Systems and methods for automated reagent validation

Abstract

A method for user-guided startup of an instrument includes: receiving an operation plan via a user interface of the instrument; indicating consumables to be provided to the instrument on the user interface based on the operation plan; detecting the presence of the consumables using a visual system; and indicating the presence of the consumables via the user interface.

Description

[0001] CROSS-REFERENCE TO RELATED APPLICATIONS

[0002] This application claims the benefit of U.S. Provisional Application No. 62 / 719,085, filed on August 16, 2018, which is incorporated herein by reference in its entirety.

[0003] This application claims the benefit of U.S. Provisional Application No. 62 / 855,643, filed May 31, 2019, which is incorporated herein by reference in its entirety. Technical Field

[0004] The present disclosure generally relates to automated monitoring of preparation tasks and validation of appropriate reagents for use in nucleic acid sequencing instruments to generate sequencing runs. Background Art

[0005] As medical science advances, new tests are developed to determine the root causes of disease, drug efficacy, and advanced immunology. In particular, tests involving gene sequencing provide more refined answers to such questions. However, such tests are often complex and expensive.

[0006] Conversely, there is increasing pressure to reduce drug costs despite the need for complex and expensive tests. This has increased the drive to provide integrated and automated instruments into clinical settings. However, the more complex the test, the more reagents and other consumables are provided for the test within the instrument, increasing the potential for human error and the costs associated with invalid tests. BRIEF DESCRIPTION OF THE DRAWINGS

[0007] The present disclosure may be better understood, and its numerous features and advantages made apparent to those skilled in the art by referencing the accompanying drawings.

[0008] Figure 1 Includes illustrations of example instruments.

[0009] Figure 2 Included is a diagram of an example deck of the instrument.

[0010] Figure 3 Included is an illustration of an example reagent reservoir for the instrument.

[0011] Figure 4 Includes a diagram of the example system used to perform the testing.

[0012] Figure 5 Includes illustration of example methods used to start instrumentation in preparation for running a test.

[0013] Figure 6 Illustration of the coverage area of ​​an example camera including one within a vision system.

[0014] Figure 7Included is a block flow diagram of an example method for starting an instrument to run a test.

[0015] Figure 8 Included is a block flow diagram of an example method for starting an instrument to run a test.

[0016] Fig. 9 and Fig.10 Includes the instance image associated with launching the instrument.

[0017] Fig.11 Includes illustrations of example consumables.

[0018] Fig.12 Included is an example picture of what the instrument deck looks like when the instrument is powered on.

[0019] Fig.13 A block flow diagram illustrating an example method for starting an instrument is included.

[0020] Fig.14 Included is an illustration of a portion of the instrument deck when starting the instrument.

[0021] Fig.15 and Fig.16 Included is an image of an example deck of the instrument.

[0022] Fig.17 A block flow diagram illustrating an example method for aligning a camera of a vision system is included.

[0023] Fig.18 Includes a picture of the example video stream used to align the camera with the instrument.

[0024] Fig.19 Included is an illustration of a block flow diagram showing an example method for starting an instrument.

[0025] Fig. 20 and Fig.21 Includes illustrations of example consumables associated with the instrument.

[0026] Figure 22 to Figure 93 Included is an illustration of an example screenshot associated with launching an instrument for running a test.

[0027] Fig.94 Included is a diagram of an example sequencing system.

[0028] Fig.95 Included are diagrams of example systems that include sensor arrays.

[0029] Fig.96 Included is a diagram of an example sensor and associated holes.

[0030] Fig.97Included are illustrations of example methods for preparing sequencing devices.

[0031] The use of the same reference numbers in different drawings indicates similar or identical items. DETAILED DESCRIPTION

[0032] In an embodiment, a visual system is used in an instrument such as a sequencing instrument to help a user prepare the instrument to run a test. The visual system can help a user detect the correct positioning and supply of consumables, such as reagent strips, pipette tips, microwell arrays, or other consumables associated with the test. In particular, the visual system can check to see that the consumables are locked in place and identified as the correct consumables associated with the running plan of the test. In addition, the visual system can detect used reagent containers and guide the user to properly remove such used containers according to a predetermined running plan. The system can also include other consumable detection systems, such as radio frequency identification (RFID) detection systems. Such systems are particularly suitable for integrated sequencing equipment.

[0033] Figure 1 An illustration of an example instrument 100 incorporating a three-axis liquid handling robot is included. In an example, the instrument 100 can be a sequencer incorporating a sample pre-preparation platform. For example, the instrument 100 can include an upper portion 102 and a lower portion 104. The upper portion can include a door 106 to access a deck 110 on which samples, reagent containers, and other consumables are placed. The lower portion can include a cabinet for storing additional reagent solutions and other components of the instrument 100. In addition, the instrument can include a user interface, such as a touch screen display 108.

[0034] In a specific example, the instrument 100 can be a sequencing instrument. In some embodiments, the sequencing instrument includes a top section, a display screen, and a bottom section. In some embodiments, the top section can include a platen support component for the sequencing instrument and consumables, and the consumables include a sample preparation section, a sequencing chip, and a reagent strip tube and a carrier. In some embodiments, the bottom section can accommodate reagent bottles and waste containers for sequencing.

[0035] In some embodiments, one or more cameras mounted in a cabinet in the top section of the instrument are oriented toward the platen to monitor which items are in place when preparing for sequencing runs. The camera can acquire video or images at time intervals. For example, images can be acquired at intervals of 1 to 4 seconds or at any suitable interval. In another example, frames of a video stream can be extracted at intervals such as in a range of 0.5 seconds to 4 seconds. A computer or processor analyzes the image to detect that the user has completed a task. The computer or processor can provide feedback and instructions for the next task in preparation via a display screen. The display screen can present a graphical representation of instrument components and consumables to show instructions to the user.

[0036] Example instrument panel 110 in Figure 2 200. The deck is contained in the top section of the instrument in the view of one or more cameras. The sample preparation deck may include multiple positions configured to accommodate reagent strips, supplies, sequencing chips, and other consumables. As used herein, consumables are components used by the instrument that are regularly replaced during use. For example, consumables include reagent and solution strips or containers, pipette tips, microwell arrays and flow cells and associated sensors, and other disposable components that are not part of the permanent components of the instrument.

[0037] In an example, system 200 includes a pipetting robot 202 that accesses various reagent strips and containers, pipette tips, microwell arrays, and other consumables to implement testing. In addition, the system may include a mechanism 204 for performing the test. Example mechanism 204 includes a mechanical conveyor or slide and a fluid system.

[0038] In an example, the deck 200 includes a tray 206 or 208 to hold a solution or reagent strip in a particular configuration. In the example of a sequencing instrument, the tray 206 can be used for library and template solutions in appropriately configured strips, and the tray 208 can hold library and template reagents in an appropriately configured manner.

[0039] In addition, the instrument can be configured to accommodate microwell arrays 210 and 212 at specific locations on the deck. For example, samples can be provided in a hole array such as microwell array 212. In another example, the system can be configured to accommodate additional reagents 214 in different strip configurations. In another example, reagent solutions can be provided in array 216. In yet another example, container array 220 can be provided with instrumentation such as a thermal cycler. In addition, the system can include other instrumentation, such as a centrifuge, which can be provided with consumables such as tubes. In addition, a tray can be provided to accommodate pipette tips 222.

[0040] The appropriate supply of consumables in each of these positions can be monitored by a visual system including one or more cameras. The platen can be provided with one or more cameras to track the supply and fixation of reagents and other consumables. When the reagent for executing a plan is missing or when the reagent consumables are present in a use state, the user can be prompted by the user interface.

[0041] Figure 3An illustration of a reagent storage cabinet 104 for storing larger volume reagents and solution containers is included. For example, the cabinet storage 104 includes an interface 302 for accommodating a reagent kit. In another example, the storage 104 can provide space for a container 304 or 306. In yet another example, the storage 104 can include space for a waste container 308. As an alternative to a visual system, the reagent storage area 104 can utilize an RFID tag and a detector to determine whether a reagent container is present.

[0042] Figure 4 Included are illustrations of exemplary systems for interfacing with instrumentation and instrumentation. In the examples, Figure 4 A computing system 400 is shown. For example, the system 400 may include a management module 402 in communication with a vision module 404, a control module 406, a sequencing module 408, a reporting module 410, and optionally an RFID module 420. The management module 402 works with various other modules 404, 406, 408, 410, or 420 to implement a run plan. The run plan includes identification of one or more tests and associated parameters.

[0043] The vision module 404 can interact with the camera 412 to collect images that are analyzed to determine whether the instrument has been properly provided for the established operation plan. In an example, the vision module 404 can collect pictures from the camera 412. In another example, the vision module 404 collects frames of a video captured by the camera 412. In particular, frames can be extracted from the video stream at least every second, two seconds, or five seconds. The vision module 404 can detect the presence of consumables. In addition, the vision system can detect whether the consumable has been used or is about to be replaced.

[0044] The vision module 404 can use various techniques to determine the presence of consumables and their usage status. For example, the vision module 404 can use heuristics to compare one or more pixels with expected values. In another example, the vision module 404 can use artificial intelligence, such as a neural network trained to detect features on the instrument plate.

[0045] The control module 406 can interact with various device interfaces 416 to implement tests according to the run plan managed by the management module 402. For example, the control module 406 can interface with a three-axis pipetting robot to implement parts of the run plan. In another example, the control module can interact with other instruments associated with the instrument deck, such as a centrifuge, a thermal cycler plate, a magnetic separator, or a microfluidic circuit.

[0046] The system 400 can further include an RFID module 420 that can interact with the RFID antenna 418 to determine the presence of a larger volume container having an RFID tag. The system 400 can further track the amount of solution used from the container or sent to the container to determine whether the remaining volume is sufficient to complete the proposed run plan.

[0047] In the case of a sequencing instrument, the system 400 may further include a sequencing module 408 that interacts with the instrument to collect sequencing data. In addition, the system may include a reporting module 410 to further process the sequencing data and provide useful reports to the user, such as variant call reports.

[0048] To interact with the user, the system may further include a user interface 414 such as a computer screen, mouse, keyboard or touch screen to interact with the user during run planning, instrument setup and result reporting. In an example, the user interface interacts with the user to guide the user to provide and clear the instrument.

[0049] Figure 5 An illustration of an example method 500 for starting an instrument is included. For example, by using a vision system, the system can detect the presence of used consumables, as shown in block 502. In particular, the vision system can detect that the foil has been pierced. In another example, the system can recognize a barcode of the sample and determine that the consumable has been used in a previous run. In another example, an RFID system can be used to detect consumables and track consumables to determine if they have been used.

[0050] If consumables are present, as shown in box 504, the presence can be indicated on the user interface, as shown in box 506. In particular, the presence can be indicated on a touch screen. For example, the presence of used consumables to be removed can be indicated using a flashing icon above a background that shows the deck or storage area of ​​the instrument. Alternatively, an audible or tactile indication can be used to indicate the presence. The process can be repeated until all used consumables have been removed from the device. At this point, the door of the instrument can be closed, as shown in box 508, and the instrument can initiate cleaning, as shown in box 510. For example, the internal deck can be exposed to ultraviolet light or a cleaning solution.

[0051] As shown in block 512, the system can receive a run plan for performing one or more specific tests. Alternatively, the system can receive the run plan before detecting the presence of used consumables. A given run plan or test uses a specific number and type of solutions and reagents and other consumables. Therefore, the system determines which consumables will be provided for the run plan, as shown in block 514.

[0052] As shown in box 516, the presence of consumables for executing the run plan is detected. When the desired consumables do not exist, as shown in box 518, the system can indicate that they do not exist, as shown in box 520. For example, the system can prompt the user to locate specific consumables and apply the consumables to a specified location on the instrument platform. In an example, the consumables to be supplied are named and shown in a diagram of the location where the consumables are placed. For the consumables under the platform, the system can alternatively use RFID to detect their presence, and prompt the user to add missing reagents or solutions. When all consumables for executing the run plan exist, the instrument can perform the run, as shown in box 522.

[0053] exist Figure 6 In the example shown, the visual system can include one or more cameras designated for observing portions of the platen 200. For example, camera 602 can observe a portion of the platen for specific consumables. In another example, camera 604 can observe reagent trays and solution trays. In yet another example, camera 606 can observe locations designated for providing unused pipette tips and various microwell arrays. In addition, the angle of camera 606 can be angled so as to observe and read codes displayed on the edge of the microwell array, such as bar codes or QR codes.

[0054] In the example, Figure 7 A method 700 for starting an instrument to prepare for operation is shown. In particular, for consumables that can be used for multiple runs, the system detects whether a sufficient number of solution containers are available to complete a given operation plan. For example, as shown in block 702, the system can detect a used container in a container group. The system can then determine the number of unused containers, as shown in block 704. The system can compare the number of unused containers with the operation plan, as shown in block 706. If a sufficient number of containers are not found, as shown in block 708, the system can indicate that the consumables are ready to be replaced, as shown in block 710. If there are a sufficient number of unused containers to run a given operation plan, the system can continue the startup method, as shown in block 712.

[0055] In particular, the comparison of pixel values ​​can be used to perform the detection of used containers. In another example, the vision system can be trained to determine or detect unused containers or used containers using artificial intelligence methods such as neural networks.

[0056] Figure 8 An illustration of a method 800 for determining that a particular consumable is present and secured is included. For example, as shown in block 802, the system can detect the presence of a consumable. In an example, the consumable can have a code, such as a barcode or QR code, that can be read by a vision system to determine that the correct consumable is in place.

[0057] If the consumable has an associated latch to fold the consumable so as to hold the consumable in place, the system can detect whether the latch is closed, as shown in block 804. In an example, the latch can include a symbol, indicator, or dot printed on the top surface of the latch. Based on the presence of the symbol or their number, the system can determine whether the latch is closed or open. For example, the latch can have three indicators, such as dots, on the top surface of the latch. When the vision system detects three dots, the latch is closed.

[0058] If the latch is not closed, the system may indicate to the user via the user interface that the latch is open, as shown in block 806. If the latch is closed, the system may determine whether the latch is locked, as shown in block 808. In an example, a locked latch may add a symbol or indicator for visual system detection. In another example, a locked latch hides the symbol or indicator. In the example of three dots, the lock may hide one of the dots. Thus, if there are three dots, the latch is closed and unlocked. When there are two dots, the latch is closed and locked.

[0059] If the latch is not locked, the system can indicate that the latch is not locked, as shown in block 810. If the latch is locked, the system can continue initialization, as shown in block 812.

[0060] Fig. 9 An illustration of an example image taken in association with a consumable 902 is included. For example, the consumable 902 has a group of containers. A subset of containers 904 has been used, while a different subset of containers 906 remains unused. For example, the system can detect that the foil has been pierced on a subset of containers 904 that have been used. When the latch 908 is located above the consumable 902, there may be an indicator readable by the visual system to determine that the latch is closed. For example, the system can observe three dots 910 in a row, indicating that the latch is in place or closed. When there is no latch locked, three dots may appear. When the latch is closed and locked, the clip 912 can block one of the indicators or dots 910. Therefore, when the latch is not in place, no dots appear. When the latch is in place and not locked, there are three dots. When the latch is positioned and locked, two dots appear.

[0061] exist Fig.10 In another example shown, a slot 1002 for accommodating a reagent strip is provided. A slide lock 1004 can secure the reagent strip in place. A visual system can detect the position of an indicator, such as indicator 1006, to determine whether the slide lock is in place or open.

[0062] exist Fig.111002 is shown in an example consumable such as a solution or reagent strip configured to fit in a slot 1002. In the example, the strip includes a base 1102 and a top 1104 coupled to the base 1102. The top 1104 includes a window 1106 that allows access to the hole 1110 or 1112. Optionally, the top 1104 can provide a window 1108 to allow access to a tube 1114 inserted into a tube holder of the base 1102.

[0063] The top portion may further include a handle 1116. For example, the handle 1116 may be used to hold the reagent container 1100 when inserting or removing the reagent container 1100 from the analytical device. In addition, the top portion 1104 may define an end structure 1118 or 1120 configured to engage a complementary structure on the instrument and limit the orientation of the strip relative to the position within the instrument. In addition, a code 1122 such as a bar code or a QR code may be present on the top portion 1104.

[0064] In particular, the vision system can detect the relative position of the indicator to determine whether the sliding lock is open or closed. Fig.12 As shown, slide lock 1204 is in an open position and slide lock 1210 is in a closed position. In the open position, consumables such as solutions or reagent strips can be applied to position 1202. As shown, when slide lock 1210 is in the locked position, an indicator such as dot or symbol 1206 on slide lock 1210 is positioned further into the instrument than dot or symbol 1208 on slide lock 1204.

[0065] like Fig.13 As shown, method 1300 includes detecting the presence of a consumable, as shown in block 1302. When the consumable is not present, as shown in block 1304, the system can indicate the absence of the consumable through a user interface, as shown in block 1306. For example, the absence can be determined based on features detected by a vision system. The features can include, for example, a symbol indicating the absence of the consumable that will be covered when the consumable is present. When the consumable is present, different indicator symbols and codes such as bar codes or QR codes can be present.

[0066] Certain consumables may further include or be supplied with a lid. As shown in block 1308, the system may determine whether the lid is open. If the lid is open, the system may indicate the presence of the lid, as shown in block 1310. If the lid is not open, the system may continue to boot, as shown in block 1312.

[0067] For example, Fig.14As shown, the platen may include a slot 1402 to accommodate consumables such as two-container consumables. When the consumables are not present, a symbol or dot 1408 may be seen that would be covered if the consumables were present. For example, when the consumables are present, consumable 1404 or consumable 1406 blocks the view of the symbol or dot 1408. As shown at 1410, a different symbol (e.g., a line) or the absence of a symbol may indicate the presence of a consumable. The vision system may detect the presence of a symbol or dot or the absence of such a symbol or dot to determine whether the consumable is present.

[0068] When this consumable is provided with a lid 1412, the system can determine that the lid is open and guide the lid to be removed. In particular, the lid can have a symbol readable by a visual system. In another example, the pixel values ​​can be compared to determine whether the lid is open or closed. In another example, the system can be trained with artificial intelligence to detect the presence 1412 of the lid or the absence 1414 of the lid.

[0069] In yet another example, as shown at 1416, the vision system can detect the presence of a consumable such as an array based on an ordered sequence of symbols such as letters or numbers.

[0070] Fig.15 and Fig.16 Further included are graphical representations for detecting the presence or absence of consumables. For example, for a pipette tip tray, a location 1502 for accommodating the tray may include an indicator 1504, such as a dot or hidden screw, detectable by a vision system. Similarly, empty holders 1506 and 1508 for accommodating microwell arrays may be detected based on the absence of the consumables by, for example, determining the absence of consumables using the presence of symbols that would block the consumables or image processing or artificial intelligence.

[0071] like Fig.16 As shown, when the pipette tip tray 1602 is in place, the indicator 1504 is hidden. Similarly, the system can determine when microwell arrays 1604 and 1608 are present based on the presence or absence of markings associated with the holders 1506 or 1508. In addition, the system can read a code such as a barcode 1606 or 1610 to determine that the microwell array is in the correct position and is the correct type.

[0072] Fig.17 An illustration of an example method 1700 for aligning a camera system is included. The method 1700 includes detecting features in an image, as shown in block 1702. These features can be indicators, symbols, or points, such as those described above. In another example, the features can be various aspects or geometric shapes of an instrument deck imaged by a camera aligned with the deck.

[0073] As shown in block 1704, the system can determine where the feature would appear in a given image. In other words, the feature has an expected location within the given image and can be detected at a location different from the expected location. When the feature is not aligned with the location where the feature appears in the given image, as shown in block 1706, the system can indicate the lack of alignment, as shown in block 1708. For example, as the technician attempts to align the detected feature within the image with the expected location of the feature within the image, the process can be repeated, as shown in block 1710.

[0074] For example, Fig.18 As shown, the feature can be identified and the area around the detected feature 1802 can be indicated on the user interface. The system can further draw the expected location of the feature within the image 1804. In practice, the frame can be extracted from the real-time video, or the real-time video can be displayed on the user interface with overlapping circles. Therefore, the technician can aim the camera so that the feature location overlaps with its expected location within the image overlap. In another example, the camera can be adjusted based on whether the camera can read the code 1806 on the consumable side.

[0075] In certain embodiments, radio frequency identification (RFID) tags can be attached to reagent bottles and nucleotide boxes. RFID sensors can be located at the bottom section communicating with a computer or processor. RFID sensors can detect the presence of specific reagent bottles and nucleotide boxes. Computers or processors can analyze the information about reagent bottles and nucleotide boxes detected from RFID sensors, and provide feedback information to users via display screens.

[0076] exist Fig.19 In another example shown, the method 1900 for starting the instrument includes detecting the presence of consumables, as shown in block 1902. In particular, the consumables can be detected based on the RFID code of the consumables. In the case of a larger volume container for more than one run, the system can track its use and determine whether it will be replaced. For example, the system can determine the presence of consumables, as shown in block 1904. When the consumables do not exist, the system can, for example, use a flashing or alternatively colored icon on the user interface to indicate that it does not exist, as shown in block 1906.

[0077] For the consumables detected, the system can determine whether the consumable has sufficient remaining volume after the previous run to meet the usage of the current run plan, as shown in block 1908. When there is insufficient volume, the system can indicate that there is a problem, such as shown in block 1910, so that the consumable is replaced. If the consumable has sufficient volume, the system can continue its startup, as shown in block 1912.

[0078] For example, Fig. 20The apparatus includes an illustration of example consumables within a reagent reservoir of the apparatus. For example, box 2002 includes various reagent containers 2004 for activating the apparatus. Fig.21 As shown, bottle 2102 includes a fluid interface 2104 for connection to the instrument. The system can track the volume of previous runs to determine if sufficient volume remains in a container such as container 2102, or if the reagents of cartridge 2002 are to be replaced.

[0079] Figure 22 to Figure 93 are examples of graphical displays that may be presented to a user on a display screen. These graphical displays guide the user through a series of steps to prepare the instrument for, for example, a sequencing run.

[0080] Figure 22 to Figure 24 Shown is an example of a display associated with selection of the type of sequencing run to be prepared as part of a proposed run plan. Fig.23 Several examples of operating plans that may be selected by a user are shown.

[0081] Fig.25 An example of a graphical display instructing a user to open a door of a deck located in the top section of a sequencing instrument is shown, as shown in FIG. Figure 1 shown.

[0082] Fig.26 Shown include Figure 2 An example of a graphical display of a deck of the top section of the top templated section is shown. In the event that the vision system does not detect a used consumable, the system indicates that the deck is clean.

[0083] In the event that the vision system detects a used consumable, Figures 27 to 40 An example of a graphical display and instructions for instructing a user to remove used parts of a templated section is shown. For a particular step, each item to be removed is highlighted in the display. Each display screen is automatically displayed in response to detecting an action by a user or a human error in the procedure.

[0084] Fig.41 An example of a graphical display instructing a user to close a deck door is shown. Fig.42 and Fig.43 An example of a graphical display that informs a user about an ultraviolet (UV) cleaning of a platen and when the cleaning is complete is shown.

[0085] Fig.44 An example of a graphical display instructing the user to open the door of the deck is shown. This will begin a series of tasks to prepare the instrument for a new sequencing run.

[0086] Figures 45 to 62An example of a graphical display and instructions for instructing a user to install components to a deck is shown. For a particular step, each item to be installed is highlighted in the display. Each display screen is automatically displayed in response to detecting a user's action or human error in the procedure using the vision system. Fig.63 An interface is shown that guides the user to lock the consumable in place. The vision system can detect whether the consumable is locked in place based on detecting the position of the locking mechanism or associated symbol.

[0087] Fig.64 An example of a graphical display indicating to the user that deck setup is complete is shown. Fig.65 An example of a graphical display instructing a user to close a deck door is shown.

[0088] Fig.66 An example of a graphical display instructing a user to open a sequencing reagent compartment door of a bottom section of a sequencing instrument is shown, Figure 3 shown.

[0089] Figures 67 to 70 An example of a graphical display and instructions for instructing a user to remove a used bottle from a reagent storage compartment is shown. For a particular step, each bottle to be removed is highlighted in the display. Each display screen is automatically displayed in response to detecting a user's action or human error in the procedure, such as using RFID detection or a weighing scale.

[0090] Fig.71 An example of a graphical display instructing a user to remove a used sequencing reagent cartridge or nucleotide cartridge is shown.

[0091] Fig.72 An example of a graphical display instructing a user to empty a waste carboy located in a reagent compartment is shown.

[0092] Figure 73 to Figure 77 An example of a graphical display and instructions for instructing a user to install a waste carboy and a new reagent bottle into a reagent compartment is shown. For a particular step, each new item to be installed is highlighted in the display. Each display screen is automatically displayed in response to, for example, a user's action or a human error in the procedure detected by an RFID.

[0093] Fig.78 An example of a graphical display instructing a user to install a new sequencing reagent kit or nucleotide box is shown. In some embodiments, RFID tags on installed bottles and nucleotide boxes can be detected to verify the presence of correct reagents and nucleotide boxes.

[0094] Fig.79 An example of a graphical display informing the user that all reagents have been installed is shown.

[0095] Fig.80An example of a graphical display is shown instructing the user to close the door of the reagent compartment and press the start run button.

[0096] The display can further be used to indicate the progress of the various steps of the operational plan. For example, Fig.81 An example of a graphical display informing a user of the progress of library preparation is shown. Fig.82 An example of a graphical display that informs a user of the progress of a template is shown. Fig.83 An example of a graphical display informing the user of the progress of sequencing is shown. In addition, Fig.84 An example of a graphical display notifying a user that a sequencing run is complete is shown.

[0097] In another example, a method for loading and unloading reagent containers or consumables from a system may include monitoring which containers or device consumables are inserted and suggesting which containers and device consumables to remove in what order. Figures 85 to 93 An example method for following the progress of system loading and unloading using machine vision is shown. Fig.85 As shown, the user interface instructs the user to open the door of the system.

[0098] When the door is detected to be open, the user can be instructed to load the parts, e.g. Fig.86 For example, the system can highlight the parts to be loaded. As the parts are loaded, the system can show which parts are loaded correctly by changing colors, patterns, or other visual cues to indicate that the appropriate parts or containers have been loaded into the appropriate locations, such as Fig.87 In the event that a component is loaded incorrectly, the system may further use color, sound, or other cues to indicate incorrect loading to warn the user.

[0099] like Fig.88 As shown, once the parts are properly loaded, the system can instruct the user to close the system door and initiate subsequent operation steps.

[0100] In order to unload the device as soon as other operating steps are completed, the system can instruct the user to open the door of the system, such as Fig.89 As shown. Fig.90 As shown, the system can indicate which containers and consumables to remove first. For example, the system may produce samples located in specific compartments. The system can notify the user to remove these samples first and may seal the samples for use in other devices. Fig.90 As shown, the sample to be removed may be highlighted with a particular color, may flash, may change color, or have an icon indicating that the sample is to be removed first.

[0101] like Fig.91As shown, once the sample is removed, other consumables or containers can be identified for removal. In an example, a flashing or blinking icon can be used to indicate which consumables or containers are to be removed. Alternatively, a change in color, sound or other indicators can be used to indicate which containers are to be removed.

[0102] like Fig.92 As shown, when a container or consumable is removed, the space graphically associated with the removed consumable may be shown as empty. Once the device is empty, the user may be instructed to close the door, such as Fig.93 shown.

[0103] The above methods and systems are particularly suitable for starting a sequencing instrument. Example sequencing instruments include ion sequencing instruments or optical sequencing instruments. Fig.94 In the particular example shown, a system 9400 including a fluid circuit 9402 is connected to at least two reagent reservoirs (9404, 9406, 9408, 9410, or 9412) via inlets, to a waste reservoir 9420, and to a biosensor 9434 via a fluid path 9432 that connects a fluid node 9430 to an inlet 9438 of the biosensor 9434 for fluid communication. Reagents from the reservoirs (9404, 9406, 9408, 9410, or 9412) can be driven to the fluid circuit 9402 by a variety of methods including pressure, pumps (such as syringe pumps, gravity feeds, etc.), and selected by control valves 9414. Reagents from the fluid circuit 9402 can be driven to a waste container 9420 via valves 9414 that receive signals from a control system 9418. Reagents from the fluid circuit 9402 may also be driven through the biosensor 9434 to a waste container 9436. The control system 9418 includes a controller for the valve, which generates signals through the electrical connection 9416 for opening and closing.

[0104] The control system 9418 also includes controllers for other components of the system, such as a wash solution valve 9424 and a reference electrode 9428 connected thereto by electrical connections 9422. The control system 9418 may also include control and data acquisition functions for the biosensor 9434. In one mode of operation, the fluid circuit 9402 delivers a series of selected reagents 1, 2, 3, 4, or 5 to the biosensor 9434 under program control of the control system 9418, such that between selected reagent flows, the fluid circuit 9402 is filled and cleaned, and the biosensor 9434 is also cleaned. Fluid entering the biosensor 9434 is discharged through the outlet 9440 and deposited in the waste container 9436 by control of the pinch valve regulator 9444. The valve 9444 is in fluid communication with the sensor fluid output 9440 of the biosensor 9434.

[0105] The device including a dielectric layer defining an aperture formed by a first inlet and a second inlet and exposing a sensor pad is particularly suitable for detecting chemical reactions and byproducts, such as detecting the release of hydrogen ions in response to nucleotide incorporation, for genetic sequencing and other applications. In a specific embodiment, the sequencing system includes a flow cell in which a sensor array is disposed, a communication circuit in electronic communication with the sensor array, and a container and a fluid controller in fluid communication with the flow cell. In an example, Fig.95 An enlarged cross-sectional view of a flow cell 9500 is shown and a portion of a flow chamber 9506 is shown. A reagent stream 9508 flows over the surface of the well array 9502, wherein the reagent stream 9508 flows over the open ends of the wells of the well array 9502. The well array 9502 and the sensor array 9505 together can form an integrated unit that forms the lower wall (or floor) of the flow cell 9500. A reference electrode 9504 can be fluidically coupled to the flow chamber 9506. In addition, a flow cell cover 9530 encapsulates the flow chamber 9506 to contain the reagent stream 9508 within a defined area.

[0106] Fig.96 An expanded view of the hole 9601 and the sensor 9614 is shown, as Fig.95 9510. The volume, shape, aspect ratio (such as the ratio of base width to hole depth) and other dimensional characteristics of the hole can be selected based on the nature of the reaction occurring and the reagents, byproducts or labeling techniques used (if any). Sensor 9614 can be a chemical field effect transistor (chemFET), more specifically an ion sensitive FET (ISFET), which has a floating gate 9618, and the floating gate 9618 has a sensor plate 9620 that is optionally separated from the interior of the hole by a material layer 9616. Sensor 9614 can respond to (and generate an output signal related to) the amount of charge 9624 present on a material layer 9616 opposite to the sensor plate 9620. Material layer 9616 can be a ceramic layer, such as an oxide of zirconium, hafnium, tantalum, aluminum or titanium, or a nitride of titanium. Alternatively, material layer 9616 can be formed of a metal such as titanium, tungsten, gold, silver, platinum, aluminum, copper or a combination thereof. In an example, the thickness of the material layer 9616 can be in the range of 5 nm to 100 nm, such as in the range of 10 nm to 70 nm, in the range of 15 nm to 65 nm, or even in the range of 20 nm to 50 nm.

[0107] Although the material layer 9616 is shown extending beyond the boundaries of the FET component shown, the material layer 9616 can extend along the bottom of the hole 9601 and optionally along the walls of the hole 9601. The sensor 9614 can respond to (and generate an output signal related to) the amount of charge 9624 present on the material layer 9616 opposite the sensor plate 9620. Changes in charge 9624 can cause changes in the current between the source 9621 and the drain 9622 of the chemFET. In turn, the chemFET can be used directly to provide a current-based output signal, or indirectly with additional circuitry to provide a voltage-based output signal. Reactants, wash solutions, and other reagents can move into and out of the hole through the diffusion mechanism 9640.

[0108] The holes 9601 may be defined by a wall structure, which may be formed by one or more layers of material. In an example, the wall structure may have a thickness extending from the lower surface of the hole to the upper surface, the thickness being in the range of 0.01 micron to 10 microns, such as in the range of 0.05 micron to 10 microns, in the range of 0.1 micron to 10 microns, in the range of 0.3 micron to 10 microns, or in the range of 0.5 micron to 6 microns. In particular, the thickness may be in the range of 0.01 micron to 1 micron, such as in the range of 0.05 micron to 0.5 micron, or in the range of 0.05 micron to 0.3 micron. The holes 9601 of the array 9502 may have a characteristic diameter of no greater than 5 microns, such as no greater than 3.5 microns, no greater than 2.0 microns, no greater than 1.6 microns, no greater than 1.0 microns, no greater than 0.8 microns, or even no greater than 0.6 microns, the characteristic diameter being defined as the cross-sectional area (A) divided by the square root of 4 times Pi (e.g., sqrt(4*A / π)). In an example, the pores 9601 can have a characteristic diameter of at least 0.01 microns. In yet another example, the pores 9601 can define a volume in the range of 0.05 fL to 10 pL, such as in the range of 0.05 fL to 1 pL, in the range of 0.05 fL to 100 fL, in the range of 0.05 fL to 10 fL, or even in the range of 0.1 fL to 5 fL.

[0109] In an embodiment, the reaction carried out in hole 9601 can be an analytical reaction for identifying or determining the characteristics or properties of the analyte of interest. These reactions can directly or indirectly produce byproducts that affect the amount of charge adjacent to sensor plate 9620. If such byproducts are produced in small amounts or rapidly decay or react with other components, multiple copies of the same analyte can be analyzed in hole 9601 at the same time to increase the output signal generated. In an embodiment, multiple copies of the analyte can be attached to solid phase carrier 9612 before or after being deposited in hole 9601. Solid phase carrier 9612 can be microparticles, nanoparticles, beads, solid or porous gels, etc. For simplicity and ease of explanation, solid phase carrier 9612 is also referred to as particles or beads in this article. For nucleic acid analytes, multiple connected copies can be prepared by rolling circle amplification (RCA), exponential RCA or similar techniques to produce amplicons without the need for solid carriers.

[0110] In particular, a solid support such as a bead support may include copies of the polynucleotide. Fig.97 In the specific examples shown, polymer particles can be used as carriers of polynucleotides during sequencing techniques. For example, such hydrophilic particles can fix polynucleotides to be sequenced using fluorescent sequencing techniques. In another example, hydrophilic particles can fix multiple copies of polynucleotides for sequencing using ion sensing techniques. Alternatively, the treatment described above can improve the adhesion of the polymer matrix to the sensor array surface. The polymer matrix can capture analytes, such as polynucleotides for sequencing.

[0111] Bead carriers can include organic polymers such as polystyrene, polyethylene, polypropylene, polyfluoroethylene, polyethyleneoxy and polyacrylamide and copolymers and grafts thereof. The carrier can also be inorganic, such as glass, silica, controlled pore glass (CPG) or reversed silica. The configuration of the carrier can be beads, balls, particles, granules, gels or surface forms. The carrier can be porous or non-porous and can have swelling or non-swelling characteristics. In some embodiments, the carrier is an ionic spherical particle. Examples of bead carriers are disclosed in US 9,243,085 entitled "Hydrophilic polymer particles and methods for preparing and using them" and US 9,868,826 entitled "Polymer substrates formed by carboxyl functional acrylamides", each of which is incorporated herein by reference.

[0112] In some embodiments, the solid support is a "microparticle", "bead", "microbead", etc. (optionally but not necessarily spherical in shape) having a minimum cross-sectional length (e.g., diameter) of 50 microns or less, preferably 10 microns or less, 3 microns or less, approximately 1 micron or less, approximately 0.5 microns or less, such as approximately 0.1, 0.2, 0.3 or 0.4 microns or less (e.g., less than 1 nanometer, about 1-10 nanometers, about 10-100 nanometers, or about 100-500 nanometers). In an example, the support is at least 0.1 micron. Microparticle or bead supports can be made of a variety of inorganic or organic materials, including but not limited to glass (e.g., controlled pore glass), silica, zirconium oxide, cross-linked polystyrene, polyacrylate, polymethyl methacrylate, titanium dioxide, latex, polystyrene, etc. Magnetization can facilitate the collection and concentration of reagents (e.g., polynucleotides or ligases) attached to the microparticles after amplification, and can also facilitate additional steps (e.g., washing, reagent removal, etc.). In certain embodiments, populations of microparticles having different shapes sizes and / or colors are used.The microparticles may optionally be encoded, for example with quantum dots, so that each microparticle or group of microparticles may be individually or uniquely identified.

[0113] Magnetic beads (e.g., Dynabeads from Dynal, Oslo, Norway) can have a size in the range of 1 micron to 100 microns, such as 2 microns to 100 microns. The magnetic beads can be formed from inorganic or organic materials, including but not limited to glass (e.g., controlled pore glass), silica, zirconium oxide, cross-linked polystyrene, polystyrene, or a combination thereof.

[0114] In some embodiments, the bead carrier is functionalized to attach the first primer population. In some embodiments, the bead is any size that can be placed in a reaction chamber. For example, one bead can be placed in a reaction chamber. In some embodiments, more than one bead is placed in a reaction chamber. In some embodiments, the minimum cross-sectional length (e.g., diameter) of the bead is about 50 microns or less, or about 10 microns or less, or about 3 microns or less, about 1 micron or less, about 0.5 micron or less, such as about 0.1, 0.2, 0.3 or 0.4 microns or less (e.g., less than 1 nanometer, about 1-10 nanometers, about 10-100 nanometers, or about 100-500 nanometers).

[0115] In general, the bead carrier can be processed to include biomolecules, including nucleosides, nucleotides, nucleic acids (oligonucleotides and polynucleotides), polypeptides, sugars, polysaccharides, lipids or derivatives or analogs thereof. For example, the polymer particles can be bound or attached to the biomolecule. The end or any internal part of the biomolecule can be bound or connected to the polymer particles. Using a connection chemical method, the polymer particles can be bound or connected to the biomolecule. The connection chemical method includes covalent or non-covalent bonds, including ionic bonds, hydrogen bonds, affinity bonds, dipole-dipole bonds, van der Waals bonds and hydrophobic bonds. Linking chemistry methods include affinity between binding partners, such as affinity between: an avidin portion and a biotin portion; an antigenic epitope and an antibody or an immunoreactive fragment thereof; an antibody and a hapten; a digoxigenin portion and an anti-digoxigenin antibody; a fluorescein portion and an anti-fluorescein antibody; an operator and an inhibitor; a nuclease and a nucleotide; a lectin and a polysaccharide; a steroid and a steroid binding protein; an active compound and an active compound receptor; a hormone and a hormone receptor; an enzyme and a substrate; an immunoglobulin and protein A; or an oligonucleotide or polynucleotide and its corresponding complementary sequence.

[0116] like Fig.97 As shown, a plurality of bead carriers 9704 can be placed in a solution with a plurality of polynucleotides 9702 (target or template polynucleotides). The plurality of bead carriers 9704 can be activated or otherwise prepared to bind to the polynucleotides 9702. For example, the bead carriers 9704 can include oligonucleotides (capture primers) that are complementary to a portion of the polynucleotides of the plurality of polynucleotides 9702. In another example, the bead carriers 9704 can be modified with target polynucleotides 9702 using techniques such as biotin-streptavidin binding.

[0117] In some embodiments, the template nucleic acid molecule (template polynucleotide or target polynucleotide) can be derived from a sample that can be from a natural or non-natural source. The nucleic acid molecule in the sample can be derived from a living organism or a cell. Any nucleic acid molecule can be used, for example, the sample can include a genomic DNA covering part or all of the genome, mRNA or miRNA from a living organism or a cell. In other embodiments, the template nucleic acid molecule can be synthetic or recombinant. In some embodiments, the sample contains nucleic acid molecules with a substantially consistent sequence or a mixture with different sequences. Illustrative embodiments are usually performed using nucleic acid molecules produced in living cells and produced by living cells. Such nucleic acid molecules are usually directly separated from natural sources, such as cells or body fluids, without any in vitro amplification. Therefore, the sample nucleic acid molecule is directly used in subsequent steps. In some embodiments, the nucleic acid molecule in the sample can include two or more nucleic acid molecules with different sequences.

[0118] Method optionally can include the target enrichment step before, during or after library preparation and before pre-implantation reaction.Can for example enrichment comprise target locus or the target nucleic acid molecule of paid attention to region by multiple nucleic acid amplification or hybridization.Multiple methods can be used for carrying out multiple nucleic acid amplification to produce the amplicon such as multiple PCR, and described multiple methods can be used in embodiment.Before template nucleic acid molecule is added in the pre-implantation reaction mixture, can carry out universal amplification reaction after enrichment by any method. Any embodiment of the present teachings can include enriching for a plurality of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 125, 150, 175, 200, 250, 300, 400, 500, 600, 700, 800, 900, 1,000, 2,000, 3,000, 4,000, 5,000, 6,000, 7,000, 8,000, 9,000, or 10,000 target nucleic acid molecules, target loci, or regions of interest. In any disclosed embodiment, the target locus or region of interest can be at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 50, 75, 100, 125, 150, 200, 250, 300, 400, 500, 600, 700, 800, 900, or 1,000 nucleotides long and include a portion or all of a template nucleic acid molecule. In other embodiments, the target locus or region of interest can be between about 1 and 10,000 nucleotides in length, such as between about 2 and 5,000 nucleotides in length, between about 2 and 3,000 nucleotides in length, or between about 2 and 2,000 nucleotides in length. In any embodiment of the present teachings, multiplex nucleic acid amplification can include generating at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 125, 150, 175, 200, 250, 300, 400, 500, 600, 700, 800, 900, 1,000, 2,000, 3,000, 4,000, 5,000, 6,000, 7,000, 8,000, 9,000, or 10,000 copies of each target nucleic acid molecule, target locus, or region of interest.

[0119] In some embodiments, after library preparation and optional enrichment steps, the template nucleic acid molecule library can be templated onto one or more carriers. One or more carriers can be templated in two reactions, i.e., an implantation reaction of a pre-implanted solid carrier is produced and a templated reaction of a template nucleic acid molecule attached is further amplified using one or more pre-implanted carriers. The pre-implantation reaction is generally an amplification reaction, and various methods can be used to carry out. For example, the pre-implantation reaction can be carried out in an RPA reaction, a template walking reaction, or a PCR. In the RPA reaction, in the presence of primers and nucleotides, a recombinase, a polymerase, and optionally a recombinase auxiliary protein are used to amplify the template nucleic acid molecule. The recombinase and optionally the recombinase auxiliary protein can dissociate at least a portion of the double-stranded template nucleic acid molecules to allow primer hybridization, and then the polymerase can be combined to start replication. In some embodiments, the recombinase auxiliary protein can be a single-stranded binding protein (single-stranded binding protein; SSB) that prevents the dissociated template nucleic acid molecules from re-hybridizing. Typically, the RPA reaction can be carried out at an isothermal temperature. In the template walking reaction, in the reaction conditions that allow at least a portion of the double-stranded template nucleic acid molecules to dissociate so that the primers can hybridize and the polymerase can subsequently bind to start replication, in the presence of primers and nucleotides, the template nucleic acid molecules are amplified using a polymerase. In PCR, the double-stranded template nucleic acid molecules are dissociated by thermal cycling. After cooling, the primers bind to the complementary sequence and can be used for the replication of the polymerase. In any aspect of the content taught by the present invention, a pre-implantation reaction can be carried out in a pre-implantation reaction mixture, and the pre-implantation reaction mixture is formed by the components necessary for amplifying the template nucleic acid molecules. In any disclosed aspect, the pre-implantation reaction mixture may include some or all of the following: a template nucleic acid molecule population, a polymerase, one or more solid supports with an attached first primer population, nucleotides, and a cofactor such as a divalent cation. In some embodiments, the pre-implantation reaction mixture may further include a second primer and optionally a diffusion limiting agent. In some embodiments, the template nucleic acid molecule population includes a template nucleic acid molecule joined to at least one adapter sequence hybridized with the first or second primer. In some embodiments, as in emulsion RPA or emulsion PCR, the reaction mixture forms an emulsion. In a preimplantation reaction performed by an RPA reaction, the preimplantation reaction mixture may include a recombinase and optionally a recombinase auxiliary protein. The various components of the reaction mixture are discussed in further detail herein.

[0120] In a specific embodiment of implantation, the hydrophilic particles and polynucleotides are subjected to polymerase chain reaction (PCR) amplification or recombinase polymerase amplification (RPA). In an example, particle 9704 includes a capture primer complementary to a portion of template polynucleotide 9702. The template polynucleotide can hybridize with the capture primer. The capture primer can be extended to form a bead 9706 including a target polynucleotide attached thereto. Other beads can remain unattached to the target nucleic acid, and other template polynucleotides can float freely in the solution.

[0121] In an example, a bead carrier 9706 including a target polynucleotide can be attached to a magnetic bead 9710 to form a bead assembly 9712. In particular, the magnetic bead 9710 is attached to the bead carrier 9706 by a double-stranded polynucleotide connection. In an example, an additional probe including a linker portion can hybridize with a portion of the target polynucleotide on the bead carrier 9706. The linker portion can be attached to a complementary linker portion on the magnetic bead 9710. In another example, a template polynucleotide for forming a target nucleic acid attached to the bead 9706 can include a linker portion attached to the magnetic bead 9710. In another example, a template polynucleotide complementary to the target polynucleotide attached to the bead carrier 9706 can be generated from a primer modified with a linker attached to the magnetic bead 9710.

[0122] The linker portion attached to the polynucleotide and the linker portion attached to the magnetic bead can be complementary and attached to each other. In an example, the linker portion has affinity and can include: an avidin portion and a biotin portion; an antigenic epitope and an antibody or an immunoreactive fragment thereof; an antibody and a hapten; a digoxin portion and an anti-digoxin antibody; a fluorescein portion and an anti-fluorescein antibody; an operator and an inhibitor; a nuclease and a nucleotide; a lectin and a polysaccharide; a steroid and a steroid-binding protein; an active compound and an active compound receptor; a hormone and a hormone receptor; an enzyme and a substrate; an immunoglobulin and a protein A; or an oligonucleotide or a polynucleotide and its corresponding complementary sequence. In a specific example, the linker portion attached to the polynucleotide includes biotin, and the linker portion attached to the magnetic bead includes streptavidin.

[0123] The bead assembly 9712 can be applied over a substrate 9716 of a sequencing device that includes a well 9718. In an example, a magnetic field can be applied to the substrate 9716 to pull the magnetic beads 9710 of the bead assembly 9712 toward the well 9718. The bead carrier 9706 enters the well 9718. For example, the magnet can be moved parallel to the surface of the substrate 9716 so that the bead carrier 9706 is deposited in the 9718 well.

[0124] The bead assembly 9712 can be denatured to remove the magnetic beads 9710, thereby leaving the bead carrier 9706 in the well 9718. For example, the hybridized double-stranded DNA of the bead assembly 9712 can be denatured using thermal cycling or ionic solutions to release the magnetic beads 9710 and the template polynucleotide having a linker portion attached to the magnetic beads 9710. For example, the double-stranded DNA can be treated with a low ion content aqueous solution such as deionized water to denature and separate the strands. In an example, a foam wash can be used to remove the magnetic beads.

[0125] Optionally, the target polynucleotide 9706 can be amplified (referred to herein as templated) while in the well 9718 to provide a bead carrier 9714 having multiple copies of the target polynucleotide. In particular, the beads 9714 have a monoclonal population of the target polynucleotide. This amplification reaction can be performed using polymerase chain reaction (PCR) amplification, recombinant polymerase amplification (RPA), or a combination thereof. Alternatively, the amplification can be performed before the bead carrier 9714 is deposited in the well.

[0126] In a specific embodiment, an enzyme such as a polymerase is present in, bound to, or in close proximity to a particle or bead. In an example, a polymerase is present in a solution or in a hole to promote the replication of a polynucleotide. A variety of nucleic acid polymerases can be used in the methods described herein. In an example embodiment, a polymerase can include an enzyme, a fragment or a subunit thereof that can catalyze the replication of a polynucleotide. In another embodiment, a polymerase can be a naturally occurring polymerase, a recombinant polymerase, a mutant polymerase, a variant polymerase, a fusion or other engineering polymerase, a chemically modified polymerase, a synthetic molecule, or an analog, derivative or fragment thereof. Examples of enzymes, solutions, compositions, and amplification methods can be found in WO2019 / 094,524, entitled "Methods and compositions for manipulating nucleic acids," which are incorporated herein by reference in their entirety.

[0127] Although the polynucleotides of the bead carrier 9714 are shown on the surface, the polynucleotides can extend within the bead carrier 9714. Hydrogels and hydrophilic particles with low concentrations of polymers relative to water can include polynucleotide fragments inside and throughout the bead carrier 9714, or the polynucleotides can be present in the orifices and other openings. In particular, the bead carrier 9714 can allow for diffusion of enzymes, nucleotides, primers, and reaction products used to monitor the reaction. Large numbers of polynucleotides per particle produce better signals.

[0128] In an example embodiment, the bead carrier 9714 can be used in a sequencing device. For example, the sequencing device 9716 can include an array of wells 9718.

[0129] In an example, a sequencing primer can be added to the well 9718, or the bead carrier 9714 can be pre-exposed to the primer before being placed in the well 9718. In particular, the bead carrier 9714 can include a bound sequencing primer. The sequencing primer and the polynucleotide form a nucleic acid duplex including a polynucleotide (e.g., a template nucleic acid) that hybridizes to the sequencing primer. The nucleic acid duplex is a polynucleotide that is at least partially double-stranded. Enzymes and nucleotides can be provided to the well 9718 to promote a detectable reaction, such as nucleotide incorporation.

[0130] Sequencing can be performed by detecting nucleotide addition. Nucleotide addition can be detected using methods such as fluorescence emission or ion detection. For example, a fluorescently labeled group of nucleotides can be provided to system 9716 and can migrate to hole 9718. Excitation energy can also be provided to hole 9718. When a nucleotide is captured by a polymerase and added to the end of an extended primer, the label of the nucleotide can fluoresce, indicating which type of nucleotide has been added.

[0131] In an alternative example, a solution comprising a single type of nucleotide may be added sequentially. In response to the addition of nucleotides, the pH within the local environment of the pore 9718 may change. This change in pH may be detected by an ion sensitive field effect transistor (ISFET). Thus, the change in pH may be used to generate a signal indicating the sequence of nucleotides complementary to the polynucleotide of the particle 9710.

[0132] In particular, the sequencing system may include a hole or multiple holes disposed on a sensor pad of an ion sensor, such as a field effect transistor (FET). In an embodiment, the system includes one or more polymer particles loaded into a hole disposed on a sensor pad of an ion sensor (e.g., a FET), or one or more polymer particles loaded into multiple holes disposed on a sensor pad of an ion sensor (e.g., a FET). In an embodiment, the FET may be a chemFET or an ISFET. A "chemFET" or chemical field effect transistor includes a field effect transistor used as a chemical sensor. The structure of a chemFET is similar to a MOSFET transistor, in which a charge on a gate electrode is applied by a chemical process. An "ISFET" or ion sensitive field effect transistor can be used to measure the concentration of ions in a solution; when the ion concentration (such as H+) changes, the current through the transistor changes accordingly.

[0133] In an embodiment, the FET may be an array of FETs. As used herein, an "array" is a planar arrangement of elements such as sensors or pores. An array may be one-dimensional or two-dimensional. A one-dimensional array may be an array having one column (or row) of elements in a first dimension and multiple columns (or rows) of elements in a second dimension. The number of columns (or rows) in the first dimension and the second dimension may be the same or different. A FET or array may contain 102 , 10 3 , 10 4 , 10 5 , 10 6 , 10 7 or more FETs.

[0134] In embodiments, one or more microfluidic structures may be fabricated above an array of FET sensors to provide containment or confinement of biological or chemical reactions. For example, in one embodiment, the microfluidic structure may be configured as one or more wells (or wells, or reaction chambers, or reaction wells, as the terms are used interchangeably herein) disposed above one or more sensors of the array, such that one or more sensors disposed on a given well detect and measure the presence, level, or concentration of an analyte in the given well. In embodiments, there may be a 1:1 correspondence of FET sensors and reaction wells.

[0135] Back to Fig.97 In another example, the holes 9718 of the hole array can be operably connected to a measuring device. For example, for a fluorescence emission method, the holes 9718 can be operably coupled to a light detection device. In the case of ion detection, the lower surface of the hole 9718 can be disposed on a sensor pad of an ion sensor (such as a field effect transistor).

[0136] An example system involving sequencing by detecting the ionic byproducts of nucleotide incorporation is the Ion TorrentPGM TM 、Proton TM or S5 TM Sequencer (Thermo Fisher Scientific), an ion-based sequencing system that sequences nucleic acid templates by detecting hydrogen ions produced as a byproduct of nucleotide incorporation. Typically, hydrogen ions are released as a byproduct of nucleotide incorporation that occurs during template-dependent nucleic acid synthesis using a polymerase. Ion Torrent PGM TM 、Proton TM or S5 TM The sequencer detects nucleotide incorporation by detecting the hydrogen ion byproduct of nucleotide incorporation. IonTorrent PGM TM 、Proton TM or S5 TMThe sequencer may include a plurality of template polynucleotides to be sequenced, each template being disposed in each sequencing reaction well in the array. Each well of the array is coupled to at least one ion sensor, which can detect the release of H+ ions or the change in solution pH produced as a byproduct of nucleotide incorporation. The ion sensor comprises a field effect transistor (FET) coupled to an ion-sensitive detection layer, which can sense the presence of H+ ions or the change in solution pH. The ion sensor may provide an output signal indicating the incorporation of nucleotides, which may be expressed as a voltage change, the magnitude of which is related to the H+ ion concentration in the respective wells or reaction chambers. Different nucleotide types may flow continuously into the reaction chamber, and may be incorporated into the extension primer (or polymerization site) in an order determined by the template sequence by the polymerase. Each nucleotide incorporation may be accompanied by the release of H+ ions in the reaction well, as well as a change in local pH. The release of H+ ions may be recorded by the FET of the sensor, which generates a signal indicating that the incorporation of nucleotides has occurred. Nucleotides that are not incorporated during the flow of a particular nucleotide may not generate a signal. The amplitude of the signal from the FET may also be related to the number of nucleotides of a particular type incorporated into the extended nucleic acid molecule, thereby permitting homopolymer regions to be resolved. Thus, during a sequencer run, multiple nucleotide flows into the reaction chamber for simultaneous incorporation, and monitoring through multiple wells or reaction chambers can allow the instrument to resolve the sequences of many nucleic acid templates simultaneously.

[0137] In an embodiment, the system monitors the location and type of consumable items, determines the next step in the process, and displays a notification indicating the location and type of the next consumable to be placed in or removed from the instrument. Monitoring is performed through images from a camera or through radio frequency identification. Consumable items include sample preparation supplies, reagent strips or bottles, or sequencing chips and adapters. In particular, the system can track the setup and cleaning of the instrument to ensure proper cleaning and setup for subsequent sequencing runs.

[0138] According to various exemplary embodiments, appropriately configured and / or programmed hardware and / or software elements may be used to perform or implement one or more features of any one or more of the above teachings and / or exemplary embodiments. Determining whether to use hardware and / or software elements to implement an embodiment may be based on any number of factors, such as desired computing rate, power level, thermal tolerance, processing cycle budget, input data rate, output data rate, memory resources, data bus speed, etc., as well as other design or performance constraints.

[0139] Examples of hardware elements may include a processor, a microprocessor, one or more input devices, and / or one or more output devices (I / O) (or peripheral devices) coupled in a communicative manner by: a local interface circuit, a circuit element (e.g., a transistor, a resistor, a capacitor, an inductor, etc.), an integrated circuit, an application specific integrated circuit (ASIC), a programmable logic device (PLD), a digital signal processor (DSP), a field programmable gate array (FPGA), a logic gate, a register, a semiconductor device, a chip, a microchip, a chipset, etc. The local interface may include, for example, one or more buses or other wired or wireless connections, controllers, buffers (caches), drivers, repeaters, and receivers, etc., to allow appropriate communication between hardware components. A processor is a hardware device for executing software, especially software stored in a memory. A processor may be any custom or commercially available processor, a central processing unit (CPU), an auxiliary processor in several processors associated with a computer, a semiconductor-based microprocessor (e.g., in the form of a microchip or chipset), a macroprocessor, or any device generally used to execute software instructions. A processor may also represent a distributed processing architecture. I / O devices may include input devices such as keyboards, mice, scanners, microphones, touch screens, interfaces for various medical devices and / or laboratory instruments, bar code readers, styluses, laser readers, radio frequency device readers, etc. In addition, I / O devices may also include output devices such as printers, bar code printers, displays, etc. Finally, I / O devices may also include devices that communicate in the form of input and output, such as modulators / demodulators (modems; used to access another device, system or network), radio frequency (RF) or other transceivers, telephone interfaces, bridges, routers, etc.

[0140] Examples of software may include software components, programs, applications, computer programs, applications, system programs, machine programs, operating system software, middleware, firmware, software modules, routines, subroutines, functions, methods, operating procedures, software interfaces, application program interfaces (APIs), instruction sets, computing codes, computer codes, code segments, computer code segments, words, values, symbols, or any combination thereof. The software in memory may include one or more independent programs, which may include ordered lists of executable instructions for performing logical functions. The software in memory may include a system for identifying data flows according to the teachings of the present invention and any suitable custom or commercially available operating system (O / S) that may control the execution of other computer programs such as the system, and provide scheduling, input-output control, file and data management, memory management, communication control, etc.

[0141] According to various exemplary embodiments, one or more features of any one or more of the above teachings and / or exemplary embodiments may be performed or implemented using a properly configured and / or programmed non-transitory machine-readable medium or object that can store instructions or instruction sets, which, if executed by a machine, can cause the machine to perform methods and / or operations according to the exemplary embodiments. Such machines may include, for example, any suitable processing platform, computing platform, computing device, processing device, computing system, processing system, computer, processor, scientific or laboratory instrument, etc., and may be implemented using any suitable combination of hardware and / or software. The machine-readable medium or object may include, for example, any suitable type of memory unit, memory device, memory object, memory medium, storage device, storage object, storage medium and / or storage unit, such as memory, removable or non-removable medium, erasable or non-erasable medium, writable or rewritable medium, digital or analog medium, hard disk, floppy disk, CD-ROM, CD-R, CD-RW, optical disk, magnetic medium, magneto-optical medium, removable memory card or disk, various types of digital versatile disks (DVD), magnetic tape, cassette, etc., including any medium suitable for a computer. The memory may include any one or combination of volatile memory elements (such as random access memory (RAM, such as DRAM, SRAM, SDRAM, etc.) and non-volatile memory elements (such as ROM, EPROM, EEROM, flash memory, hard disk drive, magnetic tape, CDROM, etc.). In addition, the memory may incorporate electronic, magnetic, optical and / or other types of storage media. The memory may have a distributed structure in which various components are located away from each other but are still accessed by the processor. The instructions may include any suitable type of code implemented using any suitable high-level, low-level, object-oriented, visual, compiled and / or interpreted programming language, such as source code, compiled code, interpreted code, executable code, static code, dynamic code, encrypted code, etc.

[0142] According to various exemplary embodiments, one or more features of any one or more of the above teachings and / or exemplary embodiments may be performed or implemented, at least in part, using distributed, clustered, remote, or cloud computing resources.

[0143] According to various exemplary embodiments, one or more features of any one or more of the above teachings and / or exemplary embodiments may be executed or implemented using a source program, an executable program (object code), a script, or any other entity containing a set of instructions to be executed. In the case of a source program, the program may be translated by a compiler, assembler, interpreter, etc., which may or may not be included in the memory, so as to operate correctly with the O / S. The instructions may be written using: (a) an object-oriented programming language with data classes and method classes; or (b) a procedural programming language with routines, subroutines, and / or functions, which may include, for example, C, C++, R, Pascal, Basic, Fortran, Cobol, Perl, Java, and Ada.

[0144] Although preferred embodiments of the present invention have been shown and described herein, it will be clear to those skilled in the art that such embodiments are provided by way of example only. Without departing from the present invention, those skilled in the art will now recognize many variations, changes and substitutes. It should be understood that each alternative of the embodiments of the present invention described herein can be used to practice the present invention. It is intended that the appended claims define the scope of the present invention, and thus cover methods and structures within the scope of these claims and their equivalents.

[0145] In a first embodiment, a method for user-guided startup of an instrument includes: receiving an operation plan via a user interface of the instrument; indicating consumables to be provided to the instrument on the user interface based on the operation plan; detecting the presence of the consumables using a visual system; and indicating the presence of the consumables via the user interface.

[0146] In an example of the first embodiment, the method further includes repeating: indicating a consumable product to be provided; detecting the presence of the consumable product; and indicating the presence of the consumable product.

[0147] In another example of the first embodiment and the above example, the instrument is a nucleic acid sequencing instrument.

[0148] In another example of the first embodiment and the above example, the method further includes: using a visual system to determine the presence of used consumables, and indicating the position and presence of the used consumables to the user via the user interface. For example, determining the presence of used consumables includes: using a visual system to determine the number of unused reagent containers in the reagent container group, and determining whether the number of unused reagent containers is sufficient to execute the operation plan. In an example, determining the number of unused reagent containers includes determining the number of used reagent containers by detecting foil punctures of used reagent containers with a visual system. In another example, the method further includes: when the number of unused reagent containers is not enough to implement the operation plan, indicating that the reagent container group will be replaced through the user interface. For example, the method further includes: using a visual system to detect the position of a latch associated with the reagent container group. In an example, detecting the position includes detecting an indicator group with a visual system. In another example, the method further includes detecting the locking state of the latch using a visual system. For example, detecting the locking state includes detecting a change in an indicator associated with the latch in a closed position.

[0149] In additional examples of the first embodiment and the above examples, the method further includes: reading a code of the consumable product using a vision system, and indicating the presence of the consumable product via a user interface when the code is correct.

[0150] In another example of the first embodiment and the above example, the method further includes determining the presence of the consumable product using the RFID system and indicating the presence of the consumable product via the user interface.

[0151] In yet another example of the first embodiment and the above example, the method further includes: detecting a cap disposed on the consumable product using a vision system and indicating the presence of the cap via a user interface.

[0152] In a second embodiment, a method for starting an instrument includes: determining the number of unused reagent containers in a reagent container group using a vision module that communicates with a camera of the instrument; receiving an operation plan at an interface of the instrument; and determining whether the number of unused reagent containers is sufficient to execute the operation plan.

[0153] In an example of the second embodiment, determining the number of unused reagent containers includes detecting the number of used reagent containers.

[0154] In a third embodiment, a method for preparing an instrument vision system includes: detecting a position of an instrument feature within a video stream of an instrument plate captured by a camera; determining a position within a frame of the video stream where the instrument feature will appear; displaying the position of the instrument feature as displayed on a user interface and the position where the instrument feature will appear in the video stream; and aligning the position of the instrument feature with the position where the instrument feature will appear by adjusting the camera.

[0155] In the example of the third embodiment, the positions are indicated by circles, and aligning includes overlapping the circles.

[0156] In a fourth embodiment, the instrument includes: a management system for receiving an operation plan; a visual system including a visual module and a camera group, the visual module communicating with the management system; and a user interface communicating with the management module; wherein the visual system is used to detect the presence or absence of a consumable group associated with the operation plan; wherein the management system is used to display a series of interfaces on the user interface, the interfaces indicating the presence or absence of consumables in the consumable group.

[0157] In an example of the fourth embodiment, the instrument further includes an RFID module in communication with the management module and an RFID antenna for detecting consumables in the second consumables group.

[0158] Note that not all activities described in the general description or examples are required, that a portion of a specific activity may not be required, and that one or more further activities may be performed in addition to the activities described. Furthermore, the order in which the activities are listed is not necessarily the order in which they are performed.

[0159] In the foregoing description, concepts have been described with reference to specific embodiments. However, it will be appreciated by those skilled in the art that various modifications and changes may be made without departing from the scope of the invention as set forth in the appended claims. Therefore, the description and drawings are to be regarded as illustrative rather than restrictive, and all such modifications are intended to be included within the scope of the invention.

[0160] As used herein, the terms "comprises / comprising", "includes / including", "has / having" or any other variation thereof are intended to cover a non-exclusive inclusion. For example, a process, method, article, or apparatus that includes a list of features is not necessarily limited to only those features, but may include other features not expressly listed or inherent to such process, method, article, or apparatus. In addition, unless expressly stated to the contrary, "or" refers to an inclusive or, not an exclusive or. For example, any of the following satisfies condition A or B: A is true (or exists) and B is false (or does not exist), A is false (or does not exist) and B is true (or exists), and both A and B are true (or exist).

[0161] In addition, the use of "a" or "an" is used to describe the elements and components described herein. This is done only for convenience and to give a general sense of the scope of the invention. The description should be interpreted as including one or at least one, and the singular also includes the plural, unless it is obvious that it is otherwise intended.

[0162] Benefits, other advantages, and solutions to problems have been described above with respect to specific embodiments. However, benefits, advantages, solutions to problems, and any features that may make any benefit, advantage, or solution or make it more apparent should not be construed as a critical, required, or essential feature of any or all of the claims.

[0163] After reading this specification, the skilled person will appreciate that, for the sake of clarity, certain features described herein in the context of separate embodiments may also be provided in combination in a single embodiment. Conversely, for the sake of brevity, various features described in the context of a single embodiment may also be provided individually or in any sub-combination. In addition, reference to values ​​stated in ranges includes every value within that range.

Claims

1. A method for user-guided startup of an instrument, the method comprising: receiving, via a user interface of the instrument, a run plan, the run plan identifying a test to be performed by the instrument and parameters associated with the test, the test utilizing a set of consumables; when implementing the operation plan, indicating on the user interface the set of consumables to be used by the instrument based on the operation plan; detecting the presence of consumables in the consumable group using a vision system including a camera; Determining, using the visual system, that the consumables are used consumables, wherein the used consumables include a reagent container set; determining the number of unused reagent containers in the reagent container set using the vision system, wherein determining the number of unused reagent containers includes determining the number of used reagent containers by detecting foil punctures of used reagent containers using the vision system based on comparison of pixel values ​​of an image acquired by the vision system using the camera with expected values; determining whether the number of unused reagent containers is sufficient to execute the run plan; as well as The presence of the used consumable is indicated via the user interface.

2. The method according to claim 1, further comprising: Indicate another consumable item to be provided; detecting said presence of said another consumable; and The presence of the another consumable is indicated.

3. The method according to claim 1 or claim 2, wherein: The instrument is a nucleic acid sequencing instrument.

4. The method according to claim 1 further comprises: when the number of the unused reagent containers is insufficient to execute the run plan, indicating through the user interface that the used consumables are to be replaced.

5. The method according to claim 1, further comprising: The vision system is used to detect the position of a latch that, when in a locked position, holds an associated reagent container in the reagent container group in place.

6. The method according to claim 5, wherein: Detecting the position includes detecting a set of indicators using the vision system.

7. The method of claim 5, further comprising: detecting the latch in a locked position using the vision system.

8. The method according to claim 7, wherein: Detecting the locked position includes detecting a change in a detected amount of a visual indicator of the consumable product.

9. The method of claim 1, further comprising: reading a code of a second consumable product in the set of consumable products using the vision system, and indicating the presence of the second consumable product via the user interface when the code is correct.

10. The method of claim 1, further comprising determining the presence of a second consumable product using an RFID system, and indicating the presence of the second consumable product via the user interface.

11. The method of claim 1 , further comprising detecting, using the vision system, a cap disposed on the consumable product and indicating the presence of the cap via the user interface.

12. An apparatus comprising: a management system for receiving a run plan, the run plan identifying a test to be performed by the instrument and parameters associated with the test, the test utilizing a set of consumables; include a vision system of a vision module and a camera group, wherein the vision module communicates with the management system; as well as a user interface in communication with the management system; wherein the user interface indicates the set of consumables to be used by the instrument based on the operation plan when the operation plan is implemented; The vision system detects the presence of consumables in the consumables group; The visual system determines that the consumables are used consumables, and the used consumables include a reagent container set; the vision system determining a number of unused reagent containers in the set of reagent containers, wherein determining the number of unused reagent containers comprises determining the number of used reagent containers by detecting foil punctures of used reagent containers using the vision system based on comparison of pixel values ​​of an image acquired by the vision system using the camera with expected values; The vision system determines whether the number of unused reagent containers is sufficient to execute the run plan; and The user interface indicates the presence of the used consumable.

13. The apparatus of claim 12, further comprising an RFID module in communication with the management system and an RFID antenna for detecting consumables in the second consumables group.

14. The apparatus according to claim 12, wherein: The visual system is prepared by the following method: detecting a location of an instrument feature within a video stream of the instrument panel captured by a camera; determining a location within a frame of the video stream where the instrument feature will appear; showing the location of the instrument feature as displayed on a user interface and the location where the instrument feature will appear in the video stream; as well as The camera is adjusted to align the position of the instrument feature with the position where the instrument feature will appear.

15. The apparatus according to claim 14, wherein: The positions are indicated by circles, and aligning comprises overlapping the circles.

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