BR112018074169B1 - SYSTEM AND METHODS FOR SELECTIVE COLLECTION OF EFFLUENTS - Google Patents

Abstract

The present invention relates to a system that may include a flow cell through which a plurality of reagents may be pumped during a genetic sequencing operation, an effluent line that, in operation, conducts a spent reaction, a spent reagent valve for receiving the spent reagent from the effluent line and that is controllable to select one of a plurality of elimination (or disposal) pathways for the spent reagent, and control circuitry coupled to the spent reagent valve that, in operation, controls the spent reagent valve to select one of the elimination pathways depending on which reagent is being pumped through the flow cell.

Description

CROSS-REFERENCE TO RELATED ORDERS

[0001] This application claims priority benefit over U.S. Patent Application No. 15/841,082, filed December 13, 2017, which claims priority benefit over U.S. Patent Application No. 62/442,742, filed January 5, 2017, and also claims priority benefit over U.S. Patent Application No. 1704766.3, filed March 24, 2017, which also claims priority benefit over U.S. Patent Application No. 62/442,742; all such prior applications are incorporated herein by reference in their entirety.

BACKGROUND OF THE INVENTION

[0002] Instruments have been developed and continue to evolve to sequence molecules of interest, particularly DNA, RNA, and other biological samples. Prior to sequencing operations, samples of the molecules of interest are prepared to form a library or template that will be mixed with reagents and finally introduced into a flow cell where individual molecules will bind to sites and are amplified to enhance detectability. The sequencing operation then includes repeating a cycle of steps to bind the molecules to the sites, label the bound components, visualize the components at the sites, and process the resulting image data.

[0003] In such sequencing systems, fluidic systems (or subsystems) provide flow of substances (e.g., reagents) under the control of a control system, such as a programmed computer and appropriate interfaces.

SUMMARY OF THE INVENTION

[0004] Details of one or more embodiments of the subject matter described in this application are set forth in the accompanying figures and in the description below. Other features, aspects and advantages will become apparent from the description, figures and claims.

[0005] In some embodiments, a system may be provided that includes: one or more effluent flow paths for fluidically connecting to a flow cell through which a plurality of reagents are to be pumped during a genetic sequencing operation, wherein the effluent paths are to receive spent reagents from the flow cell; one or more pumps for pumping the spent reagents through the effluent flow paths; a spent reagent selector valve for receiving spent reagents from one or more pumps through an effluent line, and is controllable to select one of a plurality of disposal (or waste) paths for the spent reagents; and control circuitry operatively coupled to the spent reagent selector valve, the control circuitry having one or more processors and a memory for storing (or that stores) machine executable instructions that, when executed by the one or more processors, control the one or more processors to cause the spent reagent selector valve to select one of the desired disposal pathways depending on which spent reagent is being pumped through the effluent pathways.

[0006] In some embodiments of the system, the system may additionally include a flow meter that, in operation, will detect the flow of reagents used and provide flow data relating to the flow of reagents used to the control circuit.

[0007] In some such system embodiments, the flow meter may be fluidically coupled to one of the elimination pathways, and the memory may be for storing (or may store) additional machine-executable instructions that, when executed by one or more processors, further control the one or more processors to determine whether the reagent used is flowing through the desired flow pathway based on feedback from the flow meter.

[0008] In some embodiments of the system, a first elimination lane of the elimination lanes may carry more used reagents than a second elimination lane of the elimination lanes during the sequencing operation, and the flow meter may be coupled to the first elimination lane.

[0009] In some embodiments of the system, the memory may be for storing (or may store) additional machine-executable instructions that, when executed by one or more processors, additionally control the one or more processors to control the reagent selector valve used based on a sequencing protocol prescribed for a genetic sequencer.

[0010] In some embodiments of the system, it may additionally include at least one valve for selecting a reagent and a reagent flow path, and the memory may be for storing (or may store) additional machine-executable instructions that, when executed by one or more processors, additionally control the one or more processors to control the at least one valve and the reagent selector valve used based on the prescribed sequencing protocol.

[0011] In some embodiments of the system, it may additionally include a reagent pump fluidly interposed between the reagent flow path and the effluent line.

[0012] In some embodiments of the system, it may further include a first used reagent container for receiving used reagent from a first disposal pathway of the disposal pathways and a second reagent container for receiving used reagent from a second disposal pathway of the disposal pathways.

[0013] In some embodiments of the system, the first used reagent container may direct fluid to be directed away from an opening of the first used reagent container when fluid is moved during removal or transport of the first used reagent container.

[0014] In some embodiments, a system may be provided that includes: a flow cell through which a plurality of reagents are pumped during a genetic sequencing operation to produce the spent reagents; at least one reagent selector valve for selecting a reagent and a reagent flow path from a plurality of reagent flow paths, at least one of the reagent flow paths passing through the flow cell; an effluent line that, in operation, is to carry the spent reagent; a spent reagent selector valve for receiving spent reagent from the effluent line, and is controllable to select one of a plurality of disposal paths for the spent reagent; and control circuitry operatively coupled to the at least one reagent select valve and the spent reagent select valve, the control circuitry having one or more processors and a memory for storing machine executable instructions that, when executed by the one or more processors, control the one or more processors to control the at least one reagent select valve and the spent reagent select valve based on a sequencing protocol prescribed for genetic sequencing operation.

[0015] In some embodiments of the system, the memory may be for storing (or may store) other machine executable instructions that, when executed by one or more processors, additionally control the one or more processors to select one of the desired elimination pathways depending on which reagent is being pumped through the flow cell.

[0016] In some embodiments of the system, it may additionally include a flow meter that, in operation, must detect the flow of the reagents and provide flow data to the control circuit.

[0017] In some such system embodiments, the flow meter may be coupled to one of the disposal pathways, and the memory may be for storing (or may store) additional machine-executable instructions that, when executed by one or more processors, additionally control one or more processors to determine whether reactants are flowing through the desired flow pathway based on the response of the flow meter.

[0018] In some embodiments of the system, a first elimination pathway of the elimination pathways may carry more used reagent than a second elimination pathway of the elimination pathways during the sequencing operation, and the flow meter may be fluidically coupled to the first elimination pathway.

[0019] In some embodiments, a method may be provided that includes: performing a genetic sequencing operation by pumping a plurality of reagents through a flow cell to produce spent reagents; during the genetic sequencing operation, controlling at least one reagent selector valve to select the desired reagents to be pumped through the flow cell in accordance with a protocol for genetic sequencing operation; and during the genetic sequencing operation, controlling a spent reagent selector valve to select one of a plurality of disposal pathways for the spent reagents after the spent reagents exit the flow cell, and controlling the spent reagent selector valve with the aid of the protocol for genetic sequencing operation.

[0020] In some embodiments of the method, it may additionally include detecting flow through at least one of the elimination pathways to verify that reagents used are flowing through the selected elimination pathway.

[0021] In some embodiments of the method, the flow may be detected by a flow meter fluidically coupled to one of the elimination pathways.

[0022] In some embodiments of the method, a first elimination pathway of the elimination pathways may carry more used reagent than a second elimination pathway of the elimination pathways during the sequencing operation, and the flow meter may be fluidically coupled to the first elimination pathway.

[0023] In some embodiments of the method, the method may additionally include collecting the used reagents in at least two different containers, with each disposal container positioned to receive used reagents from a different disposal pathway.

[0024] Details of one or more embodiments of the subject matter described in this application are set forth in the accompanying figures and in the description below. Other features, aspects, and advantages will become apparent from the description, figures, and claims. It should be noted that the relative dimensions of the following figures may not be drawn to scale.

BRIEF DESCRIPTION OF THE FIGURES

[0025] These and other features, aspects and advantages of the present disclosure will be better understood when the following detailed description is read with reference to the accompanying figures, in which like characters represent like parts throughout the figures, wherein:

[0026] Figure 1 is a diagrammatic overview of an example sequencing system in which the disclosed techniques may be utilized;

[0027] Figure 2 is a diagrammatic overview of an example fluidic system of the sequencing system of Figure 1;

[0028] Figure 3 is a diagrammatic overview of an example processing and control system of the sequencing system of Figure 1;

[0029] Figure 4 is a flowchart of an example process for operating the sequencing system of Figure 1 during a sequencing operation;

[0030] Figure 5A illustrates, in one example, the liquid squirting into a used reagent container experiencing a lateral load of 0.5 G, simulating the removal or transport of the container at a time instant 0.0 seconds;

[0031] Figure 5B illustrates, in one example, the used reagent container of Figure 5A at the time instant 0.1 seconds after the 0.5G lateral load was applied; and

[0032] Figure 5C illustrates, in one example, the used reagent container of Figure 5A at an instant time 0.2 seconds after the 0.5G lateral load was applied.

DETAILED DESCRIPTION

[0033] Figure 1 illustrates one embodiment of a sequencing system 10 configured to process molecular samples that can be sequenced to determine their components, determine the order of the components, and generally determine the structure of the sample. The system includes an instrument 12 that receives and processes a biological sample. A sample source 14 that provides the sample 16, and which in many cases will include a tissue sample. The sample source may include, for example, an individual, such as a human, animal, microorganism, plant, or other donor (including environmental samples), or any other individual that includes organic molecules of interest whose sequence is to be determined. The system may be used with samples other than those taken from organisms, including synthesized molecules. In many cases, the molecules will include DNA, RNA, or other molecules that have base pairs whose sequence can define genes and variants that have particular functions of ultimate interest.

[0034] Sample 16 is introduced into a sample/library preparation system 18. This system can isolate, disrupt, and prepare the sample for analysis. The resulting library includes the molecules of interest at lengths that facilitate the sequencing operation. The resulting library is then supplied to the instrument 12 where the sequencing operation is performed.

[0035] In the embodiment illustrated in Figure 1, the instrument includes a flow cell or array 20 that receives the sample library. The flow cell includes one or more fluid channels that allow the sequencing chemistry to occur, including binding of library molecules and amplification at sites or locations that can be detected during the sequencing operation. For example, the flow cell/array 20 may include sequencing templates immobilized on one or more surfaces at the sites or locations. A “flow cell” may include a patterned array, such as a microarray, a nanoarray, and so on. In practice, the sites or locations may be arranged in a regular, repeating pattern, a complex non-repeating pattern, or a random combination on one or more surfaces of a support. To allow the sequencing chemistry to occur, the flow cell also allows for the introduction of substances, such as the inclusion of various reagents, buffers, and other reaction media, that are used for reactions, washing, and so on. Substances flow through the flow cell and can come into contact with the molecules of interest at individual sites.

[0036] In the instrument 12, the flow cell 20 is mounted on a movable stage 22 which, in this embodiment, can be moved in one or more directions, as indicated by reference numeral 24. The flow cell 20 may, for example, be provided in the form of a removable and replaceable cartridge that can interact with openings in the movable stage 22 or other components of the system to allow for the dispensing of reagents and other fluids to or from the flow cell 20. The stage is associated with an optical detection system 26 which can direct radiation or light 28 to the flow cell during sequencing. The optical detection system may employ various methods, such as fluorescence microscopy methods, for detecting the analytes disposed at the sites of the flow cell. By way of non-limiting example, optical detection system 26 may employ linear scanning confocal microscopy to produce progressive pixelated image data that may be analyzed to locate individual sites on the flow cell and to determine the type of nucleotide that was most recently bound or attached to each site. Other imaging techniques may also be suitably employed, such as techniques in which one or more spots of radiation are scanned across the sample, or techniques that employ “step and shot” imaging approaches. Optical detection system 26 and stage 22 may cooperate to maintain the flow cell and detection system in a static relationship while an image of the area is obtained, or, as noted, the flow cell may be scanned in any suitable mode (e.g., spot scanning, linear scanning, step and shot scanning).

[0037] Although many different technologies can be used to image, or more generally, to detect, the molecules at the sites, currently contemplated embodiments may make use of confocal optical imaging at wavelengths that cause excitation of fluorescent labels. The labels, excited by virtue of their absorption spectrum, return fluorescent signals by virtue of their emission spectrum. The optical detection system 26 is configured to capture such signals, to process pixelated image data at a resolution that allows analysis of the signal-emitting sites, and to process and store the resulting image data (or data derived therefrom).

[0038] In a sequencing operation, cyclic operations or processes are implemented in an automatic or semi-automatic manner in which reactions are promoted, such as with individual nucleotides or with oligonucleotides, followed by washing, imaging, and deblocking in preparation for a subsequent cycle. The sample library, prepared for sequencing and immobilized on the flow cell, may undergo several such cycles before all useful information is extracted from the library. The optical detection system may generate image data from scans of the flow cell (and its sites) during each cycle of the sequencing operation through the use of detection electronics (e.g., cameras or imaging electronics or chips). The resulting image data can then be analyzed to locate individual sites in the image data and to analyze and characterize the molecules present at the sites, such as by reference to a specific color or wavelength of light (a characteristic emission spectrum of a particular fluorescence marker) that was detected at a specific site, as indicated by a group or cluster of pixels in the image data at that site. In a DNA or RNA sequencing application, for example, the four common nucleotides might be represented by distinct fluorescence emission spectra (wavelengths or wavelength ranges of light). Each emission spectrum can then be assigned a value corresponding to that nucleotide. Based on this analysis, and by tracking the cycle values determined for each site, the individual nucleotides and their order can be determined for each site. These sequences can then be processed to assemble longer segments that include genes, chromosomes, and so on. As used in this application, the terms “automated” and “semi-automated” mean that operations are performed by programming or system configuration with little or no human interaction from the time the operations are initiated or when the processes, including the operations, are initiated.

[0039] In the illustrated embodiment, reagents 30 are drawn or aspirated into the flow cell through valve 32. The valve may access reagents from containers or reservoirs in which they are stored, such as through pipettes or sippers (not shown in Figure 1). Valve 32 may allow selection of reagents based on a prescribed sequence of operations performed. The valve may further receive commands to direct reagents through flow paths 34 into flow cell 20. Effluent or outlet flow paths 36 direct spent reagents from flow cell 20. In the illustrated embodiment, a pump 38 serves to move reagents through system 10. The pump may also serve other useful functions, such as metering reagents or other fluids through the system, aspirating air or other fluids, and so on. Additional valves 40 downstream of pump 38 allow for appropriate routing of used reagent to disposal containers or reservoirs 42.

[0040] The instrument 12 further includes a variety of circuits that help control the operation of the various components of the system, monitoring their operation via sensor feedback, collecting image data, and at least partially processing the image data. In the embodiment illustrated in Figure 1, a control/supervisory system 44 includes a control system 46 and a data acquisition and analysis system 48. Both systems will include one or more processors (e.g., digital processing circuits such as microprocessors, multicore processors, FPGAs, or any other suitable processing circuits) and associated memory circuits 50 (e.g., solid-state memory devices, dynamic memory devices, and/or off-board memory devices, and so on) that can store machine-executable instructions for controlling, for example, one or more computers, processors, or other similar logic devices to provide certain functionalities. Application-specific or general-purpose computers may, at least in part, comprise the control system and the data acquisition and analysis system. The control system may include, for example, circuitry configured (e.g., programmed) to process commands for fluidic, optical, stage control, and any other useful functions of the instrument. The data acquisition and analysis system 48 interacts with the optical detection system 26 to control the movement of the optical detection system 26 or the stage 22, or both, the emission of light for cyclic detection, the reception and processing of returned signals, and so forth. The instrument may also include various interfaces, in the same manner as indicated in reference 52, such as an operator interface that allows control and monitoring of the instrument 12, loading of samples, launching of automated or semi-automated sequencing operations, generation of reports, and so forth. Finally, in the embodiment of Figure 1, external networks or systems 54 may be coupled to and cooperate with the instrument 12, for example, for analysis, control, monitoring, maintenance, and other operations.

[0041] It will be appreciated that while a single flow cell and fluid path, and a single optical detection system is illustrated in Figure 1, in some instruments 12, more than one flow cell and fluid path may be accommodated. For example, in one currently contemplated embodiment, two such arrangements are provided to improve sequencing and throughput. In practice, any number of cells and flow paths may be provided. These may make use of the same or different reagent receptacles, disposal receptacles, control systems, image analysis systems, and so forth. When provided, multiple fluid systems may be individually controlled or controlled in a coordinated manner. It should be understood that the phrase “fluidically connected” or the like may be used herein to describe connections between two or more components that place such components in fluid communication with one another, much in the same manner that “electrically connected” may be used to describe an electrical connection between two or more components. The expression “fluidically interposed” can be used, for example, to describe a specific order of components. For example, if component B is fluidically interposed between components A and C, then fluid flowing from component A to component C will flow through component B before reaching component C.

[0042] Figure 2 illustrates an example fluidic system of the sequencing system of Figure 1. In the illustrated embodiment, the flow cell 20 includes a plurality of pathways or lanes 56A and 56B that may be grouped in pairs to receive fluidic substances (e.g., reagents, buffers, reaction media) during sequencing operations. Lanes 56A are coupled to a common line 58 (a first common line), while lanes 56B are coupled to a second common line 60. A bypass line 62 is also provided to allow fluids to bypass the flow cell 20 without entering it. As noted above, a plurality of reservoirs or containers 64 allow for the storage of reagents and other fluids that may be used during the sequencing operation. A reagent selector valve 66 is mechanically coupled to a motor or actuator (not shown) to allow selection of one or more of the reagents to be introduced into the flow cell. The selected reagents are then advanced to a common line selector valve 68 that similarly includes a motor (not shown). The common line selector valve 68 may be controlled to select one or more of the common lines 58 and 60, or both common lines, to cause reagents 64 to flow into lanes 56A and/or 56B in a controlled manner, or to control the bypass line 62 to flow one or more reagents through the bypass line.

[0043] The used reagents exit the flow cell through outlet lines 36 coupled between the flow cell and the pump 38. In the illustrated embodiment, the pump 38 includes a syringe pump with a pair of syringes 70 that are controlled and moved by actuators 72 to aspirate the reagents and other fluids and expel the reagents and fluids during the different operations of the test, verification, and sequencing cycles. The pump assembly may include various other parts and components, including valves, instrumentation, actuators, and so on (not shown). In the illustrated embodiment, pressure sensors 74A and 74B sense pressure in the pump inlet lines, while a pressure sensor 74C is provided to sense pressures output by the syringe pump.

[0044] Fluids used by the system enter a used reagent selector valve 76 via the pump. This valve 76 allows selection of one of multiple flow paths for used reagents and other fluids. In the illustrated embodiment, a first flow path leads to a first used reagent receptacle 78, while a second flow path leads, via a flow meter 80, to a second used reagent receptacle 82. Depending on the reagents used, it may be advantageous to collect the reagents, or some of the reagents, in separate containers for disposal, and the used reagent selector valve 76 allows this control.

[0045] It should be appreciated that the valve within the pump assembly may permit various fluids, including reagents, solvents, cleaners, air, and so forth, to be drawn into the pump and injected or bypassed through one or more of the common lines, bypass line, and flow cell. Furthermore, as noted above, in a presently contemplated embodiment, two parallel embodiments of the fluidic system shown in Figure 2 are provided under common control. Each of the fluidic systems may be part of a single sequencing instrument and may perform functions including sequencing operations on different flow cells and sample libraries in parallel.

[0046] The fluidic system operates under the command of the control system 46, which implements prescribed protocols for testing, verification, sequencing, and so forth. The prescribed protocols will be established in advance and will include a series of events or operations for activities such as aspiration of reagents, air, other fluids, and expulsion of such reagents, air, and fluids, and so forth. The protocols will allow coordination of such fluidic operations with other instrument operations, such as reactions occurring in the flow cell, imaging of the flow cell and its sites, and so forth. In the illustrated embodiment, the control system 46 employs one or more valve interfaces 84 that are configured to provide command signals to the valves, as well as a pump interface 86 configured to command operation of the pump actuator 72. Various input/output circuits 88 may also be provided to receive responses and process such responses, such as from the pressure sensor 74A-C and the flow meter 80.

[0047] Figure 3 illustrates certain functional components of the control/supervisory system 44. As illustrated, the memory circuit 50 stores prescribed routines that are executed during testing, commissioning, troubleshooting, maintenance, and sequencing operations. Many such protocols and routines may be implemented and stored in the memory circuit, and these may be updated or changed from time to time. As illustrated in Figure 3, these may include a fluid control protocol 90 for controlling the various valves, pumps, and any other fluid actuators, as well as for receiving and processing the response from fluid sensors, such as valves and flow and pressure sensors. A stage control protocol 92 allows the flow cell to be moved as desired, such as during imaging. An optical control protocol 94 allows commands to be issued to the imaging components to illuminate portions of the flow cell and to receive feedback signals for processing. An image acquisition and processing protocol 96 allows the image data to be at least partially processed to extract data useful for sequencing. Other protocols and routines may be provided on the same or different memory circuits, as indicated by reference 98. In practice, the memory circuits may be provided as one or more memory devices, such as volatile and non-volatile memory. Such memories may be within the instrument and/or off-board.

[0048] One or more processors 100 access the stored protocols and implement them in the instrument. As noted above, the processing circuitry may be part of application-specific computers, general-purpose computers, or any suitable hardware, firmware, and software platform. The processors and operation of the instrument may be controlled by human operators through an operator interface 101. The operator interface may allow for testing, commissioning, troubleshooting, and maintenance, as well as for reporting any problems that may arise in the instrument. The operator interface may also allow for the launching and monitoring of sequencing operations.

[0049] Returning to Figure 2, syringes 70 of pump 38 may aspirate used reagents from flow cell 20 via outlet lines 36. Used reagent selector valve 76 may receive used reagents and route the used reagents to one of multiple used reagent receptacles 78, 82. Although two used reagent receptacles 78, 82 are shown in Figure 2, embodiments with more than two used reagent receptacles 78, 82 are also envisioned. Since various reagents used by the instrument may have different disposal procedures, use of used reagent valve 76 to separate used reagents into multiple used reagent receptacles 78, 82 may allow disposal of the various used reagents through different means.

[0050] For example, based on a known sequencing protocol, the control system 46 may know that next a first used reagent will be pumped out of the flow cell 20 (e.g., the reagent selected by the reagent selector valve 66). The control system 46, via the valve interface 84, may actuate the used reagent select valve 76 to a first position such that the used reagent select valve 76 receives the first used reagent and routes the first used reagent to the first used reagent receptacle 78 via the first disposal pathway. As the sequencing operation proceeds according to the sequencing protocol, a second reagent may be pumped through the flow cell 20. The control system 46, via the valve interface, may actuate the used reagent selector valve 76 to a second position such that the used reagent selector valve 76 receives the second used reagent and routes the second used reagent to the second used reagent receptacle 82 via the second disposal pathway.

[0051] The second disposal pathway may include a flow meter 80 for detecting reagent flow through the second disposal pathway. It should be understood, however, that in some embodiments, the flow meter may detect reagent flow through the first disposal pathway rather than the second disposal pathway. The flow meter 80 communicates with the control system 46 via input/output circuitry 88, such that the control system 46 may consider the outputs from the flow meter 80 when determining the position of the used reagent selector valve 76. In some embodiments, the flow meter 80 may be placed upstream of the used reagent selector valve 76, but this may prevent such embodiments from being able to detect whether liquids are flowing through the correct disposal pathway. In other additional embodiments, flow meters may be installed in each disposal pathway downstream of the spent reagent selector valve 76 and may be used to directly measure flow through each disposal pathway, although this may require additional flow meters and expense.

[0052] For example, if the spent reagent selector valve 76 is assumed to be, or is indicated to be, in the first position to select the first disposal path for the first spent reagent receptacle 78, but the flow meter 80 indicates that fluid is flowing through the second disposal path, the control system 46 may cease operations and notify the operator. On the other hand, if the spent reagent selector valve 76 is in the first position to select the first disposal path for the first spent reagent receptacle 78 and the flow meter 80 indicates that fluid is not flowing through the second disposal path, then sequencing operations may continue since the fluid appears to be flowing correctly (or at least not through an incorrect flow path). Correspondingly, if the used reagent selector valve 76 is in the second position to select the second disposal path for the second used reagent container 82 and the flow meter 80 indicates that fluid is flowing through the second disposal path, then sequencing operations may continue. However, if the used reagent selector valve 76 is in the second position to select the second disposal path for the second used reagent receptacle 82, but the flow meter 80 indicates that fluid is not flowing through the second disposal path, the control system 46 may cease operations and notify the operator.

[0053] System 10 may use significantly more of one reagent than another. For example, the first reagent may represent about 1%, 2%, 3%, 4%, 5%, 8%, 10%, 15%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 85%, 90%, 92%, 95%, 96%, 97%, 98%, 99% or any other value of the total effluent volume, wherein the term “about” indicates a variation of up to 10% of the indicated values. For example, the system may use more of the second reagent than the first reagent. In such an embodiment, flow meter 80 may be coupled to the disposal path corresponding to the most used reagent. The second spent reagent receptacle 82 may be substantially larger than the first spent reagent receptacle 78, accommodating a greater volume of fluid. In other embodiments, the receptacles 78, 82 may be the same or similar sizes but be emptied at different times.

[0054] Figure 4 is a flowchart of a process 104 for operating the instrument 12 shown in Figure 1 during a sequencing operation. At 106, a sequencing protocol may be selected. As discussed above, the sequencing protocol may be selected by an operator through the interface shown in Figure 1, or remotely through external systems/networks. In other embodiments, the sequencing protocol may be selected automatically based on a pre-programmed schedule.

[0055] The sequencing operation may begin at 108 based on the selected sequencing protocol. The control system controls the instrument in performing the sequencing operation. At 110, the reagent selector valve, under the control of the control system, may select a specific reagent or set of reagents (in some embodiments, multiple reagents and/or other substances may be premixed or mixed prior to being guided through the flow cell (reference to “the reagent,” the “selected reagent,” and so forth, should be understood to include both single reagents and combinations of reagents). This selection may be based on the selected sequencing protocol. At 112, the common line selector valve and the used reagent selector valve, under the control of the control system, may select a reagent flow path through the flow cell (or bypass line) and a downstream disposal flow path, respectively. As discussed above, the common line selector valve may direct the selected reagent to the A lanes of the flow cell via the first common line, to the B lanes of the flow cell via the second common line, to the A and B lanes of the flow cell via the first common line and second common line respectively, or the common line selector valve may route the selected reagent to the bypass line to bypass the flow cell. Similarly, based on the selected reagent, the used reagent selector valve may select a disposal path such that the used reagent flows to the used reagent receptacle corresponding to the selected reagent. The used reagent selector valve may be actuated such that the used reagent received from the effluent line(s) leading to the used reagent selector valve flows along the selected disposal path to the corresponding used reagent receptacle.

[0056] At 114, a reagent is pumped through the reagent selector valve, the common line selector valve, and the common lines and through the flow cell (or, alternatively, through the bypass line). As discussed above, reagents are pumped by the pump. For example, an actuator may move the syringe plungers to draw reagents through the flow cell or bypass line into the syringes. The actuator may then move the syringe plungers in the opposite direction to expel the spent reagent through the effluent line(s) to the spent reagent selector valve. The spent reagents flow from the selected reagent path through the spent reagent selector valve and into one of the spent reagent containers via one of the disposal paths.

[0057] At 116, the flow meter may detect the flow rate of fluid along the second disposal path to the second spent reagent receptacle and may provide a signal indicative of the flow rate to the control system. At 118, the control system may determine whether spent reagent is flowing along the selected disposal path. The flow rate of fluid through the second disposal path may assist the control system in determining whether or not the spent reagent selector valve is in the selected position, as discussed previously. If spent reagent is not flowing along the selected disposal path, or if spent reagent is flowing along a disposal path that is not selected, the control system may stop operations and notify the operator (at 120). At 122, if spent reagent is flowing along the selected elimination pathway or if spent reagent is not flowing along an unselected elimination pathway, the control system may assume that the spent reagent selector valve is in the correct position and continue the sequencing operation.

[0058] For example, if the first disposal path is selected (i.e., spent reagent flows through the spent reagent selector valve along the first disposal path and into the first spent reagent receptacle), but the flow meter indicates that fluid is flowing through the second disposal path, the control system may cease operations and notify the operator. Conversely, if the first disposal path is selected (i.e., spent reagent flows through the spent reagent selector valve along the first disposal path to the first spent reagent receptacle), and the flow meter indicates that fluid is not flowing through the second disposal path, the sequencing operation will continue. Correspondingly, if the second disposal path is selected (i.e., spent reagent flows through the spent reagent selector valve along the second disposal path and into the second spent reagent receptacle), and the flow meter indicates that fluid is flowing through the second disposal path, then the sequencing operation will continue. However, if the second disposal path is selected (i.e., spent reagent flows through the spent reagent selector valve along the second disposal path and into the second spent reagent receptacle), but the flow meter indicates that fluid is not flowing through the second disposal path, the control system may cease operations and notify the operator.

[0059] At 124, the control system may determine whether the sequencing operation is complete. If the sequencing operation is complete, the system may exit process 104. If the sequencing operation is not complete, process 104 may return to 110 to select another reagent (or reagents).

[0060] Figures 5A through 5C illustrate liquid squirting into a used reagent container 126 that experiences a lateral load of 0.5G that simulates removal or transportation of container 126. However, it should be understood that 0.5G is merely an example of typical loads on container 126 during installation, removal, and transportation. Accordingly, in the application, container 126 may withstand loads less than and/or greater than 0.5G. Figure 5A shows container 126 at a time instant 0.0 seconds. As illustrated, container 126 is partially filled with spent reagent 128. The remaining volume of container 126 is filled with ambient air 130. Container 126 includes an opening 132 through which spent reagent 128 enters and exits container 126. Container 126 also includes a recess 134 defined on one side by a redirection surface 136 to prevent the splash of spent reagent 128 from exiting reservoir 126 through opening 132. A top handle 138 and a side handle 140 assist in removing and carrying container 126.

[0061] Figure 5B shows container 126 at a time instant 0.1 seconds after a 0.5 G lateral load has been applied. As shown, a wave 142 forms in spent reagent 128 and propagates toward opening 132. However, once wave 142 reaches redirecting surface 136, redirecting surface 136 redirects wave 142 away from opening 132 such that spent reagent 128 does not exit opening 132.

[0062] Figure 5C shows container 126 at a time instant 0.2 seconds after a 0.5 G lateral load has been applied. As shown, wave 142 has been redirected by redirection surface 136, forming a secondary wave 144 that propagates back through container 126 in a direction opposite to first wave 142. Accordingly, container can withstand a large amount of fluid spray during removal or transport of container 126 (e.g., to dispose of used reagent 128) without used reagent 128 exiting opening 132 of container 126. As previously described, it should be understood that the 0.5 G lateral load described is merely an example of typical handling conditions. Accordingly, container 126 may be capable of withstanding substantially more than 0.5 G without used reagent 128 exiting opening 132.

[0063] The sequencing system may flow multiple reagents through one or more flow cells in performance of a sequencing operation. The various reagents may have different characteristics from one another, such that disposal procedures may differ from reagent to reagent. Accordingly, the instrument includes a used reagent selector valve configured to direct a used reagent to an appropriate used reagent receptacle based on the reagent currently pumped through the flow cell in accordance with a sequencing protocol, such that the various used reagents may be disposed of in different manners.

[0064] In addition to being used to detect whether liquids are flowing through the correct elimination pathways, the flow meter may also be used to determine whether there are leaks in the fluid system. For example, a syringe pump may be actuated to draw a predefined quantity of fluids from one or more reagent containers, through the flow cell, and into the syringe; the syringe pump may then be actuated to expel these liquids through the elimination pathways. If the quantity of liquid that is measured by the flow meter is outside an allowable limit amount by the predefined value, an error notification may be generated to alert the user to a possible leak or other failure.

[0065] It should also be understood that the various techniques discussed above may be implemented in a diagnostic mode separately from normal analysis/processing operations. For example, after installing a flow cell cartridge and/or reagent cartridges into an analysis system, one or more (or all) of the fluidic flow paths passing through the flow cell cartridge and/or reagent cartridges may be tested using a flow meter as discussed above. For example, pre-defined quantities of reagents associated with each fluidic flow path may be pumped through the fluidic system and through the flow meter in order to measure how much of each reagent is actually delivered to the elimination paths; if the measured quantity of fluid passing through the flow meter is outside a threshold value, e.g., ±10% of the predetermined value, then the elimination path may be determined to be defective, and a notification may be generated to alert the user. Similarly, different elimination pathways may be selected during such test flows, and the flow meter may be used to determine whether fluid flow is detected in an unselected elimination pathway, as discussed earlier in this document. If this is the case, a notification may be generated to alert the user. If the diagnostic mode is completed without any errors or warnings, the apparatus may continue to be used for routine analysis. In some of these embodiments, there may be no further measurements by the flow meter, although in other embodiments, flow meter measurements may continue and may be used to determine, for example, whether there are leaks or potential failures in the elimination pathway selection.

[0066] The use, if any, of ordinal indicators, e.g., (a), (b), (c)... or the like, in this application and the claims, should be understood as not conveying any particular order or sequence, except to the extent that such order or sequence is explicitly indicated. For example, if there are three steps labeled (i), (ii) and (iii), it should be understood that these steps may be performed in any order (or even concurrently, if not contraindicated) unless otherwise indicated. For example, if step (ii) involves the manipulation of an element that is created in step (i), then step (ii) can be viewed as occurring sometime after step (i). Likewise, if step (i) involves the handling of an element created in step (ii), the reverse should be understood.

[0067] It should also be understood that the use of the word "for", e.g., "a valve for switching between two flow paths", may be replaceable by language such as "configured for", e.g., "a valve configured to switch" between two flow paths", or the like.

[0068] Terms such as “about,” “approximately,” “substantially,” “nominal,” or the like, when used in reference to similar quantifiable quantities or properties, should be understood to include values within ± 10% of the specified values, unless otherwise indicated.

[0069] In addition to the claims listed in this application, the following additional embodiments are to be understood as incorporated within the scope of this application:

[0070] Embodiment 1: A system including: a flow cell through which a plurality of reagents are pumped during a genetic sequencing operation; an effluent line that, in operation, carries a spent reagent; a spent reagent valve configured to receive the spent reagent from the effluent line and is controllable to select one of a plurality of elimination pathways for the spent reagent; and control circuitry coupled to the spent reagent valve that, in operation, controls the spent reagent valve to select one of the desired elimination pathways depending on which reagent is being pumped through the flow cell.

[0071] Embodiment 2: The system of embodiment 1, which includes a flow meter that, in operation, shall detect the flow of reagent and provide flow data to the control circuit.

[0072] Embodiment 3: The system of embodiment 2, wherein the flow meter is coupled to one of the elimination pathways, and wherein the control circuit must determine whether the desired pathway and flow is appropriately selected based on the response of the flow meter.

[0073] Embodiment 5: The system of embodiment 3, wherein a first elimination pathway transmits more used reagent than a second elimination pathway during the sequencing operation, and wherein the flow meter is coupled to the first elimination pathway.

[0074] Embodiment 6: The system of embodiment 1, wherein the control circuit is to control the reagent waste valve based on a sequencing protocol prescribed for a genetic sequencer.

[0075] Embodiment 7: The system of embodiment 6, including at least one valve for selecting a reagent and a reagent elimination pathway, and wherein the control circuitry is to control the at least one valve and the reagent valve used based on the prescribed sequencing protocol.

[0076] Embodiment 8: The system of embodiment 7, which includes a reagent pump disposed between the reagent disposal pathway and the effluent line.

[0077] Embodiment 9: The system of embodiment 1, including a first reagent container used to receive effluent from a first disposal pathway and a second reagent container for receiving effluent from a second disposal pathway.

[0078] Embodiment 10: The system of embodiment 1, wherein the first used reagent container will direct fluid to be directed outward from an opening of the first used reagent container when fluid is displaced during removal or transport of the first used reagent container.

[0079] Embodiment 11: A system including: a flow cell through which a plurality of reagents are pumped during a genetic sequencing operation; at least one reagent valve for selecting a reagent and a reagent flow path, at least one of the reagent flow paths passing through the flow cell; an effluent line that, in operation, is to carry spent reagent; a spent reagent valve configured to receive spent reagent from the effluent line that is controllable to select one of a plurality of disposal paths for the spent reagent; and control circuitry coupled to the at least one reagent valve and the spent reagent valve, the control circuitry, in operation, controlling the at least one reagent valve and the spent reagent valve based on a sequencing protocol prescribed for genetic sequencing operation.

[0080] Embodiment 12: The system of embodiment 11, wherein the control circuit, in operation, shall select one of the desired elimination pathways, depending on which reagent is being pumped through the flow cell.

[0081] Embodiment 13: The system of embodiment 11, including a flow meter that, in operation, must detect reagent flow and provide flow data to the control circuit.

[0082] Embodiment 14: The system of embodiment 13, wherein the flow meter is coupled to one of the elimination pathways, and wherein the control circuit determines whether the desired flow pathway is properly selected based on the response of the flow meter.

[0083] Embodiment 15: The system of embodiment 14, wherein a first elimination pathway transmits more used reagent than a second elimination pathway during the sequencing operation, and wherein the flow meter is coupled to the first elimination pathway.

[0084] Embodiment 16: A method including: performing a genetic sequencing operation by pumping a plurality of reagents through a flow cell; during the genetic sequencing operation, controlling at least one reagent selector valve to select desired reagents to be pumped through a flow cell in accordance with a protocol for genetic sequencing operation; and controlling a spent reagent valve, during the genetic sequencing operation, to select one of a plurality of elimination pathways for the spent reagent after being pumped through the flow cell based on the protocol for genetic sequencing operation.

[0085] Embodiment 17: The method of embodiment 16, including detecting flux through at least one of the elimination pathways to verify that a desired elimination pathway is appropriately selected based on the protocol for genetic sequencing operation.

[0086] Embodiment 18: The method of embodiment 17, wherein flow is detected by a flow meter coupled to one of the elimination pathways, and wherein the control circuitry is to determine whether the desired flow pathway is properly selected based on the response of the flow meter.

[0087] Embodiment 19: The method of embodiment 18, wherein a first elimination pathway is expected to carry more used reagent than a second elimination pathway during the sequencing operation, and wherein the flow meter is coupled to the first elimination pathway.

[0088] Embodiment 20: The method of embodiment 16 including collecting used reagent in at least two different containers is based on which elimination pathway is selected.

[0089] It should be appreciated that all combinations of the foregoing concepts (so long as such concepts are not mutually inconsistent) are contemplated as being part of the disclosed subject matter. All combinations of the claimed subject matter appearing at the end of this disclosure are contemplated as being part of the inventive subject matter disclosed herein. It should also be appreciated that terminology explicitly employed herein, which may also appear in any application incorporated by reference, should be given a meaning most consistent with the particular concepts disclosed herein.

Claims (10)

1. A system comprising: one or more effluent flow paths (36) for fluidly connecting to a flow cell (20) through which a plurality of reagents (30) are to be pumped during a genetic sequencing operation, wherein the one or more effluent paths are to receive used reagents from the flow cell; one or more pumps (38) for pumping used reagents through the effluent flow paths; a reagent selector valve (76) for receiving used reagents from the one or more pumps through an effluent line and controllable to select one of the disposal paths for the used reagents; a flow meter (80) fluidly coupled to one of the elimination pathways, the flow meter for detecting the flow of reagents used and measuring how much of each reagent is delivered to a measured elimination pathway wherein if the measured amount of fluid passing through the flow meter is outside a threshold amount of a pre-detergent amount an alert notification is produced; control circuitry operatively coupled to the spent reagent selector valve and the flow meter, the control circuitry having one or more processors and a memory for storing machine executable instructions that, when executed by the one or more processors, control the one or more processors to cause the spent reagent selector valve to select a desired one of the plurality of waste paths depending on which spent reagent is being pumped through the effluent flow paths, and to determine that spent reagents are not flowing through the desired one of the plurality of waste paths based on the detected flow state and to provide a notification based on the determination that spent reagent is not flowing through the desired one of the plurality of waste paths; and used reagent vessels, each used reagent vessel must receive used reagent from a respective disposal path of the plurality of disposal paths and direct, by means of a redirection surface therein, fluid therein to be directed away from an opening of the used reagent vessel when the fluid is moved during removal or transportation of the used reagent vessel, to prevent used reagent from exiting the used reagent vessel through the opening. 2. The system of claim 1, wherein a first elimination pathway of the elimination pathways transmits more used reagent than a second elimination pathway of the elimination pathways during the sequencing operation, and wherein the flow meter is coupled to the first elimination pathway. 3. The system of claim 1, wherein the memory is for storing machine-executable instructions that, when executed by one or more processors, additionally control one or more processors to control the reagent selector valve used based on a sequencing protocol prescribed for a genetic sequencer. 4. The system of claim 3, further comprising at least one valve (66) for selecting a reagent and a reagent flow path, and wherein the memory shall store machine executable instructions that, when executed by one or more processors, further control the one or more processors to control the minimum valve and the reagent selector valve used based on the prescribed sequencing protocol. 5. The system of claim 4, further comprising a reagent pump fluidly interposed between the reagent flow path and the effluent line. 6. A system for collecting effluents, comprising: a flow cell through which a plurality of reagents are pumped during a genetic sequencing operation to produce spent reagents; at least one reagent selector valve for selecting a reagent and a reagent flow path from a plurality of reagent flow paths, at least one of the plurality of reagent flow paths passing through the flow cell; an effluent line that, in operation, is to carry the spent reagent; a spent reagent selector valve for receiving the spent reagent from the effluent line and controllable to select one of a plurality of waste paths for the spent reagent; a flow meter (80) fluidly coupled to one of the plurality of waste paths, the flow meter for detecting a flow state of the spent reagents; and control circuitry operatively coupled to at least one reagent selector valve, the spent reagent selector valve, and the flow meter, the control circuitry having one or more processors and a memory for storing machine executable instructions that, when executed by the one or more processors, control the one or more processors to control the at least one reagent selector valve and the spent reagent selector valve based on a sequencing protocol prescribed for the genetic sequencing operation and to determine whether spent reagents are not flowing through the desired one of the plurality of waste paths based on the detected flow state and to provide a notification based on the determination that spent reagent is not flowing through the desired one of the plurality of waste paths; and at least two spent reagent vessels, each spent reagent vessel must receive spent reagent from a respective waste path of the plurality of waste paths and direct, by a redirection surface therein, fluid to be directed away from an opening of the spent reagent vessel when the fluid is moved during removal or transport of the spent reagent vessel, to prevent spent reagent from exiting the spent reagent vessel through the opening. 7. The system of claim 6, wherein the flowmeter is coupled to one of the plurality of disposal paths and wherein the memory is for storing further machine executable instructions that, when executed by the one or more processors, further control the one or more processors to determine whether spent reagents are flowing through the desired disposal path based on feedback from the flowmeter. 8. The system of claim 1 or 7, wherein a first waste path of the plurality of waste paths transports more used reagent than a second waste path of the plurality of waste paths during the sequencing operation and wherein the flow meter is fluidly coupled to the first waste path. 9. A method comprising: performing a genetic sequencing operation by pumping a plurality of reagents (30) through the flow cell (20) of the system according to any one of claims 1 to 7 to produce used reagents; during the genetic sequencing operation, controlling at least one reagent selector valve (66) to select desired reagents to be pumped through the flow cell in accordance with a protocol for the genetic sequencing operation; during the genetic sequencing operation, controlling the used reagent selector valve (76) to select one of the elimination pathways for the used reagents after the used reagents exit the flow cell, controlling the used reagent selector valve using the protocol for the genetic sequencing operation; detecting, using a flow meter fluidly coupled to one of the plurality of waste paths, a flow state of used reagents through at least one of the plurality of waste paths to verify that used reagents are flowing through the selected one of the plurality of waste paths; determining that used reagents are not flowing through the selected waste path based on the detected flow state; and providing a notification based on the determination that used reagents are not flowing through the selected waste path; receiving, in each used reagent container of at least two used reagent containers, used reagent from a respective waste path of the plurality of waste paths, and directing, by means of a redirection surface, fluid contained therein to be directed away from an opening of the used reagent vessel when fluid is moved during removal or transport of the used reagent vessel, to prevent used reagent from exiting the used reagent vessel through the opening. 10. The method of claim 9, wherein a first elimination pathway of the elimination pathways transmits more used reagent than a second elimination pathway of the elimination pathways during the sequencing operation, and wherein the flow meter is fluidically connected to the first elimination pathway.