. The electronics may optionally be housed in a reusable docking unit. The PCA 1501, including the electronics, is preferably constructed of low thermal mass materials and surface mount electronics. An array of surface mount resistors and proximally located temperature sensors provides one means of regulating the chamber temperature within the test cassette. The surface mount resistor and temperature sensor array of the PCA 1501 are positioned to align with the test cassette when the test cassette is loaded into the docking unit. An integrated sample-to-result cassette is shown in FIG. 16. FIG. 17 shows an integrated cassette with an underlying electronics layer based on traditional printed circuit boards and surface mount components. In some embodiments, a flexible circuit may be bonded to the rear of the test cassette.

[0098] <Electronic equipment> In some embodiments, it is desirable to place the electronic components on the reusable components such that heaters, sensors and other electronics are interfaced to the disposable test cassette by means that can establish a preferred thermal interface and precise alignment of the electronics with elements on the disposable test cassette with which they must interface. In other embodiments, it is desirable to use a combination of reusable and disposable components for temperature control. For example, standoff temperature monitoring may be accomplished by infrared sensors located on the reusable docking unit, while resistive heating elements for temperature and fluid control are located on flexible circuitry integrated into the disposable test cassette.

[0099] In some embodiments, the printed circuit board (PCB) comprises standard 0.062 inch thick FR4 copper clad laminate material, although other standard board materials and thicknesses can be used. Electronic components such as resistors, thermistors, LEDs and microcontrollers preferably comprise off-the-shelf surface mount devices (SMD) and are arranged according to industry standard methodologies.

[0100] In another embodiment, the PCA could be integrated with the cassette wall and could include a flexible plastic circuit. Flexible circuit materials such as PET and polyimide could be used as shown in FIG. 8. The use of flexible plastic circuits is well known in the art. In another embodiment, heating elements and temperature sensors could be screen printed onto the plastic fluidic parts using technology developed by companies such as Soligie, Inc.

[0101] In some embodiments of the present invention, the thickness of the PCB and the amount and placement of copper in the area surrounding the resistive heating element are tailored for thermal management of the reactive solution within the fluidic component, which can be accomplished by use of standard manufacturing techniques as previously mentioned.

[0102] In some embodiments of the invention, the resistor is a thick film 2512 package, although other resistors may be used. The heating chamber in the fluidic component is preferably sized similarly to the resistor dimensions to ensure uniform heating throughout the chamber. A single resistor of this size is sufficient to heat approximately 15 μL of solution, assuming a fluidic component thickness of 0.5 mm. The drawing in FIG. 2D shows two resistors 100 forming a heater sufficient to heat approximately 30 μL of solution, assuming a fluidic component thickness of 0.5 mm. In this case, the resistors are preferably 40 Ω each and are arranged in a parallel configuration.

[0103] In some embodiments of the invention, the temperature sensor 110 preferably includes a thermistor such as a 0402 NTC device, or a temperature sensor such as an Atmel AT30TS750, each of which has a height similar to that of a 2512 resistor package. The thermistor is preferably aligned adjacent to or between the resistive heating element in the case of a one resistor or two resistor configuration, respectively. By closely aligning these electronic elements, only a very thin air gap results between them. Additionally, applying the thermal compound prior to assembling the fluidic layer with the electronic layer ensures good thermal contact between the fluidic components, resistors and thermistors.

[0104] In some embodiments of the present invention, the vent resistors 70, 71 include a thick film 0805 package, although similar resistors can also be used. Small gauge Nichrome wire heating elements, such as 40 gauge Nichrome wire, may be used in place of resistors.

[0105] In some embodiments of the invention, the microcontroller is a Microchip Technologies PIC16F1789. The microcontroller is preferably matched to the complexity of the fluid system. For example, in the case of multiplexing, the number of individual vents and heaters is commensurate with the number of I / O lines of the microcontroller. The memory size can be selected to match the program size.

[0106] In certain embodiments of the present invention, N-channel MOSFETs in a SOT-23 package operating in an on-off mode are used to modulate the current load to the vent and heater resistors. The modulation signal is sent via a microcontroller. In alternative embodiments, pulse width modulation schemes and / or other control algorithms could be used for more advanced thermal management of the fluidics. This is typically handled by the microcontroller and may require additional hardware and / or software functionality known to those skilled in the art.

[0107] Depending on the application, some embodiments include a device in which a miniature control docking unit or docking unit operates a smaller disposable unit that includes a fluid system in contact with biological material, called a test cassette. In one such embodiment, the docking unit includes the electronic components. The elimination of electrical components from the disposable test cassette reduces costs and possibly reduces environmental impact. In another embodiment, some electronic components are included in both the docking unit and the test cassette. In this particular embodiment, the test cassette includes a preferably low-cost PCA or preferably flexible circuit to provide some electrical functions such as temperature control, fluid flow control and temperature sensing that are energized, controlled and / or interrogated by the docking unit through a suitable interface. As mentioned above, the electronic functions of such a device are preferably split into two separate subassemblies. The disposable cassette 2500 preferably includes a backside designed to interface with the resistive heating and sensing elements of the docking unit. The material that constitutes the backside of the test cassette is preferably selected to provide suitable thermal conductivity and stability while allowing fluid flow control via vent ruptures. In some embodiments, the backside of the test cassette, or a portion thereof, includes a flexible circuit fabricated on a substrate such as polyimide. Flexible circuits can be used to provide low-cost resistive heating elements with low thermal mass. The flexible circuit board can be preferably placed in direct contact with the solutions present in the fluidic network of the test cassette to allow for very efficient and rapid heating and cooling. A connector 810, shown in FIG. 8, preferably provides current to the resistive heater along with power and signal lines to an optional thermistor(s).

[0108] When using a flexible circuit 799, one or more IR sensors located in the docking unit can monitor the temperature of the heated chamber (e.g., amplification or detection chamber) by reading the signal through a window in the backing 805 or directly from the rear of the flexible circuit 799. Optionally, a thermistor on the PCA or flexible circuit 799 can be used to monitor the temperature. Optionally, a weighted average of the IR sensor and thermistor outputs is performed to improve correlation between the readings and the fluid temperature in the cassette. Additionally, the sensor can also detect the ambient temperature, allowing the system to compensate for the ambient temperature to ensure the sample fluid quickly equilibrates to the desired temperature.

[0109] 33, the docking unit includes a reusable component subassembly 3980, preferably including a microcontroller, MOSFETs, switches, a power supply or power jack and / or battery, optional cooling fan 903, optional user interface, infrared temperature sensors 901, 902, and a connector 900 compatible with connector 810 of cassette 2500. When the subassemblies are mated via connectors 810 and 900, the docking unit preferably supports the disposable cassette 2500 in a substantially vertical or near vertical orientation. Although a substantially vertical orientation is preferred in some embodiments described herein, similar results can be obtained when operating the device at an angle, particularly when coating certain paths to reduce the wetting angle of the solution used.

[0110] Another embodiment of the device may be used to minimize operating costs by reducing the cost of consumable parts of the system by eliminating all electronic circuitry located on the disposables. The microcontroller, heaters, sensors, power supplies and all other circuitry are located on multiple PCAs and are electrically connected to each other via high conductor count industry standard ribbon cables. A display may be added to assist the user in operating the device. An optional serial control port may also be utilized to allow the user to upload changes to test parameters and monitor the progress of any test. One version of this embodiment includes five different PCAs. The main board PCA contains the control circuitry, serial port, power supply and connectors to interface with other boards in the system. The heater board PCA contains the heating resistors, temperature sensor and vent burn heating elements. To facilitate a thermal interface between this heater board and the disposable fluid cassette, this board is mounted on a spring loaded carrier that moves towards the back of the fluid cassette with the closing action of the lid until it makes contact with the fluid cassette. A thin thermally conductive heating pad is attached to the top of the chamber heater resistors and temperature sensor to improve heat transfer between the heater board and the fluid cassette. A durable vented burning heating element can be realized using nichrome wire wound around a small ceramic carrier. An IR sensor board PCA is mounted a short distance away from the opposite side of the cassette and used to monitor the temperature of the heating chamber. This allows for closed loop temperature control of the heating and cooling process and adapts to ambient temperature changes. The IR sensor board may also be fitted with a number of reflective sensing photocouplers that allow for detection of the presence of a cassette and may be used to identify the type of cassette as indicated by a configurable reflective pattern located on the cassette. A display board PCA may be located approximately behind the IR board to allow the user to view the display from the front of the device.The final PCA, the shutter board, is positioned laterally from the top edge of the cassette and contains a switch and reflective optical coupler used to sense if the cassette has already been used and, once the lid is closed, locks the cassette in place for inspection.

[0111] Cooling of the system is optionally augmented using a fan, such as a muffin fan, that is turned on by the microcontroller only during the cooling phase of the test. A system of vents is preferably used to direct cooler outside air into the heating chamber and exhaust it out the side of the device.

[0112] To provide a complete sample-to-result molecular test, any of the above embodiments of the invention can be interfaced to a sample preparation system 1300 that provides nucleic acid as an output to the sample chamber 1402. This has been demonstrated using the sample preparation techniques described in International Publication WO 2009 / 137059, entitled "Highly Simplified Lateral Flow-Based Nucleic Acid Sample Preparation and Passive Fluid Flow Control." One embodiment of the resulting integrated device is illustrated in Figures 15 and 16.

[0113] <Docking unit> The reusable docking unit contains the electronics necessary to perform the test cassette functions. Various docking unit embodiments have been invented to interface with corresponding variations in test cassette design. In one embodiment, the docking unit shown in FIG. 18 and FIG. 19 contains all the electronics necessary to perform the test, eliminating the need for electronics in the test cassette. Referring now to FIG. 18, before adding the sample, the cassette 2500 is inserted into the docking unit 2501. The docking unit 2501 includes a display, such as an LCD display 2502, to communicate information such as the test protocol and test status to the user. After inserting the cassette into the docking unit 2501, the sample is introduced into the sample port 20 of the cassette 2500 and the docking unit lid 2503 is closed to begin the test. A docking unit with an inserted test cassette is shown in FIG. 19, and the docking unit 2501 with the lid in the closed position is illustrated in FIG. 18B.

[0114] In some embodiments of the docking unit, a mechanism is built into the hinge of the lid 2503 to move the sliding seal 91 of the test cassette to the closed position. A sealed test cassette helps ensure that the amplified nucleic acid remains contained within the test cassette. Now referring to FIG. 20, either a manual or automatic method may be used to slide the valve over the sample port to seal the cassette. In some embodiments, the slide seals the sample port by engaging an O-ring. An expansion chamber cover holds the valve slide in place over the O-ring of the sample port. The seal is moved into position by a servo motor or by a manual action such as closing the reusable docking unit lid, which in turn activates a mechanism that closes the cassette seal. In the illustrated embodiment, a rack and pinion mechanism 2504 moves the sliding seal 91 to the closed position using a sliding seal actuator 3979. The rack and pinion mechanism 2504 can be motorized or moved by the closing action of the docking unit lid 2503 through a mechanical connection to the lid hinge. Optionally, a sensor such as an optical sensor 2505, as shown in FIG. 21, can be positioned to check the position of the sliding seal 91 to ensure proper seal placement before the start of the assay. The optical sensor detects the state (i.e., position) of the cassette sample port seal. The optical sensor allows the docking unit to be programmed to detect accidental insertion of a previously used test cassette and to detect successful closure of the test cassette seal. An error message indicating a seal malfunction can be displayed on the display 2502 and the test program is aborted if the sensor 2505 fails to detect seal closure. In other embodiments of the test cassette and docking unit, the sealing mechanism can include other means of mechanically sealing the chamber, such as a rotating valve as shown in FIG. 22. In yet another embodiment, the test cassette seal can be placed on a hinged cassette lid positioned such that insertion into the docking unit is not possible without first closing the cassette lid and seating the seal.In this embodiment, the sample is added to the test cassette prior to insertion into the docking unit. A test cassette including a hinged lid with a seal is shown in Figure 23. Generally, after the cassette is inserted into the docking unit and the sample is loaded into the cassette, the assay is preferably initiated simultaneously with automatic sealing of the cassette by closing the lid of the docking unit, preferably without the use of servo motors or other mechanical devices.

[0115] In some docking unit embodiments, the electronic components that must interface with the test cassette do not physically impede cassette insertion, but a set of components preferably facilitates proper test cassette insertion while ensuring a reliable thermal interface during testing. These components form a mechanism that holds the PCA 75 away from the cassette insertion path until the lid 2503 is closed. Referring now to FIG. 24, within the docking unit the heater board is mounted on the PCA holder 2506, preferably acting as a low thermal mass scaffolding, while the test cassette is loaded into the low thermal mass cassette holder 2507, and rails 2509 guide the cassette into the docking unit and hold it in the correct position, such as parallel to the heater board surface, for interfacing with the PCA 75 attached to the PCA holder 2506. In the lid open position, protrusions 2508 on the cassette holder 2507 interfere with the PCA holder 2506, maintaining an open path along the rails 2509 for cassette insertion. Preferably, the ramp spans the distance between the projection 2508 and the lower ridge of the part 2507, facilitating smooth movement of the projection 2508 into the recess 2511 on the PCA holder 2506 upon closing of the lid 2503. When the docking unit lid is closed, the projection 2508 engages the recess 2511, thereby bringing the heater board mount closer to the rear of the test cassette 2500. Closing of the lid 2503 exerts a downward force on the cassette holder 2507, which moves the cassette holder 2507 to a position where the projection 2508 rests in the recess 2511, and the PCA holder 2506 moves so that the PCA 75 is pressed against the rear of the cassette 2500. Preferably, the PCA holder 2506 is under a constant force, such as a spring force, to allow a reproducible pressure to be exerted by the PCA 75 against the rear of the cassette after the lid is closed. The placement of the PCA 75 against the rear of the cassette 2500 forms a thermal interface that conducts heat from the resistive heating elements on the PCA to the temperature controlled chamber and vents of the test cassette. Preferably, components 2506 and 2507 are configured to provide minimal thermal mass to the system and provide access to the test cassette surface for cooling devices such as fans and temperature monitoring by sensors such as infrared sensors.Thus, after lid closure, the heater board is preferably pressed firmly against the rear of the test cassette, forming a thermal interface that allows microheaters on the heater board, preferably under microcontroller or microprocessor control, to heat solutions in the fluid chambers of the test cassette and melt the thermally labile vent film of the test cassette. Figure 25 shows the cassette-PCA interface mechanism in cross section in both the disengaged (lid open) and engaged (lid closed) positions.

[0116] In some embodiments, the docking unit includes additional sensors for applications such as temperature sensing, detecting the presence or removal of a test cassette, and detecting a particular test cassette to enable automatic selection of test parameters. Referring now to FIG. 26, an infrared sensor 2600 detects the temperature of the test cassette in an area covering a temperature-controlled chamber, such as chambers 30 and 90. The sensor allows for the collection of temperature data in addition to or instead of the temperature data collected by a PCA75 local temperature sensor, such as sensor 110. An optical sensor may optionally but preferably be used to detect a particular test cassette to identify the cassette for a particular disease or condition and enable automatic selection of an appropriate temperature profile for a particular test. Referring now to FIGS. 27A and 27B, an optical sensor or optical sensor array, such as optical sensor array 2601, may be used in conjunction with a barcode or barcode-like feature 2602 on the test cassette to determine the type of test cassette, as well as to confirm complete insertion and correct seating of the test cassette. The sensor array 2602 in conjunction with sensor 2505 may be used to detect the insertion of a previously used test cassette by detecting a hermetic seal prior to closing the lid. The docking unit may include sensors to detect the type of test cassette inserted into the docking unit and / or to verify correct insertion, positioning and alignment of the cassette within the docking unit. Detection of an Influenza A / B test cassette is illustrated in the docking unit and test cassette system shown in Figure 19. The docking unit is preferably capable of reading a barcode or other symbol on each cassette and altering the programming according to programs stored for various assays.

[0117] In some embodiments of the present invention, it may be desirable to heat both sides of the test cassette. A dual heater PCA configuration, in which the test cassette is inserted between two heater PCAs, is depicted in Figures 28A and 28B.

[0118] In another embodiment, the docking unit includes a servo actuator, an optical subsystem for automatic result readout, a wireless data communication subsystem, a touch screen user interface, a rechargeable battery power source, and a test cassette receiver that accepts a test cassette that constitutes an integrated sample preparation subsystem. With reference to Figs. 29A, 29B, and 30, a docking unit 2700 accepts a test cassette 1500 and places it in thermal contact with a PCA 1501 to allow for temperature and fluid flow control of the test cassette. The test cassette 1500 is inserted into a cassette receiver slot 3605 of a pivoting docking unit door 2702. After adding a crude sample or lysate to the test cassette, the docking unit door is closed, placing the rear of the test cassette in alignment and contact with the PCA 1501 and in alignment with the servo actuator. The servo actuator 3602 is positioned to provide the mechanical force required to access the solution compartmentalization component 1303 through the actuator port 1310 of the cassette 1500 and rupture the seal 1305. Rupture of the mechanical seal 1305 releases the crude lysate and wash buffer to flow through the sample preparation capillary material of the sample preparation subsystem described above. After completion of capillary fluid transport, a servo actuator 3601 positioned to access the elution reservoir 1317 through an actuator port 1320 of the cassette 1500 provides a mechanical force to move the part 1317 such that the attached conduit 1318 forms a seal with the seal 1316 and moves the binding matrix 1306 to the elution compartment 1321. A servo actuator 3604 positioned to access the elution plunger 1319 through an actuator port 1322 of the cassette 1500 then provides a mechanical force to the plunger 1319 to expel the elution buffer from the elution reservoir 1317 through the binding matrix 1306, resulting in elution of the nucleic acid into the sample cup 1402 of the cassette 1500. A servo actuator 3603 seals the cassette after elution as described above. Actuator control is preferably provided by a microcontroller or microprocessor on the control electronics PCA3606 according to firmware or software instructions.Similarly, temperature and fluid flow control within the test cassette follow instructions provided in firmware or software routines stored in the memory of the microcontroller or microprocessor. An optical subsystem 3607 including an LED light source 3608 and a CMOS sensor 3609 shown in FIG. 31 digitizes the detection strip signal data. The collected detection strip images are stored in a memory in the docking unit and interpretation of the results can be achieved using an on-board processor and reported to the LCD display 2701. A ring of LEDs provides uniform illumination during image collection by a CMOS-based digital camera. Images collected with a postage stamp-sized device can provide high-resolution data (5 megapixels, 10 bits) suitable for lateral flow signal analysis by colorimetry. The preferably low profile (approximately 1 cm) along with a short working distance optics allows the system to be incorporated into a thin device housing.

[0119] Optionally, the digitized results can be transmitted for offline analysis, storage and / or visualization via a wireless communication system built into the docking unit using either standard WiFi or cellular communication networks. Photographs of an embodiment of this docking unit are shown in Figures 32A and 32B. EXAMPLES

[0120] Example 1: Method for multiplex amplification and detection of purified viral RNA (infA / B) and an internal positive control virus The Influenza A and B test cassette was placed in the docking unit. 40 μL of sample solution was added to the sample port. The sample solution contained 5000 TCID 50 Purified A / Puerto Rico influenza RNA at a concentration equivalent to 500 TCID 50The 40 μL sample contained either purified B / Brisbane influenza RNA at a concentration equal to 1000 μL / mL, or molecular grade water (no template control sample). Upon entering the sample port, 40 μL of sample mixes with lyophilized beads as it flows into the first chamber of the test cassette. The lyophilized beads consisted of MS2 phage virus particles and DTT as a positive internal control. In the first chamber of the cassette, the sample was heated to 90° C. for 1 minute to promote viral lysis and then cooled to 50° C. before opening the vent connected to the second chamber. Opening the vent connected to the second chamber allows the sample to flow into the second chamber by allowing the air in the second chamber to move into the expansion chamber. As the sample moved into the second chamber, it mixed with oligonucleotide amplification primers for influenza A, influenza B, and MS2 phage, present as a lyophilized pellet in the recess of the flow path between the first and second chambers, as well as reverse transcription and nucleic acid amplification reagents and enzymes.

[0121] The amplification chamber was heated to 47 °C for 6 minutes, during which the RNA template was reverse transcribed into cDNA. After reverse transcription was completed, 40 cycles of thermal cycle amplification were performed in the second chamber. After thermal cycling was completed, the vent connected to the third chamber was opened to allow the reaction solution to flow into the third chamber. The third chamber contained a test strip and lyophilized beads containing three blue-stained polystyrene microsphere conjugates used as detection particles. The conjugates consisted of 300 nm polystyrene microspheres covalently linked to oligonucleotide probes complementary to the amplified sequences of influenza A or influenza B or MS2 phage. The solution reconstituted the lyophilized detection particles as it flowed into the third chamber. Three capture lines were fixed on the lateral flow membrane, from the bottom of the device they were: a negative control oligonucleotide not complementary to any assay target; a capture probe complementary to the amplified product of influenza B; a capture probe complementary to the amplified product of influenza A; and an oligonucleotide complementary to the amplified product of MS2 phage. The lateral flow strips were allowed to develop for 6 minutes prior to visual interpretation of the results. Once the lateral flow strips were developed, influenza A positive samples showed the formation of a blue test line at the location of influenza A and the MS2 phage, influenza B positive samples showed the formation of a blue test line at the location of influenza B and the MS2 phage, and negative samples showed the formation of a blue test line only at the location of the MS2 phage, as shown in FIG.

[0122] Example 2: Method for multiplex amplification and detection of viral lysates in buffer and internal positive control virus The Influenza A and B test cassette was placed in the docking unit. 40 μL of sample solution was added to the sample port. The sample solution contained 5000 TCID 50 / mL equivalent concentration of A / Puerto Rico influenza virus, 500 TCID 50The 40 μL sample contained either influenza B / Brisbane virus at a concentration equal to 100 μL / mL, or molecular grade water (no template control sample). Upon entering the sample port, 40 μL of sample mixes with lyophilized beads as it flows into the first chamber of the test cassette. The lyophilized beads consisted of MS2 phage virus particles and DTT as a positive internal control. In the first chamber of the cassette, the sample was heated to 90° C. for 1 minute to promote viral lysis and then cooled to 50° C. before opening the vent connected to the second chamber. Opening the vent connected to the second chamber allows the sample to flow into the second chamber by allowing the air in the second chamber to move into the expansion chamber. As the sample moves into the second chamber, it mixes with oligonucleotide amplification primers for influenza A, influenza B, and MS2 phage, present as a lyophilized pellet in the recess of the flow path between the first and second chambers, as well as reverse transcription and nucleic acid amplification reagents and enzymes.

[0123] The amplification chamber was heated to 47 °C for 6 minutes, during which the RNA template was reverse transcribed into cDNA. After reverse transcription was completed, 40 cycles of thermal cycle amplification were performed in the second chamber. After thermal cycling was completed, the vent connected to the third chamber was opened to allow the reaction solution to flow into the third chamber. The third chamber contained a test strip and lyophilized beads containing three blue-stained polystyrene microsphere conjugates used as detection particles. The conjugates consisted of 300 nm polystyrene microspheres covalently linked to oligonucleotide probes complementary to the amplified sequences of influenza A or influenza B or MS2 phage. The solution reconstituted the lyophilized detection particles as it flowed into the third chamber. Three capture lines were fixed on the lateral flow membrane, from the bottom of the device they were: a negative control oligonucleotide not complementary to any assay target; a capture probe complementary to the amplified product of influenza B; a capture probe complementary to the amplified product of influenza A; and an oligonucleotide complementary to the amplified product of MS2 phage. The lateral flow strips were allowed to develop for 6 minutes prior to visual interpretation of the results. Once the lateral flow strips were developed, influenza A positive samples showed the formation of a blue test line at the location of influenza A and the MS2 phage, influenza B positive samples showed the formation of a blue test line at the location of influenza B and the MS2 phage, and negative samples showed the formation of a blue test line only at the location of the MS2 phage, as shown in Figure 35.

[0124] Example 3: Method for multiplex amplification and detection of influenza virus (purified) and an internal positive control virus spiked into negative clinical nasal samples. Nasal swab samples collected from human subjects were placed in 3 mL of 0.025% Triton X-100, 10 mM Tris, pH 8.3 and tested for the presence of influenza A and influenza B using an FDA-approved real-time RT-PCR test. Prior to use in this test, samples were confirmed to be negative for influenza A and influenza B. Confirmed influenza-negative nasal samples were dosed with 5000 TCID 50A confirmed influenza negative nasal sample was spiked with A / Puerto Rico influenza virus at a concentration equivalent to 100 µL / mL or used without the addition of virus as a negative control. 40 µL of the resulting spiked or negative control sample was added to the sample port of the Influenza A and B test cassette. Upon entering the sample port, the 40 µL of sample mixes with the lyophilized beads as it flows into the first chamber of the test cassette. The lyophilized beads consisted of MS2 phage virus particles and DTT as a positive internal control. In the first chamber of the cassette, the sample was heated to 90 °C for 1 min to promote viral lysis and then cooled to 50 °C before opening the vent connected to the second chamber. Opening the vent connected to the second chamber allows the sample to flow into the second chamber by allowing the movement of air in the second chamber into the expansion chamber. As the sample moved into the second chamber, it mixed with oligonucleotide amplification primers for influenza A, influenza B and MS2 phage, as well as reverse transcription and nucleic acid amplification reagents and enzymes, which were present as a lyophilized pellet in the recess of the flow path between the first and second chambers.

[0125] The amplification chamber was heated to 47 °C for 6 minutes, during which the RNA template was reverse transcribed into cDNA. After reverse transcription was completed, 40 cycles of thermal cycle amplification were performed in the second chamber. After thermal cycling was completed, the vent connected to the third chamber was opened to allow the reaction solution to flow into the third chamber. The third chamber contained a test strip and lyophilized beads containing three blue-stained polystyrene microsphere conjugates used as detection particles. The conjugates consisted of 300 nm polystyrene microspheres covalently linked to oligonucleotide probes complementary to the amplified sequences of influenza A or influenza B or MS2 phage. The solution reconstituted the lyophilized detection particles as it flowed into the third chamber. Three capture lines were fixed on the lateral flow membrane, from the bottom of the device they were: a negative control oligonucleotide not complementary to any assay target; a capture probe complementary to the amplified product of influenza B; a capture probe complementary to the amplified product of influenza A; and an oligonucleotide complementary to the amplified product of MS2 phage. The lateral flow strips were allowed to develop for 6 minutes prior to visual interpretation of the results. Once the lateral flow strips were developed, the Influenza A positive samples showed the formation of a blue test line at the location of Influenza A and the MS2 phage, while the negative control samples showed the formation of a blue test line only at the location of the MS2 phage, as shown in Figure 36.

[0126] Although the present invention has been described in detail with particular reference to the disclosed embodiment, other embodiments can achieve the same results. Variations and modifications of the present invention will be obvious to those skilled in the art, and it is intended to cover all such modifications and equivalents. The entire disclosures of all patents and publications cited above are hereby incorporated by reference into this specification. [Explanation of symbols]

[0127] "OPEN" in Figure 21A means "open." "CLOSED" in Figure 21C means "closed." [Related to Figures 1 and 2] 15,37 Recess 30,90 Chamber 35,40 Channel 50,54 Vent pocket 72 Thermally stable materials 75 Printed Circuit Board or PCA 80 Heat-unstable vent pocket seal material (heat-unstable material) 7004 (Figure 45) Dimple (protrusion) 230 Detection Chamber 235 Detection Strips 93 Capillary pool or space in the detection chamber [Related to Figures 7 and 8] 400 Fluid Parts 410 Thermally unstable materials 420 Gasket 430 Thermally stable materials 440 Air Gap 799 Flexible Circuits [Related to Figure 44] 7001 Ridges (or ridges) (structures to help guide fluids) [Related to Figures 39 to 43] 4001 Triangle Flow Control Feature 4003 Reaction Chamber 4005 Tapered outlet 4101 Triangle Flow Control Feature 4103 Reaction Chamber 4201 Trapezoidal flow control feature 4203 Reaction Chamber 4303 Triangle flow control feature 4305 Reaction Chamber 4306 Exit Channel 4401 Flow Control Features 4403 Reaction Chamber

Claims

1. A cassette for detecting a target nucleic acid, comprising: a vertically oriented detection chamber; The detection chamber comprises: a lateral flow detection strip disposed within the detection chamber and oriented such that a sample receiving end of the lateral flow detection strip is a lower end of the lateral flow detection strip; a capillary pool at the sample receiving end of the lateral flow detection strip for receiving a fluid containing amplified target nucleic acid; Equipped with The cassette further comprises a chamber fluidly connected to and upstream of the detection chamber, the chamber having a feature that prevents fluid entering vertically at the top of the chamber from flowing directly into the outlet of the chamber.

2. The cassette of claim 1 , wherein the capillary pool contains detection particles.

3. 3. The cassette of claim 2, wherein the detection particles are selected from the group consisting of dye polystyrene microspheres, latex, colloidal gold, colloidal cellulose, nanogold and semiconductor nanocrystals.

4. 3. The cassette of claim 2, wherein the detection particles comprise an oligonucleotide complementary to a sequence of the amplified target nucleic acid or a ligand capable of binding to the amplified target nucleic acid.

5. 5. The cassette of claim 4, wherein the ligand is selected from the group consisting of biotin, streptavidin, a hapten, or an antibody.

6. 3. The cassette of claim 2, wherein the detection particles are dried, lyophilized, or present on at least a portion of the interior surface as a dry mixture of detection particles in a carrier to facilitate resuspension of the detection particles.

7. The cassette of claim 6 , wherein the carrier comprises a polysaccharide, a detergent or a protein.

8. 10. The cassette of claim 1 for performing an assay having a volume of less than 200 μL.

9. 9. The cassette of claim 8, wherein the assay has a volume of less than 60 μL.

10. The cassette of claim 1 , wherein the features are triangular or trapezoidal in shape.

11. The cassette of claim 1 , wherein said outlet is tapered.

12. The cassette of claim 1 , wherein the lateral flow detection strip comprises a porous material.

13. 13. The cassette of claim 12, wherein the porous material comprises cellulose, nitrocellulose, polyethersulfone, polyvinylidine fluoride, nylon, charge-modified nylon, polytetrafluoroethylene, or a combination thereof.

14. 13. The cassette of claim 12, wherein the porous material comprises a binding moiety capable of specifically binding, directly or indirectly, to the amplified target nucleic acid.

15. 15. The cassette of claim 14, wherein the porous material is patterned with lines, dots, microarrays or other visually identifiable elements that include the binding moieties.

16. The cassette of claim 12 , wherein the porous material contains detector particles.

17. 17. The cassette of claim 16, wherein the detection particles are dried or lyophilized.

Images