Systems and methods for at least one of sample preparation or sample analysis including a rotary valve

Abstract

The present application relates to systems and methods including a rotary valve for at least one of sample preparation or sample analysis. Systems and methods for conducting a specified reaction including a fluidic network having a sample channel, a reaction chamber, and a reservoir. The sample channel is in flow communication with a sample port. The system further includes a rotary valve having a flow channel and configured to rotate between a first valve position and a second valve position. When the rotary valve is in the first valve position, the flow channel fluidly couples the reaction chamber and the sample channel, and when the rotary valve is in the second valve position, the flow channel fluidly couples the reservoir and the reaction chamber. When the rotary valve is in the first valve position, a pump assembly induces a biological sample to flow toward the reaction chamber, and when the rotary valve is in the second valve position, the pump assembly induces a reaction component to flow from the reservoir to the reaction chamber.

Description

[0001] This application is a divisional application of the application filed on June 3, 2015, with application number 201580040821.0 and entitled "System and method including a rotary valve for at least one of sample preparation or sample analysis". Technical Field

[0002] The embodiments of this application generally relate to systems and methods for generating samples for biochemical analysis and / or for carrying out biochemical reactions, and more specifically, to systems and methods utilizing rotary valves. background

[0003] Various biochemical assays involve a large number of controlled reactions carried out on a carrier surface or within a designated reaction chamber. Controlled reactions can be performed to analyze biological samples or prepare biological samples for subsequent analysis. This analysis can identify or reveal the properties of the chemicals involved in the reaction. For example, in array-based cyclic sequencing assays (e.g., sequencing-by-synthesis (SBS)), DNA features (e.g., template nucleic acids) of a dense array are sequenced via enzymatically manipulated iterative cycles. After each cycle, an image can be captured and subsequently analyzed with other images to determine the sequence of the DNA features. In another biochemical assay, an unknown analyte with an identifiable label (e.g., a fluorescent label) can be exposed to a known probe array with predetermined addresses within the array. Observing the chemical reactions occurring between the probes and the unknown analyte can help identify or reveal the properties of the analyte.

[0004] There is a general need for systems that automate assays, such as those described above, where the system requires less user work or intervention. Currently, most platforms require the user to prepare the biological sample separately before loading it into the system for analysis. Users may expect to load one or more biological samples into the system, select the assay to be performed by the system, and obtain results from the analysis within a predetermined time period, such as one day or less. At least some currently used systems are unable to perform certain protocols that provide data with sufficient quality at a reasonable cost, such as whole-genome sequencing.

[0005] Brief

[0006] According to an embodiment, a system is provided comprising a fluid network having a sample channel, a reaction chamber, and a reservoir. The sample channel is in flow communication with a sample port configured to receive a biological sample. The system also includes a pump assembly configured to be in flow communication with the fluid network. The system further includes a rotary valve having a flow channel and configured to rotate between a first valve position and a second valve position. When the rotary valve is in the first valve position, the flow channel fluidly connects the reaction chamber and the sample channel, and when the rotary valve is in the second valve position, the flow channel fluidly connects the reservoir and the reaction chamber. When the rotary valve is in the first valve position, the pump assembly induces the biological sample to flow toward the reaction chamber, and when the rotary valve is in the second valve position, the pump assembly induces reaction components to flow from the reservoir to the reaction chamber.

[0007] In one embodiment, the pump assembly includes a system pump that is in flow communication with the reaction chamber and is located downstream of the reaction chamber.

[0008] In one embodiment, the rotary valve is configured to hold the biological sample in the flow channel when the rotary valve is rotated from the first valve position to the second valve position, and the pump assembly is configured to induce the biological sample to flow into the reservoir when the rotary valve is in the second valve position.

[0009] In one embodiment, the sample channel is a first sample channel and the biological sample is a first biological sample, the fluid network includes a second sample channel having a second biological sample, the rotary valve is configured to rotate to a third valve position such that the flow channel is in flow communication with the second sample channel, the pump assembly is configured to induce the second biological sample in the second sample channel to flow into the flow channel, wherein the rotary valve is configured to hold the second biological sample in the flow channel when the rotary valve is rotated from the third valve position to the second valve position, and the pump assembly is configured to induce the second biological sample therein to flow into the reservoir when the rotary valve is in the second valve position.

[0010] In one embodiment, the pump assembly is configured to induce the first and second biological samples to flow from the reservoir toward the reaction chamber.

[0011] In one embodiment, the reservoir is a first reservoir, and the fluid network further includes a second reservoir, wherein the rotary valve is configured to move to a third valve position such that the flow channel fluidly connects the second reservoir and the reaction chamber.

[0012] In one embodiment, the sample channel is a first sample channel and the fluid network includes a second sample channel.

[0013] In one embodiment, each of the first sample channel and the second sample channel is in flow communication with the rotary valve via a common supply port.

[0014] In one embodiment, the system further includes a channel valve coupled to the sample channel, the channel valve being configured to move between a first position and a second position to respectively block flow through the sample channel and allow flow through the sample channel.

[0015] In one embodiment, the rotary valve rotates about an axis, and the fluid network includes a feed port aligned with the axis and fluidly connecting the flow channel and the reaction chamber.

[0016] In one embodiment, the fluid network further includes a reagent channel, the sample channel and the reagent channel being in flow communication with a common supply port located upstream of the flow channel, the supply port fluidly connecting the sample channel and the reagent channel to the flow channel.

[0017] In one embodiment, the system further includes a detection component configured to detect a specified reaction within the reaction chamber.

[0018] In one embodiment, the detection component includes an imaging detector positioned to detect light signals from the reaction chamber.

[0019] In one embodiment, the imaging detector has a fixed position relative to the fluid network.

[0020] In one embodiment, the system further includes a system controller configured to automatically control the rotary valve and the pump assembly for iterative cycles of a sequencing synthesis (SBS) protocol.

[0021] In one embodiment, a method is provided that includes rotating a rotary valve having a flow channel to a first valve position. When in the first valve position, the flow channel is in flow communication with a reaction chamber. The method may further include allowing a biological sample to flow from a sample channel or a first reservoir through the flow channel and into the reaction chamber while the rotary valve is in the first valve position. The method further includes rotating the rotary valve to a second valve position. When in the second valve position, the flow channel is fluidly connected to a second reservoir and the reaction chamber. The method further includes allowing a reaction component to flow from the second reservoir into the reaction chamber. The reaction component interacts with the biological sample within the reaction chamber.

[0022] In one embodiment, the method further includes detecting a specified reaction between the reaction component and the biological sample within the reaction chamber.

[0023] In one embodiment, detecting the designated reaction includes detecting a light signal from the reaction chamber, the light signal characterizing the designated reaction.

[0024] In one embodiment, the method further includes allowing multiple biological samples to flow into the reservoir respectively, thereby combining the biological samples in the reservoir, wherein the biological samples simultaneously flow through the flow channel and into the reaction chamber when the rotary valve is in the first valve position.

[0025] In one embodiment, the method further includes rotating the rotary valve to a third valve position and allowing the washing solution to flow from the third reservoir into the reaction chamber, and the method further includes rotating the rotary valve to a second valve position and allowing the reaction component to flow from the second reservoir into the reaction chamber.

[0026] In one implementation, the method includes performing an iterative cycle of a sequencing-by-synthesis (SBS) protocol.

[0027] In one embodiment, the method further includes amplifying the biological sample in the sample channel or the reservoir before allowing the biological sample to flow through the flow channel and into the reaction chamber.

[0028] In one embodiment, the rotary valve rotates about an axis and a feed port fluidly connects the flow channel and the reaction chamber, the axis extending through the feed port.

[0029] In one embodiment, a system is provided comprising a flow control system having a fluid network and a pump assembly in flow communication with the fluid network. The fluid network includes a sample channel configured to receive a biological sample, multiple reservoirs, and a reaction chamber. The system also includes a rotary valve having a flow channel. The rotary valve is configured to rotate to different valve positions to fluidly connect the reaction chamber to either the sample channel or one of the reservoirs. The system further includes a detection device configured to detect a light signal from the reaction chamber during an assay. The system also includes a system controller configured to control the rotary valve and pump assembly to allow the biological sample to flow from the sample channel and into the reaction chamber. The system controller is also configured to control a rotary valve, a pump assembly, and a detection device during multiple scenario cycles, each of which includes: (a) rotating the rotary valve to a first reservoir valve position, such that the reaction chamber is in flow communication with a first reservoir among a plurality of reservoirs; (b) controlling the pump assembly to induce fluid to flow from the first reservoir into the reaction chamber; (c) rotating the rotary valve to a second reservoir valve position, such that the reaction chamber is in flow communication with a second reservoir among a plurality of reservoirs; (d) controlling the pump assembly to induce fluid to flow from the second reservoir into the reaction chamber; and (e) controlling the detection device to detect an optical signal from the reaction chamber when or after fluid from the second reservoir flows through the reaction chamber.

[0030] In one embodiment, the sample channel includes a sample preparation area, and the system further includes a thermal circulator configured to control the temperature of the biological sample within the sample preparation area. The system controller controls the thermal circulator to amplify the biological sample within the sample preparation area before the biological sample flows from the sample channel into the reaction chamber.

[0031] In one embodiment, each of the scheme cycles further includes rotating the rotary valve to a third reservoir valve position, such that the reaction chamber is in third reservoir flow communication with the plurality of reservoirs, and controlling the pump assembly to induce fluid to flow from the third reservoir into the reaction chamber.

[0032] In one embodiment, the detection device includes a CMOS imaging detector.

[0033] In one embodiment, the system further includes a flow unit coupled to the detection device, the flow unit defining the reaction chamber.

[0034] In one embodiment, the flow unit is fixed in a fixed position relative to the detection device.

[0035] In one embodiment, the flow control system includes a microfluidic body having a body side including a plurality of ports opening toward the body side, wherein a rotary valve seals a plurality of the ports when the flow channel is fluidly connected to at least one of the other ports.

[0036] In one implementation, the system is configured to perform a synthetic sequencing (SBS) protocol.

[0037] According to an embodiment, a method is provided comprising providing a microfluidic body and a rotary valve. The microfluidic body has a body side and a fluid network including a supply port and a feed port. The supply port opens toward the body side. The rotary valve is rotatably mounted to the body side. The rotary valve has a first channel port, a second channel port, and a flow channel extending between the first channel port and the second channel port. The method further comprises rotating the rotary valve to a first valve position in which the first channel port is in flow communication with the supply port of the microfluidic body. The method further comprises, when the rotary valve is in the first valve position, allowing a biological sample to flow through the first channel port and into the flow channel. The method further comprises, with the biological sample within the flow channel, rotating the rotary valve to a second valve position such that the first channel port is sealed by the body side. The method further comprises performing a thermal cycling operation to change the temperature of the biological sample in the flow channel to a selected temperature.

[0038] In one embodiment, the microfluidic body includes a reservoir port opening toward the body side and in flow communication with a reservoir, and the method further includes rotating the rotary valve to align the first channel port and the reservoir port, and inducing the biological sample within the flow channel to flow through the first channel port into the reservoir.

[0039] In one embodiment, the method further includes inducing the biological sample to flow from the reservoir through the flow channel and through the feed port of the microfluidic body.

[0040] In one embodiment, when the rotary valve is in the second valve position, the second channel port is aligned with the feed port.

[0041] In one embodiment, when the rotary valve is in the second valve position, the second channel port is sealed by the body side.

[0042] In one embodiment, the first channel port is a first inlet port and the flow channel is a first flow channel, and the rotary valve includes a second inlet port and a second flow channel extending between the second inlet port and the second channel port.

[0043] In one embodiment, the first channel port is a first inlet port and the second channel port is a first outlet port, the rotary valve includes a second inlet port and a second outlet port, and a flow channel extends between the second inlet port and the second outlet port.

[0044] In one embodiment, the rotary valve includes a fluid side and an operating side facing opposite directions, and the thermal circulator engages the operating side to control the temperature of the biological sample.

[0045] In one embodiment, the method further includes inducing the biological sample to flow from the reservoir through the flow channel and through the feed port of the microfluidic body into the reaction chamber, and the method further includes detecting an optical signal from the reaction chamber.

[0046] In one embodiment, the reaction chamber has a remote position relative to the rotary valve.

[0047] In one embodiment, the flow unit includes the reaction chamber, and wherein detecting the optical signal from the reaction chamber includes detecting the optical signal using an imaging detector coupled to the flow unit.

[0048] In one embodiment, the imaging detector and the flow unit are fixed to each other.

[0049] According to an embodiment, a system is provided comprising a microfluidic body having a body side and a fluid network including a supply port and a feed port. The supply port opens toward the body side. The system also includes a rotary valve rotatably mounted to the body side. The rotary valve has a first channel port, a second channel port, and a flow channel extending between the first and second channel ports. The rotary valve is configured to rotate between a first valve position and a second valve position. When the rotary valve is in the first valve position, the first channel port is in flow communication with the supply port of the microfluidic body. When the rotary valve is in the second valve position, the first channel port is sealed by the microfluidic body. The system also includes a pump assembly configured to induce fluid flow through the supply port and into the flow channel when the rotary valve is in the first valve position. The system also includes a thermal circulator positioned relative to the rotary valve and configured to control the temperature experienced by the fluid within the flow channel when the rotary valve is in the second valve position.

[0050] In one embodiment, the microfluidic body includes a reservoir port opening toward the body side and in flow communication with a reservoir, the rotary valve being rotatable to a third valve position in which the first channel port and the reservoir port are aligned, and the pump assembly being configured to induce fluid flow in the flow channel through the reservoir port and into the reservoir.

[0051] In one embodiment, the pump assembly is configured to induce the fluid to flow from the reservoir through the flow channel and through the feed port of the microfluidic body.

[0052] In one embodiment, the rotary valve is configured to rotate about an axis, with the second channel port and the feed port aligned with the axis.

[0053] In one embodiment, the flow channel is a first flow channel, and the rotary valve includes a second flow channel extending between corresponding channel ports.

[0054] In one embodiment, the system further includes a reaction chamber in flow communication with the feed port and a detection device positioned to detect a specified reaction within the reaction chamber.

[0055] In one embodiment, the reaction chamber has a remote position relative to the rotary valve.

[0056] In one embodiment, the flow unit includes the reaction chamber, and the detection device is an imaging detector located adjacent to the flow unit.

[0057] In one embodiment, the imaging detector and the flow unit are fixed to each other.

[0058] According to an embodiment, a system is provided comprising a microfluidic body having a fluid network having an inlet port, an outlet port, and a sample reservoir. The system also includes a rotary valve rotatably coupled to the microfluidic body. The rotary valve has a first channel section and a second channel section. When the rotary valve is in a first valve position, the first channel section fluidly connects the inlet port and the sample reservoir. When the rotary valve is in the first valve position, the second channel section fluidly connects the outlet port and the sample reservoir. The system also includes a pump assembly configured to allow fluid to flow through the inlet port and the first channel section into the sample reservoir when the rotary valve is in the first valve position. The rotary valve is configured to move to a second valve position in which the sample reservoir is sealed by the rotary valve. The system may further include a thermal circulator positioned relative to the microfluidic body to provide heat to the sample reservoir when the rotary valve is in the second valve position.

[0059] In one embodiment, the rotary valve includes a closed gas reservoir that, when the rotary valve is in the second valve position, is aligned with the sample reservoir, and the closed gas reservoir and the sample reservoir are combined to form a reaction chamber.

[0060] In one embodiment, the system further includes a feed channel in fluid communication with the outlet port, the feed channel fluidly connecting the outlet port to the reaction chamber, wherein the system includes the reaction chamber and a detection device positioned to detect a specified reaction within the reaction chamber.

[0061] In one embodiment, the reaction chamber has a remote position relative to the rotary valve.

[0062] In one embodiment, the flow unit includes the reaction chamber, and the detection device is an imaging detector located adjacent to the flow unit.

[0063] According to an embodiment, a system is provided comprising a microfluidic body having a fluid network having a sample reservoir and a separate measurement channel. The measurement channel extends between a first port and a second port. The fluid network also includes a feed port. The system may further include a thermal circulator positioned adjacent to a thermally controlled region of the microfluidic body. The measurement channel extends through the thermally controlled region. The thermal circulator is configured to provide thermal energy to the thermally controlled region. The system also includes a rotary valve rotatably coupled to the microfluidic body and configured to move between a first valve position and a second valve position. The rotary valve has a bridge channel and a separate flow channel. When the rotary valve is in the first valve position, the bridge channel fluidly connects the sample reservoir and the first port of the measurement channel, and the flow channel fluidly connects the second port of the measurement channel and the feed port. The rotary valve is configured to move to the second valve position to seal the first and second ports of the measurement channel.

[0064] In one embodiment, the flow channel is configured to receive a biological sample from the measurement channel, and the rotary valve is configured to rotate to a third valve position, in which the flow channel is fluidly connected to a reservoir, allowing the biological sample to flow through the flow channel into the reservoir.

[0065] In one embodiment, the system further includes a reaction chamber in flow communication with the feed port and a detection device positioned to detect a specified reaction within the reaction chamber.

[0066] In one embodiment, the reaction chamber has a remote position relative to the rotary valve.

[0067] In one embodiment, the flow unit includes the reaction chamber, and the detection device is an imaging detector located adjacent to the flow unit.

[0068] In one embodiment, the imaging detector and the flow unit are fixed to each other. Attached Figure Description

[0069] Figure 1It is a schematic diagram of a system formed according to the implementation plan, which is configured to perform at least one of biochemical analysis or sample preparation.

[0070] Figure 2 This is a plan view of the flow control system formed according to the implementation plan, which is related to... Figure 1 Used together with the system.

[0071] Figure 3 It is possible to be with Figure 2 A cross-sectional view of a valve mechanism in its first state or condition, used in conjunction with a flow control system.

[0072] Figure 4 It is in the second state or condition. Figure 3 Cross-sectional view of the valve mechanism.

[0073] Figure 5 It is possible to be with Figure 2 A cross-sectional view of a valve mechanism in its first state or condition, used in conjunction with a flow control system.

[0074] Figure 6 It is in the second state or condition. Figure 5 Cross-sectional view of the valve mechanism.

[0075] Figure 7 It is possible to be with Figure 2 A cross-sectional view of a valve mechanism in its first state or condition, used in conjunction with a flow control system.

[0076] Figure 8 It is in the second state or condition. Figure 7 Cross-sectional view of the valve mechanism.

[0077] Figure 9 It is the cross-section of the rotary valve installed on the microfluidic body according to the implementation plan.

[0078] Figure 10 yes Figure 9 A plan view of the microfluidic host.

[0079] Figure 11 It is a cross-section of a detection component that can be used to detect a specified reaction from a reaction chamber.

[0080] Figure 12 It is a flowchart of the method according to the implementation plan.

[0081] Figure 13 It is a plan view of a rotary valve formed according to the implementation scheme and rotatably mounted to the microfluidic body.

[0082] Figure 14 It is rotatably mounted to the microfluidic body. Figure 13A cross-sectional view of the rotary valve.

[0083] Figure 15A-15L The different rotational positions of the rotary valve are shown during different stages of the measurement scheme.

[0084] Figure 16 It is a plan view of the rotary valve formed according to the implementation plan.

[0085] Figure 17 During the amplification protocol Figure 16 A plan view of the rotary valve.

[0086] Figure 18 It is a plan view of the rotary valve formed according to the implementation plan.

[0087] Figure 19 It is based on the method of the implementation plan.

[0088] Figure 20 This is a perspective view of a flow control system formed according to the implementation plan, which includes a rotary valve and a microfluidic body.

[0089] Figure 21 When the rotary valve is in the designated position for the amplification scheme Figure 20 A perspective view of the flow control system.

[0090] Figure 22 yes Figure 20 The separated cross section of the flow control system.

[0091] Figure 23 It is a schematic diagram of a system formed according to the implementation plan, which is configured to perform at least one of biochemical analysis or sample preparation.

[0092] Figure 24 This is a plan view of the flow control system formed according to the implementation plan, which utilizes a bridge-type channel.

[0093] Figure 25 yes Figure 24 A partial exploded perspective view of the flow control system.

[0094] Figure 26 This is a bottom perspective view of the rotary valve according to the implementation plan.

[0095] Figure 27 yes Figure 26 Side perspective view of the rotary valve.

[0096] Figure 28 Show Figure 26 A cross-sectional view of the rotary valve.

[0097] Figure 29 yes Figure 26An enlarged cross-sectional view of the rotary valve. Detailed Implementation

[0098] The embodiments described herein can be used to perform specified reactions for sample preparation and / or biochemical analysis. As used herein, the term "biochemical analysis" can include at least one of biological analysis or chemical analysis. Figure 1 This is a schematic diagram of a system 100 configured to perform biochemical analysis and / or sample preparation. System 100 includes a base instrument 102 and a removable cartridge 104 configured to detachably engage with the base instrument 102. The base instrument 102 and the removable cartridge 104 may be configured to interact with each other to transport biological samples to different locations within system 100, perform specified reactions including the biological samples to prepare biological samples for subsequent analysis, and optionally, detect one or more events with the biological samples. The event may indicate a specified reaction accompanying the biological sample. The removable cartridge 104 may be similar to an integrated microfluidic cartridge, for example, those shown and described in, for example, U.S. Provisional Patent Application No. 62 / 003,264, filed May 27, 2014, which is incorporated herein by reference in its entirety. However, the embodiments set forth herein are not limited to integrated devices but may also be used in larger systems.

[0099] Although the following is for reference Figure 1 The basic instrument 102 and removable cartridge 104 are shown, but it should be understood that the basic instrument 102 and removable cartridge 104 only illustrate one exemplary embodiment of system 100, and other embodiments exist. For example, the basic instrument 102 and removable cartridge 104 include various components and features that jointly perform multiple operations for preparing and / or analyzing biological samples. In the illustrated embodiment, each of the basic instrument 102 and removable cartridge 104 is capable of performing certain functions. However, it should be understood that the basic instrument 102 and removable cartridge 104 may perform different functions and / or may share such functions. For example, in the illustrated embodiment, removable cartridge 104 is configured to detect a specified reaction using a detection component (e.g., an imaging device). In an alternative embodiment, the basic instrument 102 may include this detection component. As another example, in the illustrated embodiment, the basic instrument 102 is a "dry" instrument that does not provide, receive, or exchange liquids with the removable cartridge 104. In an alternative implementation, the base instrument 102 may provide the removable cartridge 104 with reagents or other liquids, for example, that are subsequently consumed by the removable cartridge 104 (e.g., used in a specified reaction).

[0100] As used herein, biological samples may include one or more biological substances or chemical substances, such as nucleosides, nucleic acids, polynucleotides, oligonucleotides, proteins, enzymes, polypeptides, antibodies, antigens, ligands, receptors, polysaccharides, carbohydrates, organelles, lipid layers, cells, tissues, organisms, and / or bioactive chemical compounds, such as analogs or simulants of the aforementioned species. In some examples, biological samples may include whole blood, lymph, serum, plasma, sweat, tears, saliva, sputum, cerebrospinal fluid, amniotic fluid, semen, vaginal secretions, serous fluid, synovial fluid, pericardial fluid, peritoneal fluid, exudate, cystic fluid, bile, urine, gastric juice, intestinal juice, fecal samples, fluids containing single or multiple cells, fluids containing organelles, fluidized tissues, fluidized organisms, fluids containing multicellular organisms, biological swabs, and biological washes.

[0101] In some implementations, the biological sample may include added materials such as water, deionized water, saline solution, acidic solution, alkaline solution, detergent solution, and / or pH buffer. The added materials may also include reagents that will be used during the specified assay protocol to perform biochemical reactions. For example, the added liquid may include materials that undergo multiple polymerase chain reaction (PCR) cycles with the biological sample.

[0102] However, it should be understood that the biological sample being analyzed may be in a different form or state than the biological sample loaded into system 100. For example, the biological sample loaded into system 100 may include whole blood or saliva that is subsequently processed (e.g., via an isolation or amplification procedure) to provide prepared nucleic acids. The prepared nucleic acids can then be analyzed by system 100 (e.g., quantitatively by PCR or by SBS sequencing). Therefore, when the term "biological sample" is used in describing a first operation such as PCR and again in describing a subsequent second operation, such as sequencing, it should be understood that the biological sample in the second operation may be altered relative to the biological sample prior to or during the first operation. For example, the sequencing step (e.g., SBS) may be performed on amplicon nucleic acids, which are generated from template nucleic acids amplified in a previous amplification step (e.g., PCR). In this case, the amplicon is a copy of the template, and the amplicon is present in a higher amount than the template.

[0103] In some embodiments, system 100 can automatically prepare samples for biochemical analysis based on user-provided materials (e.g., whole blood or saliva). However, in some embodiments, system 100 can analyze biological samples that are partially or preliminarily prepared for analysis by a user. For example, the user can provide a solution containing nucleic acids that have been isolated and / or amplified from whole blood.

[0104] As used herein, a “specified reaction” includes a change in at least one aspect of the chemical, electrical, physical, or optical properties (or characteristics) of the analyte in question. In a particular embodiment, the specified reaction is an associative binding event (e.g., the co-incorporation of the analyte in question with a fluorescently labeled biomolecule). The specified reaction can be a dissociative binding event (e.g., the release of a fluorescently labeled biomolecule from the analyte in question). The specified reaction can be a chemical transformation, chemical change, or chemical interaction. The specified reaction can also be a change in electrical properties. For example, the specified reaction can be a change in the concentration of ions in solution. Exemplary reactions include, but are not limited to, chemical reactions such as reduction, oxidation, addition, elimination, rearrangement, esterification, amidation, etherification, cyclization, or substitution; binding interactions in which a first chemical substance binds to a second chemical substance; dissociation reactions in which two or more chemical substances separate from each other; fluorescence; luminescence; bioluminescence; chemiluminescence; and biological reactions such as nucleic acid replication, nucleic acid amplification, nucleic acid hybridization, nucleic acid ligation, phosphorylation, enzyme catalysis, receptor binding, or ligand binding. The specified reaction can also be the addition or elimination of protons, for example, detectable as a change in the pH of the surrounding solution or environment. Another specified reaction could be the detection of ion flow through a membrane (e.g., a natural or synthetic bilayer membrane), where, for example, the current is interrupted and the interruption can be detected when ions flow through the membrane. Field sensing using charged tags can also be used as thermal sensing and other analytical sensing techniques known in the art.

[0105] In a particular embodiment, the specified reaction involves incorporating a fluorescently labeled molecule into an analyte. The analyte may be an oligonucleotide, and the fluorescently labeled molecule may be a nucleotide. The specified reaction can be detected when excitation light is directed at the oligonucleotide containing the labeled nucleotide, and the fluorophore emits a detectable fluorescent signal. In an alternative embodiment, the detected fluorescence is a result of chemiluminescence or bioluminescence. The specified reaction can also increase fluorescence resonance energy transfer (FRET), for example, by bringing the donor fluorophore closer to the acceptor fluorophore. Resonance energy transfer (FRET) can be reduced by separating the donor fluorophore and the acceptor fluorophore, and increased by separating the quencher from the fluorophore or by co-localizing the quencher and the fluorophore.

[0106] As used herein, "reaction component" includes any substance that can be used to obtain a specified reaction. For example, reaction components include reagents, such as catalysts for enzymes, reactants for the reaction, samples, reaction products, other biomolecules, salts, metal cofactors, chelating agents, and buffer solutions (e.g., hydrogenation buffers). Reaction components may be delivered individually in solution or in combination with one or more mixtures to different locations in a fluid network. For example, reaction components may be delivered to a reaction chamber in which a biological sample is immobilized. Reaction components may interact directly or indirectly with the biological sample. In some embodiments, removable cartridge 104 is pre-loaded with one or more reaction components necessary to perform a specified assay. Pre-loading may occur at a location (e.g., a manufacturing facility) before cartridge 104 is received by a user (e.g., at a consumer facility).

[0107] In some embodiments, the base instrument 102 may be configured such that each stage interacts with a removable cartridge 104. After a stage, the removable cartridge 104 may be replaced by another removable cartridge 104. In some embodiments, the base instrument 102 may be configured such that each stage interacts with more than one removable cartridge 104. As used herein, the term "stage" includes performing at least one of a sample preparation and / or biochemical analysis protocol. Sample preparation may include isolating, isolating, modifying, and / or amplifying one or more components of a biological sample such that the prepared biological sample is suitable for analysis. In some embodiments, a stage may include a continuous activity in which multiple controlled reactions are performed until (a) a specified number of reactions have been performed, (b) a specified number of events have been detected, (c) a specified period of system time has elapsed, (d) the signal-to-noise ratio has decreased to a specified threshold, (e) a target component has been identified, (f) a system failure or malfunction has been detected, and / or (g) one or more resources used to perform the reactions have been exhausted. Optionally, a phase may include pausing system activity for a period of time (e.g., minutes, hours, days, weeks) and completing the phase later until at least one of (a)-(g) occurs.

[0108] An assay protocol may include a series of operations for performing a specified reaction, detecting a specified reaction, and / or analyzing a specified reaction. Commonly, the removable cartridge 104 and the base instrument 102 may include components required to perform the various operations. Operations of the assay protocol may include fluid manipulation, thermal control manipulation, detection manipulation, and / or mechanical manipulation. Fluid manipulation includes controlling the flow of fluid (e.g., liquid or gas) through system 100, which may be actuated by base instrument 102 and / or removable cartridge 104. For example, fluid manipulation may include controlling a pump to induce the inflow of a biological sample or reaction component into a reaction chamber. Thermal control manipulation may include controlling the temperature of a designated portion of system 100. For example, thermal control manipulation may include raising or lowering the temperature of a polymerase chain reaction (PCR) region in which a fluid containing a biological sample is stored. Detection manipulation may include controlling the actuation of a detector or monitoring the activity of a detector to detect a predetermined property, characteristic, or feature of the biological sample. As an example, detection manipulation may include capturing an image of a designated area comprising a biological sample to detect fluorescence emission from the designated area. Detection manipulation may include controlling a light source to illuminate the biological sample or controlling a detector to observe the biological sample. Mechanical operations may include controlling the movement or position of designated components. For example, mechanical operations may include controlling a motor to move a valve control component in base instrument 102 that is operatively engaged with a movable valve in removable cartridge 104. In some examples, combinations of different operations may occur simultaneously. For example, a detector may capture an image of the reaction chamber while a pump controls the flow of fluid through it. In some examples, different operations targeting different biological samples may occur simultaneously. For example, a first biological sample may undergo amplification (e.g., PCR) while a second biological sample undergoes detection.

[0109] Similar or identical fluid elements (e.g., channels, ports, reservoirs, etc.) may be labeled differently to more easily distinguish these fluid elements. For example, a port may be referred to as a reservoir port, supply port, network port, feed port, etc. It should be understood that two or more fluid elements (e.g., reservoir channels, sample channels, flow channels, bridging channels) that are labeled differently do not require the fluid elements to be structurally different. Furthermore, the claims may be amended to add such designations to more easily distinguish such fluid elements in the claims.

[0110] As used herein, "liquid" refers to a relatively incompressible substance that has the ability to flow and conform to the shape of a container or channel that retains the substance. Liquids may be water-based and include polar molecules that exhibit surface tension that holds the liquid together. Liquids may also include nonpolar molecules, for example, in oil-based or non-aqueous substances. It should be understood that liquids mentioned in this application may include liquids formed by a combination of two or more liquids. For example, individual reagent solutions may be subsequently combined to carry out a specified reaction.

[0111] The removable cartridge 104 is configured to be detachably engaged or removably coupled to the base instrument 102. As used herein, when the terms “detachably engaged” or “removably coupled” (etc.) are used to describe the relationship between the removable cartridge and the base instrument, the term is intended to mean that the connection between the removable cartridge and the base instrument is easily detachable without damaging the base instrument. Thus, the removable cartridge can be electrically detachably engaged to the base instrument such that the electrical contacts of the base instrument are not damaged. The removable cartridge can be mechanically detachably engaged to the base instrument such that the characteristics of the base instrument holding the removable cartridge are not damaged. The removable cartridge can be fluidly detachably engaged to the base instrument such that the ports of the base instrument are not damaged. For example, if only simple adjustments to the components are required (e.g., realignment) or simple replacements are required (e.g., nozzle replacement), the base instrument is not considered “damaged.” Components (e.g., removable cartridge 104 and base instrument 102) can be easily detachable when components can be separated from each other without excessive effort or spending a significant amount of time separating the components. In some implementations, the removable case 104 and the base instrument 102 can be easily separable without damaging the removable case 104 or the base instrument 102.

[0112] In some embodiments, the removable cartridge 104 may be permanently altered or partially damaged during the period it is with the base instrument 102. For example, the container holding the liquid may include a foil cap that is punctured to allow the liquid to flow through the system 100. In such embodiments, the foil cap may be damaged, making it necessary to replace the damaged container with another one. In certain embodiments, the removable cartridge 104 is a single-use cartridge, such that the removable cartridge 104 can be replaced after a single use and optionally disposed of.

[0113] In other embodiments, the removable cartridge 104 can be used for more than one stage when coupled to the base instrument 102, and / or can be removed from the base instrument 102, reloaded with reagents, and recoupled to the base instrument 102 for additional specified reactions. Therefore, in some cases, the removable cartridge 104 can be refurbished so that the same removable cartridge 104 can be used with different consumables (e.g., reaction components and biological samples). Refurbishment can be performed at the manufacturing facility after the cartridge has been removed from the base instrument located at the customer facility.

[0114] As in Figure 1As shown, the removable cartridge 104 includes a fluid network 106 that can contain and guide fluid (e.g., liquid or gas) through it. The fluid network 106 includes a plurality of interconnected fluid elements capable of storing fluid and / or allowing fluid to flow through it. Non-limiting examples of fluid elements include channels, ports of channels, cavities, storage modules, reservoirs of storage modules, reaction chambers, waste reservoirs, detection chambers, multi-purpose chambers for reaction and detection, etc. The fluid elements can be fluidly coupled to each other in a specified manner, enabling system 100 to perform sample preparation and / or analysis.

[0115] As used herein, the term "fluidly coupled" (or a similar term) refers to two spatial regions connected together, allowing a liquid or gas to be guided between the two spatial regions. In some examples, a fluid coupling allows fluid to be guided back and forth between the two spatial regions. In other examples, the fluid coupling is unidirectional, allowing only one flow direction between the two spatial regions. For example, a measurement reservoir may be fluidly coupled to a channel, allowing liquid to be delivered from the measurement reservoir into the channel. However, in some embodiments, it may not be possible to guide fluid in the channel back to the measurement reservoir. In a particular embodiment, fluid network 106 is configured to receive biological samples and guide them through sample preparation and / or sample analysis. Fluid network 106 may guide biological samples and other reactants to a waste reservoir.

[0116] One or more embodiments may include retaining a biological sample (e.g., a template nucleic acid) at a designated location on the analytical biological sample. As used herein, the term "retention" when relating to the use of a biological sample includes substantially attaching the biological sample to a surface or confining the biological sample within a designated space. As used herein, the term "fixation" when relating to the use of a biological sample includes substantially attaching the biological sample to a surface in a solid support or a surface on a solid support. Fixation may include attaching the biological sample to the surface at the molecular level. For example, adsorption techniques including non-covalent interactions (e.g., electrostatic forces, van der Waals forces, and dehydration at hydrophobic interfaces) and covalent binding techniques can be used to fix the biological sample to a substrate surface, wherein functional groups or linkers facilitate attachment of the biological sample to the surface. The surface on which the biological sample is fixed to the substrate may be based on the properties of the substrate surface, the liquid medium carrying the biological sample, and the properties of the biological sample itself. In some examples, the substrate surface may be functionalized (e.g., chemically or physically modified) to facilitate fixation of the biological sample to the substrate surface. The substrate surface may first be modified to have functional groups that bind to the surface. The functional groups can then bind to the biological sample to immobilize it thereon. In some instances, the biological sample can be immobilized to the surface via a gel, such as the gels described in U.S. Patent Publications 2011 / 0059865A1 and 2014 / 0079923A1, each of which is incorporated herein by reference in its entirety.

[0117] In some embodiments, nucleic acids can be immobilized to a surface and amplified using bridging amplification. Useful bridging amplification methods are described, for example, in U.S. Patent Nos. 5,641,658; WO 07 / 010251, 6,090,592; 2002 / 0055100A1; 7,115,400; 2004 / 0096853A1; 2004 / 0002090A1; 2007 / 0128624A1; and 2008 / 0009420A1, each of which is incorporated herein by reference in its entirety. Another useful method for amplifying nucleic acids on a surface is rolling circle amplification (RCA), for example, using methods further detailed below. In some embodiments, nucleic acids can be attached to a surface and amplified using one or more primer pairs. For example, one primer may be in solution, and another primer may be immobilized on a surface (e.g., 5'-attachment). For instance, a nucleic acid molecule may hybridize with one of the primers on the surface, followed by extension of the immobilized primer to produce a first copy of the nucleic acid. The primer in solution then hybridizes with the first copy of the nucleic acid, which can be extended using the first copy of the nucleic acid as a template. Optionally, after producing the first copy of the nucleic acid, the original nucleic acid molecule may hybridize with a second immobilized primer on the surface, and may be extended simultaneously with or after the primer extension in solution. In any embodiment, multiple copies of the nucleic acid are provided using immobilized primers in solution and repeated cycles of primer extension (e.g., amplification). In some embodiments, the biological sample may be confined within a predetermined space along with reaction components configured for use during amplification of the biological sample (e.g., PCR).

[0118] One or more embodiments described herein can be configured to perform an amplification (or PCR) protocol or an assay protocol including an amplification (or PCR) protocol. During the amplification protocol, the temperature of the biological sample within the reservoir or channel can be varied to amplify the biological sample (e.g., DNA of the biological sample). For example, the biological sample may undergo (1) a preheating phase at approximately 95°C for approximately 75 seconds; (2) a denaturation phase at approximately 95°C for approximately 15 seconds; (3) an annealing-extension stage at approximately 59°C for approximately 45 seconds; and (4) a temperature holding phase at approximately 72°C for approximately 60 seconds. Multiple amplification cycles can be performed in the embodiments. It should be noted that the above cycles describe only one specific embodiment, and alternative embodiments may include modifications to the amplification protocol.

[0119] The methods and systems described in this paper can use arrays of features with any density of various kinds, for example, at least about 10 features / cm². 2 100 features / cm 2 500 features / cm 2 1,000 features / cm 2 5,000 features / cm 2 10,000 features / cm 2 50,000 features / cm 2 100,000 features / cm 2 1,000,000 features / cm 2 5,000,000 features / cm 2 Or higher. The methods and apparatus described herein may include detection components or devices having a resolution sufficient to resolve individual features at one or more of these exemplary densities.

[0120] In the illustrated embodiment, the removable cartridge 104 includes a cartridge housing 110 having a plurality of housing sides 111-114. Housing sides 111-114 include non-mating sides 111-113 and mating sides 114. The mating sides 114 are configured to engage with the base instrument 102. In the illustrated embodiment, the cartridge housing 110 forms a generally integral structure. In an alternative embodiment, the cartridge housing 110 may be constructed from one or more sub-components that are assembled by a user of the system 100. The sub-components may be assembled before the removable cartridge 104 is detachably engaged with the base instrument 102 or after one of the sub-components is detachably engaged with the base instrument 102. For example, a storage module 150 may be held by a first sub-housing (not shown), and the remainder of the removable cartridge 104 (e.g., a fluid network and imaging equipment) may include a second sub-housing (not shown). The first and second sub-housings may be combined to form the cartridge housing 110.

[0121] The fluid network 106 is held by the housing 110 and includes a plurality of sample ports 116 opening toward the non-contact side 112. In an alternative embodiment, the sample ports 116 may be positioned along the non-contact side 111 or 113 or along the contact side 114. Each of the sample ports 116 is configured to receive a biological sample. For example only, the biological sample may be whole blood or saliva. In some embodiments, the biological sample may be nucleic acids and other materials (e.g., reagents, buffers, etc.) for performing PCR. Although in Figure 1 The diagram shows three sample ports 116, but the implementation may include only one sample port, two sample ports, or more than three sample ports.

[0122] The fluid network 106 also includes a fluid connection port 118, which opens toward the mating side 114 and is exposed to the exterior of the housing 110. The fluid connection port 118 is configured to fluidly connect to a system pump 119 of the base instrument 102. The fluid connection port 118 is in flow communication with a pump channel 133, which is part of the fluid network 106. During operation of the system 100, the system pump 119 is configured to provide negative pressure to induce fluid flow through the pump channel 133 and through the remainder of the fluid network 106. For example, the system pump 119 can induce a biological sample from the sample port 116 into the sample preparation area 132, where the biological sample can be prepared for subsequent analysis. The system pump 119 can induce a biological sample from the sample preparation area 132 into the reaction chamber, where detection operations are performed to obtain data (e.g., imaging data) of the biological sample. The system pump 119 can also induce fluid from reservoirs 151, 152 of the storage module 150 into the reaction chamber 126. After the detection operation is performed, the system pump 119 can induce fluid to flow into the waste reservoir 128.

[0123] In addition to the fluid network 106, the removable housing 104 may include one or more mechanical interfaces 117 that can be controlled by the base instrument 102. For example, the removable housing 104 may include a valve assembly 120 having a plurality of flow control valves 121-123 operatively coupled to the flow network 106. Each of the flow control valves 121-123 may represent a mechanical interface 117 controlled by the base instrument 102. For example, the flow control valves 121-123 may be selectively actuated or controlled via the base instrument 102 in conjunction with selective actuation of the system pump 119 to control the flow of fluid within the fluid network 106.

[0124] For example, in the illustrated embodiment, the fluid network 106 includes a sample channel 131 that is immediately downstream of and in flow communication with the sample port 116. Figure 1 The diagram shows only a single sample channel 131, but alternative embodiments may include multiple sample channels 131. Sample channel 131 may include a sample preparation area 132. Valve assembly 120 includes a pair of channel valves 121, 122, which may also be referred to as flow control valves. Channel valves 121, 122 may be selectively actuated by base instrument 102 to prevent or block fluid flow through sample channel 131. In a particular embodiment, channel valves 121, 122 may be actuated to form a seal that retains a specified volume of liquid within the sample preparation area 132 of sample channel 131. The specified volume within sample preparation area 132 may include a biological sample.

[0125] Valve assembly 120 may further include a movable valve 123. The movable valve 123 has a valve body 138, which may include at least one flow passage 140 extending between corresponding ports. The valve body 138 is movable between different positions to align the ports with corresponding ports of the fluid network 106. For example, the position of the movable valve 123 may determine the type of fluid flowing into the reaction chamber 126. In a first position, the movable valve 123 may be aligned with a corresponding port of sample passage 131 to provide a biological sample to the reaction chamber 126. In a second position, the movable valve 123 may be aligned with one or more corresponding ports of reservoir passages 161, 162 that are in flow communication with reservoirs 151, 152 of storage module 150, respectively. Each reservoir 151, 152 is configured to store reaction components that can be used to perform a specified reaction. Reservoir passages 161, 162 are located downstream of and in flow communication with reservoirs 151, 152, respectively. In some implementations, the movable valve 123 can be moved individually to different positions to align with the corresponding port of the reservoir channel.

[0126] In the illustrated embodiment, the movable valve 123 is a rotary valve (or rotatable valve) configured to rotate about axis 142. The movable valve 123 can be similar to the rotary valve 216 (in... Figure 2 (As shown in the figure). However, it should be understood that alternative embodiments may include movable valves that do not rotate to different positions. In such embodiments, the movable valve can slide in one or more linear directions to align corresponding ports. The rotary valves and linear motion valves described herein may be similar to the devices described in International Application No. PCT / US2013 / 032309, filed March 15, 2013, which is incorporated herein by reference in its entirety.

[0127] In some embodiments, the biological sample is illuminated by a light source 158 of the base instrument 102. Optionally, the light source 158 may be combined with a removable cartridge 104. For example, the biological sample may include one or more fluorophores that provide light emission when excited by light of a suitable wavelength. In the illustrated embodiment, the removable cartridge 104 has an optical path 154. The optical path 154 is configured to allow illumination light 156 from the light source 158 of the base instrument 102 to be incident on the biological sample within the reaction chamber 126. Thus, the reaction chamber may have one or more optically transmissive sides or windows. The optical path 154 may include one or more optical elements, such as lenses, reflectors, fiber optic cables, etc., that actively guide the illumination light 156 to the reaction chamber 126. In an exemplary embodiment, the light source 158 may be a light-emitting diode (LED). However, in alternative embodiments, the light source 158 may include other types of light-generating devices, such as lasers or lamps.

[0128] In some embodiments, detection component 108 includes an imaging detector 109 and a reaction chamber 126. The imaging detector 109 is configured to detect a specific reaction within the reaction chamber 126. In some embodiments, the imaging detector 109 may be positioned relative to the reaction chamber 126 to detect light signals (e.g., absorbance, reflection / refraction, or light emission) from the reaction chamber 126. The imaging detector 109 may include one or more imaging devices, such as a charge-coupled device (CCD) camera or a complementary metal-oxide-semiconductor (CMOS) imager. In some embodiments, the imaging detector 109 may detect light signals emitted from chemiluminescence. However, in other embodiments, detection component 108 may not be limited to imaging applications. For example, detection component 108 may be one or more electrodes for detecting the electrical properties of a liquid.

[0129] As described herein, the base instrument 102 is configured to operatively engage the removable cartridge 104 and control various operations within the removable cartridge 104 to perform specified reactions and / or obtain data from biological samples. For this purpose, the mating side 114 is configured to allow or permit the base instrument 102 to control the operation of one or more components of the removable cartridge 104. For example, the mating side 114 may include a plurality of access openings 171-173 that allow valves 121-123 to be controlled by the base instrument 102. The mating side 114 may also include an access opening 174 configured to receive a thermal circulator 186 (e.g., a heat or heat transfer block) of the base instrument 102. In the illustrated embodiment, the thermal circulator 186 is a heat block. The access opening 174 extends along the sample channel 131. As shown, the access openings 171-174 open toward the mating side 114.

[0130] In some embodiments, fluid network 106 and valve assembly 123 may constitute flow control system 164. Flow control system 164 may include multiple components that cooperate to control the flow of one or more fluids through system 100 or, more specifically, control removable housing 104 to perform one or more specified operations. In other embodiments, flow control system 164 may include additional components, such as system pump 119. Flow control system 164 may be integrated with flow control system 200 (… Figure 2 (as shown in the image) similar or identical.

[0131] The base instrument 102 has a control side 198 configured to detachably engage a mating side 114 of the removable cartridge 104. The mating side 114 of the removable cartridge 104 and the control side 198 of the base instrument 102 can jointly define a system interface 195. The system interface 195 represents a common boundary between the removable cartridge 104 and the base instrument 102, through which the base instrument 102 and the removable cartridge 104 are operatively engaged. More specifically, the base instrument 102 and the removable cartridge 104 are operatively engaged along the system interface 195 such that the base instrument 102 can control various features of the removable cartridge 104 through the mating side 114. For example, the base instrument 102 may have one or more controllable components that control corresponding parts of the removable cartridge 104.

[0132] In some embodiments, the base instrument 102 and the removable cartridge 104 are operatively coupled such that the base instrument 102 and the removable cartridge 104 are secured to each other at a system interface 195, wherein at least one of an electrical connection, thermal connection, optical connection, valve connection, or fluid connection is established through the system interface 195. In the illustrated embodiment, the base instrument 102 and the removable cartridge 104 are configured to have electrical connections, thermal connections, valve connections, and optical connections. More specifically, the base instrument 102 and the removable cartridge 104 can transmit data and / or power via electrical connections. The base instrument 102 and the removable cartridge 104 can transfer thermal energy to and / or from each other via thermal connections, and the base instrument 102 and the removable cartridge 104 can transmit optical signals (e.g., illumination light) via optical connections.

[0133] In the illustrated embodiment, system interface 195 is a single-sided interface. For example, control side 198 and housing side 114 are generally planar and face opposite directions. The single-sided nature of system interface 195 allows removable housing 104 and base instrument 102 to be operatively coupled to each other only via mating side 114 and control side 198. In alternative embodiments, the system interface may be multi-sided. For example, at least two, three, four, or five sides of the removable housing may be mating sides configured to be coupled to the base instrument. Multiple sides may be planar and may be arranged orthogonally or opposite to each other (e.g., around all or part of a rectangular volume).

[0134] To control the operation of the removable cartridge 104, the base instrument 102 may include valve actuators 181, 182, and 183, a thermal circulator 186, and a contact array 188 of electrical contacts. The actuators 181, 182, and 183 are configured to operatively engage flow control valves 121-123, and the thermal circulator 186 is configured to supply and / or remove thermal energy from the sample preparation region 132. The base instrument 102 may also include a light source 158 positioned along a control side 198. The base instrument 102 may also include a system pump 119 having a control port 199 positioned along the control side 198.

[0135] System 100 may also include a locking mechanism 176. In the illustrated embodiment, locking mechanism 176 includes a rotatable latch 177 configured to engage a latch engagement element 178 of removable cartridge 104. Optionally, removable cartridge 104 may include rotatable latch 177, and base instrument 102 may include latch engagement element 178. When removable cartridge 104 is mounted to base instrument 102, rotatable latch 177 can rotate and engage latch engagement element 178. A cam effect generated by locking mechanism 176 can push or drive removable cartridge 104 toward base instrument 102 to secure removable cartridge 104 thereto.

[0136] The base instrument 102 may include a user interface 125 configured to receive user input for performing a specified measurement protocol and / or configured to transmit information about the measurement to the user. The user interface 125 may be integrated with the base instrument 102. For example, the user interface 125 may include a touchscreen attached to the housing of the base instrument 102 and configured to recognize touches from the user and the position of the touch relative to information displayed on the touchscreen. Alternatively, the user interface 125 may be positioned remotely relative to the base instrument 102.

[0137] The basic instrument 102 may also include a system controller 180, which is configured to control the operation of at least one of the following: valve actuators 181, 182, 183; thermal circulator 186; contact array 188; light source 158; or system pump 119. The system controller 180 is conceptually shown as a collection of circuit modules, but can be implemented using any combination of dedicated hardware boards, DSPs, processors, etc. Optionally, the system controller 180 can be implemented using an off-the-shelf PC with a single processor or multiple processors, where functional operations are distributed among the processors. Alternatively, the circuit modules described below can be implemented using a hybrid configuration in which dedicated hardware is used to perform some module functions, while an off-the-shelf PC, etc., is used to perform the remaining module functions.

[0138] System controller 180 may include multiple circuit modules 190-193 configured to control the operation of certain components of basic instrument 102 and / or removable housing 104. For example, circuit module 190 may be a flow control module 190 configured to control the flow of fluid through fluid network 106. Flow control module 190 may be operatively coupled to valve actuators 181, 182, 183 and system pump 119. Flow control module 190 may selectively actuate valve actuators 181, 182, 183 and system pump 119 to induce fluid flow through one or more paths and / or prevent fluid flow through one or more paths.

[0139] For example only, valve actuator 183 may be rotatably engaged with movable valve 123. Valve actuator 183 may include a rotary motor 189 configured to drive (e.g., rotate) valve actuator 183. Flow control module 190 may actuate valve actuator 183 to move movable valve 123 to a first rotational position. With movable valve 123 in the first rotational position, flow control module 190 may actuate system pump 119 to extract a biological sample from sample preparation area 132 and into reaction chamber 126. Flow control module 190 may then actuate valve actuator 183 to move movable valve 123 to a second rotational position. With movable valve 123 in the second rotational position, flow control module 190 may actuate system pump 119 to extract one or more reaction components from a corresponding reservoir and into reaction chamber 126. In some embodiments, system pump 119 may be configured to provide positive pressure, such that fluid is actively pumped in the opposite direction. This operation can be used to add multiple liquids to a common reservoir, thereby mixing the liquids in the reservoir. Therefore, the fluid connection port 118 can allow fluid (e.g., gas) to leave the housing 110, or can receive fluid into the housing 110.

[0140] The system controller 180 may also include a thermal control module 191. The thermal control module 191 can control the thermal circulator 186 to provide and / or remove heat from the sample preparation area 132. In a particular example, the thermal circulator 186 can increase and / or decrease the temperature experienced by the biological sample within the sample channel 131 according to a PCR protocol. Although not shown, the system 100 may include additional thermal devices located adjacent to the sample preparation area 132.

[0141] The system controller 180 may also include a detection module 192 configured to control the detection assembly 108 to obtain data about the biological sample. The detection module 192 can control the operation of the detection assembly 108 via a contact array 188. For example, the detection assembly 108 may communicatively engage along a mating side 114 to an array of contacts 194 of electrical contacts 196. In some embodiments, the electrical contacts 196 may be flexible contacts (e.g., spring contacts or contact posts) capable of being repositioned to and from the mating side 114. The electrical contacts 196 are exposed outside the housing and electrically coupled to the detection assembly 108. The electrical contacts 196 may be referred to as input / output (I / O) contacts. When the base instrument 102 and the removable housing 104 are operatively engaged, the detection module 192 can control the detection assembly 108 to obtain data at a predetermined time or for a predetermined period of time. For example, when a biological sample has a fluorophore attached thereto, the detection module 192 can control the detection component 108 to capture an image of the reaction chamber 126. Multiple images can be obtained.

[0142] Optionally, the system controller 180 includes an analysis module 193, which configures analytical data to provide at least partial results to a user of the system 100. For example, the analysis module 193 may analyze imaging data provided by the imaging detector 109. This analysis may include identifying nucleic acid sequences of biological samples.

[0143] System controller 180 and / or circuit modules 190-193 may include one or more logic-based devices, including one or more microcontrollers, processors, reduced instruction set computers (RISC), application-specific integrated circuits (ASICs), field-programmable gate arrays (FPGAs), logic circuits, and any other circuits capable of performing the functions described herein. In an illustrative embodiment, system controller 180 and / or circuit modules 190-193 execute a set of instructions stored therein to perform one or more assay protocols. Storage elements may be in the form of information sources or physical storage elements within base instrument 102 and / or removable cartridge 104. Protocols performed by assay system 100 may include, for example, quantitative analysis of DNA or RNA, protein analysis, DNA sequencing (e.g., sequencing by synthesis (SBS)), sample preparation, and / or preparation of fragment libraries for sequencing.

[0144] The instruction set may include various commands of the instruction system 100 to perform specific operations of methods and processes such as those described herein. The instruction set may be in the form of a software program. As used herein, the terms “software” and “firmware” are interchangeable and include any computer program stored in memory, including RAM memory, ROM memory, EPROM memory, EEPROM memory, and non-volatile RAM (NVRAM) memory, for execution by a computer. The memory types described above are merely exemplary and therefore do not limit the types of memory that can be used to store computer programs.

[0145] Software can take various forms, such as system software or application software. Furthermore, software can be a collection of individual programs or a program module within a larger program or program module. Software can also include modular programming in the form of object-oriented programming. After obtaining the detection data, the detection data can be processed automatically by system 100, in response to user input, or in response to a request made by another processing machine (e.g., a remote request via a communication link).

[0146] System controller 180 can be connected to other components or subsystems of system 100 via a communication link, which can be hardwired or wireless. System controller 180 can also be communicatively connected to an off-site system or server. System controller 180 can receive user input or commands from a user interface (not shown). The user interface may include a keyboard, mouse, touchscreen panel, and / or voice recognition system, etc.

[0147] System controller 180 is used to provide processing capabilities, such as storing, interpreting, and / or executing software instructions, and to control the overall operation of system 100. System controller 180 can be configured and programmed to control the data and / or power aspects of various components. Although system controller 180... Figure 1 While represented as a single structure, it should be understood that the system controller 180 may include multiple individual components (e.g., processors) distributed throughout the system 100 at various locations. In some embodiments, one or more components may be integrated with the base instrument, and one or more components may be located remotely relative to the base instrument.

[0148] Figure 2 This is a plan view of the flow control system 200 formed according to the implementation scheme. The flow control system 200 may be part of a system (not shown) for sample preparation and / or sample analysis, such as system 100. Figure 1 (as shown) is part of the system. In some embodiments, the flow control system 200 is entirely within an integrated device, such as in a removable housing 104. Figure 1Within. However, in other embodiments, the flow control system 200 may be part of a standard system (e.g., a desktop system). Figure 2 In one embodiment, the components of the flow control system 200 are located within a local area. In other embodiments, the components of the flow control system 200 may be separated from each other and distributed in different areas.

[0149] In the illustrated embodiment, the flow control system 200 includes a fluid network 202 configured to have one or more fluids (e.g., gas or liquid) flowing through it. The fluid network 202 includes an arrangement of interconnected fluid elements. The fluid elements may be configured to direct fluid to a designated region within the fluid network 202, where, for example, the fluid may be subjected to predetermined conditions and / or undergo a designated reaction. The fluid elements may be selectively interconnected via one or more valves, such that one or more fluid elements can be disconnected relative to one or more other fluid elements during operation.

[0150] In the illustrated embodiment, the fluid network 202 includes sample ports 204A, 204B, 204C, and 204D and sample channels 206A, 206B, 206C, and 206D, which are in flow communication with the sample ports 204A, 204B, 204C, and 204D, respectively. The sample channels 206A, 206B, 206C, and 206D extend from the corresponding sample ports 204A, 204B, 204C, and 204D to a common node or intersection 209. The fluid network 202 also includes a supply port 210 extending from node 209. Figure 9 The sample channel 208 is a combination of the two (shown in the diagram). The rotary valve 216 is located above the supply port 210.

[0151] Fluid network 202 also includes feed port 226 ( Figure 9 (Shown in the diagram) and a feed channel 224 extending from the feed port 226. The feed channel 224 extends between the feed port 226 of the fluid network 202 and the flow cell 320. The flow cell 320 includes an inlet port 322, an outlet port 324, and a reaction chamber 326 extending between the inlet port 322 and the outlet port 324. During operation, fluid can flow through the inlet port 322 from the feed channel 224 and exit the reaction chamber 326 through the outlet port 324. After exiting the reaction chamber 326, the fluid can flow into the waste reservoir 330 of the fluid network 202. The waste reservoir 330 is in... Figure 2 The contents are indicated by small boxes, but it should be understood that the volume of waste storage 330 can be larger than, for example, storage 240-244.

[0152] As fluid flows through reaction chamber 326, it can interact with existing materials (e.g., analytes) within the chamber. A specific reaction can be detected within reaction chamber 326. For example, a detection component (not shown) can be positioned adjacent to reaction chamber 326 and detect light signals from within it.

[0153] In the illustrated embodiment, sample ports 204A, 204B, 204C, and 204D open toward the body side or surface 214 of the microfluidic body 212, such that sample ports 204A, 204B, 204C, and 204D are exposed to the outside of the microfluidic body 212. Sample channels 206A, 206B, 206C, and 206D, and the combined sample channel 208 extend through (within) the microfluidic body 212. Supply port 210 may open toward the body side 214. Alternatively, supply port 210 may open toward the underside (not shown) or the outside of the microfluidic body 212. Thus, sample channels 206A, 206B, 206C, and 206D are in flow communication with a single port, such as supply port 210. However, in an alternative implementation, sample channels 206A, 206B, 206C, and 206D can be in flow communication with individual supply ports opening toward the body side 214. In such an alternative implementation, each sample channel can extend between its corresponding sample port and its corresponding port.

[0154] In the illustrated embodiment, the fluid network 202 further includes a plurality of reservoir channels 220. Each of the reservoir channels 220 is fluidly located between a reservoir port 222. Figure 10 (shown in the diagram) and reservoir 240. Reservoir port 222 opens toward body side 214. Similar to supply port 210, reservoir port 222 may be covered by rotary valve 216. Optionally, fluid network 202 may include reservoir channel 228 fluidly located between common sample channel 208 and reservoir 230.

[0155] In the illustrated embodiment, the flow control system 200 includes a microfluidic body 212. The microfluidic body 212 can be a physical structure defining fluid elements of a fluid network 202. For example, the microfluidic body 212 can include stacked PCB layers, wherein one or more layers are etched or shaped to form one or more channels (e.g., sample channels 206A, 206B, 206C, 206D, common sample channel 208, reservoir channels 220, 228, and feed channel 224) and one or more ports of the fluid network 202 (e.g., sample ports 204A, 204B, 204C, 204D, reservoir port 222, supply port 210, and feed port 226). Flow units 320 can be attached to the microfluidic body 212. Such microfluidic bodies are shown and described in U.S. Provisional Application No. 62 / 003,264 and U.S. Provisional Application No. 61 / 951,462. Each of these provisional applications is incorporated herein by reference in its entirety. Alternatively, materials other than the PCB layer, such as glass or plastic, can be used. In alternative embodiments, the microfluidic body 212 can be formed from multiple body components. In some examples, the microfluidic body 212 is at least partially formed by channels.

[0156] Rotary valve 216 is configured to rotate about axis 299 to different valve positions (e.g., a rotary position) to fluidly connect different channels of fluid network 202. Rotary valve 216 may be slidably coupled to body side 214 and may be positioned to cover multiple ports opening onto body side 214, such as reservoir port 222, supply port 210, and feed port 226. Rotary valve 216 includes at least one flow channel 218 configured to fluidly connect discrete channels. Figure 9 (As shown in the diagram). For example, when the rotary valve 216 is in the first valve position, the flow passage 218 can fluidly connect the sample passage 208 to the feed passage 224. When the rotary valve 216 is in the second valve position, the flow passage 218 can fluidly connect a reservoir passage 220 to the feed passage 224.

[0157] Each of sample ports 204A, 204B, 204C, and 204D is configured to receive a corresponding biological sample. For example, a user of the flow control system 200, such as a technician or laboratory worker, may load (e.g., aspirate with a pipette) a biological sample into one or more of sample ports 204A, 204B, 204C, and 204D. The biological sample may be for the same individual from a population (e.g., a human) or may be for multiple different individuals from a population. It should be understood that the biological sample may originate from other species, such as animals, plants, bacteria, or fungi. In the illustrated embodiment, sample ports 204A, 204B, 204C, and 204D are configured to be accessible from outside the flow control system 200. In an alternative embodiment, sample ports 204A, 204B, 204C, and 204D may be part of a larger fluid network through which the biological sample is delivered to sample ports 204A, 204B, 204C, and 204D.

[0158] As in Figure 2 As shown, each of sample channels 206A, 206B, 206C, and 206D may include a sample preparation region 232. In the illustrated embodiment, sample channels 206A, 206B, 206C, and 206D have corresponding wavy or serpentine paths along their respective sample preparation regions 232. Wavy or serpentine paths may allow for larger volumes of biological samples to be contained within the thermal control region 234. In an alternative embodiment, the sample preparation region 232 may have different dimensions than other portions of the corresponding sample channel. For example, the sample preparation region 232 may form a wide chamber or a groove with increased depth.

[0159] In sample preparation area 232, a biological sample may undergo a process to prepare it for subsequent reactions and / or analyses. For example, the biological sample may be subjected to changes in pressure and / or temperature. Optionally or additionally, the biological sample may be mixed with one or more reaction components within sample preparation area 232. In some embodiments, flow control system 200 may include a thermal control strip or band 236 (indicated by a dashed line) extending along a thermal control area 234 adjacent to the sample preparation areas 232 of sample channels 206A, 206B, 206C, 206D. In some embodiments, thermal control strip 236 may be a flexible PCB heater, such as the flexible PCB heater described in U.S. Provisional Application No. 61 / 951,462, which is incorporated herein by reference in its entirety. The flexible PCB heater may extend along thermal control area 234 and have conductive lines therein that generate heat when an electric current is allowed to flow through it.

[0160] Thermal control strip 236 is configured to control the temperature of biological samples within corresponding sample channels 206A, 206B, 206C, and 206D along thermal control region 234. The temperature can be controlled during an amplification protocol, wherein the biological samples undergo temperature increases / decreases according to a predetermined schedule to amplify the biological samples. In such an embodiment, the biological samples can be loaded together with an amplification (e.g., PCR) mixture of reagents into sample ports 204A, 204B, 204C, and 204D. Optionally, the amplification mixture can be separately delivered through fluid network 202 to sample preparation region 232. For example, sample preparation region 232 can be in flow communication with another channel (not shown) through which the amplification mixture can be delivered.

[0161] In some embodiments, the flow control system 200 includes a storage component or module 238. As shown, the storage component 238 includes a plurality of reservoirs 240-244. Each of the reservoirs 240-244 is configured to hold a reaction element that can be used during a predetermined assay protocol (e.g., an SBS protocol). Each of the reservoirs 240-244 is in flow communication with a corresponding port via one of the reservoir channels 220. As described herein, a rotary valve 216 is configured to rotate to different valve positions according to a predetermined schedule to fluidly connect the feed channel 224 to the other channels of the fluid network 202.

[0162] In some embodiments, the flow control system 200 further includes channel valves 246, 248. As shown, each of the sample channels 206A, 206B, 206C, 206D is coupled to a pair of channel valves 246, 248. A corresponding sample preparation region 232 for each sample channel 206A, 206B, 206C, 206D extends between the corresponding channel valves 246, 248. Each pair of channel valves 246, 248 is configured to seal the corresponding biological sample within the sample preparation region 232 as the biological sample undergoes different conditions. For example, the channel valves 246, 248 can seal the corresponding biological sample therebetween as the biological sample undergoes thermal cycling in a PCR protocol.

[0163] To induce flow throughout the fluid network 202, the flow control system 200 may include a pump assembly 332. In the illustrated embodiment, the flow control system 200 includes only a single pump located downstream of the reaction chamber 326 and drawing or aspirating fluid through the fluid network 202. In an alternative embodiment, one or more pumps may be used to propel fluid through the fluid network 202. For example, one or more pumps may be fluidly positioned upstream of reservoirs 240-243 and / or reservoir 244. Samples 204A, 204B, 204C, and 204D may also be fluidly connected to the upstream pump, which induces flow of the biological sample toward sample channel 208.

[0164] Figures 3-8 Different valve mechanisms are shown in the flow control system 200. Figure 2 The valve mechanism can control (e.g., regulate) the flow through the fluid network 202. Figure 2 The flow of ). More specifically, Figure 3 and Figure 4 A cross-section of the valve mechanism 250, including the channel valve 246, is shown. Although the following pertains to the channel valve 246, the channel valve 248 ( Figure 2 Other valves may include similar or identical features. As shown, the microfluidic body 212 includes multiple layers 252, 253, 254 stacked side-by-side. Layers 252, 253, 254 may be printed circuit board (PCB) layers. One or more of layers 252, 253, 254 may be etched such that when layers 252, 253, 254 are stacked side-by-side, the microfluidic body 212 forms a sample channel 206. The sample channel 206 includes a valve or cavity 256.

[0165] Channel valve 246 is configured to regulate the flow of fluid through sample channel 206. For example, channel valve 246 may allow a maximum clearance so that fluid can flow unimpeded. Channel valve 246 may also prevent fluid from flowing through it. As used herein, the term "prevent" can include slowing the flow of fluid or completely blocking the flow of fluid. As shown, sample channel 206 includes a first port and a second port 258, 260 in flow communication with valve chamber 256. The channel is configured for fluid to flow into valve chamber 256 through the first port 258 and out of valve chamber 256 through the second port. In the illustrated embodiment, channel valve 246 constitutes a flexible membrane capable of bending between a first condition and a second condition. This flexible membrane... Figure 3 In the first condition and in Figure 4The second condition is met. In a particular embodiment, the flexible membrane is a flexible layer. This flexible layer is configured to be pushed into the valve chamber 256 and cover the first port 258 to block fluid flow through it. In an alternative embodiment, the channel valve 246 may be another physical element capable of moving between different conditions or positions to regulate fluid flow.

[0166] Flow control system 200 ( Figure 2 It may also include a valve actuator 262 configured to actuate channel valve 246. For example, valve actuator 262 can bend the flexible diaphragm between a first condition and a second condition. Valve actuator 262 includes an elongated body 264, such as a post or rod, extending through an inlet or opening 266. Inlet or opening 266 allows valve actuator 262 to directly engage channel valve 246, which, in the illustrated embodiment, is a flexible diaphragm. Figure 3 In this state, valve actuator 262 is in the first state or position. Figure 4 In the second state or position, valve actuator 262 engages channel valve 246 and has moved a distance toward first port 258. Valve actuator 262 can deform channel valve 246 so that channel valve 246 covers first port 258. Therefore, fluid flowing through first port 258 is blocked by channel valve 246.

[0167] Figure 5 and Figure 6 A cross-section of the valve mechanism 270, including the channel valve 272, is shown. In some embodiments, the channel valve 246 ( Figure 2 The channel valve 272 can be used instead. Valve mechanism 270 can be similar to valve mechanism 250. For example, the valve mechanism includes a channel valve 272 and a valve actuator 274. Valve actuator 274 has an elongated body 276, such as a nozzle, extending into an inlet or opening 278. Inlet or opening 278 can form a closed or sealed chamber. In an exemplary embodiment, channel valve 272, which may be a flexible diaphragm, is pneumatically actuated by valve actuator 274. More specifically, valve actuator 274 is configured to provide fluid (e.g., air) to increase the pressure within the closed chamber, thereby causing channel valve 272 to deform. When channel valve 272 deforms, the channel valve can cover port 277 of sample channel 279, thereby blocking flow through sample channel 279.

[0168] Figure 7 and Figure 8 A valve mechanism 280 including a channel valve 282 is shown. The valve mechanism 280 may include a valve mechanism 250 (…). Figure 3 ), 270 Figure 5Similar features. Channel valve 282 is rotatably engaged with valve actuator 284. Channel valve 282 is a planar body shaped to be in a first rotational position ( Figure 7 (as shown in the diagram) allows flow through sample channel 286, and when in the second rotational position ( Figure 8 (As shown in the diagram) when flow is blocked through sample channel 286. More specifically, when in the second rotational position, channel valve 282 can cover port 288.

[0169] Figure 9 A cross-section of a rotary valve 216 operably engaged with valve actuator 290 is shown. Rotary valve 216 is slidably engaged to the body side 214 of microfluidic body 212. Valve actuator 290 is configured to rotate rotary valve 216 about axis 299 to a designated valve position (or rotational position) to fluidly connect fluid network 202. Figure 1 The rotary valve 216 includes a valve body 292 having a flow side 294 and an operating side 296. The operating side 296 may include a mechanical interface 298 configured to engage a valve actuator 290. In the illustrated embodiment, the mechanical interface 298 includes a flat body or plate coinciding with an axis 299. The valve actuator 290 includes a slot 300 configured to receive the mechanical interface 298 such that the valve actuator 290 operatively engages the rotary valve 216. More specifically, the valve actuator 290 may engage the rotary valve 216 such that the valve actuator 290 is capable of rotating the rotary valve 216 about an axis 299.

[0170] The main body side 214 includes a supply port 210 and a feed port 226. The main body side 214 also includes storage ports 222A-222E. Figure 10 (As shown in the diagram). Flow passage 218 extends between first and second channel ports 306, 308. First and second channel ports 306, 308 open to the fluid side 294 of valve body 292. In an exemplary embodiment, rotary valve 216 includes only two channel ports 306, 308 and only one flow passage 218. However, in other embodiments, rotary valve 216 may include two or more channel ports and / or more than one flow passage. Such embodiments enable fluid connection of two or more channels at a single rotational position of rotary valve 216.

[0171] As in Figure 9As shown, feed port 226 is aligned with and fluidly connected to channel port 308, and supply port 210 is aligned with and fluidly connected to channel port 306. Depending on the rotational position of rotary valve 216, channel port 306 may also be fluidly connected to one of reservoir ports 222A-222E. As noted above, rotary valve 216 is configured to rotate about axis 299. In some embodiments, feed port 226 and channel port 308 are positioned such that feed port 226 and channel port 308 are aligned with axis 299. More specifically, axis 299 extends through each of feed port 226 and channel port 308.

[0172] When valve actuator 290 is operably engaged with rotary valve 216, valve actuator 290 can apply actuator force 310 in the direction against the body side. In such an embodiment, actuator force 310 may be sufficient to seal flow passage 218 between channel ports 306, 308 and seal reservoir port 222 and / or supply port 210.

[0173] Therefore, the rotary valve 216 can fluidly connect the feed port 226 and the supply port 210 at a first rotational position, and fluidly connect the feed port 226 and the corresponding reservoir port 222 at a second rotational position. When the rotary valve 216 rotates between different rotational positions, the rotary valve 216 effectively changes the flow path of the fluid network.

[0174] Fluid can flow through flow channel 218 in either direction. For example, system pump 119 ( Figure 1 A system pump (not shown) may be in flow communication with feed port 226. The system pump may generate a suction force that draws fluid through supply port 210 (or the corresponding reservoir port 222) into flow channel 218 and through feed port 226. Optionally, the system pump may provide a positive pressure that displaces the fluid within flow channel 218, causing fluid to flow through feed port 226 into flow channel 218 and through supply port 210 (or the corresponding reservoir port 222).

[0175] Figure 10 This is a top view of the main body side 214, showing the supply port 210, feed port 226, and storage ports 222A-222E. Figure 10 In this diagram, flow channel 218 is shown in two different rotational positions; however, it should be understood that flow channel 218 can have other rotational positions. The rotational position of flow channel 218 is related to that of rotary valve 216. Figure 2The valve position is related to the reservoir position. Reservoir ports 222A-222E are fluidly connected to the corresponding reservoirs through the corresponding reservoir passages. For example, reservoir port 222A is fluidly connected to reservoir 243; reservoir port 222B is fluidly connected to reservoir 242; reservoir port 222C is fluidly connected to reservoir 241; reservoir port 222D is fluidly connected to reservoir 240; and reservoir port 222E is fluidly connected to reservoir 244. As described above, according to rotary valve 216 ( Figure 2 By rotating the flow channel 218 to the position of the feed port 226, the flow channel 218 can fluidly connect the feed port 226 to the supply port 210 or one of the corresponding storage ports 222A-222E.

[0176] Table 1 illustrates the various stages of a sequencing-by-synthesis (SBS) protocol. In an exemplary embodiment, reservoir 244 includes a hydrogenation buffer, reservoir 243 includes a nucleotide solution, reservoir 242 includes a washing solution, and reservoir 241 includes a lysis solution. While Table 1 provides a summary of SBS protocols, it should be understood that various summaries may be provided depending on the desired assay protocol. In the example below, the biological sample has been prepared according to the PCR protocol in the corresponding sample preparation area 232 (…). Figure 2 It is amplified within.

[0177] In stage 1, flow channel 218 has valve positions that fluidly connect supply port 210 and feed port 226. In stage 1, channel valves 246 and 248 are connected to sample channel 206A. Figure 2 The pump assembly 332 is deactivated (e.g., under the first condition) to allow the first biological sample to flow through sample channels 206A and 208. However, channel valves 246 and 248 connected to sample channels 206B, 206C, and 206D are actuated to seal the second, third, and fourth biological samples within the corresponding sample preparation areas 232. Therefore, in stage 1, the pump assembly 332 ( Figure 2 The first biological sample can be induced to flow into the flow channel 218. In stage 2, the rotary valve 216 rotates to the second valve position, while the first biological sample is stored in the flow channel 218, such that the flow channel 218 fluidly connects the reservoir port 222E and the feed port 226. In the second valve position, the pump assembly 332 can induce fluid to flow within the flow channel 218, such that the first biological sample flows through the reservoir port 222E and into the hydrogenation buffer.

[0178] In stage 3, rotary valve 216 rotates back to the first valve position, and channel valves 246 and 248 are selectively actuated to allow the second biological sample to flow into flow channel 218, while the third and fourth biological samples are sealed within sample preparation area 232. In stage 4, rotary valve 216 rotates back to the second valve position, while the second biological sample is stored within flow channel 218, and the second biological sample is added to the hydrogenation buffer along with the first biological sample. During stages 5-8, the third and fourth biological samples are removed from their respective sample preparation areas and added to the hydrogenation buffer. Thus, four biological samples can be stored in a single reservoir containing hydrogenation buffer. While in reservoir 243, a reaction can occur with the biological sample and hydrogenation buffer to prepare the biological sample for SBS sequencing.

[0179] In stage 9, pump assembly 332 draws the combined biological sample / hydrogenation buffer through reservoir port 222E, through flow channel 218, through feed port 226, and into reaction chamber 326. Figure 2 In the reaction chamber, biological samples can be immobilized onto the surface defining the reaction chamber. For example, clusters comprising biological samples can be formed. Stages 10-13 represent the sequencing cycle. In stage 10, rotary valve 216 can be in the third valve position, allowing the nucleotide solution to be drawn through flow channel 218 and into the reaction chamber. At this point, nucleotides can be incorporated into the corresponding biological sample (e.g., primers annealed with template nucleic acids). In stage 11, rotary valve 216 can be in the fourth valve position, allowing the washing solution to flow through the reaction chamber and carry the nucleotide solution out of the reaction chamber. After stage 11, the reaction chamber can be monitored by an imaging detector, such as detection device 404. Figure 11 Imaging. The color of the light emitted from the cluster can be used to identify the bases incorporated through the cluster. After stage 12, rotary valve 216 can be in the fourth valve position, allowing the lysis solution to flow through the reaction chamber and removing the fluorophore (and, if present, the reversible terminator portion) from the cluster. In stage 13, rotary valve 216 can again be in the third valve position, and washing solution can flow through the reaction chamber to remove the lysis solution. Stages 10-13 can be repeated until sequencing is complete and / or until reagents are exhausted.

[0180] Table 1

[0181]

[0182]

[0183] Figure 11A cross-section of a portion of the detection assembly 400 is shown. In the illustrated embodiment, the detection assembly 400 is integrally formed with the flow unit 320. More specifically, the detection assembly includes a detection device 404 positioned adjacent to the flow unit 320 and the reaction chamber 326. The flow unit 320 may be mounted to the detection device 404. In the illustrated embodiment, the flow unit 320 is directly secured to the detection device 404 by one or more fixing mechanisms (e.g., adhesives, bonding agents, fasteners, etc.). In some embodiments, the flow unit 320 may be removably coupled to the detection device 404. In a particular embodiment, the detection device 404 is configured to detect optical signals from the reaction chamber 326. Therefore, in some embodiments, the detection device 404 may be referred to as an imaging detector.

[0184] In the illustrated embodiment, the detection device 404 includes a device base 425. In a particular embodiment, the detection device 404 includes multiple stacked layers (e.g., silicon layers, dielectric layers, metal-dielectric layers, etc.). The device base 425 may include a sensor array 424 of photosensors 440, a guide array 426 of light guides 462, and a reaction array 428 having reaction recesses 408 with corresponding reaction sites 414. In some embodiments, the components are arranged such that each photosensor 440 is aligned with a single light guide 462 and a single reaction site 414. However, in some embodiments, a single photosensor 440 may receive photons through more than one light guide 462 and / or from more than one reaction site 414. As used herein, a single photosensor may include one or more pixels. The detection device 404 may be fabricated using complementary metal-oxide-semiconductor (CMOS) technology. In a particular embodiment, the detection device 404 is a CMOS imaging detector.

[0185] It should be noted that the terms "array" or "subarray" do not necessarily include every item of a particular type that a detection device may have. For example, sensor array 424 may not include every photosensor in detection device 404. Instead, detection device 404 may include other photosensors (e.g., other arrays of photosensors). As another example, guide array 426 may not include every light guide of the detection device. Instead, there may be other light guides that are constructed differently from light guide 462 or have different relationships with other elements of detection device 404. Therefore, unless explicitly stated otherwise, the term "array" may or may not include all such items of the detection device.

[0186] In the illustrated embodiment, the flow unit 320 includes a sidewall 406 and a flow cap 410 supported by the sidewall 406 and other sidewalls (not shown). The sidewalls are coupled to a detector surface 412 and extend between the flow cap 410 and the detector surface 412. In some embodiments, the sidewalls are formed of a curable adhesive layer that bonds the flow cap 410 to the detection device 404.

[0187] The flow unit 320 is sized and shaped such that a reaction chamber 326 exists between the flow cap 410 and the detection device 404. As shown, the reaction chamber 326 may include a height H1. By way of example only, the height H1 may be between approximately 50-400 μm (micrometers), or more specifically, between approximately 80-200 μm. In the illustrated embodiment, the height H1 is approximately 100 μm. The flow cap 410 may include a material that is transmissible to excitation light 401 propagating from the outside of the detection assembly 400 into the reaction chamber 326. Figure 7 As shown, the excitation beam 401 approaches the flow cap 410 at a non-orthogonal angle. However, this is merely for illustrative purposes, as the excitation beam 401 can approach the flow cap 410 from different angles. The reaction chamber 326 is sized and shaped to guide fluid along the detector surface 412. The height H1 and other dimensions of the reaction chamber 326 can be configured to maintain a generally uniform flow of fluid along the detector surface 412. The dimensions of the reaction chamber 326 can also be configured to control bubble formation.

[0188] The sidewall 406 and the flow cover 410 may be separate components connected to each other. In other embodiments, the sidewall 406 and the flow cover 410 may be integrally formed such that the sidewall 406 and the flow cover 410 are formed from a continuous sheet of material. For example, the flow cover 410 (or flow unit 320) may comprise a translucent material such as glass or plastic. The flow cover 410 may be formed as a generally rectangular block having a planar outer surface and a planar inner surface defining the reaction chamber 326. This block may be mounted onto the sidewall 406. Alternatively, the flow unit 320 may be etched to define the flow cover 410 and the sidewall 406. For example, a recess may be etched into the translucent material. When the etched material is mounted onto the detection device 404, the recess may become the reaction chamber 326.

[0189] The detection device 404 has a detector surface 412, which can be functionalized (e.g., chemically or physically modified in a suitable manner to perform a specified reaction). For example, the detector surface 412 can be functionalized and may include a plurality of reaction sites 414 having one or more biomolecules anchored thereto. The detector surface 412 has an array of reaction recesses or side-opening reaction recesses 408. Each of the reaction recesses 408 may include one or more reaction sites 414. The reaction recesses 408 may be defined by, for example, notches or variations in depth along the detector surface 412. In other embodiments, the detector surface 412 may be substantially planar.

[0190] As in Figure 11 As shown, reaction sites 414 can be distributed in a patterned manner along the detector surface 412. For example, reaction sites 414 can be located in rows and columns along the detector surface 412 in a manner similar to a microarray. However, it should be understood that various patterns of reaction sites can be used. Reaction sites can include biological or chemical substances that emit light signals. For example, the biological or chemical substances of the reaction sites can produce light emission in response to excitation light 401. In a particular embodiment, reaction sites 414 include clusters or aggregates of biomolecules (e.g., nucleic acids) immobilized on the detector surface 412.

[0191] Figure 12 This is a flowchart of method 470. In some embodiments, method 470 may include a specified reaction for preparing a biological sample and / or detecting the biological sample for analysis. Method 470 may, for example, use the structure or aspects of the various embodiments (e.g., systems and / or methods) discussed herein. In various embodiments, certain steps may be omitted or added, certain steps may be combined, certain steps may be performed simultaneously, certain steps may be performed concurrently, certain steps may be divided into multiple steps, certain steps may be performed in a different order, or certain steps or a series of steps may be re-executed iteratively.

[0192] Method 470 can be used with flow control system 200 ( Figure 2A similar or identical flow control system may be used to perform or execute the method. Method 470 includes (at 472) rotating a rotary valve to a first valve position. The rotary valve has at least one flow passage. In the first valve position, the flow passage may be in flow communication with a sample passage (or other reservoir of the flow control system) and with a reaction chamber, such that the flow passage fluidly connects the sample passage and the reaction chamber. For example, the rotary valve may have a first channel port and a second channel port. The first channel port may be aligned with a port (e.g., a supply port or reservoir port), and the second channel port may be aligned with a feed port. When the rotary valve is in the first valve position, the other ports may be sealed by the rotary valve, such that fluid flow is blocked through the other ports.

[0193] Method 470 may further include allowing a biological sample to flow from the sample channel (or the first reservoir) into the flow channel (at 474) when the rotary valve is in the first valve position. For example, the biological sample may flow through the supply port into the flow channel of the rotary valve. As another example, the biological sample may be disposed within a reservoir, such as a reservoir containing hydrogenation buffer. The biological sample (containing hydrogenation buffer) may flow through the reservoir port and into the flow channel.

[0194] Optionally, the biological sample may continue to flow into the reaction chamber (at 476). Optionally, method 470 may include rotating the rotary valve to a second valve position while the biological sample is arranged within the flow channel (at 478). In the second valve position, the flow channel may be fluidly coupled to another reservoir, such as a reservoir containing hydrogenation buffer. At 480, the biological sample within the flow channel may be induced to flow (e.g., via a pump assembly) into the reservoir. Method 470 may then include repeating steps 472, 474, 478, and 480 until each of the desired biological samples is arranged in a common reservoir. At 482, the biological sample with hydrogenation buffer may simultaneously flow through the flow channel and into the reaction chamber.

[0195] Therefore, one or more biological samples can be directed into the reaction chamber using a rotary valve. In an alternative embodiment, the biological sample (or samples) has a direct passage to the reaction chamber and does not flow through the rotary valve. Optionally, method 470 can be initiated by a specified operation, such as the operation described with respect to Table 1, to perform a specified reaction. For example, the rotary valve can be rotated (at 484) to another valve position to fluidly connect the reaction chamber to a specified reservoir. At 486, the reaction components can flow into the reaction chamber to interact with the biological sample therein. Optionally, at 488, method 470 includes detecting the specified reaction within the reaction chamber. Method 470 can then return to step 484.

[0196] Figure 13This is a plan view of a rotary valve 500 formed according to an embodiment, wherein the rotary valve 500 is rotatably mounted to the body side 502 of the microfluidic body 504. The rotary valve 500 may include components similar to rotary valve 216. Figure 2 The microfluidic body 504 includes multiple reservoirs 506-510 configured to hold reaction components and / or biological samples. More specifically, reservoirs 506-509 hold first, second, third, and fourth biological samples (or sample liquids). Reservoir 510 includes a hydrogenation buffer. Each of reservoirs 506-510 is characterized by... Figure 13 The corresponding reservoir channels 516-520, indicated by lines, are fluidly connected to the corresponding ports. As shown, the ports include reservoir or supply ports 526-530 that open toward the body side 502 and are in flow communication with the reservoirs 506-510. The microfluidic body 504 also includes a feed port 524 opening toward the body side 502. Figure 13 (as shown in the image).

[0197] Rotary valve 500 includes a fluid side 513 ( Figure 14 The valve body 512 (shown in the diagram) has a fluid side 513 engaging the body side 502 and an opposing operating side 514. The valve body 512 includes first, second, third, and fourth flow channels 536-539. Each of the flow channels 536-539 is configured to hold a biological sample during amplification or PCR protocol. Each of the flow channels 536-539 has a centrally located common channel port (or outlet port) 544. In other embodiments, the flow channels 536-539 do not share the same channel port. The common channel port 544 is located at an axis 542 about which the rotary valve 500 rotates. The flow channels 536-539 include corresponding first channel ports (or inlet ports) 546-549. Thus, each of the flow channels 536-539 extends from its corresponding first channel port 546-549 to the common channel port 544. Similar to rotary valve 216 (… Figure 2 Rotary valve 500 is configured to rotate to different valve positions to fluidly connect the reservoir and the passage. However, unlike rotary valve 500, rotary valve 500 can be used during expansion programs. More specifically, valve body 512 can engage heat circulator 570. Figure 14 (As shown in the diagram), while the biological sample is kept within the flow channels 536-539.

[0198] In some implementations, flow channels 536-539 may have an anti-diffusion section 545. The anti-diffusion section 545 is configured to reduce the likelihood of diffusion when a biological sample within flow channels 536-539 undergoes a PCR protocol. For example, Figure 13The flow channels 536-539 shown have a non-linear path and dimensions that vary along the path. More specifically, the flow channels 536-539 have a serpentine or wavy path that loops back and forth as the flow channels extend from the corresponding first channel port toward the common channel port 544. The first channel ports 546-549 have a radially outward position. In addition to the shape of the flow channels 536-539, the flow channels 536-539 have dimensions that decrease as the flow channels 536-539 extend from the corresponding first channel port to the common channel port 544. In other embodiments, the anti-diffusion section 545 does not have a serpentine path. The segment of the flow channels 536-539 excluding the anti-diffusion section 545 may be referred to as a sample preparation region 543, which represents a portion of the corresponding flow channel in which the biological sample may undergo different conditions, such as temperature changes. However, it should be understood that for at least some embodiments, the biological sample may also be present within the anti-diffusion section 545.

[0199] Figure 14 The diagram shows a side section of the rotary valve 500 when the heat circulator 570 is mounted to the operating side 514. In some embodiments, the heat circulator 570 can provide a mounting force 572 against the body side 502 of the microfluidic body 504 to press the valve body 512. Although in Figure 14 As not shown, valve body 512 may include one or more mechanical interfaces (e.g., non-planar features, such as fins) engaged by thermal circulator 570. Thermal circulator 570 is configured to control the temperature of flow channels 536-539. In a particular embodiment, thermal circulator 570 controls the temperature of each of flow channels 536-539 simultaneously. In other embodiments, thermal circulator 570 may selectively engage fewer than all flow channels at a time.

[0200] As in Figure 14 As shown, the common channel port 544 is fluidly connected to the feed port 524. An axis 542 extends through the common channel port 544 and the feed port 524. The first channel port 547 of the flow channel 537 is fluidly connected to the reservoir port 527. However, the first channel port 549 of the flow channel 539 is sealed by the body side 502. Therefore, in Figure 14 In the valve position shown, fluid (e.g., fluid containing a biological sample) can flow from reservoir 507. Figure 13 It flows and enters the flow channel 537.

[0201] Figures 15A-15L This is a plan view of the rotary valve 500 and shows the different valve positions where different operations can occur. This is to prepare for expansion schemes, such as system controller 180 ( Figure 1The system controller is configured to selectively control a pump assembly (not shown) and a rotary valve 500. The pump assembly may be similar to pump assembly 332 and include one or more flow pumps. In some embodiments, a single pump may be located downstream of the rotary valve 500 and configured to operate via a common channel port 544 ( Figure 15A (Drawing fluid.)

[0202] Optional location, flow channels 536-539 ( Figure 15A It can be filled with fluid before receiving biological samples. For example, Figures 15A-15D A first channel port corresponding to a flow channel is shown, which is fluidly connected to a reservoir port 530 in flow communication with reservoir 510. Therefore, the first channel port of each flow channel can be individually connected to reservoir 510. When a flow channel is in flow communication with reservoir 510, the system controller can selectively actuate the pump assembly to induce the flow of the reactants within reservoir 510, causing the reactants to flow into the corresponding flow channel.

[0203] Therefore, in Figure 15D Subsequently, each of flow channels 536-539 is filled with a reactive component. Although the reactive component is associated with reservoir 510, other reactive components may fill flow channels 536-539. For example, flow channels 536-539 may be fluidly coupled to a separate reservoir (not shown) containing, for example, water or a buffer solution. In the illustrated embodiment, each of flow channels 536-539 is detachably coupled to reservoir 510. In an alternative embodiment, one or more of flow channels 536-539 may be simultaneously coupled to reservoir 510 or a separate reservoir.

[0204] After flow channels 536-539 have been filled, the water from reservoirs 506-509... Figure 15E Biological samples can be loaded into flow channels 536-539 respectively. Figure 15E In. For example, such as Figure 15E As shown, flow channel 538 is fluidly connected to reservoir port 528 and thus in flow communication with reservoir 508. Flow channels 536, 537, and 539 are covered by body side 502. The pump assembly can induce flow of biological samples within reservoir 508, causing the biological samples to flow into flow channel 538. The flow rate can be based on the amount of fluid within reservoir 508. After the biological samples have been loaded into flow channel 538, rotary valve 500 can be selectively rotated, and the pump assembly can be selectively actuated in a similar manner to load biological samples from reservoirs 506, 507, and 509 into flow channels 536, 537, and 539, respectively. Figures 15F-15H As shown in the image.

[0205] With the biological sample loaded within the corresponding flow channels 536-539, the rotary valve 500 can be selectively rotated such that each of the first channel ports 546-549 is covered (or sealed) by the body side 502 of the microfluidic body 504. The valve position within which the first channel ports 546-549 are sealed is... Figure 15I As shown in the diagram. Then the heat circulator 570 can be controlled ( Figure 14 The flow channels 536-539 are cyclically circulated through temperature changes according to the specified amplification protocol. Although the flow channels 536-539 are sealed only at one end, the pump assembly and anti-diffusion section 545 prevent biological samples (e.g., PCR plugs) from moving and / or diffusing into or through the feed port 524. Figure 14 ).

[0206] Following the amplification protocol, biological samples can be loaded into a shared storage container. For example, such as... Figure 15J-15L As shown, the biological samples within flow channels 536-538 can be fluidly coupled to reservoir 510. A pump assembly can be selectively operated to induce the biological samples to flow into reservoir 510. Although not shown, flow channel 536 can also be fluidly coupled to reservoir 510 such that the biological samples within flow channel 536 can be loaded into reservoir 510. Therefore, each biological sample from reservoirs 506-509 can be loaded into a common reservoir 510 after the amplification protocol. The pump assembly can then be selectively actuated to induce the mixed biological samples to flow through feed port 524. The biological samples can be fluidly delivered to a reaction chamber, such as reaction chamber 326. Figure 2 The biological sample can then undergo the specified reaction as described herein. In certain embodiments, the biological sample can be used during the SBS protocol.

[0207] Figure 16 This is a plan view of a rotary valve 600 formed according to an embodiment, which is mounted to the body side 616 of a microfluidic body 618. The rotary valve 600 may include components similar to rotary valve 216. Figure 2 ) and rotary valve 500 ( Figure 13 The rotary valve 600 includes a valve body 602 having flow channels 604-606. Each of the flow channels 604-606 extends between a first channel port (or inlet port) and a second channel port (or outlet port) 610. Unlike the rotary valve 500, the flow channels 604-606 are not in flow communication with a common channel port.

[0208] In the illustrated embodiment, each of flow channels 604-606 is in flow communication with upstream channel 612 and downstream channel 614. Figure 16In this configuration, rotary valve 600 is in the valve position, allowing each of flow channels 604-606 to receive biological samples from its corresponding upstream channel 612. For example, flow channels 604-606 can simultaneously receive corresponding biological samples. The flow of biological samples into flow channels 604-606 can be induced by a common pump. For example, downstream channels 614 can be combined and fluidly coupled to a single pump. Alternatively, individual pumps can be fluidly coupled to flow channels 604-606.

[0209] Figure 17 This is a plan view of the rotary valve 600 after it has been rotated to the valve position, wherein the first and second channel ports 608, 610 for each of the flow channels 604-606 are sealed by the body side 616 of the microfluidic body 618. Figure 17 In the valve position shown, a thermal circulator (not shown) can engage the valve body 602 to control the temperature experienced within the flow channels 604-606. Therefore, biological samples can undergo the amplification protocol described herein. Unlike in... Figure 13-1 In the embodiment shown in 5, the flow channels 604-606 are sealed at both ends to reduce the possibility of diffusion and movement of the PCR plug.

[0210] Figure 18 This is a plan view of rotary valve 602 formed according to the implementation scheme. Rotary valve 620 can be used with rotary valve 600 ( Figure 16 Similar to or identical to, and including multiple flow channels 624-626. As shown, the rotary valve 600 is divided into three thermal control regions or zones 634-636. Thermal control regions 634-636 are represented by pie-shaped areas indicated by dashed lines. Each thermal control region 634-636 represents a different temperature range controlled by one or more thermal circulators (not shown). More specifically, after a biological sample is loaded into the flow channels 624-626, the rotary valve 620 can be selectively rotated to different positions. The flow channels within thermal control region 634 can experience a specified temperature for denaturing nucleic acids. The flow channels within thermal control region 635 can experience a specified temperature for the annealing-extension phase, and the flow channels within thermal control region 636 can experience a specified temperature for the preheating and / or temperature holding phase. The system controller can selectively rotate the rotary valve 620 to three different valve positions to cycle the biological sample through multiple PCR amplification phases. Therefore, unlike the flow passage of rotary valve 600, flow passages 624-626 experience different temperatures.

[0211] Figure 19This is a flowchart illustrating method 650. In some embodiments, method 650 may include preparing a biological sample and optionally detecting a specified reaction of the biological sample for analysis. Method 650 may, for example, utilize the structure or aspects of the various embodiments (e.g., systems and / or methods) described herein, for example, regarding... Figures 13-18 The implementation scheme is described. In various implementation schemes, some steps may be omitted or added, some steps may be combined, some steps may be executed simultaneously, some steps may be executed concurrently, some steps may be divided into multiple steps, some steps may be executed in different orders, or some steps or a series of steps may be re-executed in an iterative manner.

[0212] Method 650 may include (at 652) providing a microfluidic body and a rotary valve. The microfluidic body may have a body side and a fluid network, the fluid network including a supply port (e.g., reservoir ports 526-529) and a feed port. The supply port opens toward the body side. The rotary valve is rotatably mounted to the body side and has a first channel port, a second channel port, and a flow channel extending between the first and second channel ports. In some embodiments, multiple flow channels may be used, wherein the flow channels have separate second channel ports, for example... Figures 16-18 The implementation scheme, or sharing a second channel port, for example Figure 13-Figure 1 Implementation scheme 5. In such an implementation scheme in which the second channel port is shared, the second channel port may be referred to as the common channel port.

[0213] Method 650 may include (at 654) rotating a rotary valve to a first valve position, wherein a first channel port is in flow communication with a supply port of the microfluidic body. Method 650 may further include (at 656) allowing a biological sample to flow through the first channel port and into the flow channel while the rotary valve is in the first valve position. The biological sample may flow from the first channel port toward a second channel port. This flow (at 656) may include selectively controlling the flow rate and / or duration such that the biological sample substantially does not flow through the second channel port or the feed port. For embodiments including multiple flow channels, such as rotary valve 500, steps 654 and 656 may be repeated until each flow channel has a corresponding biological sample. However, the rotation (at 654) of each flow channel is not to the same valve position. More specifically, while a biological sample flows into a corresponding flow channel, the other flow channels may be sealed at one or both ends.

[0214] Method 650 may further include (at 658) rotating the rotary valve to a second valve position while the biological sample is within the flow channel, such that the first channel port is sealed by the body side, and performing (at 660) a thermal cycling operation to change the temperature of the biological sample in the flow channel to a selected temperature. This execution (at 660) can be based on a predetermined protocol. For example, the list may specify the biological sample to be analyzed for subsequent analysis.

[0215] Optionally, after this execution (at 660), a biological sample or multiple biological samples may be loaded (at 662) into a reservoir. For example, the reservoir may include a hydrogenated buffer solution for preparing biological samples for subsequent analysis. At 664, the biological sample (or a combination of biological samples) may be delivered to a reaction chamber for subsequent analysis at 666.

[0216] Figure 20 This is a perspective view of a flow control system 700 formed according to an implementation scheme, which includes a microfluidic body 702 and a rotary valve 704. Unlike rotary valve 500 ( Figure 13 ), Rotary valve 600 ( Figure 16 ) and rotary valve 620 ( Figure 18 The amplification does not occur solely within the rotary valve 704. Instead, it occurs at least partially within the microfluidic body 702. More specifically, the microfluidic body 702 has a first body side 706 facing opposite directions. Figure 22 (shown in the middle) and the second main body side 708 ( Figure 22 (As shown in the diagram). The microfluidic body 702 has a fluid network 705, which includes multiple sample reservoirs 711-714, multiple supply channels 721-724 with corresponding inlet ports 731-734, and a common outlet port 736. The inlet ports 731-734 and the outlet port 736 open toward the first body side 706 ( Figure 22 ).

[0217] Rotary valve 704 is rotatably mounted to microfluidic body 702 along a first body side 706. In the illustrated embodiment, rotary valve 704 has a first channel section 726 and a second channel section 728. The first and second channel sections 726 and 728 open toward the fluid side 709 of valve body 704. Figure 22 (As shown). Optionally, the first and second channel segments 726, 728 may extend between corresponding channel ports opening toward the fluid side 709. The first and second channel segments 726, 728 are separate from each other and extend only a portion of the fluid side 709. In the illustrated embodiment, the second channel segment 728 is in flow communication with the outlet port 736 at any rotational position of the rotary valve 704.

[0218] Figure 20A rotary valve 704 is shown in a designated position, with a sample reservoir 711 in flow communication with the pump assembly. More specifically, a first channel section 726 is fluidly located between an inlet port 731 and the sample reservoir 711. A second channel section 726 is fluidly located between the sample reservoir 711 and an outlet port 736. Thus, a supply channel 721 is in flow communication with a feed channel 756 via the first channel section 726, the sample reservoir 711, and the second channel section 728.

[0219] Although not shown, the flow control system 700 may include a pump assembly configured to induce fluid flow through inlet port 731 and a first channel segment 726 into sample reservoir 711. The fluid may include a biological sample loaded in, for example, a remote reservoir (not shown) in fluid communication with supply channel 721. The fluid flow and the size of the sample reservoir may be configured such that the biological sample does not substantially exit sample reservoir 711 through second channel segment 728. After the biological sample is loaded into sample reservoir 711, rotary valve 704 can be selectively rotated such that first channel segment 726 and second channel segment 728 are fluidly coupled to sample reservoir 712. Sample reservoir 712 may contain the biological sample flowing from supply channel 722. Sample reservoirs 713 and 714 may contain corresponding biological samples in a similar manner.

[0220] Figure 21 This is a perspective view of the flow control system 700 after the sample reservoirs 711-714 have been loaded with the corresponding biological samples. In some embodiments, the rotary valve 704 includes gas reservoirs 741-744, which... Figure 20 As shown in the diagram. During the amplification protocol, gas reservoirs 741-744 are configured to align with sample reservoirs 711-714. For example, as... Figure 22 As shown, sample reservoir 711 and gas reservoir 741 are combined to form sample preparation chamber 751. The gas in gas reservoir 741 can be used as a gas ballast in sample preparation chamber 751. After thermal cycling, the biological sample can flow through feed channel 756, which is in flow communication with outlet port 736. Figure 20 As described herein, biological samples can be guided into a reaction chamber, such as reaction chamber 326. Figure 2 ), where the specified reaction can occur and be detected.

[0221] Figure 23 This is a schematic diagram of system 800 formed according to the implementation scheme. System 800 may include systems similar to system 100 ( Figure 1Features of the system. For example, system 800 includes a flow control system 802 having a fluid network 804. The fluid network 804 may include multiple interconnected channels, ports, reservoirs, and other spatial regions configured to maintain fluid flow through it or to allow fluid flow therethrough. For example, fluid network 804 includes rotary valves 806 and 808. Rotary valve 806 is configured to be used during a sample preparation phase, and rotary valve 808 is configured to be used during a sample analysis phase. Rotary valves 806 and 808 are fluidly connected via a central channel 810 of fluid network 804. Fluid network 804 also includes a feed channel 812, a reaction chamber 814, and a waste reservoir 816. Flow control system 802 includes a pump assembly 818 in flow communication with fluid network 804. In the illustrated embodiment, pump assembly 818 includes a single pump, but in other embodiments, multiple pumps may be included. System 800 may include a microfluidic body (not shown) having a body side 819. Rotary valves 806 and 808 are rotatably mounted to the body side 819. The microfluidic body may also include or define an intermediate channel 810 and a feed channel 812.

[0222] The fluid network 804 also includes a plurality of measurement channels 821-824 and a plurality of sample reservoirs 831-834. Each measurement channel 821-824 extends between corresponding first and second ports 826, 828 and is configured to fluidly connect the corresponding sample reservoir to the intermediate channel 810. As shown, the measurement channels 821-824 extend through a thermal control region 825. In the illustrated embodiment, the measurement channels 821-824 have a wavy path 825 through the thermal control region 825. The portions of the measurement channels 821-824 extending through the thermal control region 825 may constitute a sample preparation region 827. Optionally, or in addition to a non-linear path, the measurement channels 821-824 may have different dimensions to accommodate a specified volume of corresponding biological sample.

[0223] Rotary valve 806 is configured to move between multiple valve positions. Rotary valve 806 includes a bridge passage 840 and a flow passage 842. Bridge passage 840 and flow passage 842 are configured to fluidly connect one of sample reservoirs 831-834 to an intermediate passage 810. For example, as... Figure 23 As shown, the bridge channel 840 fluidly connects the reservoir port (or supply port) of the sample reservoir 833 to the first port 826 of the measurement channel 823. Simultaneously, the flow channel 842 fluidly connects the second port 828 to the intermediate port 856. The intermediate port 856 opens along the body side 819 and is in flow communication with the intermediate channel 810.

[0224] Therefore, the system controller (not shown) can selectively rotate the rotary valve 806 to fluidly connect sample reservoirs 831-834 to the corresponding measurement channels 821-824, respectively. The system controller can selectively control the pump assembly 818 to induce the flow of biological samples within the sample reservoirs, such that the biological samples are arranged within the sample preparation areas 827 of the measurement channels 821-824.

[0225] When a biological sample (or multiple samples) is located within its corresponding assay channel, the rotary valve 806 can be rotated by the system controller to another valve position in which the first and second ports 826, 828 for each assay channel 821-824 are covered or sealed by the body side 819. With the assay channel sealed, the biological sample can undergo an amplification protocol. For example, a thermal circulator (not shown) can be positioned adjacent to the thermal control region 825 and apply heat according to the amplification protocol. In a particular embodiment, each of the biological samples can be located within the thermal control region 825 simultaneously. In an alternative embodiment, the biological samples can be located within the thermal control region 825 at separate times.

[0226] After the biological sample has been amplified, rotary valve 806 can return to its corresponding valve position to load the corresponding biological sample into flow channel 842. With the biological sample arranged within flow channel 842, the rotary valve can be rotated to another position where flow channel 842 is in flow communication with reservoir 835. Reservoir 835 may contain, for example, a hydrogenated buffer solution. The biological sample can be loaded into reservoir 835. Optionally, rotary valve 806 and pump assembly 818 can operate in a similar manner to load biological samples from other assay channels into reservoir 835. The biological sample can then be directed toward another stage. For example, the biological sample can flow through flow channel 842, through intermediate port 856, and into intermediate channel 810. In an alternative embodiment, the biological sample can be directed toward rotary valve 808 without first being loaded into reservoir 835.

[0227] like Figure 23 As shown, rotary valve 808 includes a flow channel 870 and a plurality of reagent reservoirs 871-878. After a biological sample has been prepared using rotary valve 806, the biological sample can be delivered to reaction chamber 814. Optionally, before delivering the biological sample to reaction chamber 814, rotary valve 808 can be rotated to fluidly connect one or more of the reagent reservoirs 871-878 to reaction chamber 814. More specifically, flow channel 870 can be rotated to a designated position to fluidly connect one of the reagent reservoirs 871-878 to reaction chamber 814. Thus, rotary valve 808 can be used to prepare reaction chamber 814 to receive biological samples. For example, reagent reservoirs 871-878 may include clustering reagents, enzymes, and / or capture probes.

[0228] After the biological sample is delivered to the reaction chamber 814, the rotary valve 808 can be selectively rotated to different valve positions. For example, the rotary valve 808 can be rotated according to a predetermined cycle to repeatedly deliver the reaction components used for the SBS protocol. This cycle can be similar to the cycle shown in Table 1 above. Therefore, the rotary valve 808 can be used to prepare the reaction chamber to receive biological samples and / or for performing assays.

[0229] Figure 24 and Figure 25 Another embodiment utilizing a rotary valve with a bridge-type channel is shown. Figure 24 This is a plan view of the flow control system 900, and... Figure 25 This is a partial exploded perspective view of the flow control system 900. As shown, the flow control system 900 includes first and second body sides 904, 906 with opposite sides. Figure 25 The microfluidic body 902 includes a plurality of flow channels 908 and a plurality of sample reservoirs 910. Each of the flow channels 908 is configured to be fluidly connected to a corresponding sample reservoir 910. The flow channels 908 may be similar in shape and size to flow channels 536-539. Figure 13 )similar.

[0230] The flow control system 900 also includes a rotary valve 912. The rotary valve 912 includes a plurality of bridge-type channels 913-916 configured to fluidly connect a corresponding flow channel 908 and a sample reservoir 910. In a particular embodiment, each of the bridge-type channels 913-916 is a side-opening recess along the exterior of the rotary valve 912. In an alternative embodiment, the bridge-type channels 913-916 are not side-opening but extend between a first port and a second port leading to the exterior. For example, Figure 24 Bridge channel 916 fluidly connects the corresponding sample reservoir 910 to the corresponding flow channel 908 based on the rotational position of rotary valve 912. When a biological sample flows through bridge channel 913, the other bridge channels 914-916 are not fluidly connected to the corresponding sample reservoir 910. More specifically, the other bridge channels 914-916 are sealed by rotary valve 912.

[0231] A thermal circulator (not shown) can alter the temperature experienced by the biological sample within the flow channel 908 in a manner similar to that described in other embodiments. For example, one or both of the body sides 904, 906 can be coupled with a thermal circulator. After the amplification protocol, the biological sample can be transported to another spatial region for further modification / preparation and / or analysis.

[0232] As described above, in various embodiments, the rotary valve and microfluidic body may include different fluid elements that cooperate to control the flow of one or more fluids in a specified manner. It should be understood that the embodiments described above are merely illustrative and not limiting. For example, the embodiments described above (and / or aspects thereof) may be used in combination with each other. Furthermore, many modifications can be made to adapt specific situations or materials to the teachings of the various embodiments without departing from their scope.

[0233] Figures 26-29 Various views of a rotary valve 950 formed according to an embodiment are shown. The rotary valve 950 can be used as a rotary valve in various embodiments, for example, rotary valve 216 (…). Figure 2 ). Figure 26 and Figure 27 A bottom perspective view and a side perspective view of a rotary valve 950 are shown, respectively. The rotary valve 950 includes a fluid side 952 and an operating side 954. The operating side 954 includes a mechanical interface 956 configured to engage a valve actuator (not shown).

[0234] Figure 28 A cross-section of a rotary valve 950 is shown; as illustrated, the rotary valve 950 includes a housing cover 960 and a side cover 964 fixed in a fixed position relative to each other. The housing cover 960 defines a valve cavity 962, and the side cover 964 closes one end of the valve cavity 962 along the fluid side 952. The rotary valve 950 also includes a rotor shaft 966, which includes a mechanical interface 956, a valve spring 968, a manifold body 970, and a compressible diaphragm 972, all disposed within the valve cavity 962. The rotor shaft 966 is configured to rotate the manifold body 970 and the compressible diaphragm 972 about an axis 978 along the side cover 964.

[0235] The manifold body 970 is fixed to the rotor shaft 966 on one side and to the compressible diaphragm 972 on the opposite side. A valve spring 968 can bias or push the manifold body 970 and the compressible diaphragm 972 against the inner surface of the side cover 964. In certain embodiments, the compressible diaphragm 972 may be polypropylene or other similar materials. (Back to...) Figure 26 The side cover 964 includes a central flow port 980, a discharge port 981, and an external flow port 982. The side cover 964... Figure 26 The area is partially transparent to show the central flow port 980, the discharge port 981, and the external flow ports 982. A total of nine external flow ports 982 are shown, but other embodiments may include a different number of ports.

[0236] Figure 29This is an enlarged cross-section of a rotary valve 950 representing the interaction between the manifold body 970, the compressible diaphragm 972, and the side cap 964. As shown, the side cap 964 and the compressible diaphragm 972 may define a lubricant reservoir 990 between them. The lubricant reservoir 990 may extend about axis 978. In some embodiments, an external lubricant reservoir 991 may also be provided. Figure 26 The diagram also shows a lubricant reservoir 990. A discharge port 981 is in flow communication with the lubricant reservoir 990, allowing lubricant to be loaded into the reservoir 990. As shown, a flow passage 984 is defined between the manifold body 970 and the compressible diaphragm 972. When the rotor shaft 966 rotates the compressible diaphragm 972 and the manifold body 970 together, the flow passage 984 rotates with it. Due to the compressible diaphragm 972 and the lubricant reservoir 980, frictional forces resisting rotation are reduced. Therefore, the operating life of the rotary valve 950 can be longer than that of other known valves.

[0237] According to an embodiment, a system is provided comprising a fluid network having a sample channel, a reaction chamber, and a reservoir. The sample channel is in flow communication with a bioport configured to receive a biological sample. The system also includes a pump assembly configured to be in flow communication with the fluid network. The system further includes a rotary valve having a flow channel and configured to rotate between a first valve position and a second valve position. When the rotary valve is in the first valve position, the flow channel fluidly connects the reaction chamber and the sample channel, and when the rotary valve is in the second valve position, the flow channel fluidly connects the reservoir and the reaction chamber. When the rotary valve is in the first valve position, the pump assembly induces the biological sample to flow toward the reaction chamber, and when the rotary valve is in the second valve position, the pump assembly induces reaction components to flow from the reservoir to the reaction chamber.

[0238] On one hand, the pump assembly may include a system pump that is in flow communication with the reaction chamber and is located downstream of the reaction chamber.

[0239] On the other hand, the rotary valve can be configured to hold the biological sample in the flow channel when the rotary valve is rotated from the first valve position to the second valve position. The pump assembly can be configured to induce the biological sample to flow into the reservoir when the rotary valve is in the second valve position.

[0240] Optionally, the sample channel may be a first sample channel, and the biological sample may be a first biological sample. The fluid network may include a second sample channel having a second biological sample. The rotary valve may be configured to rotate to a third valve position such that the flow channel is in flow communication with the second sample channel. The pump assembly may be configured to induce the second biological sample in the second sample channel to flow into the flow channel, wherein the rotary valve is configured to hold the second biological sample in the flow channel when the rotary valve is rotated from the third valve position to the second valve position. The pump assembly may be configured to induce the second biological sample therein to flow into a reservoir when the rotary valve is in the second valve position. In some embodiments, the pump assembly may be configured to induce the first and second biological samples to flow from the reservoir toward the reaction chamber.

[0241] On the other hand, the reservoir can be a first reservoir. The fluid network can also include a second reservoir, wherein the rotary valve can be configured to move to a third valve position, such that the flow passage fluidly connects the second reservoir and the reaction chamber.

[0242] On the other hand, the sample channel can be a first sample channel and the fluid network includes a second sample channel. Optionally, each of the first and second sample channels is in flow communication with a rotary valve via a common supply port. Optionally, the system may also include a channel valve coupled to the sample channel. The valve channel may be configured to move between a first position and a second position to respectively block flow through the sample channel and allow flow through the sample channel.

[0243] On the other hand, the rotary valve can rotate about an axis. The fluid network may include a feed port that is aligned with the axis and fluidly connects the flow channel and the reaction chamber.

[0244] On the other hand, the fluid network may also include reagent channels. The sample channels and reagent channels may be in flow communication with a common supply port located upstream of the flow channel. The supply port fluidly connects the sample channels and reagent channels to the flow channel.

[0245] On the other hand, the system may include a detection component configured to detect a specified reaction within the reaction chamber. Optionally, the detection component includes an imaging detector that can be positioned to detect light signals from the reaction chamber. Optionally, the imaging detector may have a fixed position relative to the fluid network.

[0246] On the other hand, the system includes a system controller that can be configured to automatically control rotary valves and pump assemblies for iterative cycles of the sequencing-by-synthesis (SBS) protocol.

[0247] In one embodiment, a method is provided that includes rotating a rotary valve having a flow channel to a first valve position. When in the first valve position, the flow channel is in flow communication with a reaction chamber. The method may further include allowing a biological sample to flow from a sample channel or a first reservoir through the flow channel and into the reaction chamber while the rotary valve is in the first valve position. The method further includes rotating the rotary valve to a second valve position. When in the second valve position, the flow channel is fluidly connected to a second reservoir and the reaction chamber. The method further includes allowing a reaction component to flow from the second reservoir into the reaction chamber. The reaction component interacts with the biological sample within the reaction chamber.

[0248] On one hand, the method may include detecting a specified reaction between the reaction components and the biological sample within the reaction chamber. Optionally, detecting the specified reaction may include detecting a light signal from the reaction chamber. The light signal may indicate the specified reaction.

[0249] On the other hand, the method also includes combining multiple biological samples by individually flowing them into the reservoir. When the rotary valve is in the first valve position, the biological samples can simultaneously flow through the flow channel and into the reaction chamber.

[0250] Alternatively, the method also includes rotating the rotary valve to the third valve position and allowing the washing solution to flow from the third reservoir into the reaction chamber. The method may also include rotating the rotary valve to the second valve position and allowing the reaction components to flow from the second reservoir into the reaction chamber. Optionally, the method includes performing an iterative cycle of a sequencing-by-synthesis (SBS) protocol.

[0251] On the other hand, the method also includes amplifying the biological sample in the sample channel or reservoir before allowing the biological sample to flow through the flow channel and into the reaction chamber.

[0252] In one embodiment, a system is provided comprising a flow control system having a fluid network and a pump assembly in flow communication with the fluid network. The fluid network includes a sample channel, a plurality of reservoirs, and a reaction chamber, the sample channel being configured to receive a biological sample. The system also includes a rotary valve having a flow channel. The rotary valve is configured to rotate to different valve positions to fluidly connect the reaction chamber to either the sample channel or one of the reservoirs. The system further includes a detection device configured to detect a light signal from the reaction chamber during an assay. The system also includes a system controller configured to control the rotary valve and pump assembly to cause the biological sample to flow from the sample channel and into the reaction chamber. The system controller is also configured to control a rotary valve, a pump assembly, and a detection device during multiple scenario cycles, each of which includes: (a) rotating the rotary valve to a first reservoir valve position, such that the reaction chamber is in flow communication with a first reservoir among a plurality of reservoirs; (b) controlling the pump assembly to induce fluid to flow from the first reservoir into the reaction chamber; (c) rotating the rotary valve to a second reservoir valve position, such that the reaction chamber is in flow communication with a second reservoir among a plurality of reservoirs; (d) controlling the pump assembly to induce fluid to flow from the second reservoir into the reaction chamber; and (e) controlling the detection device to detect an optical signal from the reaction chamber when or after fluid from the second reservoir flows through the reaction chamber.

[0253] On one hand, the sample channel may include a sample preparation area. The system may also include a thermal circulator configured to control the temperature of the biological sample within the sample preparation area. The system controller may control the thermal circulator to amplify the biological sample within the sample preparation area before the biological sample flows from the sample channel into the reaction chamber.

[0254] Optionally, each cycle includes rotating the rotary valve to the third reservoir valve position, thereby establishing flow communication between the reaction chamber and the third reservoir of the plurality of reservoirs, and controlling the pump assembly to induce fluid to flow from the third reservoir into the reaction chamber.

[0255] On the other hand, the detection device includes a CMOS imaging detector. On the other hand, a flow unit is coupled to the detection device. The flow unit can define a reaction chamber. Optionally, the flow unit is fixed in a fixed position relative to the detection device.

[0256] On the other hand, the flow control system includes a microfluidic body having a body side. The body side may include multiple ports opening toward the body side, wherein a rotary valve seals multiple of these ports, provided that a flow channel is fluidly coupled to at least one of the other ports. In a particular embodiment, the system is configured to perform a sequencing synthesis (SBS) protocol.

[0257] According to an embodiment, a method is provided comprising providing a microfluidic body and a rotary valve. The microfluidic body has a body side and a fluid network including a supply port and a feed port. The supply port opens toward the body side. The rotary valve is rotatably mounted to the body side. The rotary valve has a first channel port, a second channel port, and a flow channel extending between the first channel port and the second channel port. The method further comprises rotating the rotary valve to a first valve position, wherein the first channel port is in flow communication with the supply port of the microfluidic body. The method further comprises, when the rotary valve is in the first valve position, allowing a biological sample to flow through the first channel port and into the flow channel. The method further comprises, with the biological sample within the flow channel, rotating the rotary valve to a second valve position, such that the first channel port is sealed by the body side. The method further comprises performing a thermal cycling operation to change the temperature of the biological sample in the flow channel to a selected temperature.

[0258] On one hand, the microfluidic body may include a reservoir port opening toward the body side and flowing in communication with a reservoir. The method may further include rotating a rotary valve to align a first channel port and a reservoir port, and inducing a biological sample within the flow channel to flow through the first channel port into the reservoir. Optionally, the method includes inducing a biological sample to flow from the reservoir through the flow channel and through a feed port of the microfluidic body.

[0259] On the other hand, when the rotary valve is in the second valve position, the second channel port can be aligned with the feed port.

[0260] On the other hand, when the rotary valve is in the second valve position, the second channel port can be sealed by the main body side.

[0261] On the other hand, the first channel port is a first inlet port, and the flow channel is a first flow channel. The rotary valve may include a second inlet port and a second flow channel. The second flow channel may extend between the second inlet port and the second channel port.

[0262] On the other hand, the first channel port is a first inlet port, and the second channel port is a first outlet port. The rotary valve may include a second inlet port and a second outlet port through which a flow channel extends.

[0263] On the other hand, a rotary valve may include a fluid side and an operating side facing opposite directions. A thermal circulator may engage the operating side to control the temperature of the biological sample.

[0264] Alternatively, the method may include inducing a biological sample to flow from a reservoir through a flow channel and through a feed port of a microfluidic body into a reaction chamber. The method may also include detecting an optical signal from the reaction chamber. Optionally, the reaction chamber has a remote position relative to the rotary valve.

[0265] On the other hand, the flow unit includes a reaction chamber. Detecting the light signal from the reaction chamber can include detecting the light signal using an imaging detector coupled to the flow unit. Optionally, the imaging detector and the flow unit are fixed to each other.

[0266] According to an embodiment, a system is provided comprising a microfluidic body having a body side and a fluid network including a supply port and a feed port. The supply port opens toward the body side. The system also includes a rotary valve rotatably mounted to the body side. The rotary valve has a first channel port, a second channel port, and a flow channel extending between the first and second channel ports. The rotary valve is configured to rotate between a first valve position and a second valve position. When the rotary valve is in the first valve position, the first channel port is in flow communication with the supply port of the microfluidic body. When the rotary valve is in the second valve position, the first channel port is sealed by the microfluidic body. The system also includes a pump assembly configured to induce fluid flow through the supply port and into the flow channel when the rotary valve is in the first valve position. The system also includes a thermal circulator positioned relative to the rotary valve and configured to control the temperature experienced by the fluid within the flow channel when the rotary valve is in the second valve position.

[0267] On one hand, the microfluidic body may include a reservoir port that opens toward the body side and flows in communication with a reservoir. A rotary valve may be rotatable to a third valve position where the first channel port and the reservoir port are aligned. A pump assembly may be configured to induce fluid in the flow channel to flow through the reservoir port and into the reservoir. Optionally, the pump assembly is configured to induce fluid to flow from the reservoir through the flow channel and through a feed port of the microfluidic body.

[0268] On the other hand, the rotary valve is configured to rotate about an axis. The second channel port and the feed port can be aligned with the axis.

[0269] On the other hand, the flow channel can be a first flow channel. A rotary valve may include a second flow channel extending between the corresponding channel ports.

[0270] On the other hand, the system includes a reaction chamber in flow communication with a feed port and a detection device positioned to detect a specified reaction within the reaction chamber. Optionally, the reaction chamber has a remote position relative to the rotary valve. Optionally, the system includes a flow unit having the reaction chamber. The detection device may be an imaging detector positioned adjacent to the flow unit. In some embodiments, the imaging detector and the flow unit are fixed to each other.

[0271] According to an embodiment, a system is provided comprising a microfluidic body having a fluid network having an inlet port, an outlet port, and a sample reservoir. The system also includes a rotary valve rotatably coupled to the microfluidic body. The rotary valve has a first channel section and a second channel section. When the rotary valve is in the first valve position, the first channel section fluidly connects the inlet port and the sample reservoir. When the rotary valve is in the first valve position, the second channel section fluidly connects the outlet port and the sample reservoir. The system also includes a pump assembly configured to allow fluid to flow through the inlet port and the first channel section into the sample reservoir when the rotary valve is in the first valve position. The rotary valve is configured to move to a second valve position in which the sample reservoir is sealed by the rotary valve. The system may further include a thermal circulator positioned relative to the microfluidic body to provide heat to the sample reservoir when the rotary valve is in the second valve position.

[0272] On one hand, the rotary valve may include a sealed gas reservoir. When the rotary valve is in the second valve position, the sealed gas reservoir can be aligned with the sample reservoir. The sealed gas reservoir and the sample reservoir can be combined to form a reaction chamber.

[0273] On the other hand, the system also includes a feed channel in flow communication with the outlet port. The feed channel fluidly connects the outlet port to the reaction chamber. The system includes the reaction chamber and a detection device positioned to detect a specified reaction within the reaction chamber.

[0274] On the other hand, the reaction chamber can be located remotely relative to the rotary valve. Optionally, the system may include a flow unit having a reaction chamber. The detection device may be an imaging detector positioned adjacent to the flow unit.

[0275] According to an embodiment, a system is provided comprising a microfluidic body having a fluid network having a sample reservoir and a separate measurement channel. The measurement channel extends between a first port and a second port. The fluid network also includes a feed port. The system may further include a thermal circulator positioned adjacent to a thermally controlled region of the microfluidic body. The measurement channel extends through the thermally controlled region. The thermal circulator is configured to provide thermal energy to the thermally controlled region. The system also includes a rotary valve rotatably coupled to the microfluidic body and configured to move between a first valve position and a second valve position. The rotary valve has a bridge channel and a separate flow channel. When the rotary valve is in the first valve position, the bridge channel fluidly connects the sample reservoir and the first port of the measurement channel, and the flow channel fluidly connects the second port of the measurement channel and the feed port. The rotary valve is configured to move to the second valve position to seal the first and second ports of the measurement channel.

[0276] On one hand, the flow channel can be configured to receive biological samples from the measurement channel. The rotary valve can be configured to rotate to a third valve position where the flow channel is fluidly connected to the reservoir. This allows the biological sample to flow through the flow channel into the reservoir.

[0277] On the other hand, the system includes a reaction chamber in flow communication with a feed port and a detection device positioned to detect a specified reaction within the reaction chamber. Optionally, the reaction chamber may have a remote position relative to the rotary valve. Optionally, the system also includes a flow unit having the reaction chamber. The detection device may be an imaging detector positioned adjacent to the flow unit.

[0278] As used herein, elements or steps described in the singular and beginning with the words “a” or “an” should be understood to not exclude multiple said elements or steps unless such exclusion is explicitly stated. Furthermore, references to “an embodiment” are not intended to exclude the existence of other embodiments that also include the stated features. Additionally, unless explicitly stated to the contrary, embodiments “comprising” or “having” one or more elements having a particular characteristic may include additional elements, regardless of whether they possess that characteristic.

[0279] It should be noted that in various alternative embodiments, the specific arrangement of the components in the illustrated embodiments (e.g., quantity, type, placement, etc.) can be modified. In various embodiments, different numbers of given modules or units can be used, different types or categories of given modules or units can be used, given modules or units can be added, or given modules or units can be omitted.

[0280] It should be understood that the above description is intended to be illustrative and not restrictive. For example, the above embodiments (and / or aspects thereof) can be used in combination with each other. Furthermore, many modifications can be made to adapt particular situations or materials to the teachings of various embodiments without departing from their scope. The dimensions, material types, orientations of various components, and the number and location of various components described herein are intended to define parameters of certain embodiments and are by no means restrictive, but merely exemplary embodiments. Many other embodiments and modifications within the spirit and scope of the claims will be apparent to those skilled in the art upon reviewing the above description. Therefore, the scope of the patentable works should be determined by reference to the appended claims and the full scope of their equivalents.

[0281] As used in the specification, phrases such as “in an exemplary embodiment” mean that the described embodiment is merely one example. This phrase is not intended to limit the subject matter of the invention to that embodiment. Other embodiments of the subject matter of the invention may exclude the stated features or structures. In the appended claims, the terms “including” and “inwhich” are used as concise English equivalents to the corresponding terms “comprising” and “wherein.” Furthermore, in the appended claims, the terms “first,” “second,” and “third,” etc., are used only as designations and are not intended to impose numerical claims on the objects to which they are applied. Additionally, the limitations of the following claims are not drafted in a means-plus-function format and are not intended to be interpreted based on 35 U.S.SC §112(f), unless and until such a claim limitation is explicitly expressed using the phrase “means for…” followed by a functional statement without further structure.

Claims

1. A method comprising: Rotate the rotary valve with the flow channel to the first valve position. When in the first valve position, the flow channel is in flow communication with the reaction chamber. When the rotary valve is in the first valve position, the biological sample flows from the sample channel or the first reservoir through the flow channel and into the reaction chamber; Rotate the rotary valve to the second valve position. When in the second valve position, the flow channel fluidly connects the second reservoir and the reaction chamber. The reaction components flow from the second reservoir into the reaction chamber, where they interact with the biological sample. The method further includes rotating the rotary valve to the third valve position and allowing the washing solution to flow from the third reservoir into the reaction chamber, and also includes rotating the rotary valve to the second valve position and allowing the reaction component to flow from the second reservoir into the reaction chamber.

2. The method of claim 1, further comprising detecting a specified reaction between the reaction component and the biological sample in the reaction chamber.

3. The method according to claim 2, wherein, Detecting the specified reaction includes detecting a light signal from the reaction chamber, the light signal characterizing the specified reaction.

4. The method according to any one of claims 1-3, further comprising allowing a plurality of the biological samples to flow into the first reservoir respectively, thereby combining the biological samples in the first reservoir, wherein the biological samples simultaneously flow through the flow channel and into the reaction chamber when the rotary valve is in the first valve position.

5. The method according to any one of claims 1-3, wherein, The method includes performing an iterative cycle of a sequencing-by-synthesis (SBS) protocol.

6. The method according to any one of claims 1-3, further comprising amplifying the biological sample in the sample channel or the first reservoir before allowing the biological sample to flow through the flow channel and into the reaction chamber.

7. The method according to any one of claims 1-3, wherein, The rotary valve rotates about an axis and a feed port fluidly connects the flow channel and the reaction chamber, the axis extending through the feed port.

8. A system comprising: A flow control system includes a fluid network and a pump assembly in flow communication with the fluid network, the fluid network including sample channels, multiple reservoirs and a reaction chamber, the sample channels being configured to receive biological samples; A rotary valve including a flow passage, the rotary valve being configured to rotate to different valve positions to fluidly connect the reaction chamber to the sample passage or to one of the reservoirs; A detection device configured to detect light signals from the reaction chamber during a measurement procedure; as well as A system controller configured to control the rotary valve and the pump assembly to allow the biological sample to flow from the sample channel and into the reaction chamber, the system controller further configured to control the rotary valve, the pump assembly, and the detection device during multiple protocol cycles, each of said protocol cycles including: -- Rotate the rotary valve to the first reservoir valve position, so that the reaction chamber is in flow communication with the first reservoir among the plurality of reservoirs; --Control the pump assembly to induce fluid from the first reservoir into the reaction chamber; -- Rotate the rotary valve to the second reservoir valve position, so that the reaction chamber is in flow communication with the second reservoir among the plurality of reservoirs; --Control the pump assembly to induce fluid from the second reservoir into the reaction chamber; and --Control the detection device to detect the optical signal from the reaction chamber when fluid from the second reservoir flows through the reaction chamber or after fluid from the second reservoir has flowed through the reaction chamber; --Each of the scheme cycles further includes rotating the rotary valve to the third reservoir valve position, such that the reaction chamber is in flow communication with the third reservoir of the plurality of reservoirs, and controlling the pump assembly to induce fluid to flow from the third reservoir into the reaction chamber.

9. The system according to claim 8, wherein, The sample channel includes a sample preparation area, and the system further includes a thermal circulator configured to control the temperature of the biological sample in the sample preparation area. The system controller controls the thermal circulator to amplify the biological sample in the sample preparation area before the biological sample flows from the sample channel into the reaction chamber.

10. The system according to claim 8 or 9, wherein, The detection equipment includes a CMOS imaging detector.

11. The system of claim 8 or 9 further includes a flow unit coupled to the detection device, the flow unit defining the reaction chamber.

12. The system according to claim 11, wherein, The flow unit is fixed in a fixed position relative to the detection device.

13. The system according to any one of claims 8-9 and 12, wherein, The flow control system includes a microfluidic body having a main body side, the main body side including a plurality of ports opening toward the main body side, wherein a rotary valve seals a plurality of the ports, provided that the flow channel is fluidly connected to at least one of the other ports.

14. The system according to any one of claims 8-9 and 12, wherein, The system is configured to perform a synthesis sequencing (SBS) protocol.

15. A system comprising: A microfluidic body having a body side and a fluid network including a supply port and a feed port, the supply port opening toward the body side; A rotary valve is rotatably mounted to the body side, the rotary valve having a first channel port, a second channel port, and a flow channel extending between the first channel port and the second channel port, the rotary valve being configured to rotate between a first valve position and a second valve position, wherein when the rotary valve is in the first valve position, the first channel port is in flow communication with the supply port of the microfluidic body, and when the rotary valve is in the second valve position, the first channel port is sealed by the microfluidic body; and A pump assembly configured to induce fluid flow through the supply port and into the flow passage when the rotary valve is in the first valve position; as well as A heat circulator, positioned relative to the rotary valve and configured to control the temperature experienced by the fluid in the flow passage when the rotary valve is in the second valve position; The microfluidic body includes a reservoir port that opens toward the body side and flows in communication with the reservoir. The rotary valve is rotatable to a third valve position in which the first channel port and the reservoir port are aligned. The pump assembly is configured to induce the fluid in the flow channel to flow through the reservoir port and into the reservoir.

16. The system according to claim 15, wherein, The pump assembly is configured to induce the fluid to flow from the reservoir through the flow channel and through the feed port of the microfluidic body.

17. The system according to any one of claims 15-16, wherein, The rotary valve is configured to rotate about an axis, with the second channel port and the feed port aligned with the axis.

18. The system according to any one of claims 15-16, wherein, The flow channel is a first flow channel, and the rotary valve includes a second flow channel extending between the corresponding channel ports.

19. The system according to any one of claims 15-16, further comprising a reaction chamber in flow communication with the feed port and a detection device positioned to detect a specified reaction within the reaction chamber.

20. The system according to claim 19, wherein, The reaction chamber is located at a distance from the rotary valve.

21. The system according to claim 19, wherein, The flow unit includes the reaction chamber, and the detection device is an imaging detector located adjacent to the flow unit.

22. The system according to claim 21, wherein, The imaging detector and the flow unit are fixed to each other.

23. A system comprising: A microfluidic body having a fluid network including a sample reservoir and separate measurement channels extending between a first port and a second port, the fluid network also including a feed port; A thermal circulator is positioned adjacent to the thermal control region of the microfluidic body, the measurement channel extends through the thermal control region, and the thermal circulator is configured to provide thermal energy to the thermal control region; as well as A rotary valve, rotatably coupled to the microfluidic body and configured to move between a first valve position and a second valve position, the rotary valve having a bridge channel and a separate flow channel, wherein when the rotary valve is in the first valve position, the bridge channel fluidly connects the sample reservoir and the first port of the measurement channel, and the flow channel fluidly connects the feed port and the second port of the measurement channel, wherein the rotary valve is configured to move to the second valve position to seal the first port and the second port of the measurement channel; The flow channel is configured to receive a biological sample from the measurement channel, and the rotary valve is configured to rotate to a third valve position, in which the flow channel is fluidly connected to a reservoir, allowing the biological sample to flow through the flow channel into the reservoir.

24. The system of claim 23 further includes a reaction chamber in flow communication with the feed port and a detection device positioned to detect a specified reaction within the reaction chamber.

25. The system according to claim 24, wherein, The reaction chamber is located at a distance from the rotary valve.

26. The system according to claim 24, wherein, The flow unit includes the reaction chamber, and the detection device is an imaging detector located adjacent to the flow unit.

27. The system according to claim 26, wherein, The imaging detector and the flow unit are fixed to each other.

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