Systems and methods for nanopore sequencing

Abstract

An analyzer instrument for performing sequencing operations includes a housing, a piercing tip member, at least one sealed container, a fluid transfer system, and an interface assembly for receiving a chip package included in a consumable device. The piercing tip member is movable within the housing, and the sealed container holds a fluid and includes a seal that is penetrable by the piercing tip member. The fluid transfer system is configured to access and produce a flow of the fluid from the sealed container to the consumable device. The chip package of the consumable device contains at least one fluidic lane. The interface assembly is configured to fluidically couple the chip package to the fluid transfer system. The fluid transfer system includes an inlet portion for directing fluid flows towards the chip package and an outlet portion for directing fluid flows away from the chip package.

Description

Attorney Docket No.: P37148-WO-1SYSTEMS AND METHODS FOR NANOPORE SEQUENCINGCross-Reference to Related Applications

[0001] This application claims priority to and the filing date benefit of U.S. Provisional Application No. 63 / 684,163, entitled '’Systems and Methods for Nanopore Sequencing,” filed August 16, 2024, which is incorporated herein by reference in its entirety.Background

[0002] The ability to rapidly and accurately assess biological and biochemical samples, including those containing or otherwise derived from biopolymers such as DNA, is of considerable significance for analytical as well as diagnostic purposes. In DNA sequencing, for example, nanopore-based assays and techniques — leveraging tiny apertures on the cell membrane on the order of one nanometer in internal diameter — have shown promise for fast and reliable testing. In some instances, the nanopores may be maintained on synthetic membranes in a semiconductor-based biochip.

[0003] Recent advances in micro-miniaturization within the semiconductor industry, moreover, have enabled biotechnologists to begin packing traditionally bulky sensing tools into smaller and smaller form factors, including onto biochips and chip-based consumable devices. For example, it is now possible to use semiconductor-based electronic systems to detect unique electrical signals associated with individual molecules as they enter and / or pass through a nanopore, which may be created in situ on a biochip or test consumable. In some instances, a voltage in a circuit including the nanopore is measured (e.g., at an integrating capacitor) as a way of measuring the resistance associated with a particular molecule that has entered and / or passed through the nanopore, thus allowing the particular molecule to be detected and identified.

[0004] In the context of DNA sequencing, the molecules that may be detected using semiconductor-based nanopore systems can include a particular nucleotide (e.g., as part of a nucleic acid), a particular surrogate molecule derived from a particular nucleotide, or a particular tag attached to a particular nucleotide. Semiconductor-based nanopore sequencing technology offers several advantages over other existing modalities that use optical or pH change methods to detect DNA sequences, including flexibility and versatility, both short and longer read lengths, rapid data generation and analysis, and cost-effectiveness.Attorney Docket No.: P37148-WO-1

[0005] Some known analyzer or diagnostic systems used to assess biochemical samples are research-based systems that, while potentially offering flexibility in sample processing, require considerable reconfiguration between tests and are therefore not well-suited for high throughput testing and analysis. Further, some diagnostic systems and analyzers may purport to provide high throughput testing, but are limited in their ability to make and maintain effective mechanical, electrical, thermal, and / or fluidic coupling with different biochips and semiconductor chip packages.

[0006] Moreover, in systems that couple and use a nanopore chip or test consumable together with a processor-controlled analyzer instrument, such as a DNA sequencer, it is important to provide the electrical coupling in a manner that minimizes electrostatic and other electrical noise, which can adversely affect the detection of biomolecules in a nanopore, and, as a consequence, reduce the accuracy of test results. It is also important to maintain consistent ambient conditions, such as temperature and thermal uniformity, in a nanopore chip or consumable device while testing procedures are conducted using the nanopores.

[0007] Thus, a need exists for improved systems, devices, and methods for processing and analyzing biological and biochemical samples, including those used in nanopore sequencing technologies.Summary

[0008] The embodiments described herein relate to systems and methods for conducting biological or biochemical assays, including but not limited to DNA sequencing. More particularly, the embodiments described herein relate to a consumable device as well as an analyzer or sequencer instrument that can be used together in assay systems and methods, such as DNA sequencing.

[0009] In some embodiments, an analyzer instrument includes a housing, a piercing tip member, at least one sealed container, a fluid transfer system, and an interface assembly. The piercing tip member is movable within the housing in response to control signals generated by a processor. The sealed container holds a fluid and is sealed via a seal that is penetrable by the piercing tip member. The fluid transfer system is configured to access and produce a flow of the fluid from the sealed container in response to control signals generated by the processor. The interface assembly is coupled to the housing and can receive a chip package containing at least one fluidic lane. The interface assembly is configured to fluidically couple the chipAttorney Docket No.: P37148-WO-1 package to the fluid transfer system in response to control signals generated by the processor. The fluid transfer system includes an inlet portion for directing fluid flows towards the chip package and an outlet portion for directing fluid flows away from the chip package. The interface assembly includes an actuator that is movable from a first position to a second position to cause the outlet portion to become fluidically coupled to an aligned fluidic lane from the at least one fluidic lane of the chip package, the actuator being configured to move from the first position to the second position in response to a force applied to the actuator by the piercing tip member.

[0010] In some embodiments, the actuator is coupled to an outlet needle such that each movement of the actuator produces a corresponding movement of the outlet needle and the outlet needle has a lumen in fluidic connection with the outlet portion. The outlet needle is configured to fluidically engage the aligned fluidic lane from the at least one fluidic lane of the chip package, when the actuator is in the second position, such that the aligned fluidic lane is fluidically coupled to the outlet portion via the lumen.

[0011] In some embodiments, the actuator is further movable from the second position to the first position, the aligned fluidic lane being fluidically isolated from the outlet portion when the actuator is in the first position.

[0012] In some embodiments, the actuator is configured to move from the first position to the second position in response to a first force applied to the actuator by the piercing tip member. And the actuator is also configured to move from the second position to the first position in response to a second force applied by the piercing tip member.

[0013] In some embodiments, the second force is applied by the piercing tip member to an actuator pin spaced apart from the actuator, the actuator pin being configured to move from a third position to a fourth position in response to the second force. Movement of the actuator pin from the third position to the fourth position is configured to rotate a lift arm contacted by the actuator pin about a pivot disposed between the actuator pin and the actuator. Rotation of the lift arm about the pivot is configured to lift the actuator from the second position to the first position.

[0014] In some embodiments, the actuator that is movable from the first position to the second position, as well as from the second position to the first position, is a lifter actuator ofAttorney Docket No.: P37148-WO-1 the analyzer instrument. The first position corresponds to the lifter actuator being in a raised state. And the second position corresponds to the lifter actuator being in a lowered state.

[0015] In some embodiments, the lifter actuator is associated with a fluid egress portion (such as a fluid outlet port) of the chip package received (e.g., via insertion) by the analyzer instrument. When the lifter actuator is in its lowered state, the fluid egress portion of the chip package is fluidically engaged with at least aportion of the fluid transfer system (e.g., the outlet portion) of the analyzer instrument. And when the lifter actuator is in its raised state, the fluid egress portion of the chip package is fluidically disengaged with at least a portion of the fluid transfer system (e.g., the outlet portion) of the analyzer instrument.

[0016] In some embodiments, the at least one fluidic lane of the chip package includes a plurality of fluidic lanes that are each capable of being aligned with the outlet portion so as to be fluidically couplable to the outlet portion. The actuator that is movable to cause the outlet portion to become fluidically coupled to an aligned fluidic lane is a first actuator. The interface assembly includes a second actuator that is movable between a plurality of positions: (a) each position from the plurality of positions being associated with (b) a particular fluidic lane or a particular subgroup of fluidic lanes from the plurality of fluidic lanes. Movement of the second actuator to a position from the plurality of positions is configured to cause the particular fluidic lane or the particular subgroup of fluidic lanes associated the position to be aligned with the outlet portion, such that the particular fluidic lane or the particular subgroup of fluidic lanes serves as the one or more aligned fluidic lanes that are configured to become fluidically coupled to the outlet portion in response to a movement by the first actuator from the first position to the second position.

[0017] In some embodiments, the at least one sealed container includes a plurality of sealed containers each having a seal penetrable by the piercing tip member, a first sealed container from the plurality of sealed containers holding a reagent, a second sealed container from the plurality of sealed containers holding a target fluid. In some embodiments, the reagent comprises a salt buffer, a protein pore, or a lipid. The target fluid comprises a synthesized macromolecule prepared from a biological sample. In some embodiments, the synthesized macromolecule is an Xpandomer.

[0018] In some embodiments, the interface assembly includes a cooling assembly with a cap member. The cap member has a plurality of protruding surfaces for making contact withAttorney Docket No.: P37148-WO-1 the chip package on a condition that the chip package is inserted into the interface assembly. The protruding surfaces are spaced apart from one another, each being configured to make contact with the chip package at a different location on the chip package.

[0019] In some embodiments, the cooling assembly is coupled to a housing of the interface assembly via a biasing member.

[0020] In some embodiments, the interface assembly includes a set of electrical connectors surrounding the cap member of the cooling assembly. The set of electrical connectors is configured to make contact with the chip package from below on a condition that the chip package is inserted into the interface assembly.

[0021] In some embodiments, the interface assembly includes a grounding spring configured to make contact with the chip package upon insertion of the chip package into the interface assembly. The grounding spring is configured to dissipate electrostatic charge from the chip package on a condition that the chip package is inserted into the interface assembly.

[0022] In some embodiments, an analyzer instrument includes a housing, a fluid transfer system within the housing, and an interface assembly. The fluid transfer system is configured to access and produce a flow of a fluid associated with a sequencing operation. The interface assembly is configured to receive a chip package containing at least one fluidic lane. The chip package is fluidically couplable to the fluid transfer system on a condition that the chip package is inserted into the interface assembly. The fluid transfer system includes an inlet portion configured to direct the produced flow into the chip package and an outlet portion configured to direct the flow out of the chip package. The interface assembly includes a cooling assembly with a cooling interface member. The cooling interface member has a set of protruding surfaces for making contact with the chip package on the condition that the chip package is inserted into the interface assembly. The protruding surfaces are spaced apart from one another, each being configured to make contact with the chip package at a different location on the chip package.

[0023] In some embodiments, an analyzer instrument includes a housing, a processor, a fluid transfer system within the housing, and an interface assembly. The fluid transfer system is configured to access and produce a flow- of a fluid associated with a sequencing operation in response to control signals generated by the processor. The interface assembly is configured to receive a chip package containing at least one fluidic lane. The interface assembly is configured to fluidically couple the chip package to the fluid transfer system in response toAttorney Docket No.; P37148-WO-1 control signals generated by the processor. The fluid transfer system includes an inlet portion for directing fluid flows towards the chip package and an outlet portion for directing fluid flows away from the chip package. The interface assembly includes at least one electrical connector configured to make contact with the chip package and electronically couple the chip package to the processor on a condition that the chip package is inserted into the interface assembly. The interface assembly includes at least one grounding spring configured to make contact with the chip package and dissipate electrostatic discharge from the chip package on the condition that the chip package is inserted into the interface assembly.

[0024] In some embodiments, a consumable device for use with a sequencing system is provided. The consumable device can include a sequencing chip, the sequencing chip can include a plurality of wells, each well including a working electrode; a flow cell including at least one flow channel, wherein the flow cell is configured to be disposed over sequencing chip such that the at least one flow channel is disposed over the plurality of wells of the sequencing chip; at least one inlet boss having a lumen in fluid communication with the at least one flow channel; and at least one counter electrode disposed over at least a portion of the at least one flow channel; and a flow cell cover including at least one inlet boss receptacle for receiving the at least one inlet boss of the flow cell; and at least one dispense tip receptacle configured to receive a dispense tip, wherein the at least one dispense tip receptacle is in fluid communication the at least one inlet boss receptacle.

[0025] In some embodiments, a system includes a synthesis instrument for producing a synthesized macromolecule and a sequencing instrument for performing a sequencing operation. The synthesis instrument includes a first fluid transfer system configured to convey the synthesized macromolecule from a synthesis flow cell to a collection reservoir. The sequencing instrument includes the collection reservoir that can contain a target fluid comprising the synthesized macromolecule, an interface assembly, a needle, a second fluid transfer system, and an actuator assembly. The interface assembly is configured to receive a consumable device having a fluid inlet, at least one fluid outlet, and at least one fluid channel disposed between the fluid inlet and the at least one fluid outlet. The consumable device is configured to receive a flow of the target fluid from the collection reservoir via the fluid inlet and direct the flow of the target fluid through the at least one fluid channel and towards the at least one fluid outlet. The needle is configured to access at least one of the fluid inlet or the fluid outlet of the consumable device. The second fluid transfer system is configured to beAttorney Docket No.: P37148-WO-1 operably coupled to the consumable device and includes a first circuit segment and a second circuit segment. The first circuit segment is configured to direct the flow of the target fluid from the collection reservoir into the fluid inlet of the consumable device. The second circuit segment is configured to direct the flow of the target fluid from the at least one fluid outlet of the consumable device towards a waste receptacle. The actuator assembly includes an actuator pin and is configured to align and fluidically couple the at least one fluid outlet with the second circuit segment in response to a force applied to the actuator pin by the needle.

[0026] In some embodiments, a needle is configured to pierce an inlet seal covering the fluid inlet of the consumable device to access the fluid inlet.

[0027] In some embodiments, the actuator assembly further includes a force transfer link and a positioning bar. The force transfer link transfers movement of the actuator pin along a first axis into movement of the positioning bar along a second axis. The positioning bar being coupled to an outlet needle such that movement of the positioning bar along the second axis produces a corresponding movement of the outlet needle to selectively place the outlet needle in fluidic connection with the at least one fluid outlet of the consumable device.

[0028] In some embodiments, the collection reservoir is within a reagent assembly of the sequencing instrument, the reagent assembly includes at least one sealed container containing a reagent. The needle is configured to pierce a seal of the sealed container.

[0029] In some embodiments, the synthesized macromolecule comprises an Xpandomer.

[0030] In some embodiments, the first fluid transfer system includes a pump, a valve, and a fluid transfer circuit. The pump is configured to produce a flow of the synthesized macromolecule from the synthesis flow cell into the fluid transfer circuit. The valve is configured to selectively place the fluid transfer circuit in fluid communication with the collection reservoir.

[0031] In some embodiments, the first fluid transfer system includes a pipetting assembly coupled to the fluid transfer circuit. The pipetting assembly is configured to convey the synthesized macromolecule into the collection reservoir.

[0032] In some embodiments, the first fluid transfer system includes a pipetting assembly configured to convey the synthesized macromolecule into the collection reservoir.Attorney Docket No.: P37148-WO-1

[0033] In some embodiments, the synthesis instrument and the sequencing instrument are discrete instruments that are operably coupled via the first fluid transfer system. In some embodiments, the system includes a housing and the synthesis instrument and the sequencing instrument each being contained within the housing.

[0034] In some embodiments, a system includes a synthesis instrument for producing a synthesized macromolecule and a sequencing instrument for performing a sequencing operation. The synthesis instrument includes a first fluid transfer system configured to convey the synthesized macromolecule from a synthesis flow cell to a collection reservoir. The sequencing instrument includes the collection reservoir that can contain a target fluid comprising the synthesized macromolecule, an interface assembly, a second fluid transfer system, and an actuator assembly. The interface assembly is configured to receive a consumable device having a fluid inlet, at least one fluid outlet, and at least one fluid channel disposed between the fluid inlet and the at least one fluid outlet. The consumable device is configured to receive a flow of the target fluid from the collection reservoir via the fluid inlet and direct the flow of the target fluid through the at least one fluid channel and towards the at least one fluid outlet. The second fluid transfer system is configured to be operably coupled to the consumable device and includes a first circuit segment and a second circuit segment. The first circuit segment is configured to direct the flow of the target fluid from the collection reservoir into the fluid inlet of the consumable device. The second circuit segment is configured to direct the flow of the target fluid from the at least one fluid outlet of the consumable device towards a waste receptacle. The actuator assembly is configured to align and fluidically couple the at least one fluid outlet with the second circuit segment.

[0035] In some embodiments, an apparatus includes a first interface assembly, an illumination assembly, a second interface assembly, a first fluid transfer component, a second fluid transfer component, and a controller operably coupled to the illumination assembly, the first fluid transfer component and the second fluid transfer component. The first interface assembly is configured to receive a synthesis flow cell that is configured to receive a sample. The illumination assembly is configured to produce an electromagnetic radiation output and guide the electromagnetic radiation output to a portion of the synthesis flow cell to cleave a macromolecule from the sample. The first fluid transfer component is configured to convey the macromolecule from the synthesis flow cell to one of a collection reservoir or a consumable device to produce a target fluid. The second interface assembly is configured to receive theAttorney Docket No.; P37148-WO-1 consumable device that has a fluid inlet, at least one fluid outlet, and at least one fluid channel disposed between the fluid inlet and the at least one fluid outlet. The consumable device is configured to receive a flow of the target fluid via the fluid inlet and direct the flow of the target fluid through the at least one fluid channel and towards the at least one fluid outlet. The second fluid transfer component is configured to be operably coupled to the consumable device. The second fluid transfer system includes a first circuit segment and a second circuit segment. The first circuit segment directs the flow of the target fluid from the fluid inlet and through the consumable device to perform a sequencing operation. The second circuit segment directs the flow of the target fluid from the at least one fluid outlet of the consumable device towards a waste receptacle. The controller is configured to execute a set of operations, including sending, to the illumination assembly, an illumination control signal to produce the electromagnetic radiation; sending, to the first fluid transfer component, a fluid transfer signal to cause the transfer of the macromolecule from the synthesis flow cell to one of the collection reservoir or the consumable device; sending, to the second fluid transfer component, a flow signal to produce the flow of the target fluid through the consumable device; and receiving, from the consumable device, a set of signals associated with the flow of the target fluid through the consumable device, the signals associated with a sequence of the macromolecule.

[0036] In some embodiments, the macromolecule is an Xpandomer.

[0037] In some embodiments, the first fluid transfer system includes a pump, a valve, and a fluid transfer circuit. The pump is configured to produce a flow of the macromolecule from the synthesis flow cell into the fluid transfer circuit. The valve is configured to selectively place the fluid transfer circuit in fluid communication with one of the collection reservoir or the consumable device.

[0038] In some embodiments, the first fluid transfer system includes a pipetting assembly that is configured to convey the macromolecule into the consumable device.Brief Description of the Drawings

[0039] FIG. 1 is a schematic illustration of a nanopore-based sequencing chip, according to an embodiment.

[0040] FIG. 2 is an exploded view of a consumable device that includes a sequencing chip, according to an embodiment.Attorney Docket No.: P37148-WO-1

[0041] FIG. 3 is a top view of a consumable device that includes a sequencing chip, according to an embodiment, showing multiple fluidic channels.

[0042] FIGS. 4 and 5 are a top perspective view (FIG. 4) and a bottom perspective view (FIG. 5) of a consumable device that includes a sequencing chip, according to an embodiment.

[0043] FIGS. 6 and 7 are schematic illustrations of an analyzer instrument, according to an embodiment.

[0044] FIG. 8 is a schematic illustration of an electronic control system of the analyzer instrument from FIGS. 6 and 7.

[0045] FIG. 9 is a perspective view of the analyzer instrument from FIGS. 6 and 7, according to an embodiment, with the hood in an opened position.

[0046] FIG. 10 is an exploded perspective view of the housing of the analyzer instrument from FIGS. 6 and 7, according to an embodiment.

[0047] FIG. 11 is a perspective view showing the chassis of the analyzer instrument from FIGS. 6 and 7, according to an embodiment.

[0048] FIG. 12 is an exploded view of a portion of the analyzer instrument from FIGS. 6 and 7, according to an embodiment, showing the chassis, certain panels, and drip trays.

[0049] FIG. 13 is an exploded view of a portion of the analyzer instrument from FIGS. 6 and 7, according to an embodiment, showing a water level sensor.

[0050] FIG. 14 is a schematic illustration of the analyzer instrument from FIGS. 6 and 7, according to an embodiment, showing an ambient sensor.

[0051] FIG. 15 is a perspective view of a portion of the analyzer instrument from FIGS. 6 and 7, according to an embodiment, showing the drip tray.

[0052] FIG. 16 is a side view of a portion of the analyzer instrument from FIGS. 6 and 7, according to an embodiment, showing the water level sensor in the drip tray.

[0053] FIGS. 17 and 18 are schematic illustrations of a fluid transfer system, according to an embodiment, that can be used in the instrument from FIGS. 6 and 7 shown in an isolated state (FIG. 17) and a connected state (FIG. 18).Attorney Docket No.: P37148-WO-1

[0054] FIG. 19 is a schematic illustration of a fluid transfer system, according to an embodiment, that can be used in the instrument from FIGS. 6 and 7.

[0055] FIG. 20 is a perspective view of the instrument from FIGS. 6 and 7, according to an embodiment, including the reagent assembly (and the bulk reagent container assembly).

[0056] FIGS. 21 and 22 are a perspective view (FIG. 21) and a cross-sectional view (FIG. 22) of the bulk reagent container assembly shown in FIG. 19.

[0057] FIGS. 23 and 24 are a front perspective view (FIG. 23) and a rear perspective view (FIG. 24) of an outlet actuator assembly according to an embodiment.

[0058] FIG. 25 is a perspective view of an outlet needle of a fluid transfer system, according to an embodiment.

[0059] FIG. 26 is a perspective view of a portion of a fluid transfer system according to an embodiment, including the outlet needle shown in FIG. 25.

[0060] FIG. 27 is a perspective view of an outlet actuator assembly, according to an embodiment, coupled to a portion of an interface assembly of an instrument.

[0061] FIGS. 28A and 28B are cross-sectional views of the outlet actuator assembly shown in FIG. 27 in a first configuration (FIG. 28 A) and a second configuration (FIG. 28B).

[0062] FIG. 29 is a perspective view of a wash station of a fluid transfer system, according to an embodiment.

[0063] FIG. 30 is a schematic illustration of the wash station of the fluid transfer system shown in FIG. 19.

[0064] FIGS. 31A-31C are schematic illustrations of the wash station shown in FIG. 30 in different use configurations.

[0065] FIG. 32 is a perspective view of a waste container of a fluid transfer system, according to an embodiment.

[0066] FIGS. 33 and 34 are perspective views of portions of the fluid transfer system, wash station, and reagent assembly within the instrument from FIGS. 6 and 7, according to an embodiment.Attorney Docket No.: P37148-WO-1

[0067] FIG. 35 is a perspective view of an interface assembly, according to an embodiment, that can be included within the instrument from FIGS. 6 and 7.

[0068] FIGS. 36 and 37 are perspective views of the interface assembly shown in FIG. 35, with the clamp top subassembly being shown in an exploded view'.

[0069] FIG. 38 is a side view of the interface assembly shown in FIG. 35, showing the clamp top portion, electronic circuit assembly, and clamp base subassembly in an exploded view.

[0070] FIG. 39 is a perspective view of the clamp top subassembly of the interface assembly shown in FIG. 35 with the outlet actuator assembly shown in FIGS. 23 and 24 mounted thereto.

[0071] FIG. 40 is a perspective view of the clamp top subassembly of the interface assembly shown in FIG. 35 with the top plate shown in transparent view.

[0072] FIG. 41 is a perspective view of the clamp base subassembly of the interface assembly shown in FIG. 35 with portions being shown in an exploded view;

[0073] FIG. 42 is a perspective view' of the clamp base subassembly of the interface assembly shown in FIG. 35.

[0074] FIG. 43 is a perspective view of the cooling assembly of the interface assembly shown in FIG. 35.

[0075] FIGS. 44-46 are perspective view's of an inlet portion of the interface assembly shown in FIG. 35, showing the front slot cover closed (FIG. 44) and a consumable device being loaded via the inlet portion (FIGS. 45 and 46).

[0076] FIG. 47 is a perspective view of the clamp base subassembly of the interface assembly shown in FIG. 35 and the consumable device shown in FIGS. 4 and 5 with portions being shown in an exploded view;

[0077] FIGS. 48-50 are perspective views of the interface assembly shown in FIG. 35, in an opened configuration (FIG. 48), a partially loaded configuration (FIG. 49), and a fully loaded configuration (FIG. 50).Attorney Docket No.: P37148-WO-1

[0078] FIG. 51 is a schematic illustration of an instrument for synthesizing a macromolecule, according to an embodiment.

[0079] FIGS. 52A and 52B illustrate at least a portion of an illumination assembly of the synthesis instrument shown in FIG. 51.

[0080] FIG. 53 is a schematic illustration of a portion of a synthesis flow cell used with the synthesizing instrument of FIG. 51, showing the steps of synthesizing a macromolecule, according to an embodiment.

[0081] FIG. 54 illustrates the components of a surrogate macromolecule produced via the synthesis instrument of FIG. 51.

[0082] FIG. 55 is a perspective view of an instrument for synthesizing a macromolecule, according to an embodiment.

[0083] FIG. 56A-56C are a front perspective view (FIG. 56A), an exploded view (FIG. 56B), and a rear perspective view (FIG. 56C) of a synthesis flow cell, according to an embodiment.

[0084] FIG. 57 is a schematic illustration of a system for performing a sequencing operation according to an embodiment that includes a synthesis instrument and a sequencing instrument.

[0085] FIG. 58 is a front view of a system for performing a sequencing operation according to an embodiment that includes a synthesis instrument and a sequencing instrument.Detailed Description

[0086] The invention can be implemented in numerous ways, including as a process: an apparatus; a system; a composition of matter; a computer program product embodied on a computer readable storage medium; and / or a processor, such as a processor configured to execute instructions stored on and / or provided by a memory7coupled to the processor. In this specification, these implementations, or any other form that the invention may take, may be referred to as techniques. In general, the order of the steps of disclosed processes may be altered within the scope of the invention. As used herein, the term “processor’’ refers to one or moreAttorney Docket No.: P37148-WO-1 electronic devices, circuits, and / or processing cores configured to process data, such as computer program instructions.

[0087] A detailed description of one or more embodiments of the invention is provided below along with accompanying figures that illustrate the principles of the invention. The invention is described in connection with such embodiments, but the invention is not limited to any embodiment. The scope of the invention is limited only by the claims and the invention encompasses numerous alternatives, modifications and equivalents. Numerous specific details are set forth in the following description in order to provide a thorough understanding of the invention. These details are provided for the purpose of example and the invention may be practiced according to the claims without some of these specific details.

[0088] Systems for conducting biological or biochemical assays, including but not limited to nucleic acid sequencing, are described herein. In some embodiments, the instruments described herein include an interface assembly that receives a chip package (e.g., a consumable device containing a biochip) and efficiently couples the chip package (mechanically, fluidically, thermally, and / or electronically) to the other portions of the instrument. Specifically, in some embodiments, the instrument can receive a chip package that has one or more fluidic lanes, and the instrument's interface assembly can fluidically couple the chip package to a fluid transfer system of the instrument that directs fluid flows towards (e.g., biochemical fluid for nanopore-based sequencing analysis) and away from (e.g., biochemical waste fluid) the chip package. The interface assembly includes an actuator that can move (e.g., between two allowable positions) to cause a portion of the fluid transfer system to become fluidically coupled to an aligned fluidic lane from the one or more fluidic lanes of the chip package. In some embodiments, the actuator can be moved (e g., between two allowable positions) in response to a force applied thereto. More specifically, in some embodiments, the actuator is configured to move from the first position to the second position in response to a force applied to the actuator by a piercing tip member (e.g., needle). In some instances, the piercing tip member (e.g., needle) also serves to pierce or access one or more fluid containers within the instrument (e.g., container holding a particular biochemical fluid used to conduct nanopore-based sequencing).

[0089] Thus, the instrument (e.g., DNA analyzer or sequencer) can effectively align and / or fluidically couple its fluid transfer system with at least one desired fluidic lane in the chip package (e.g., semiconductor-based biochip for maintaining nanopores) by including one orAttorney Docket No.: P37148-WO-1 more actuators that are responsive to a dual-use component of the system, i.e., the piercing tip member. In this manner, the instruments described herein have reduced complexity (due to the novel use of a piercing component for multiple different instrument operations) while retaining the flexibility to couple to chip packages that have different configurations of fluidic lanes.

[0090] The instruments described herein can also provide efficient and / or spatially uniform cooling of the chip package during operation. By transferring away accumulated heat in a manner that maintains uniform temperatures across the chip package (e.g., while sequencing operations are conducted using nanopores), the systems described herein can produce more accurate results. In some embodiments, the instruments described herein include a cooling assembly (e.g.. thermoelectric cooler) that matingly engages with the chip package when the chip package is loaded or inserted into the instrument’s interface assembly. Specifically, in some embodiments, the cooling assembly includes a cooling interface member (e.g., cold plate or cold block cap) having a set of protruding surfaces that contact with the chip package. In some embodiments, the protruding surfaces are spaced apart from one another and are each configured to make contact with the chip package at a different location on the chip package. Thus, the selective areas of contact can be configured and / or arranged to produce efficient and / or spatially uniform heat transfer from the chip package during operation.

[0091] The instruments described herein can also limit undesirable electronical noise when the chip package is coupled with the interface assembly. In some embodiments, the instruments described herein include one or more springs that contact the chip package upon insertion of the chip package into the instrument's interface assembly. More specifically, in some embodiments, the one or more springs form or include electrical grounding members capable of dissipating accumulated electrical charge from the chip package when the chip package is loaded or inserted into the interface assembly. In this manner, electrostatic and other electrical noise, and the potential damage that may result therefrom, can be efficiently and effectively mitigated during operation of the chip package (e.g., without the need for the chip package to itself include electrostatic grounding mechanisms).

[0092] The instruments described herein can form a part of a system for performing end- to-end sequencing operations. For example, in some embodiments, a system can include a synthesis instrument for producing a synthesized macromolecule and a sequencing instrument for performing a sequencing operation. In some embodiments, the synthesis instrument can be separate from, but operably coupled to the sequencing instrument. Specifically, the synthesisAttorney Docket No.: P37148-WO-1 instrument and / or the sequencing instrument can include a fluid transfer system (e.g., a pump- driven system or a robotic fluid handling system with pipetting capabilities) that conveys a synthesized macromolecule produced by the synthesis instrument into a receiving portion of the synthesizing instrument (e.g., a vial, a collection reservoir, or directly into a consumable device). In this manner, the target molecule can be synthesized and sequenced with limited (or no) human intervention required. This arrangement can improve the speed of the sequencing operation and also limit contamination of the sample (due to additional handling steps).

[0093] In some embodiments, a system can include a synthesis instrument and a sequencing instrument that are integrated into one unit (i.e., that are within a shared housing and / or are supported by a shared chassis). In some embodiments, a single fluid transfer system can be used to perform fluid transfer operations associated with each of the synthesis operation and the sequencing operation.

[0094] As used in this specification, the term "reagent" includes any substance that is used in connection with any of the operations described herein, including nanopore-based sequencing operations and biochemical reactions and other operations for creating and / or maintaining nanopores and nanopore membranes. For example, a reagent can include a sequencing reagent, a PCR reagent, an elution buffer, an enzyme, a substrate, a wash solution, a blocking solution, or the like. A reagent can further include nanopore compositions, hemolysin compositions, acid and / or base compositions, lipid formulations, osmolarity buffers, or the like. Additionally, a reagent can include cleaning reagents, including but not limited to detergents, system fluids, and run buffers. A reagent can also include compositions used in nucleic acid sequencing, including but not limited to nucleotide molecules and compositions including nucleotides, surrogate molecules derived from nucleic acids and compositions including such surrogate molecules (e.g., Xpandomers), and tagged nucleotides and compositions including tagged molecules. A reagent can include a mixture of one or more constituents. A reagent can include such constituents regardless of their state of matter (e.g., solid, liquid or gas). Moreover, a reagent can include the multiple constituents that can be included in a substance in a mixed state, in an unmixed state, and / or in a partially mixed state. A reagent can include both active constituents and inert constituents. Accordingly, as used herein, a reagent can include non-active and / or inert constituents such as water, colorant, or the like.Attorney Docket No.: P37148-WO-1

[0095] As used in this specification, the term “target fluid’' includes any substance that is analyzed using any of the systems and operations described herein, including all kinds of biological and biochemical materials, for example proteins or nucleic acids, but also other molecules occurring in nature or being derivatives or synthetic analogues or variants thereof. In sequencing operations, for example, a target fluid that is analyzed can include nucleotide molecules and compositions including nucleotides, surrogate molecules derived from nucleic acids and compositions including such surrogate molecules (e.g., Xpandomers), and tagged nucleotides and compositions including tagged molecules. Furthermore, the term “biological material” comprises viruses and eukaryotic and prokaryotic cells. In some embodiments, the biological target material is nucleic acids such as DNA, RNA or PNA. The DNA can be, for example, viral DNA, genomic DNA or plasmid DNA. The biological target material can be native or modified. Native biological material is not irreversibly altered as compared to the respective naturally occurring biological material, such as DNA or RNA isolated from organisms. Modified biological material comprises, e.g., biotinylated molecules such as nucleic acids or proteins.

[0096] The term “Xpandomer” refers to a class of (simple to measure) surrogate molecules derived from nucleic acids (such as DNA), which may in turn be used in a nanopore-based sequencing technique known as sequencing by expansion (SBX) to identify an original nucleic acid sequence. Xpandomer molecules are derived or synthesized based on the natural function of DNA replication where expandable nucleoside triphosphates (X-NTPs) act as substrates for template-dependent, polymerase-based replication. Specifically, four differentiable X-NTPs are used during Xpandomer synthesis, one for each DNA base, and engineered polymerases incorporate the X-NTPs into a resulting Xpandomer, which then serves as a surrogate for the complement of the nucleic acid template. When nanopore-based sequencing is conducted using the synthesized Xpandomer, accordingly, each incorporated X-NTP within the Xpandomer will function as a high signal-to-noise reporter of the original DNA base to which the incorporated X-NTP corresponds. Thus, as the Xpandomer molecule transits through a nanopore, the distinct electrical signal of each base reporter is easily identifiable to enable highly accurate and high throughput nanopore-based nucleic acid sequencing.

[0097] The term “fluid-tight” is understood to encompass hermetic sealing (i.e., a seal that is gas-impervious) as well as a seal that is only liquid-impervious. The term “substantially” when used in connection with “fluid-tight,” “gas-impervious,” and / or “liquid-impervious” isAttorney Docket No.: P37148-WO-1 intended to convey that, while total fluid imperviousness is desirable, some minimal leakage due to manufacturing tolerances, or other practical considerations (such as, for example, the pressure applied to the seal and / or within the fluid), can occur even in a “substantially fluid- tight” seal. Thus, a “substantially fluid-tight” seal includes a seal that prevents the passage of a fluid (including gases, liquids and / or slurries) therethrough when the seal is maintained at pressures associated with normal operation of the component or seal. Any residual fluid layer that may be present on a portion of a wall of a container after component defining a “substantially-fluid tight” seal are moved past the portion of the wall are not considered as leakage.

[0098] As used in this specification, the term “about” when used in connection with a referenced numeric indication means the referenced numeric indication plus or minus up to 10% of that referenced numeric indication. For example, the language “about 50” covers the range of 45 to 55.

[0099] As used in this specification, specific words chosen to describe one or more embodiments and optional elements or features are not intended to limit the invention. For example, spatially relative terms — such as “beneath,” “below,” “lower,” “above,” “upper,” “proximate,” and the like — may be used to describe the relationship of one element or feature to another element or feature as illustrated in the figures. These spatially relative terms are intended to encompass different positions (i.e., translational placements) and orientations (i.e., rotational placements) of a device, component, element, or feature in use or operation in addition to the position and orientation shown in the figures. For example, if a device in the figures is turned over, elements described as “below” or “beneath” other elements or features would then be “above” or “over” the other elements or features. Thus, the term “below” can encompass both positions and orientations of above and below. A device component, element, or feature may be otherwise oriented (e.g., rotated 90 degrees or at other orientations) and the spatially relative descriptors used herein interpreted accordingly. Likewise, descriptions of movement along (translation) and around (rotation) various axes include various spatial device positions and orientations.

[0100] Similarly, geometric terms, such as “parallel,” “perpendicular.” “round,” or “square,” are not intended to require absolute mathematical precision, unless the context indicates otherwise. Instead, such geometric terms allow for variations due to manufacturing or equivalent functions. For example, if an element is described as “round” or “generallyAttorney Docket No.: P37148-WO-1 round,” a component that is not precisely circular (e.g., one that is slightly oblong or is a many- sided polygon) is still encompassed by this description.

[0101] In addition, the singular forms “a,” “an,” and “the” are intended to include the plural forms as well, unless the context indicates otherwise. The terms “comprises,” “includes,” “has,” and the like specify the presence of stated features, steps, operations, elements, components, etc. but do not preclude the presence or addition of one or more other features, steps, operations, elements, components, or groups.

[0102] Nanopore membrane devices having pore sizes on the order of one nanometer in internal diameter have shown promise in rapid nucleotide sequencing. When a voltage potent al is applied across a nanopore immersed in a conducting fluid, a change in an electrical signal, e.g., a change in ion current or resistance attributed to the conduction of ions across the nanopore can be observed. The magnitude of the current or resistance is sensitive to the pore size. When a molecule is passed through the nanopore, the magnitude of the current or resistance temporarily changes. By measuring the cunent or resistance as various molecules (e.g., a nucleotide as part of a nucleic acid, a particular surrogate molecule derived from a particular nucleotide, or a particular tag attached to a particular nucleotide) are conveyed through the nanopore, the individual molecules as well as the sequence of a molecular chain can be determined.

[0103] Accordingly, a nanopore-based sequencing chip or chip package may be used for DNA sequencing. Such a nanopore-based sequencing chip or chip package may be included and housed within a consumable device, which may be portable and / or disposable. A nanopore-based sequencing chip incorporates a large number of sensor cells (each including a nanopore through which target molecules can be conveyed), which may be arranged as arrays and / or grouped into sensor cell banks. For example, an array of one million cells may include 1000 rows by 1000 columns of cells. Such an array may be further divided into 16 sensor banks in a 4x4 row-column arrangement.

[0104] FIG. 1 illustrates an embodiment of a nanopore-based sequencing chip package 100. Nanopore-based sequencing chip package 100 includes a nanopore-based sequencing chip 102. Sequencing chip 102 is an example of a biochip that can be used for DNA sequencing. In some instances, sequencing chip 102 is constructed from semiconductor materials. Nanopore-based sequencing chip 102 incorporates a large number of nanopore sensor cells configured as aAttorney Docket No.: P37148-WO-1 nanopore array 104. For example, an array of one million cells may include 1000 rows by 1000 columns of cells. In some instances, although not shown in FIG. 1, nanopore array 104 may be further divided or grouped into multiple sensor banks.

[0105] With reference to FIG. 1, nanopore-based sequencing chip package 100 further includes a reservoir or flow chamber 106 that is mounted on top of nanopore-based sequencing chip 102 and encloses the nanopore cells. A fluid ingress portion 108, which may include one or more inlet ports, inlet tubes or needles, and / or inlet guides, directs fluid into the reservoir or flow chamber 106. A fluid egress portion 110, which may include one or more outlet ports, outlet tubes or needles, and / or outlet guides, directs the fluid out of reservoir or flow chamber 106.

[0106] In some instances, one or more components from the fluid ingress portion 108 and fluid egress portion 110 may be included and / or housed within the sequencing chip package 100. Additionally and / or alternatively, one or more components from the fluid ingress portion 108 and fluid egress portion 110 may be external to the sequencing chip package 100 (e.g., provided as one or more components from a separate analyzer or sequencer instrument configured to receive and / or be coupled with the chip package 100, further described in connection with FIGS. 6-10 below). In one example, a fluid inlet port from the fluid ingress portion 108 and a fluid outlet port from the fluid egress portion 110 are included and / or housed within the sequencing chip package 100, while a fluid inlet tube from the fluid ingress portion 108 and a fluid outlet tube from the fluid egress portion 110 are provided as external components configured to be coupled to the fluid inlet port and fluid outlet port, respectively, during operation of the chip package 100.

[0107] In some instances, although not shown in FIG. 1, the fluid ingress portion 108 may have one or more associated seals. For example, an inlet port of the fluid ingress portion 108 may have a seal that covers the inlet port to fluidically isolate the fluid ingress portion 108 from the surrounding environment. Such seals associated with the fluid ingress portion 108 may be configured to be peeled, pierced, or otherwise opened to allow fluid to be directed, through the fluid ingress portion 108, into the reservoir or flow chamber 106. In some instances, a seal associated with the fluid ingress portion 108 may be pierced or punctured using a piercing tip or needle.Attorney Docket No.: P37148-WO-1

[0108] In some instances, although not shown in FIG. 1, the fluid egress portion 110 may have one or more associated seals. For example, an outlet port of the egress portion 110 may have a seal that covers the outlet port to fluidically isolate the fluid egress portion 1 10 from the surrounding environment. Such seals associated with the fluid egress portion 110 may be configured to be peeled, pierced, or otherwise opened to allow' fluid to be directed, through the fluid egress portion 110, out of the reserv oir or flow chamber 106. In some instances, the same piercing tip or needle is used to open both a seal associated with the fluid ingress portion 108 as well as a seal associated with the fluid egress portion 1 10.

[0109] The reservoir or flow chamber 106 may be configured to include one or more fluidic channels or lanes (not shown in FIG. 1) that direct fluid to flow from the fluid ingress portion 108 towards the fluid egress portion 110. The fluid can be, for example, a conducting fluid across which a voltage potential is applied during a sequencing operation. Each fluidic channel or lane may be associated with (1) a respective inlet port, inlet tube or needle, and / or inlet guide from fluid ingress portion 108, and (2) a respective outlet port, outlet tube or needle, and / or outlet guide from fluid egress portion 110.

[0110] In some instances, the reservoir or flow chamber 106 includes a single fluidic channel or lane between the fluid ingress portion 108 and the fluid egress portion 110. In other instances, the reservoir or flow chamber 106 includes multiple fluidic channels or lanes (e.g., arranged in a parallel fashion) between the fluid ingress portion 108 and the fluid egress portion 110. In instances where the reservoir 106 includes a single fluidic channel or lane between the fluid ingress portion 108 and the fluid egress portion 110, the single channel or lane may be configured to provide a straight path, a curved path, or a serpentine path for fluid to flow from the fluid ingress portion 108 to the fluid egress portion 110.[OHl] FIG. 2 illustrates an embodiment of a consumable device 200 that contains and / or houses a chip or chip package, which may be similar to the nanopore-based sequencing chip package 100 from FIG. 1 or a different chip package. Consumable device 200, along with the chip(s) or chip package contained therein, may be portable and / or disposable.

[0112] FIG. 2 is an exploded view of the consumable device 200 in which various components of the consumable device are shown as being separated from one another in the vertical direction. The components of the consumable device 200 show n in FIG. 2 include a sequencing chip 202, agasket 203, counter and reference electrodes 218 connected by a flexibleAttorney Docket No.: P37148-WO-1 flat circuit 215 to a connector (not shown in FIG. 2), a top cover 222, inlet / outlet guide 226, a fluid inlet 208, and a fluid outlet 210. The sequencing chip 202 may be configured to be coupled to an optional printed circuit board 212, which may either be included with the consumable device 200, or form a part of a separate analyzer or sequencer instrument configured to receive and / or be coupled with the consumable device 200 (further described in connection with other figures below).

[0113] In some instances, although not shown in FIG. 2, the inlet / outlet guide 226, fluid inlet 208, fluid outlet 210, and / or the top cover 222, may each have an associated seal to fluidically isolate the portions of the chip 202 from the surrounding environment. Such seals may be configured to be peeled, pierced, or otherwise opened to allow fluid to be directed through the respective inlet / outlet guide 226, fluid inlet 208, and / or fluid outlet 210 and into the reservoir (and fluid channels) defined within the consumable device 200. In some instances, such seals may be pierced or punctured using a piercing tip or needle.

[0114] While FIG. 2 depicts each of the inlet / outlet guide 226, fluid inlet 208, and fluid outlet 210 as portions of the consumable device 200, in alternative embodiments, one or more of these elements may be formed (at least in part) as components external to the consumable device 200 (e.g., provided as one or more components from a separate analyzer or sequencer instrument configured to receive and / or be coupled with the consumable device 200, further described in connection with FIGS. 6-10 below). In one example, the fluid inlet 208 and fluid outlet 210 can each include a respective inlet / outlet port that is provided as part of the consumable device 200. In this example, any one of the individual fluid inlets / outlets 208 / 210 can further include an external needle configured to be coupled to the respective inlet / outlet port during operation of the consumable device 200.

[0115] FIG. 3 illustrates another embodiment of a consumable device 300 that includes a flow chamber 306 arranged into four fluidic channels 307, with each channel directing fluid to flow directly above a single column (or a single row) of sensor cell banks 304 (i.e., a portion of the nanopore chip). As shown in FIG. 3, consumable device 300 includes four fluid inlets 308 and four fluid outlets 310. Each of the individual fluid inlets / outlets 308 / 310 may include a respective inlet / outlet port, inlet / outlet tube or needle, and / or inlet / outlet guide.

[0116] In some instances, while not shown in FIG. 3, all four fluid inlets 308 may be positioned and arranged to fall along a straight line. In some instances, while not shown inAttorney Docket No.: P37148-WO-1FIG. 3, all four fluid outlets 310 may be positioned and arranged to fall along a straight line. Other arrangements or configurations of each of the individual fluid inlets / outlets 308 / 310 are also possible.

[0117] With reference to FIG. 3, fluid is directed into the consumable device 300 through the four fluid inlets 308. and this may occur either sequentially (in any order) or together in parallel. Each of the inlets 308 feeds the fluid into a separate channel of the flow chamber 306 that directs the fluid to flow directly above a single column (or a single row) of sensor cell banks 304. The fluidic channels 307 may be formed by stacking together a top plate and a gasket 303 with dividers that divide the flow chamber 306 into multiple lanes, and then mounting them on top of the sequencing chip to form the multiple (enclosed) fluidic channels 307. Once the fluid flows through an individual channel to the opposite side of the sequencing chip, the fluid is directed through a respective outlet for that channel and out of the consumable device 300.

[0118] In some instances, although not shown in FIG. 3, each of the four inlets 308 and four outlets 310 may have an associated seal that covers the respective inlet or outlet. Such seals fluidically isolate the fluidic channels 307 from the surrounding environment (e.g., prior to the consumable device 300 being used in a sequencing operation). Such seals may be configured to be peeled, pierced, or otherwise opened so as to allow fluid to be directed through the respective inlet or outlet. In some instances, such seals may be pierced or punctured using a piercing tip or needle. In some instances, the same piercing tip or needle is used to open all seals associated with inlets 308 and outlets 310.

[0119] FIGS. 4 and 5 illustrate an embodiment of a consumable device 400 that contains and / or houses a chip or chip package, which may be similar to any of the nanopore-based sequencing chip packages described herein. Consumable device 400, along with the chip(s) or chip package contained therein, may be portable and / or disposable. Consumable device 400 can be used with and manipulated by any of the analyzer instruments described herein, including the instrument 1001.

[0120] The consumable device 400 includes a sequencing chip (not shown) that is enclosed by a top cover 422. The top cover 422 includes two guide rails 427 (one of the two being visible in FIG. 4) configured to align and / or couple the consumable device 400 within any of the analyzer instruments described herein. The top cover 422 also defines a fluid inlet and aAttorney Docket No.: P37148-WO-1 fluid outlet that provide fluidic access to a flow chamber (not shown, but which is similar to any of the flow chambers described herein). The flow chamber is positioned above the nanopore-based sequencing chip. The top cover includes an inlet seal 423 that fluidically isolates the fluid inlet from the surrounding environment and an outlet seal 424 that fluidically isolates the fluid outlet from the surrounding environment. The inlet seal 423 and the outlet seal 424 are configured to be pierced or punctured by a piercing tip or needle (e.g., piercing tip 2205) as described herein.

[0121] The consumable device 400 includes a printed circuit board 412 that is coupled to the top cover 422 and that encloses the bottom portion of the consumable device 400. The printed circuit board 412 includes any electronic components (e.g., processor, memory, current measurement sensors, resistors, capacitors) that are used in performing assays or other tests within the consumable device. As described herein, the printed circuit board 412 is configured to be operably coupled to the electronic control system of any of the analyzer instruments described herein (e.g., the electronic control system 1900). The printed circuit board 412 is also configured to be mechanically coupled to any of the analyzer instruments described herein (e.g., via the interface assembly 3500) to ensure the desired electronic, mechanical, fluidic, and thermal performance of the consumable device 400 during operation. As shown in FIG. 5, the printed circuit board 412 includes a set of electrical connectors 416 that are configured to be matingly coupled to connectors of the analyzer instrument. The printed circuit board 412 also defines a central opening 414 and two alignment openings 415. As described herein, the central opening 414 is configured to receive a portion of a cooling assembly. The alignment openings 415 are configured to receive an alignment pin.

[0122] In some instances, any one of the chip-based devices 100, 200, 300, and 400 previously described can include and / or be communicably coupled to one or more processors that control (at least in part) the operation of the chip-based device, such as to enable, facilitate, and / or perform biochemical assays and sequencing methods. In one example, consumable device 200, 300 or 400 (which may be portable) may include a processor local to and / or supported by the housing of the consumable device. For the consumable device 400, the processor can be coupled to the printed circuit board 412. The processor of the consumable device may be communicably coupled to, and transmit and / or receive electronic signals to and / or from, a separate analyzer instrument configured to be functionally and / or physicallyAttorney Docket No.: P37148-WO-1 coupled with the consumable device, such as during the performance of a nanopore-based sequencing method.

[0123] In an alternative example, consumable device 200, 300 or 400 may not include its own processor, but is configured to be functionally and / or physically coupled with a separate analyzer instrument that has a processor (such as instrument 1001 described below). In this case, the processor of the analyzer instrument may be communicably coupled to, and transmit and / or receive electronic signals to and / or from, the consumable device to control the operation of the consumable device, such as during the performance of a nanopore-based sequencing method.

[0124] Moreover, in some instances, any one of the chip-based devices 100, 200, 300, and 400 previously described can further include and / or be communicably coupled to one or more memory components, input / output devices, circuit boards, sensors, motors (e.g., to drive the fluid flows), valves, resistors, capacitors, inductors, accelerometers, switches, drivers, antennas, and / or the like. Such components may also facilitate control and / or operation of the device 100, 200, 300 or 400 to perform any suitable assays or sequencing methods.

[0125] FIGS. 6 and 7 show schematic illustrations of an embodiment of an analyzer instrument 1001. The instrument 1001 may receive, house, and / or manipulate a biochip package (such as sequencing chip package 100 previously described or any other suitable chip packages) and / or a consumable device (such as consumable device 200, 300, or 400 previously- described or any other suitable consumable devices) to analyze a biological or biochemical sample. Thus, the instrument 1001 may be functionally coupled and used together with a biochip or consumable device (which may be portable and / or disposable) to conduct biological or biochemical assays, including but not limited to nanopore-based sequencing methods.

[0126] The instrument 1001 is associated with and communicably coupled to one or more processors, including CPUs and / or GPUs, that may control how the instrument 1001 operates, such as to conduct assays and sequencing methods. In instances where the instrument 1001 has been coupled with a particular consumable device, the processor(s) may also control how the consumable device operates, such as during conducted assays and sequencing methods. Any one of these processors may be physically local to the instrument 1001 or be placed somewhere remote from the instrument 1001 (e.g., in the cloud).Attorney Docket No.: P37148-WO-1

[0127] In some instances, the instrument 1001 includes an electronic control system 1900, which may be local to and / or supported by the housing 1100. Specifically, the electronic control system 1900 includes any of the electronic components to produce the desired inputs, outputs, signals or the like to control the operation of the instrument 1001 to perform any suitable assays or sequencing methods. A schematic illustration of the electronic control system 1900 is shown in FIG. 8. As shown in FIG. 8, the electronic control system 1900 can include one or more processors 1922, one or more memory devices 1923, an input module 1924, an output module 1925, a sensor module 1926, and an actuator module 1927. The input module 1924, the output module 1925, the sensor module 1926, and the actuator module 1927 can each be hardware and / or software modules that are implemented in at least one of the memory devices 1923 or processors 1922. The input module 1924 can receive inputs from the user (e.g., via the display screen, the power button, and any other input device) and provide such inputs to the processor, which can produce control signals based thereon. The output module 1925 can produce outputs to the user (e.g., via the display screen) based on signals from the processor, thereby notifying the user of the status and / or producing prompts for inputs.

[0128] The sensor module 1926 can interface with any of the sensors described herein and provide information to the processor, which can produce control signals or output signals based thereon. For example, in some embodiments, the sensor module can receive a pressure signal from a pressure sensor (e.g.. the pressure sensor 2321) that is associated with a flow of fluids (e.g., the target fluid) within the consumable device. The sensor module 1926 can communicate this information to the processor 1922. The processor 1922 can perform operations and / or an algorithm to determine the flow rate and, in turn, produce one or more control signals to the fluid transfer system 1200 to adjust or maintain the flow of the target fluid. In other embodiments, the sensor module 1926 can receive a signal associated with the current produced by a nanopore within the consumable device as the target fluid flows through the consumable device. As described above, as macromolecules are conveyed through the nanopore, the current produced varies for each nucleic acid base (Thymine (T), Cytosine (C), Adenine (A), and Guanine (G)). Thus, the sensor module 1926 can receive the current measured at one or more of the nanopores and can communicate this information to the processor 1922, the memory' device 1923, and / or any external computing system. The current measurements can be used to sequence the macromolecule.Attorney Docket No.: P37148-WO-1

[0129] The actuator module 1927 can interface with any of the actuators described herein and based on control signals from the processor. For example, in some embodiments, the actuator module 1927 can interface with the actuator assembly 2400, 3400, or 4400 to produce the desired movements of the needle as described herein. Additionally, the electronic control system 1900 can include any suitable components, including input / output devices (e.g., the display 1902 described below), circuit boards, sensors, motors (e.g., to drive the fluid pumps described herein), valves, resistors, capacitors, inductors, accelerometers, switches, drivers, antennas, and / or the like.

[0130] In some instances, one or more components of the electronic control system 1900, including one or more processors (e.g., CPUs and / or GPUs) and memory components, may be placed somewhere remote from the instrument 1001 (e.g., in the cloud) instead of being local to and / or supported by the housing 1100. In some instances the electronic control system 1900 includes one or more components that are local to the housing 1100, as well as one or more components that are remote from the housing 1100.

[0131] Referring to FIGS. 6, 7 and 9, in some embodiments, the electronic control system 1900 includes a display 1902 that can serve as an input I output device to control the operation of the instrument 1001. The display 1902, which is integrated within the housing 1100, may be embodied as an interactive touch screen. The display 1902 serves as an interface for the user who may thereby be informed about, for example, the status of specific samples within the instrument 1001, the ambient temperature inside the housing 1100 and / or temperatures of specific components within the housing, the filling status of reagent containers or waste containers, the status of any received consumable device, estimated remaining duration of an assay or sequencing method, or the like. With reference to FIGS. 7 and 9, the display 1902 may be tiltable upwards to provide the user with a better viewing angle. While not shown in FIGS. 6, 7, and 9, in alternative embodiments, the display 1902 may be provided as a part of a larger interactive interface that includes one or more of a keyboard, a microphone, a scanner (such as a barcode scanner), and / or other user input devices.

[0132] By entering commands via the display 1902, the user may influence the actions performed by and within the instrument 1001. For instance, the user may order the processing of a specific sample among other samples present within the instrument 1001 at a given point in time. In other cases, the user may schedule specific processing or sequencing steps, or adjust certain parameters of the instrument 1001 such as temperature or the like.Attorney Docket No.: P37148-WO-1

[0133] The electronic control system 1900 includes any suitable sensors that provide feedback signals to the processor to produce the desired control of the instrument 1001. As shown in FIG. 13, the electronic control system 1900 includes a liquid sensor 1931 that may be coupled to or near the bottom surface panel 1116. The liquid sensor can produce a signal associated with a level or amount of liquid in a reservoir or tray. This information can be used by the processor to adjust the operation of the instrument 1001, produce an error signal, or any other appropriate control activity. In some instances, the liquid sensor 1931 may be an optical liquid sensor.

[0134] FIG. 14 shows an ambient sensor 1932 that may be coupled to the inside surface of the openable hood 1103. In other embodiments, the ambient sensor 1932 can be fixed to a frame or deck of the instrument 1001 rather than attached to the openable hood 1103. The ambient sensor 1932 may detect ambient temperature, pressure, humidity, and the like inside the housing 1100.

[0135] FIGS. 15 and 16 show different views of the pull-out condensation collection tray 1122. As shown in FIG. 16, the pull-out condensation collection tray 1122 may be coupled with a liquid sensor 1931 for detecting liquid levels in the pull-out condensation collection tray 1122.

[0136] The instrument 1001 includes a housing 1100 within which a variety of subassemblies or modules are contained. Specifically, the instrument 1001 includes the electronic control system 1900 (described above), a fluid transfer system 1200, a reagent assembly 3300, an outlet actuator assembly 2400, and an interface assembly 1500. A description of the housing 1100 and each module or subassembly follows.

[0137] As shown in FIGS. 6 and 7, the components of the instrument 1001 are contained within, supported by. and / or surrounded by a housing 1100. protecting the interior components from external influences and vice versa. For example, the interior is protected from external sources of contamination, while a user outside of the housing 1100 is shielded from biological agents such as reagents that may be processed on the inside. The housing 1100 includes a slot or opening 1101 for receiving a consumable device, which may be consumable device 200, 300, or 400. As described in more detail below' (see, e.g., FIGS. 10 and 11), the housing also includes a chassis or frame 1110 and a set of panels coupled to the chassis 1110 that define an internal region within which the components of the instrument 1001 are contained. TheAttorney Docket No.: P37148-WO-1 housing 1100 also includes a movable hood 1103 that can be opened to provide access to the internal region within the housing 1100.

[0138] FIG. 9 is another perspective view of the instrument 1001, show n with the hood 1103 in an opened state. As shown in FIG. 9, the hood 1103 of the analyzer may be opened by the user to reveal a power button 1901 located near the front bezel (or elsewhere on the housing 1100), as well as the inner components of the instrument 1001 that are located within the housing 1100. For example, this view shows portions of the interface assembly 1500, the reagent assembly 3300, and the fluid transfer system 1200, among other inner components of the analyzer further described in relation to other figures below.

[0139] FIG. 10 is an exploded perspective view of the housing 1100 with several of the interior components of the instrument 1001 hidden to show the housing components in greater detail. The components shown in FIG. 10 include display 1902, openable hood 1103, left side panel 1112, right side panel 1113, back side panel 1114, upper surface panel 1115, bottom surface panel 1 116, and a chassis or frame 1110. The chassis or frame 1110 and bottom surface panel 1116 are show n from another perspective view in FIG. 11.

[0140] As shown in FIGS. 10 and 13, one or more of the panels coupled to the chassis 1110 may include air vents. The air vents can allow- airflow into and / or out of the internal region of the housing 1100 to produce the desired cooling. As show n in FIG. 10, one or more of the panels coupled to the chassis 1110 may include dust filters 1121 integrated with air vents.

[0141] FIG. 11 is a perspective view' of the chassis or frame 1110, along with several components coupled to the bottom surface panel 1116. As shown in FIG. 11, the components coupled to the bottom surface panel 1110 include a pull-out condensation collection tray 1122, a dust filter tray 1123, a load cell mounting bracket 1125, and a pull-out lift handle 1124.

[0142] As shown in FIG. 10, a door lock 1104 for the openable hood 1103 may be coupled to the left side panel 1112 and / or the chassis 1110.

[0143] As shown in FIG. 9 and further discussed below, the analyzer instrument 1001 (which may be aDNA sequencer) includes a fluid transfer system 1200 to produce and / or direct fluidic flow s from and / or towards different locations during the operation of the instrument. For example, the fluid transfer system may generate fluid pressures and / or forces (e.g., using a pump) to convey sample fluids, reagent fluids, target fluids, system fluids, waste fluids, and / orAttorney Docket No.: P37148-WO-1 other fluids to and from different locations and / or subsystems of the instrument 1001. In some embodiments, the fluid transfer system may operate in response to or in accordance with electronic signals (e.g., control signals) generated by the electronic control system 1900 and / or another processor associated with the analyzer instrument.

[0144] FIGS. 17 and 18 illustrate a schematic illustration of a fluid transfer system 1200 that may be used with the instrument 1001, with the fluid transfer being in an unconnected or isolated state (FIG. 17) and a connected state (FIG. 18). The fluid transfer system 1200 (and any of the fluid transfer systems described herein) may be disposed within the housing 1100 of the instrument 1001 or any other . Alternatively, one or more portions of the fluid transfer system 1200 may extend outside the housing 1100 but remain operatively coupled to the instrument 1001.

[0145] In the embodiment of FIG. 17, the fluid transfer system 1200 includes a fluidic circuit 1210 operably coupled to a pump 1220. As used herein, a "‘fluidic circuit” (such as fluidic circuit 1210) is a structure or structural assembly that includes one or more fluidic lines or channels capable of forming a fluidic path between a source location and a destination location to allow liquid flows (e.g., driven by one or more associated pumps) between those locations. The lines or channels making up a fluidic circuit may be constructed from various types of liquid conduits that are know n to those of ordinary skill in the art, including but not limited to pipes, tubes, funnels, and needles.

[0146] As shown, the fluidic circuit 1210 includes an inlet circuit segment 1211 and an outlet circuit segment 1213. The inlet circuit segment 1211 and outlet circuit segment 1213 are together capable of forming a fluidic path between a fluid source 1201 and a fluid destination 1202. Fluid source 1201 may be, for example, a container or receptacle holding either a system fluid or a non-system fluid (such as a reagent). Fluid destination 1202 may be, for example, a fluid waste container or receptacle. The fluid source 1201 and fluid destination 1202 may (but need not) be disposed physically proximate to each other in the housing 1 100 of the instrument 1001 or any other instruments described herein.

[0147] In the embodiment of FIG. 17, the fluidic path between fluid source 1201 and fluid destination 1202 travels through a fluidic channel of a consumable device 500 (which may be consumable device 200, 300, or 400 previously described, or any other suitable consumable devices containing at least one fluidic channel). Along this fluidic path, as shown in FIG. 17,Attorney Docket No.: P37148-WO-1 the inlet circuit segment 1211 is capable of directing liquid flows away from the fluid source 1201 and towards the consumable device 500, and the outlet circuit segment 1213 is capable of directing liquid flows away from the consumable device 500 and towards the fluid destination 1202. The flow of fluids along any portion of this fluidic path may be driven, at least in part, by pump 1220. The pump 1220 can operate according to any number of mechanisms known to those skilled in the art to produce and / or drive fluidic flows from one location on a fluidic path to another. For example, the pump 1220 may impart suction and / or propulsion forces or pressure to trigger the displacement of fluid and / or gas particles along the fluidic path. In some implementations, the pump 1220 may be a positive displacement hydraulic pump, such as a syringe pump, a piston pump, a vane pump, or a peristaltic pump.

[0148] In FIGS. 17 and 18, the pump 1220 is shown as being coupled to the inlet circuit segment 1211. But the pump 1220 may alternatively be placed in other locations in the fluid transfer system 1200, such as being proximate and / or coupled to any one of the fluid source 1201, consumable device 500. outlet circuit segment 1213, and fluid destination 1202. Additional pumps (not shown in FIGS. 17 and 18) may also be placed at various locations in the fluid transfer system 1200, and used together with pump 1220 to produce and / or drive fluidic flow s along any portion of the fluidic circuit 1210.

[0149] In FIG. 17, the fluidic circuit 1210 is depicted in a disconnected state. As shown in FIG. 17, an end portion 1212 of the inlet circuit segment 1211 is fluidically isolated from an end portion 1214 of the outlet circuit segment 1213. FIG. 18 depicts the fluidic circuit 1210 in a connected (or fluidically coupled) state. As shown in FIG. 18. the end portion 1212 of the inlet circuit segment 121 1 is fluidically connected to the end portion 1214 of the outlet circuit segment 1213 such that a fluidic path is formed. Specifically, as shown in FIG. 18, the end portion 1212 of the inlet circuit segment 1211 is fluidically coupled to an inlet fluidic connector 1203, which is in turn fluidically coupled to an inlet port 508 of the consumable device 500. The inlet port 508 is fluidically connected to the outlet port 510 of the consumable device through a fluidic channel 507 in the consumable device. The outlet port 510 of the consumable device is fluidically coupled to an outlet fluidic connector 1204, which is in turn fluidically coupled to the end portion 1214 of the outlet circuit segment 1213.

[0150] In at least some implementations of the fluidic circuit 1210 depicted in FIGS. 17 and 18, the fluidic circuit 1210 is capable of transitioning from a disconnected state (as shown in FIG. 17) to a connected state (as shown in FIG. 18), and vice versa, based on movements ofAttorney Docket No.: P37148-WO-1 the inlet fluidic connector 1203 and outlet fluidic connector 1204. Specifically, in at least some implementations, the inlet fluidic connector 1203 is movable to create a fluidic connection between the inlet circuit segment 1211 and a fluidic channel of the consumable device, and the outlet fluidic connector 1204 is movable to create a fluidic connection between the outlet circuit segment 1213 and a fluidic channel of the consumable device.

[0151] The inlet fluidic connector 1203 may be constructed as a movable portion or component of the inlet circuit segment 1211, a movable portion or component of the consumable device 500, a combination of movable portions or components from the inlet circuit segment 1211 and the consumable device 500, or a separate component from both the inlet circuit segment 1211 and the consumable device 500.

[0152] For example, in some embodiments, the inlet fluidic connector 1203 may take the form of a dispense tip or needle having a lumen that is fluidically coupled to the inlet circuit segment 1211 via a flexible and / or extendable end portion 1212 of the inlet circuit segment. Such a dispense tip or needle 1203 may further be mechanically coupled to a movable robotic arm controlled by a processor (e.g., the processor 1922) associated with the instrument 1001. Thus, in response to control signals generated by the processor, the dispense tip or needle 1203 may be moved to fluidically engage with the inlet port 508 of the consumable device, which may include an opening sized and shaped to receive the dispense tip or needle 1203. The dispense tip or needle 1203 may also be moved to fluidically disengage with the inlet port 508 in response to control signals generated by the processor.

[0153] The outlet fluidic connector 1204 may be constructed as a movable portion or component of the outlet circuit segment 1213, a movable portion or component of the consumable device 500, a combination of movable portions or components from the outlet circuit segment 1213 and the consumable device 500, or a separate component from both the outlet circuit segment 1213 and the consumable device 500.

[0154] For example, the outlet fluidic connector 1204 may take the form of an outlet tip or needle having a lumen that is fluidically coupled to the outlet circuit segment 1213 via a flexible and / or extendable end portion 1214 of the outlet circuit segment. Such an outlet tip or needle 1204 may further be mechanically coupled to a movable actuator of an actuator assembly controlled by a processor (e.g., the processor 1922) associated with the instrument 1001. Thus, in response to control signals generated by the processor, the outlet tip or needle 1204 may beAttorney Docket No.: P37148-WO-1 moved to fluidically engage with the outlet port 510 of the consumable device, which may include an opening sized and shaped to receive the outlet tip or needle 1204. The outlet tip or needle 1204 may also be moved to fluidically disengage with the outlet port 510 in response to control signals generated by the processor.

[0155] FIG. 19 illustrates an embodiment of a fluid transfer system 2200 with further optional features and elements added to the fluid transfer system 1200 described above in relation to FIGS. 17 and 18. Similar to fluid transfer system 1200, fluid transfer system 2200 includes a fluidic circuit 2210 operably coupled to a pump 2220, in which the fluidic circuit 2210 includes an inlet circuit segment 2211 and an outlet circuit segment 2213.

[0156] The inlet circuit segment 2211 shown in FIG. 19, however, is an optional variation of the inlet circuit segment 1211 shown in FIG. 17. Specifically, inlet circuit segment 2211 includes a flexible and / or extendable end portion in the form of an end tube 2212. End tube 2212 is mechanically and fluidically coupled to a movable dispense tip or needle 2203.

[0157] The inlet circuit segment 2211, in addition to directing fluids from fluid source 2201 towards the consumable device 600 via the end tube 2212 and dispense tip or needle 2203 (e.g., in response to propulsion forces or pressure imparted by the pump 2220 located upstream from the end tube 2212), is further capable of aspirating fluids from liquid containers and receptacles other than fluid source 2201, via the end tube 2212 and dispense tip or needle 2203 (e.g., in response to suction forces or pressure imparted by the pump 2220 located upstream from the end tube 2212). In some instances, the end tube portion 2212 of the inlet circuit segment 2211 has sufficient internal volume to hold liquids (e.g., a non-system fluid such as a reagent) aspirated from containers and receptacles other than fluid source 2201. As shown in FIG. 19, such containers and receptacles may include any number of reagent vials 2310 and a bulk reagent container assembly 2320. With reference to FIG. 19, reagent vials 2310 and bulk reagent container assembly 2320 are considered to be separate components from the fluid transfer system 2200 (which includes fluidic circuit 2210 and pump 2220), but hold one or more types of liquid capable of being accessed by the fluid transfer system 2200 (e.g., via a movable aspirate-and-dispense needle fluidically coupled to the end tube portion 2212). In some embodiments, one or more of the reagent vials 2310 can contain a target fluid that includes a synthesized macromolecule that is used for a sequencing operation. The synthesized macromolecule can be a surrogate molecule derived from a nucleic acid (e.g., Xpandomers). In some embodiments, the synthesized macromolecule is produced by any of the synthesisAttorney Docket No.: P37148-WO-1 instruments described herein and is conveyed to the reagent vial 2310 (which can function as a collection reservoir for the target fluid) by a fluid transfer system (e.g., a pump-drive fluid transfer system, a pipetting system, or any other fluid handling system that can convey the synthesized macromolecule from the synthesis instrument to the reagent vial 2310. The fluid transfer system can be within the synthesis instrument (e.g., the instrument 1002 described herein) or the sequencing instrument (e g., the instrument 1001). In other embodiments, the fluid transfer system can be a separate system that is shared by the synthesis instrument and the sequencing instrument.

[0158] As previously explained in connection with FIG. 17, the dispense tip or needle 2203 may be mechanically coupled to a movable robotic arm or gantry 2230 controlled by the electronic control system 1900 and / or another processor associated with the analyzer instrument. Thus, in response to control signals generated by the electronic control system 1900 and / or other processor, the dispense tip or needle 2203 may be moved to fluidically engage with any one of reagent vials 2310 and bulk reagent container assembly 2320. The pump 2220 located upstream from the end tube 2212 and dispense tip or needle 2203 may thereafter impart a suction force or pressure to cause fluid from the engaged container to be aspirated or drawn, via the dispense tip or needle 2203, into the end tube 2212 of the inlet circuit segment. Thus, the inlet circuit segment 2211, via end tube 2212 and dispense tip or needle 2203. is able to access fluids from any one of reagent vials 2310 and bulk reagent container assembly 2320, and this may occur in response to control signals generated by the processor (e.g., the processor 1922).

[0159] In some instances, the end tube portion 2212 of the inlet circuit segment 2211 has sufficient internal volume to hold liquids aspirated from any one of reagent vials 2310 (including, for example, the target fluid containing the synthesized macromolecule) and bulk reagent container assembly 2320. Each vial or container may hold a different type of fluid that may be accessed by the analyzer instrument during its operation, e.g.. for creating new mixtures, catalyzing reactions, carrying out assays, or performing sequencing analysis. For example, one vial or container may hold a salt buffer fluid. Another vial or container may hold a liquid containing protein pores. Another vial or container may hold a liquid containing lipids. Yet another vial or container may hold a liquid containing molecules synthesized from DNA, such as Xpandomers. In some embodiments, the synthesized molecules can be produced by any of the synthesis instruments disclosed herein and can be conveyed into one or more of theAttorney Docket No.: P37148-WO-1 reagent vials 2310 (which function as a collection reservoir for the target fluid containing the synthesized molecules).

[0160] For certain analyzer operations, such as nanopore-based sequencing, it may be desirable to aspirate a particular type of liquid from a first location, e.g.. one of reagent vials 2310 and bulk reagent container assembly 2320, and thereafter dispense or transfer that liquid to a second location within the analyzer instrument, e.g., a consumable device (such as device 100, 200, 300, or 400 described herein) or another receptacle for creating mixtures disposed within the analyzer. To accomplish this, with reference to FIG. 19, the fluid source 2201 coupled to the inlet circuit segment 2211 (and located upstream from the end tube 2212 and dispense tip or needle 2203) may house a hydraulic or system fluid whose flow through the fluidic circuit 2210 is controllable via a pump, which may either be pump 2220 or a different pump. The end tube portion 2212 of the fluidic circuit 2210, as discussed above, is capable of holding a certain volume of a liquid that had previously been aspirated via the movable dispense tip or needle 2203 from one of the reagent vials 2310 and bulk reagent container assembly 2320. Accordingly, the dispense tip or needle 2203 may thereafter be moved (e.g., by a mechanically coupled robotic arm in response to control signals generated the analyzer instrument's processor) to the second location where the aspirated liquid is to be dispensed, and the pump (e.g., pump 2220) can at that point generate a flow of the hydraulic or system fluid from fluid source 2201, through the inlet circuit segment 2211 in the direction of the end tube 2212, that in turn imparts a fluidic pressure or displacement force on the existing (aspirated) liquid in the end tube 2212 to cause that (aspirated) liquid to flow further downstream, i.e.. out of the dispense tip or needle 2203. In some instances, fluidic pressure or displacement force imparted on the existing (aspirated) liquid in the end tube 2212 can be measured using an optional pressure sensor 2321 disposed between the pump 2220 and the end tube 2212.

[0161] For example, with reference to FIG. 19, the dispense tip or needle 2203 may be moved to fluidically engage with an inlet port 608 of the consumable device 600 after having aspirated a liquid (e.g., a reagent or Xpandomer fluid) from one of the reagent vials 2310 and bulk reagent container assembly 2320. Upon a flow of the system fluid from fluid source 2201 being generated in the direction of the end tube 2212, the aspirated liquid from one of the reagent vials 2310 and bulk reagent container assembly 2320 is caused to flow back out of the dispense tip or needle 2203 and into a fluidic channel of the consumable device.Attorney Docket No.: P37148-WO-1

[0162] As another example, a particular receptacle of the bulk reagent container assembly 2320 may be used to create and house mixtures of different liquids aspirated from reagent vials 2310. In this instance, the dispense tip or needle 2203 may be moved to fluidically engage with the bulk reagent container assembly 2320 after having aspirated a reagent liquid from one of the reagent vials 2310. Upon a flow of the system fluid from fluid source 2201 being generated in the direction of the end tube 2212, the aspirated liquid from one of the reagent vials 2310 is caused to flow back out of the dispense tip or needle 2203 and into the mixture receptacle of the bulk reagent container assembly 2320.

[0163] With reference to FIG. 19, in some instances, the entirety of the inlet circuit segment 2211, including the end tube portion 2212. can be filled with the hydraulic or system fluid from fluid source 2201 before a liquid from one of the reagent vials 2310 and bulk reagent container assembly 2320 is aspirated. Thus, when a liquid from one of the reagent vials 2310 and bulk container assembly 2320 is aspirated into the end tube portion 2212 (e.g., via a movable dispense tip or needle 2203), the system fluid previously held in the end tube portion 2212 is displaced and / or replaced by the aspirated liquid. Furthermore, in instances where liquid from one of the reagent vials 2310 and bulk reagent container assembly 2320 is aspirated via a movable dispense tip or needle 2203, the dispense tip or needle 2203 may form an airtight seal with the container while liquid is being drawn into the end tube portion 2212. By filling the inlet circuit segment 2211 with system fluid prior to aspirating other liquids and additionally forming an airtight seal with the other liquid’s containers while another liquid is being drawn via the dispense tip or needle 2203, this helps ensure that no air bubbles are allowed to enter the inlet circuit segment 2211. The presence of air bubbles in the inlet circuit segment 2211 may adversely affect the subsequent dispensing of the aspirated liquid via the (movable) dispense tip or needle 2203 (e.g., out of the end tube portion 2212 and into a fluidic channel 2003 of the consumable device). For example, air bubbles present in the inlet circuit segment 2211 may introduce undesirable discontinuities in the (outgoing) flow of liquid subsequently- dispensed via the dispense tip or needle 2203.

[0164] As described above, the instrument 1001 can include an electronic control system 1900 including one or more processors that may generate electronic signals to control movement of the tip or needle 2203 as well as the aspirate-and-dispense functionality of the end tube portion 2212 coupled to the tip or needle 2203, described above.Attorney Docket No.: P37148-WO-1

[0165] With reference to FIG. 19, in some instances, one or more of reagent vials 2310 may be stored at room temperature. Additionally and / or alternatively, one or more of reagent vials 2310 may be stored at a cooled temperature below room temperature. For example, one or more of reagent vials 2310 may be disposed in or atop a reagent cooler supported by the housing 1100 of the instrument 1001, and one or more of reagent vials 2310 may be disposed at a different location outside the reagent cooler. The bulk reagent container assembly 2320 may be stored at either room temperature or at a cooled temperature. Moreover, in some embodiments, one or more of the reagent vials can be fluidically coupled to a synthesis instrument (not shown in FIG. 19, but which can be similar to the synthesis instrument 1002 or any of the synthesis instruments described herein). This arrangement can allow' for a synthesized molecule (e.g., an Xpandomer) to be conveyed from the synthesis instrument to the instrument 1001 (and in particular, to one or more reagent vials 2310, which can function as a collection reservoir). Such conveyance can occur, for example, automatically (i.e., with out human intervention).

[0166] FIGS. 20-22 provide additional details of the bulk reagent container assembly 2320 shown schematically in FIG. 19. With reference to FIG. 20, in some embodiments, a reagent assembly 3300 of the analyzer instrument (also partially visible in FIG. 9) includes all on-board reagents, which can include reagent vials 2310 (not shown in FIG. 20) and / or the bulk reagent container assembly 2320, as well as any other component for storing and / or maintaining the reagents within the instrument 1001. FIG. 21 shows one example of bulk reagent container assembly 2320 / 3320, which includes multiple different containers within a positioning container. As shown in FIG. 22, in some embodiments, one or more of the containers belonging to the bulk reagent container assembly 3320 (e.g., a receptacle used to create mixtures) may be disposed in the instrument 1001 at an angled tilt such that one section of a container’s bottom surface is lowered at angle with respect to another section of the container’s bottom surface. This causes the fluid housed in such a tilted container to tend to collect at the lowered end, which facilitates access to the fluid at the lowered end by the dispense tip or needle 2203.

[0167] As discussed, the dispense tip or needle 2203 is capable of being moved w ithin an analyzer instrument’s housing to fluidically engage with a number of other system elements as depicted in FIG. 19, including but not limited to one or more reagent vials 2310, one or more bulk reagent containers 2320, and one or more fluid inlets 608 of the consumable device. In some instances, one or more of these system elements may initially be disposed within theAttorney Docket No.: P37148-WO-1 housing of the analyzer in a sealed state. For example, any one of the reagent containers may initially have a top seal for the container so as to protect the container’s fluid from contamination, spillage, and / or evaporation. Similarly, each of the one or more fluid inlets 608 of consumable device 600 may initially have atop seal so as to protect the consumable device’s fluidic channels. For example, as described with reference to FIG. 4, in some embodiments, a top cover of the consumable device 600 (or any of the consumable devices described herein) can include a seal similar to the seal 423. In such instances, with reference to FIG. 19, one or more of those seals may be configured to be opened and / or penetrated by a movable pierce tip or needle 2205, e.g., through a downward movement or force applied by the pierce tip or needle 2205, such that an inner volume once covered by the seal may thereafter be accessed by the dispense tip or needle 2203, e.g., through a subsequent downward insertion of the dispense tip or needle 2203 into the inner volume.

[0168] The penetrable seals, which may be used with reagent vials 2310, bulk reagent containers 2320, and / or consumable device fluid inlets 608 as discussed, may be constructed from various penetrable materials and have various shapes and sizes, as known to those of ordinary skill in the art. In some embodiments, the penetrable seals are frangible members constructed from a polymer film, such as any form of polypropylene. In some embodiments, the frangible member can be constructed from bi-axially oriented polypropylene (BOP). In some embodiments, the frangible member can be constructed from a thin aluminum sheet. In yet other embodiments, the penetrable seals are thicker septums that can be penetrated by the pierce tip or needles described herein.

[0169] As previously mentioned, the dispense tip or needle 2203 may be mechanically coupled to a robotic arm controlled by the analyzer’s processor (e g., the processor 1922). Similarly, the pierce tip or needle 2205 may also be mechanically coupled to a robotic arm controlled by the analyzer’s processor (e g., the processor 1922). FIG. 19 illustrates an example where both the dispense tip or needle 2203 and the pierce tip or needle 2205 are coupled to and movable by the same robotic gantry 2230, but this is not required. As would be understood by those of ordinary7skill in the art, the mechanical actuators associated with the dispense tip or needle 2203 and the pierce tip or needle 2205 can take various forms, and a particular implementation may be chosen depending on the desired degrees of freedom in movement, range of allowable movement space or volume, movement force, and / or movement speed, among other factors.Attorney Docket No.: P37148-WO-1

[0170] With reference to FIG. 19, the consumable device 600 is schematically illustrated as having four individual fluid outlets 610. One example of a consumable device having four individual fluid outlets is consumable device 300 previously described above. In other instances, the consumable device used with the fluid transfer system 2200 and fluidic circuit 2210 may have a greater or fewer number of individual fluid outlets 610. As discussed further below, each of the individual fluid outlets 610 is capable of being fluidically aligned with and coupled to an outlet fluidic connector, shown in the example of FIG. 19 as an outlet tip or needle 2204. The outlet tip or needle 2204 has a lumen that is fluidically coupled to the outlet circuit segment 2213 via a flexible and / or extendable end tube portion 2214 of the outlet circuit segment.

[0171] As discussed in connection with FIGS. 17 and 18, and illustrated in one example in FIG. 19, outlet tip or needle 2204 is mechanically coupled to an outlet actuator assembly 2400, which is configured to generate movements of outlet tip or needle 2204 to align the outlet tip or needle 2204 with a particular individual fluid outlet 610 of the consumable device, as well as movements of outlet tip or needle 2204 to fluidically engage or disengage with an aligned fluid outlet of the consumable device. In the example of FIG. 19, the outlet actuator assembly 2400 is configured to move the outlet tip or needle 2204 in the horizontal direction to cause alignment with a particular fluid outlet, and to move the outlet tip or needle 2204 in the vertical direction to cause fluidically engagement or disengagement with an aligned fluid outlet.

[0172] The outlet actuator assembly 2400 may respond to applied electrical forces, mechanical forces, magnetic forces, or a combination of the foregoing to cause one or more movements of the outlet tip or needle 2204, such as a horizontal movement to become aligned with an individual fluid outlet of the consumable device 600 or a vertical movement to fluidically engage or disengage with an aligned fluid outlet. Such forces applied to the outlet actuator assembly 2400, and the corresponding movement triggered in the outlet tip or needle 2204, may be generated based on or in response to control signals from electronic control system 1900 and / or another processor associated with the analyzer instrument 1001.

[0173] In some implementations, the outlet actuator assembly 2400 includes one or more actuators or actuator members, such as movable pins, bars, lift brackets, and toggle cams, that are configured to move between or among various allowable positions within the outlet actuator assembly 2400 in response to an electrical, mechanical, and / or magnetic force imparted on the actuator member, such a movement by the actuator member in turn causing the outlet tip orAttorney Docket No.: P37148-WO-1 needle 2204 to move a certain way. For example, the outlet actuator assembly 2400 may include a lift bracket mechanically fastened to the outlet tip or needle 2204 that responds to a force applied to the lift bracket by moving up or down, in turn causing the outlet tip or needle 2204 to also move up (e.g., to fluidically disengage from a fluid outlet of the consumable device) or down (e.g., to fluidically engage with an aligned fluid outlet of the consumable device). In some instances, the force applied to such a lift bracket may be a mechanical force directly imparted on the lift bracket in either the upward or downward direction. For example, with reference to FIG. 19, a downward mechanical force may be directly imparted on the lift bracket by a downward movement of the pierce tip or needle 2400 that results in direct contact with the lift bracket.

[0174] Additionally or alternatively, the outlet actuator assembly 2400 may include a horizontal positioning bar coupled to the outlet tip or needle 2204 (e.g., either directly or via the above-described lift bracket). In such a case, the actuator bar member may respond to a force applied to it (either directly or indirectly) by shifting to the left or to the right, in turn causing the outlet tip or needle 2204 to also move to the left (e.g., to become fluidically aligned with a first fluid outlet of the consumable device) or to the right (e.g., to become fluidically aligned with a second fluid outlet of the consumable device). In some instances, the force applied to such a horizontal positioning bar may be a mechanical force indirectly imparted on the bar member in either the left or right direction. For example, with reference to FIG. 19. a downward mechanical force may be directly imparted on a first actuator pin (from the outlet actuator assembly 2400) by a downw ard movement of the pierce tip or needle 2205 that results in a downward movement of the contacted actuator pin, which in turn contacts a toggle cam that rotates to the left to apply a leftward mechanical force to the bar member. Similarly, a downward mechanical force may be directly imparted on a second actuator pin (from the outlet actuator assembly 2400) by a downward movement of the pierce tip or needle 2205 that results in a downw ard movement of the contacted actuator pin, which in turn contacts a toggle cam that rotates to the right to apply a rightward mechanical force to the bar member.

[0175] While FIG. 19 depicts an outlet actuator assembly 2400 that is mechanically coupled to and causes movements of outlet tip or needle 2204 to create fluidic alignment with and coupling to individual fluid outlets 610 of the consumable device, in alternative embodiments, a different outlet actuator assembly (not shown in FIG. 19) may be used to cause movements of one or more individual fluid outlets 610 of the consumable device (e.g., in theAttorney Docket No.: P37148-WO-1 horizontal and / or vertical direction), rather than movements of the outlet tip or needle 2204, to create fluidic alignment and / or coupling between a fluid outlet and the outlet tip or needle 2204.

[0176] In yet other embodiments, an outlet actuator assembly may cause movements by both (1) a fluid outlet 610 of the consumable device, and (2) the outlet tip or needle 2204, to create fluidic alignment and / or coupling between them. For example, an outlet actuator assembly may be configured to cause movements by one or more fluid outlets of the consumable device in the horizontal direction to create alignment with the outlet tip or needle 2204, and movements by the outlet tip or needle 2204 to create fluidic engagement or disengagement with an aligned fluid outlet.

[0177] FIGS. 23-24 depict two perspective views of an embodiment of outlet actuator assembly 3400, which may be used to implement the outlet actuator assembly 2400 from FIG. 19 to generate movements of an outlet needle 3204 to cause fluidic alignment and / or coupling with particular individual fluid outlets of the consumable device (e.g., the consumable device 400). With reference to FIGS. 25 and 26, the outlet needle 3204 has a lumen that is physically and fluidically coupled to a flexible and / or extendable end tube 3214 of the outlet circuit segment. When the outlet needle 3204 is fluidically engaged with a particular fluid outlet of the consumable device, the lumen of outlet needle 3204 directs fluid flows in the direction of the end tube 3214 and away from the engaged fluid outlet of the consumable device. As shown in FIGS. 25 and 26, the outlet needle 3204, via end tube 3214, directs outgoing fluid flows from the engaged fluid outlet of the consumable device tow ards an anti-siphoning valve 3225 at the other end of the end tube 3214. In some embodiments, the anti -siphoning valve 3225 may be used as the anti-siphoning valve 2225 from FIG. 19. With reference to FIG. 19. antisiphoning valve 2225 prevents outgoing fluid flows from the consumable device, which have already entered the outlet circuit segment, from flowing backwards in the direction of the consumable device. The anti-siphoning valve 2225 may also be operable to achieve reliable fluidic connections at the consumable device. In an embodiment, prior to extracting the dispense tip or needle 2203 from the consumable device fluid inlets 608, the anti-siphoning valve 2225 may be closed and a small amount of fluid is pumped into the consumable device, thereby pressurizing the fluidic channel. The dispense tip or needle 2203 is then removed from the fluid inlets 608, which causes a small amount of fluid to fdl the inlet “cone” on the backer of the consumable device. This small amount of left-over fluid is used during the reinsertion of the dispense tip or needle 2203 to achieve a liquid-to-liquid connection and preventAttorney Docket No.: P37148-WO-1 introduction of air bubbles into the fluidic lane. As shown in FIGS. 23 and 26, the outlet needle 3204, via end tube 3214, directs outgoing fluid flows from the engaged fluid outlet of the consumable device (e.g., device 400 from FIGS. 5-6 or device 600 from FIG. 19) towards an anti-siphoning valve at the other end of the end tube 3214.

[0178] With reference to FIG. 23, the outlet actuator assembly 3400 includes a lift bracket 3401 mechanically fastened to the outlet needle 3204 such that each movement of the lift bracket 3401 causes a corresponding movement by the outlet needle 3204. The lift bracket3401 and outlet needle 3204 are movably coupled to a vertical guide 3403 that guides and / or constrains both the lift bracket 3401 and outlet needle 3204 in their movements in the vertical direction.

[0179] As shown in FIGS. 23 and 24, the lift bracket 3401 has an indented upper surface3402 configured to be directly contacted by the pierce tip or needle 2205 upon a downward movement of the pierce tip or needle 2205. The lift bracket 3401 responds to a downward mechanical force directly applied to it, via the pierce tip or needle 2205, by moving down. The downward movement of the lift bracket 3401 in turn causes the outlet needle 3204 to also move dow n to fluidically engage with an aligned fluid outlet of the consumable device.

[0180] FIG. 24 show s the lift bracket 3401 when viewed from the rear. As shown in FIG.24, a portion of the lift bracket 3401 (enclosed within the vertical guide 3403) is contacted by a lift arm 3405 at a first end 3406 of the lift arm. The lift arm 3405 rotates about a pivot 3408 disposed between the first end 3406 and a second end 3407 of the lift arm. The second end 3407 of the lift arm is contacted by an actuator pin 341 1. The actuator pin 3411 has an indented upper surface 3412 configured to be directly contacted by the pierce tip or needle 2205 upon a downward movement of the pierce tip or needle 2205. With reference to FIG. 24, the actuator pin 3411 responds to a downw ard mechanical force directly applied to it, via the pierce tip or needle 2205. by moving down. The downward movement of the actuator pin 3411 in turn causes the second end 3407 of the lift arm 3405 to also move downwards, which in turn causes the lift arm 3405 to rotate about the pivot 3408 and the first end 3406 of the lift arm to move upwards. The upw ard movement of the first end 3406 of the lift arm, which contacts the lift bracket 3401 (enclosed within the vertical guide 3403), causes the lift bracket 3401 to also move upward. The upward movement of the lift bracket 3401 in turn causes the outlet needle 3204 to also move up to fluidically disengage with an aligned fluid outlet of the consumable device.Attorney Docket No.: P37148-WO-1

[0181] With reference to FIGS. 23 and 24, the outlet actuator assembly 3400 also includes a horizontal positioning bar 3420. The horizontal positioning bar 3420 is mechanically fastened to the vertical guide 3403 such that each horizontal movement of the horizontal positioning bar 3420 (to the left or right) causes a corresponding movement by vertical guide 3403 (to the left or right). As discussed, the vertical guide 3403 is coupled to the lift bracket 3401 and outlet needle 3404 and guides and / or constrains both the lift bracket 3401 and outlet needle 3204 in their movements in the vertical direction. Thus, when the vertical guide 3403 moves horizontally to the left or right in response to a movement of the horizontal positioning bar 3420, the horizontal movement of the vertical guide 3403 also causes a corresponding horizontal movement of both the lift bracket 3401 and outlet needle 3204. In some embodiments, such a horizontal movement of the outlet needle 3204 causes it to become fluidically aligned with a particular fluid outlet of the consumable device. Once the outlet needle 3204 is aligned with a particular fluid outlet, the outlet needle 3404 may be caused to fluidically engage with the aligned fluid outlet by a downward mechanical force imparted by the pierce tip or needle 2205, as previously described.

[0182] With reference to FIGS. 23 and 24, the movement of the horizontal positioning bar 3420, and thus the horizontal movement of the outlet needle 3204 to come into alignment with a particular fluid outlet, is triggered by four actuator pins 3413a, 3413b, 3413c, and 3413d. Each of the four actuator pins is associated with a particular one of four fluid outlets of the consumable device. Each of the four actuator pins 3413a, 3413b, 3413c, and 3413d has a respective indented upper surface configured to be directly contacted by the pierce tip or needle 2205 upon a downward movement of the pierce tip or needle 2205.

[0183] With reference to FIGS. 23 and 24, each of the four actuator pins 3413a, 3413b, 3413c, and 3413d responds to a downward mechanical force directly applied to it, via the pierce tip or needle 2205, by moving down. The downward movement of actuator pin 3413a in turn causes the outlet needle 3204 to become fluidically aligned with a particular fluid outlet that is associated with actuator pin 3413-a. The downward movement of actuator pin 3413b in turn causes the outlet needle 3204 to become fluidically aligned with a particular fluid outlet that is associated with actuator pin 3413-b. The downward movement of actuator pin 3413c in turn causes the outlet needle 3204 to become fluidically aligned with a particular fluid outlet that is associated with actuator pin 3413-c. The downward movement of actuator pm 3413d in turn causes the outlet needle 3204 to become fluidically aligned with a particular fluid outlet that isAttorney Docket No.: P37148-WO-1 associated with actuator pin 3413-d. This is because, with reference to FIGS. 23 and 24, the downward movement of a given actuator pin 3413a, 3413b, 3413c. or 3413d causes that actuator pin to contact one or more toggle cams configured to rotate to either the left or right to apply a leftward or rightward mechanical force to the horizontal positioning bar 3420.

[0184] As previously explained, the horizontal positioning bar 3420 is mechanically fastened to the vertical guide 3403 such that each horizontal movement of the horizontal positioning bar 3420 (to the left or right) causes a corresponding movement by vertical guide 3403 (to the left or right). And when the vertical guide 3403 moves horizontally to the left or right in response to a movement of the horizontal positioning bar 3420, the horizontal movement of the vertical guide 3420 also causes a corresponding horizontal movement of the outlet needle 3404. The movement of the outlet needle 3404 to a particular horizontal position causes the outlet needle 3404 to come into fluidic alignment with a particular fluid outlet of the consumable device.

[0185] FIGS. 27, 28A, and 28B depict an alternative embodiment of outlet actuator assembly 4400, which may also be used as the outlet actuator assembly 2400 from FIG. 19 or in any instrument described herein. The outlet actuator assembly 4400 is shown as being operably coupled to a portion of the interface assembly 1500 (described below) with the consumable device 400 (see FIGS. 4 and 5) coupled within the interface assembly. The outlet actuator assembly 4400 is configured to generate movements of two outlet needles 4204-1 and 4204-2 to cause fluidic alignment and / or coupling with particular individual fluid outlets 410A, 410B, 410C and 410D of the consumable device. Each of the outlet needles 4204-1 and 4204- 2 has a lumen that is physically and fluidically coupled to a respective flexible and / or extendable end tube portions 4214-1 or 4214-2 of the outlet circuit segment. When either outlet needle is fluidically engaged with a particular fluid outlet 410A, 410B, 410C and 410D of the consumable device 400, the lumen of the outlet needle directs fluid flows in the direction of the respective end tube portion and away from the engaged fluid outlet of the consumable device. In some instances, both of the two end tube portions 4214-1 and 4214-2 are configured to direct outgoing fluid flows from the consumable device towards an anti-siphoning valve at the other end of the end tube portions 4214-1 or 4214-2.

[0186] With reference to FIG. 27, the outlet actuator assembly 4400 includes two lift brackets 4401-1, 4401-2 mechanically fastened to a respective outlet needle 4204-1, 4204-2 such that each movement of lift bracket 4401-1 or 4401-2 causes a corresponding movementAttorney Docket No.: P37148-WO-1 by the respective outlet needle 4204-1 or 4204-2. As show n in FIG. 27, each of the tw o lift brackets 4401-1, 4401-2 has an indented upper surface configured to be directly contacted by the pierce tip or needle 4205 upon a downward movement of the pierce tip or needle 4205. Each lift bracket responds to a dow w ard mechanical force directly applied to it, via the pierce tip or needle 4205, by moving down. The downward movement of either of lift brackets 4401- 1 or 4401-2 in turn causes a respective outlet needle 4204-1 or 4204-2 to also move down to fluidically engage with an aligned fluid outlet of the consumable device.

[0187] With reference to FIGS. 27, 28A, and 28B, the outlet actuator assembly 4400 also includes a horizontal positioning bar 4420. The horizontal positioning bar 4420 is mechanically fastened to a vertical guide 4403 such that each horizontal movement of the horizontal positioning bar 4420 (to the left or right) causes a corresponding movement by vertical guide 4403 (to the left or right). The vertical guide 4403 is coupled to both (a) lift brackets 4401-1 and 4401-2 and (b) outlet needles 4204-1 and 4204-2 and guides and / or constrains those components in their movements in the vertical direction. Thus, when the vertical guide 4403 moves horizontally to the left or right in response to a movement of the horizontal positioning bar 4420, the horizontal movement of the vertical guide 4403 also causes a corresponding horizontal movement of both (a) lift brackets 4401-1 and 4401-2 and (b) outlet needles 4204-1 and 4204-2. In some embodiments, such a horizontal movement of outlet needles 4204-1 and 4204-2 causes each needle to become fluidically aligned with a particular fluid outlet of the consumable device. Once the outlet needles 4204-1 and 4204-2 are aligned with tw o respective fluid outlets, either of the outlet needles 4204-1 or 4204-2 may be caused to fluidically engage with the respective aligned fluid outlet by a downward mechanical force imparted by the pierce tip or needle 4205.

[0188] With reference to FIGS. 28A and 28B, the movement of the horizontal positioning bar 4420, and thus the horizontal movement of the outlet needles 4204-1 and 4204-2 to come into alignment with a particular pair of fluid outlets, is triggered by two actuator pins 4413 A and 4413B. Each of the two actuator pins is associated with a particular pair or subgroup of two fluid outlets of the consumable device. Each of the two actuator pins 4413A and 4413B has a respective indented upper surface configured to be directly contacted by the pierce tip or needle 4205 upon a downward movement of the pierce tip or needle 4205.

[0189] With reference to FIGS. 28A and 28B, each of the two actuator pins 4413 A and 4413B responds to a downw ard mechanical force directly applied to it, via the pierce tip orAttorney Docket No.: P37148-WO-1 needle 4205, by moving down. The downward movement of actuator pin 4413A in turn causes the outlet needles 4204-1 and 4204-2 to become fluidically aligned with a first pair or subgroup of fluid outlets of the consumable device 400. As shown in FIG. 28 A, the first pair or subgroup includes the first outlet 410A and third outlet 410C when viewed from the left. The downward movement of actuator pin 4413B in turn causes the outlet needles 4204-1 and 4204-2 to become fluidically aligned with a second pair or subgroup of fluid outlets of the consumable device 400. As shown in FIG. 28B. the second pair or subgroup includes the second outlet 410B and fourth outlet 410D when from the left.

[0190] In either case, with reference to FIGS. 28A and 28B. the downward movement of a given actuator pin 4413 A or 4413B causes that actuator pin to contact a toggle cam 4430 configured rotate to either the left or right to apply a leftward or rightward mechanical force to the horizontal positioning bar 4420. Said another way, the toggle cam 4430 functions as a force transfer link that transfers the vertical (e.g.. downw ard) movement of the actuator pins 4413 A. 4413B to a horizontal movement of the positioning bar 4420. The horizontal positioning bar 4420 is mechanically fastened to the vertical guide 4403 such that each horizontal movement of the horizontal positioning bar 4420 (to the left or right) causes a corresponding movement by vertical guide 4403 (to the left or right). And when the vertical guide 4403 moves horizontally to the left or right in response to a movement of the horizontal positioning bar 4420. the horizontal movement of the vertical guide 4403 also causes a corresponding horizontal movement of the outlet needles 4204-1 and 4204-2. The movement of the outlet needles 4204-1 and 4204-2 to a particular horizontal position causes the outlet needles 4204-1 and 4204-2 to come into fluidic alignment with a particular pair of fluid outlets of the consumable device 400.

[0191] With reference to FIG. 19, the outlet circuit segment 2213 is coupled to a wash station 2250 disposed between the anti-siphoning valve 2225 and a fluid waste container 2202, which sits at the destination end of the outlet circuit segment 2213 of the fluidic circuit 2210. FIG. 29 depicts an embodiment of the wash station 3250 that can function as the wash station 2250 shown in FIG. 19. FIG. 30 is a schematic illustration of the wash station 2250 and FIGS. 31A-31D show the w ash station 2250 in various configurations of use. In some instances, the wash station 2250 is configured to receive the movable dispense tip or needle 2203 (or any of the dispense tip or needles described herein) to allow the dispense tip or needle 2203 to wash itself using system fluid from fluid source 2201. For example, the dispense tip or needle 2203Attorney Docket No.: P37148-WO-1 may be mechanically coupled to a movable robotic arm controlled by the electronic control system 1900 and / or another processor associated with the analyzer instrument. Thus, in response to control signals generated by the electronic control system 1900 and / or other processor, the dispense tip or needle 2203 may be moved to fluidically engage with a recessed well 2251 of the wash station 2250 having a well opening sized to receive the dispense rip or needle 2203. Pump 2220 can at that point generate a flow of the system fluid from fluid source 2201, through the inlet circuit segment 2211, towards the dispense tip or needle 2203 that has been inserted into the wash station 2250. Upon dispensing the system fluid via the dispense tip or needle 2203 into the recessed well of the wash station 2250, the system fluid fills up the well 2251 and is able to cleanse the dispense tip or needle 2203 inserted into the well. The first wash pump 2252 and / or the second wash pump 2253 produce flow of the wash fluid away from the wash station 2250 (e.g., to the waste container 2202 shown in FIG. 19 or a waste container 3202 shown in FIG. 32).

[0192] Referring to FIGS. 30 and 31A-31D, when the wash station 2250 is inactive, flow from the anti-siphon valve 2225 is conveyed into the wash station as shown by arrow AA and is routed to the wash station outlet and towards the waste container as shown by arrow BB. The flow is routed via the bypass channel 2254 as shown by arrow CC in FIG. 31 A. During a wash cycle, the dispense tip 2203 is inserted into the well 2251 (FIGS. 31B and 31C) and the fluid is conveyed into the well. If the excess wash fluid is conveyed, it can be drained (via the first pump 2252 and / or the second pump 2253) from the overflow area (as shown by arrow DD) and out towards the waste container. When the tip wash is completed, the dispense tip 2203 can be moved out of the well 2251 and the remaining wash fluid can be drained (via the second pump 2253) from the overflow area (as shown by arrow EE) and out towards the waste container (e.g., waste container 2202 from FIG. 19 or waste container 3202 shown in greater detail in FIG. 32).

[0193] FIGS. 33 and 34 are perspective views that show how the different components of the fluid transfer system 1200 (one implementation of which is described schematically in connection with FIG. 19 as the fluid transfer system 2200) may be physically disposed within and supported by the housing 1100 of the analyzer instrument 1001.

[0194] In some instances, the dispense tip or needle 2203, 3203 (see FIG. 9) is a nondisposable dispense tip or needle configured to be used by the same analyzer instrumentAttorney Docket No.: P37148-WO-1 throughout multiple fluidic engagements of the dispense tip or needle with other components of the analyzer instrument (e.g., different reagent vials bulk reagent container assembly).

[0195] In some embodiments, a dispense tip 3203 can be used as the dispense tip 2203 previously described in connection with FIG. 19. Dispense tip 3203 (or any dispense tips described herein) can form a fluidic seal while it is inserted into and / or fluidically engaged with a fluid container (e.g., to aspirate liquid from one of reagent vials 2310 / 3310 and bulk reagent container assembly 2320 / 3320) or a fluid inlet of the consumable device (e.g., to dispense the previously aspirated liquid).

[0196] The dispense tip 3203 (or any dispense tips described herein) can be any suitable dispense tip, such as those described in U.S. Patent Publication No. 2022 / 0291192, entitled “Interface of Automated Fluid Injection,” which is incorporated herein by reference in its entirety. The dispense tip 3203 (or any dispense tips described herein) can be made of stainless steel or another metal or metal alloy and can be coated with a low friction, hydrophobic material, such as a fluoropolymer (i.e., polytetrafluoroethylene (PTFE) or fluorinated ethylene propylene (FEP)). Both the outer surface and the interior surface of the dispense tip 2203, 3203 can be coated. In some embodiments, the coating is at least 1, 2, 3, 4, or 5 um thick. Use of metal for the dispense tip over other materials, such as plastic, provides the dispense tip with increased structural strength and allows the dispense tip to be used repeatedly before needing to be replaced. Use of metal also allows the dispense tip to function as a probe, such as a liquid level probe using capacitive sensing. The length of the dispense tip 2203, 3203 can be sufficiently long to ensure that the dispense tip can reach the bottom of the reagent reservoirs that are used. For example, the length can be between about 20 to 200 mm, or between about 40 to 100 mm, or between about 60 to 80 mm, or at least 20, 30, 40, 50, 60, 70, 80, 90, or 100 mm in length. In some embodiments, the volume of the lumen of the dispense tip 2203, 3203 can be sufficiently large to ensure that the entire reagent and / or sample volume that is to be dispensed can be held within the lumen of the dispense tip 2203. 3203 in order to prevent the reagents and / or sample from being aspirated into the tubing, which may cause the waste of precious reagents. For example, the swept volume of the dispense tip 2203, 3203 can be between 10 and 100 ul, or at least 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100 ul.

[0197] The outer diameter of the dispense tip 2203, 3203 can be slightly greater than the diameter of a lumen of a fluid inlet of the consumable device. The tip of dispense tip 2203, 3203 may be gently tapered to facilitate insertion into the lumen of a fluid inlet of theAttorney Docket No.: P37148-WO-1 consumable device, and to facilitate formation of a fluidic seal. In some embodiments, the taper can be between about 5 to 30 degrees, or be about 5, 10, 15, 20. 25. or 30 degrees.

[0198] In some embodiments, a ferrule can be placed on the proximal end of dispense tip in order to provide an attachment feature that can be used to attached the dispense tip to another component of the analyzer instrument (e.g., the end tube 2212 of inlet circuit segment 2211 from FIG. 19). In addition, the ferrule may also act as: (1) a fluidic sealing surface between the dispense tip and another component of the fluidic circuit 2210 (e.g., end tube 2212), and / or (2) an electrical connection between the dispense tip and the analyzer instrument’s electronic control system 1900 so that the dispense tip can function as a sensor in a capacitive liquid level detection circuit. The ferrule may be uncoated and can be either straight or slightly tapered. In some embodiments, the dispense tip 2203, 3203 may also be used to puncture a seal covering one or more fluid inlets of the consumable device.

[0199] Any of the piercing tips described herein (e.g.. the piercing tip 2205 in FIG. 19 and the piercing tip 4205 in FIG. 27) can be of any suitable piercing tip or tool, such as those described in U.S. Patent Publication No. 2022 / 0291192, entitled “Interface of Automated Fluid Injection.” which is incorporated herein by reference in its entirety. In some embodiments, the piercing tool 2205, 4205 can be made of metal or metal alloy, such as stainless steel. In other embodiments, the piercing tool 2205, 4205 can be made of a polymer or ceramic material. The piercing tool 2205, 4205 can have a distal end with a sharp tip for piercing the seal and a proximal end with an attachment feature or mechanism, such as internal screw threads, for attaching the piercing tool 2205, 4205 to another component of the analyzer instrument (e.g., movable robotic arm).

[0200] FIGS. 35-50 show various views of one embodiment of the interface assembly 1500 (also partially visible in FIG. 9) of the analyzer instrument 1001. As used herein, an “interface assembly” (such as the example interface assembly 3500 from FIG. 35) is a physical interface of the analyzer instrument (such as instrument 1001) that provides one or more of a mechanical coupling, fluidic coupling, electrical coupling, and thermal coupling with a consumable device (e.g., the consumable device 400) inserted into and / or received by the analyzer instrument. In one embodiment, as shown in FIG. 36, the interface assembly 3500 includes a clamp top subassembly 3510, a clamp base subassembly 3530, and a cooling assembly 3550, and interfaces with an electronic circuit assembly 1950 of the electronic control system 1900. As shown in FIG. 35, the interface assembly 3500 is coupled to and supports the outlet actuatorAttorney Docket No.: P37148-WO-1 assembly 3400. Specifically, the outlet actuator assembly 3400 is coupled to the top plate 3514 of the top clamp subassembly 3510. In other embodiments, the interface assembly 3500 can be coupled to any suitable outlet actuator assembly (e.g., the outlet actuator assembly 4400).

[0201] The clamp top subassembly 3510 includes atop plate 3514 (see, e.g., FIGS. 38-39), a pressure plate 3516 (see, e.g., FIG. 40), a rear support 3512. a front slot cover 3522, and two side guide rails 3521. The clamp top subassembly 3510 defines an upper boundary of an internal region within which a consumable device (e.g., the consumable device 400) and / or chip package can be received. The clamp top subassembly 3510 also facilitates alignment and coupling of the consumable device 400 within the internal region. Additionally , the clamp top subassembly 3510 also facilitates mounting of the outlet actuator assembly 3400 and access to the inlet openings 408 and outlet openings 410 of the consumable device.

[0202] Referring to FIGS. 38 and 39, the top plate 3510 includes a surface to which the outlet actuator assembly 3400 is mounted and defines an opening 3515, which along with the opening 3517 provides access for any of a pierce tip (e.g., the pierce tip 2205 or the pierce tip 4205), a dispense tip (e.g., the dispense tip 2203 or the dispense tip 3203), and / or an outlet tip (e.g., the outlet tip 2204 or the outlet tip 3204) to the consumable device 400 to perform the functions described herein. For example, in use the pierce tip 4205 can access the top cover 422 of the consumable device (via the openings 3515, 3517) to puncture the seals 423, 424 to provide fluidic access to the nanopore chip within the consumable device. The dispense tip 3203 can access the inlet openings 408 (via the openings 3515, 3517) to convey fluids into the consumable device 400. The outlet tip 3204 can access the outlet openings 410 (via the openings 3515, 3517) to convey fluids out of the consumable device 400. Moreover, as described herein, the pierce tip 4205 can also manipulate the outlet actuator assembly 3400 to select the desired fluidic channels within the consumable device 400.

[0203] As shown in FIG. 40, the pressure plate 3516 is coupled below the top plate 3510 and provides a surface against which the top cover 422 of the consumable device engages when the consumable device 422 is loaded into the instrument 1001. The pressure plate is biased downward (i.e., towards the consumable device 400 and the clamp base subassembly 3530 by a set of springs 3518. The springs 3518 can be any suitable type of spring, such as a wave spring, a coil spring, or a leaf spring. In other embodiments, the pressure plate can be biased downward by an elastic member or any other suitable biasing member. Biasing the pressure plate 3516 against the consumable device 400 can ensure that the consumable device 400 isAttorney Docket No.: P37148-WO-1 coupled within the internal region of the interface assembly 3500 with a sufficient force that is maintained within a desired tolerance. As described above, the pressure plate 3516 defines the opening 3517 that is aligned with the opening 3515 of the top plate 3514.

[0204] The side guide rails 3521 are coupled to the top plate 3514 and provide guide surfaces against which portions of the consumable device 400 can ride during insertion of the consumable device into the interface assembly 3500. The inlet ramp 3520 is also coupled to the guide rails 3521 and / or the top plate 3514.

[0205] The clamp base subassembly 3530 includes the bottom mount plate 3534. two side plates 3535, a bottom chassis plate 3536 and a lifter 3537. The clamp base subassembly 3530 (and / or the electronic circuit assembly 1950) defines a lower boundary of the internal region within which the consumable device 400 and / or chip package can be received. The clamp base subassembly 3530 also facilitates alignment and coupling of the consumable device 400 within the internal region. Additionally, the clamp base subassembly 3530 also includes and / or is coupled to the clamp mechanism 3540.

[0206] Referring to FIGS. 36 and 41, the bottom mount plate 3534 includes two alignment pins 3531 and defines an opening 3533. As shown in FIGS. 36, 38 and 42. the electronic circuit assembly 1950 (which can be the printed circuit board, as shown) is coupled to the top surface of the bottom mount plate 3534. In this manner, the electronic circuit assembly 1950 defines a lower boundary' of the internal region within which the consumable device 400 and / or chip package can be received and also provides a surface (and / or components, such as the connectors 1951) that contact or engage with the consumable device. In this manner, on condition that the consumable device 400 is loaded within the interface assembly 3500, the consumable device 400 can be electronically coupled to the instrument 1001 via the electronic circuit assembly 1950. Specifically, as shown in FIG. 46 the connectors 1951 of the electronic circuit assembly 1950 can be maintained in contact with the corresponding connectors 416 of the consumable device 400.

[0207] Referring to FIGS. 36, 44 and 46, the alignment pins 3531 extend through openings in the electronic circuit assembly 1950 and into the internal region within which the consumable device 400 is loaded. The alignment pins 3531 can be aligned with corresponding openings 416 in the consumable device such that when the clamp mechanism 3540 is actuated to clamp the consumable device within the interface assembly 3500, the alignment pins 3531Attorney Docket No.: P37148-WO-1 are matingly received within the corresponding openings 416. Moreover, as shown in FIG. 46, a grounding spring 3532 is disposed about the alignment pins 3531. When the consumable device 400 is loaded, one end of the grounding spring 3532 is in contact with the printed circuit board 412 of the consumable device 400 and the other end of the grounding spring 3532 is grounded to the electronic circuit assembly 1950 or any other suitable ground. In this manner, the grounding spring 3532 can establish a conductive path from the electronics of the consumable device 400 to ground. This provides a suitable path for electrostatic discharge (ESD) and can also reduce other forms of noise that can disrupt the signals from the consumable device 400.

[0208] The opening 3533 of the bottom mount plate 3534 is aligned with an opening 1952 of the electronic circuit assembly 1950. The openings 3533 and 1952 provide access through which the cooling assembly 3550 can access the consumable device 400, as described in more detail below.

[0209] The bottom mount plate 3534 is coupled to the side plates 3535, which are themselves coupled to the bottom chassis plate 3536 to form the supporting structure for the interface assembly 3500. Referring to FIGS. 37, 38, and 41, the clamp mechanism 3540 includes two outer plates 3545, a handle 3541 and two clamp actuator arms 3542. The handle 3541 and clamp actuator arms 3542 are movably coupled to the side plates 3535 and the outer plates 3545. Additionally, each clamp actuator arm 3542 is coupled to the top plate 3514 of the top clamp assembly 3510. Specifically, each clamp actuator arm 3542 is coupled between one of the side plates 3535 and one of the outer plates 3542. Thus, when the handle 3541 is rotated (see arrow FF in FIG. 50), the clamp actuator arms 3542 rotate between the side plates 3535 and the outer plates 3545. The rotation of the clamp actuator arms 3542, in turn, produce a vertical movement of the top plate 3514. Thus, movement of the handle 3541 can move the top plate 3514 between an opened position (in which the consumable device 400 can be inserted into the interface assembly 3500, see FIG. 48) and a closed position (in which the consumable device 400 is coupled or locked within the interface assembly 3500, see FIG. 50).

[0210] The outer plates each define two cam slots 3546 and each actuator arm includes two guide pins 3543. When the clamp actuator arms 3542 are rotated between the side plates 3535 and the outer plates 3545, the guide pins 3543 move within the cam slots 3546. Thus, the movement of the actuator arms 3542 is guided by the cam slots 3546 to produce the desired motion of the clamp actuator arms 3542, and therefore the top plate 3514. Specifically, theAttorney Docket No.: P37148-WO-1 cam slots 3546 can be shaped and sized to produce motion limits for the top plate 3514. A clamp sensor 1933 is coupled to the clamp assembly to provide a signal associated with the clamp status.

[0211] FIG. 42 shows a perspective view of the electronic circuit assembly 1950 of the analyzer instrument. The electronic circuit assembly 1950 includes an electrical circuit board, which may be an FPGA. As described above, the electronic circuit assembly 1950 includes a set of electrical connectors 1951 configured to make contact with the connectors 416 of the consumable device. The electrical connectors 1951, upon contacting the consumable device, electronically couple the consumable device to the electronic control system 1950 of the analyzer instrument 1001. In some instances, the set of electrical connectors 1951 may be arranged in a rectangular fashion atop the electrical circuit board. In some instances, the set of electrical connectors 1951 surround or partially surround the opening 1952. In some instances, the two grounding springs 3532 are spaced apart from one another, with the set of electrical connectors 1951 being disposed between them.

[0212] FIG. 43 is a perspective view of the thermal interface assembly 3550 of the analyzer instrument 1001, which may be disposed underneath and / or within the clamp base subassembly- 3530 and the electronic circuit assembly 1950. The thermal interface assembly 3550 includes a cooling element 3551, a cold block 3555, a heat sink 3560, a mounting duct 3561 a fan 3570 and an outlet duct 3571. The cooling element 3551 can be any suitable mechanism for producing heat transfer (e.g., away from the consumable device 400). In some embodiments, the cooling element 3551 can be a thermoelectric cooling assembly. The cooling element 3551 can be coupled to the electronic controller 1900 of the instrument 1001 via the leads 3552. As shown, in some embodiments, the cooling assembly 3550 can include a temperature probe (e.g., a thermistor or thermocouple) that is coupled to the electronic controller 1900 of the instrument 1001 via the leads 3553.

[0213] The top (cold) side of the cooling element 3551 is coupled to the cold block 3555 and the bottom (hot) side of the cooling element is coupled to the heat sink 3560. In this manner, when heat is generated in the consumable device (i.e., during a test), the heat can be transferred via the cooling element 3551 from the cold block 3555 towards the heat sink 3560.

[0214] The cold block 3555 includes a cap 3556 that has one or more protruding surfaces 3557 for making contact with the consumable device 400 from below-. Specifically, at least aAttorney Docket No.: P37148-WO-1 portion of the cold block 3555 (including the cap 3556) extends through the opening 3533 in the bottom plate 3534 (see FIG. 41) and the opening 1952 of the electronic circuit assembly 1950 (see FIG. 36) and into the opening 414 of the consumable device 400 (see FIG. 47). Thus, when the consumable device 400 is clamped within the interface assembly 3500, the cap 3556 extends between the connectors 1951 and into the consumable device where it can contact the nanopore chip (not shown). This arrangement allows for efficient cooling of the nanopore chip package within the consumable device.

[0215] In some instances, the cooling cap block 3556 has multiple protruding surfaces 3557 spaced apart from one another, and each protruding surface may be raised upwards so as to make contact with the consumable device 400 (and / or the nanopore chip package) at a different location on the bottom surface of the consumable device. This arrangement produces spatially uniform and repeatable cooling of the nanopore chip package. In some instances, the protruding surfaces of the cooling cap block 3557 are configured to make contact with the consumable device through a layer of carbon interface material located at the bottom of the consumable device.

[0216] Referring to FIGS. 43 and 45, the cooling assembly 3550 is coupled to the bottom mount plate 3534 by a set of spring-biased screws 3563. Specifically, the screws 3563 extend through openings 3567 in the heat sink 3560 with the springs 3564 being between the mounting surface of the heat sink 3560 and the bottom portion (i.e., the head) of the screws 3563. In this manner, when the consumable device 400 is clamped within the interface assembly 3500, the amount of contact pressure between the cooling block cap 3556 and the consumable device 400 is controlled by the springs 3564.

[0217] The fan 3570 can be actuated to produce an airflow through the mounting duct 3561 and the outlet duct 3571.

[0218] FIGS. 48-50 show how- a consumable device 400 may be inserted into the interface assembly 3500 and thereafter become coupled to the analyzer instrument.

[0219] The sequencing methods performed by the instrument 1001 can include sequencing by expansion, which is a protocol based on the polymerization of (highly modified) non-natural nucleotide analogs referred to as “XNTPs” (i.e., the synthesized surrogate macromolecule can, as described below, be a polymer). In general terms, sequencing by expansion uses biochemical polymerization to transcribe the sequence of a DNA template onto a measurableAttorney Docket No.: P37148-WO-1 polymer (e.g., an Xpandomer). The transcribed sequence is encoded along the Xpandomer backbone in reporters that are separated by a predetermined distance (e.g., between 7 nm and 15 nm, further optionally approximately 10 nm). The reporters can be designed for high-signal - to-noise, well-differentiated responses. These differences can provide significant performance enhancements in sequence read efficiency and accuracy of Xpandomers relative to natural DNA (or RNA).

[0220] In some embodiments, the instrument 1001 can be included within a system that also includes an instrument for producing the synthesized macromolecules that are within (and sequenced by) the target fluid analyzed by the instrument 1001. Similarly stated, in some embodiments, a system can include a synthesis instrument configured to produce a synthesized macromolecule (i.e., a surrogate molecule), such as an Xpandomer, and a sequencing instrument configured to receive the synthesized macromolecule and perform any of the operations described herein to sequence the synthesized macromolecule. The synthesis instrument can be any of the synthesis instruments shown and described in International Patent Application No. PCT / IB2024 / 059485, bearing attorney docket no. P39142-WO and entitled “Systems, System Components and Methods for Automated Macromolecule Synthesis,” filed September 27, 2024 and / or International Patent Application No. PCT / US2025 / 015804, bearing attorney docket no. P39234-WO and entitled “Techniques for Synthesizing a Macromolecule From a Sample.” filed February 13, 2025, the disclosure of each of which is incorporated herein by reference in its entirety. In some embodiments, the system can include a fluid transfer system, such as a pump-drive system or a robotic fluid handling system with pipetting capability, to convey the synthesized macromolecule to the sequencing instrument (e.g. the instrument 1001).

[0221] FIG. 51 is a schematic illustration of an instrument 1002 for synthesizing a macromolecule that can be operably coupled to the sequencing instrument 1001 or otherwise included within a system including the sequencing instrument 1001. The instrument 1002 is configured to receive a synthesis flow' cell 150 within a mount (or interface) assembly 1620. The instrument 1002 further includes a fluid transfer system 1640, a synthesis reagent system 1660, an illumination assembly 1700, and a synthesis controller 1750.

[0222] The synthesis flow cell 150 is a fluidic device within which a synthesized macromolecule is produced from a sample. The sample can include a specimen (e.g., a nucleotide sample including a nucleotide sequence, e.g., a DNA sample or an RNA sample)Attorney Docket No.: P37148-WO-1 for which sequencing is desired. The synthesis flow cell 150 (and any of the synthesis flow cells described herein) can be a consumable device or cartridge that is disposed of after use. As shown, the synthesis flow cell 150 includes an inlet port 170 and an outlet port 171. The inlet port 170 is coupled to (or includes) a transfer tube 174, which can function as a sipper to draw in fluid from any of the vials 1661 of the reagent system 1660. The transfer tube 174 can also function as an outlet tube if the flow within the synthesis flow cell 150 is reversed. Although not shown in FIG. 51. the synthesis flow cell can include at least one flow channel (similar to the flow channel 252 described below) that is defined by an inner surface 154 (see FIG. 53). As described herein, the inner surface 154 is the structure that is functionalized to perform the synthesis methods described herein. Similarly stated, the inner surface 154 is the structure to which the capture probes are adhered as a part of the method of producing a synthesized macromolecule described herein.

[0223] The interface assembly 1620 includes a thermal block 1621 and a coupling mechanism 1622. As shown, the thermal block 1621 is coupled to the coupling mechanism 1622 and / or the synthesis flow cell 150 to control the temperature of the synthesis flow cell 150. The thermal block 1621 can have any suitable structure to facilitate rapid and accurate control of the temperature of the synthesis flow cell 150 and any fluids contained therein. The coupling mechanism f622 can include any suitable features to couple the synthesis flow cell 150 within the instrument 1002 in the desired orientation and also to thermally couple the synthesis flow cell 150 to the thermal block 1621. In some embodiments, the coupling mechanism 1622 can have a shape and / or surface features corresponding to the shape and / or surface features of the synthesis flow cell 150. In some embodiments, the coupling mechanism 1622 can include one or more clamps, such as spring-loaded clamps, magnetic clamps, or the like. In some embodiments, the coupling mechanism 1622 can include a thermal pad (not shown), thermal paste, or gel to promote high thermal conductivity between the synthesis flow cell 150 and the thermal block 1621.

[0224] The reagent assembly 1660 includes a set of vials 1661 that can hold reagents, samples, buffers, and other liquids used in the synthesis method. In some embodiments, the reagent assembly 1660 can include a 96 well plate (or plate with another well count). The reagent assembly 1660 can also include any other suitable reagent trays, bottles, and other containers for holding liquids. The openings of the containers, such as the openings of the vialsAttorney Docket No.: P37148-WO-11661 (or the wells of the well plate) can be located on the same plane or height. This arrangement can allow for efficient access to these liquids via the transfer tube 174.

[0225] The reagent assembly 1660 can be moved in all three axes with the XYZ gantry 1665. This configuration allows the synthesis flow cell 150 (and its transfer tube 174) to remain in a fixed position while the reagent assembly 1660 is moved by the gantry 1665 to a piercing tool (not shown) and to the transfer tube 174 to facilitate the desired conveyance of liquids into (or out of) the synthesis flow cell 150. Alternatively, in other embodiments, the XYZ gantry 1665 can be attached to the interface assembly 1620 and synthesis flow cell 150 to move the transfer tube and synthesis flow cell 150 relative to the fixed reagent assembly 1660.

[0226] As shown, in some embodiments, the reagent assembly 1660 can include a product collection reservoir 1662. The product collection reservoir 1662 can contain the synthesized macromolecules produced by the instrument 1002 and can be operably coupled to a transfer system for conveying the synthesized macromolecules from the instrument 1002 to a sequencing instrument (e.g., the sequencing instrument 1001). In some embodiments, the fluid transfer system 1640 can function to convey the synthesized macromolecules to the sequencing instrument 1001. In some embodiments, the XYZ gantry 1665 can facilitate transfer of the synthesized macromolecule from the instrument 1002 to the sequencing instrument (e.g., instrument 1001). Specifically, the XYZ gantry 1665 can move the collection reservoir 1662 into proximity with the sequencing instrument. In other embodiments, as described below, the fluid transfer system 1640 can function to convey the synthesized macromolecules to the sequencing instrument. In yet other embodiments, a separate fluid transfer system (e.g., a pipetting system) can be used to convey the synthesized macromolecules to the sequencing instrument.

[0227] The fluid transfer system 1640 is coupled to the outlet port 171 of the synthesis flow cell 150 and includes a pump 1641 that is selectively fluidically coupled to one or more containers or outlet circuits via a valve 1 48. Specifically, the pump 1641 can be selectively coupled to a waste reservoir 1644, a buffer container 1646, and a fluidic circuit 1649. The fluid transfer system 1640 also includes one or more sensors 1642 that monitors characteristics (e.g., pressure, temperature, flow rate) of the flow between the outlet port 171 and the various containers. In use, the pump 1641 can be used in a pull mode to draw fluid into the inlet port 170 of the synthesis flow cell 150 via the transfer tube 174, and the fluid can be drawn out of the synthesis flow cell 150 through the outlet port 171 and into the waste reservoir 1644. TheAttorney Docket No.: P37148-WO-1 pump 1641 can also be used in a push mode to pump fluid, such as a wash solution or elution buffer, from the buffer reservoir 1646 and into the synthesis flow cell 150 through the outlet port 171, and then the fluid can be pushed out of the synthesis flow cell 150 through the inlet port 170 and through the transfer tube 174 and into a product collection reservoir 1662. The pump 1641 can be a syringe pump or other type of pump that is capable of precisely metering out very small amounts of fluid (i.e., in the microliter to milliliter range).

[0228] In some embodiments, the pump 1641 can facilitate conveying the synthesized macromolecules out of the synthesis flow cell 150 and into a fluid circuit 1649 that is coupled to a sequencing instrument (e.g., the instrument 1001).

[0229] The illumination assembly 1700 is configured to produce UV radiation and guide the UV radiation to the at least one flow channel of the synthesis flow cell 150. For example, the illumination optics assembly 1700 can be configured to image a light source (e.g., a secondary light source generated by processing UV radiation emitted by the UV radiation source 1725) onto the synthesis flow cell 150. An illumination area of the illumination assembly 1700 can correspond to an outline of the synthesis flow cell 150. For instance, the illumination area of the illumination assembly 1700 can correspond to an area inscribing all flow channels of the synthesis flow cell 150.

[0230] Referring to FIGS. 52A and 52B, in some embodiments, the illumination assembly 1700 comprises a mixing component 1707 configured to mix the emitted UV radiation. Mixing the UV radiation can include increasing a spatial homogeneity of the UV radiation (i.e., a homogeneity at different locations of the illumination area). In other words, a spatial homogeneity of the UV radiation emitted from the UV radiation source 1725 is smaller than a spatial homogeneity of the UV radiation output by the mixing component 1707. For instance, in some embodiments, a lowest illumination intensity over the output of the mixing rod 1707 can be at most 12% lower than a highest illumination intensity.

[0231] In some examples, the mixing component 1707 can be a mixing rod. The mixing component 1707 can form a tube that guides the UV light received at its input via reflection at its surfaces (e.g., total internal reflection). In this manner, a spatial homogeneity of the UV radiation can be increased while the UV light travels along the tube (and undergoes multiple reflections in average). In other examples (or in addition), the mixing component 1707 can employ scatters to mix the UV light radiated by the UV light source.Attorney Docket No.: P37148-WO-1

[0232] In some examples, the mixing component 1707 can have a tapered shape (e.g., a cross-section can increase between an input and an output of the mixing component 1707). In some examples, a numerical aperture at an input of the mixing component 1707 (e.g., having a tapered shape, e.g., a mixing rod) can be larger than a numerical aperture at an output if the mixing component 1707 (e.g., aresult of atapered shape of the mixing component 1707). This can increase the efficiency of imaging optics receiving the mixed UV radiation, which can have limited numerical aperture.

[0233] In some examples, an output of the mixing component 1707 is configured to sen e as a secondary light source generating an input for the downstream components of the illumination assembly 1700. For instance, the output of the mixing component 1707 can be imaged onto the receptacle by the illumination optics assembly 103. The output of the mixing component 1707 can be an output facet 1721 or surface of the mixing component 1707 (e.g., a planar output facet 1721 or surface of the mixing component 1707).

[0234] In some examples, the illumination assembly 1700 includes imaging optics 1701 configured to image UV radiation onto the at least one receptacle (e.g., a flow cell including one or more flow channels). In some examples, the imaging optics 1701 can be configured to image an output (e.g., an output facet 1721) of the mixing component 1707 onto the synthesis flow cell 150 (including one or more flow channels therein). As described above, the imaging optics 1701 can be configured with a critical illumination setup (i.e., a light source, e.g., a secondary light source imaged onto the specimen position, which can be the receptacle 107). In some examples, the imaging optics 1701 includes a plurality of transmissive optical components (e.g.. lenses).

[0235] In some examples, an exit of the mixing component 1707 can have the same aspect ratio as the illumination area (at the synthesis flow cell 150). In these examples, the imaging optics 1701 can have a suitable magnification to illuminate an illumination area having the same aspect ratio (i.e., the aspect ratio is maintained by the imaging optics 1701 ).

[0236] In some examples, the illumination assembly 1700 further comprises a field stop 1705 arranged between the mixing component 1707 and the imaging optics 1701. The field stop 1705 can be shaped to define a field of the UV radiation entering the imaging optics 1701. In some examples, the field stop 1705 is arranged over an output of the mixing component 1707. For instance, the field stop 1705 can be arranged less than 5 mm aw ay from the outputAttorney Docket No.: P37148-WO-1 of the mixing component 1707 (e.g., as measured along a propagation direction of a central ray of the mixing component 1707). In other examples, the field stop 1705 can be arranged less than 17 mm away from the output of the mixing component 1707 (e.g., as measured along a propagation direction of a central ray of the mixing component 1707). In addition or alternatively, the field stop 1705 can be arranged spaced apart from the output of the mixing component 1707 (e.g., as measured along a propagation direction of a central ray of the mixing component 1707). For instance, the field stop 1705 can be arranged spaced apart by at least 0.5 mm (e.g., at least 1 mm) from the output of the mixing component 1707 (e.g., as measured along a propagation direction of a central ray of the mixing component 1707). In other words, there can be a gap between the output of the mixing component and the field stop 1705. This can be advantageous in some examples as the field stop itself may be located in an ideal position for generating a focused image of the field stop on the receptacle. The exit of the mixing rod is blurred. This blurring can reduce the contrast of any surface imperfections of the exit facet (e.g., scratches, digs, or dust).

[0237] In still other examples, the field stop 1705 can contact an output facet 1721 of the mixing component 1707 (e.g., as measured along a propagation direction of a central ray of the mixing component 1707).

[0238] The field stop 1705 can include a flat sheet with an opening that defines the field (e.g., a cut-out in a sheet material such as sheet metal). In the example of FIGS. 52A and 52B, that opening has a rectangular shape. In some examples, the field stop 1705 (e.g., its opening) defines a shape and size of the illuminated area on the receptacle (e.g., the flow cell). In the example of FIGS. 52A and 52B, this area also has a rectangular shape. In other examples, the field stop can define a differently shaped area (e g., a circular area). In some examples, the field stop 1705 is located at an intermediate image plane optically conjugated to the image plane of the illumination assembly 1700 on the synthesis flow cell 150. In some examples, the field stop 1705 can include multiple openings (e.g., corresponding to multiple disconnected areas to be illuminated at the receptacle, e.g., different flow channels of a flow cell).

[0239] In some examples, the illumination assembly 1700 further comprises an aperture stop 1713 arranged between the imaging optics 1701 and the mount (e.g.. at a focal plane of a field lens of the imaging optics 1701). Other positions of the aperture stop are possible in other examples. The aperture stop 1713 can be positioned to define the angular range from which the illumination assembly 1700 (and particularly the imaging optics 1701 can receiveAttorney Docket No.: P37148-WO-1UV radiation. The aperture stop 1713 can include a flat sheet with an opening (e.g., a cut-out in a sheet material such as sheet metal).

[0240] In some examples, the illumination assembly 1700 further comprises one or more folding mirrors 1715 to fold a beam path of the UV radiation one or more times. This can make the illumination assembly 1700 more compact.

[0241] In some examples, the imaging optics 1701 is configured to be telecentric at its input and / or its output. In other words, the chief rays of UV radiation entering and exiting the imaging optics 1701 are parallel. In other words, a magnification on the input / output is independent from a distance to the first / last component of the illumination optics assembly 103. Telecentricity at the input can improve a coupling of UV radiation into the imaging optics 1701. Telecentricity at the output can be advantageous in situations where the receptacle has a considerable depth and / or is at least partially covered by other elements. The telecentricity can avoid shadowing and resulting loss of radiation (e.g., vignetting) which can in turn reduce illumination homogeneity. Moreover, providing telecentricity can mean that the magnification is substantially independent from a focus error. Even when the receptacle to be illuminated is not (perfectly) in focus, this does not result in a change in size of the illumination area (it can merely be blurred).

[0242] The illumination assembly 1700 can further comprise a field lens 1719. The field lens 1719 can be configured to only provide a smaller (e.g., much smaller) contribution to the image formation compared to the other optical components (e.g., lenses) of the imaging optics 1701. The field lens 1719 can provide for (in combination with the aperture stop 1713) telecentricity at the output of the imaging optics 1701.

[0243] In use, the instrument 1002 (or any other synthesis instrument shown and described herein) can be used to produce a synthesized macromolecule, such as an Xpandomer. Referring to FIGS. 53 and 54, the method can include functionalizing a portion of a synthesis flow cell 150. Specifically, the method can include functionalizing the surface 154 that defines a portion of a flow channel of the synthesis flow cell 150. For instance, at step A, a selected molecule 156 (also referred to as capture probe in the present disclosure) can be bound to the surface 154 that defines a flow channel of a synthesis flow cell 150. The selected molecule or capture probe 156 can be bound to the surface 154 of the synthesis flow cell 150 by a linker molecule 155 which itself is attached to the surface 154 (e.g., in a solid phase).Attorney Docket No.: P37148-WO-1The selected molecule or capture probe 156 is designed to capture (bind with) a strand of nucleotides in the sample. Even though FIG. 53 only shows a single selected molecule or capture probe 156, the functionalization of the surface 154 within the synthesis flow cell 150 can include a plurality of selected molecules or capture probes 156 attached to the surface 154. In some examples, when carrying out the techniques of the present disclosure, a surface of the receptacle has already been functionalized (i.e., the process starts with a receptacle having a functionalized surface). In other words, in some embodiments, the operations of step A are optional.

[0244] In step B. a target nucleotide 158 can be conveyed into the synthesis flow cell 150 (e.g., via the fluid transfer system 1640). The target nucleotide 158 is captured by (e.g., bound to) the selected molecule or capture probe 156. For instance, the selected molecule or capture probe 156 can include a sequence of nucleotides that can bind to a complementary sequence of nucleotides of the target nucleotide 158 (e g., by hybridization). In this manner, the target nucleotide 158 can be bound to the receptacle (e.g., its surface) for the synthetization of a macromolecule described herein.

[0245] In step C, a macromolecule 160 is synthesized as described in the present disclosure. For instance, the macromolecule 160 can be an Xpandomer as described in the present disclosure or the cited references (particularly in the following section and in connection with FIG. 54). The macromolecule 160 can encode a nucleotide sequence of the target nucleotide 158.

[0246] Specifically, FIG. 54 (not to scale) shows components of one example of a surrogate polymer (which are synthesized macromolecules, e.g., Xpandomers). Xpandomers include a sequence of ordered XNTPs which correspond to the order of the target DNA sequence. XNTPs can be expandable, 5’ triphosphate modified non-natural nucleotide analogs compatible with template dependent enzymatic polymerization. An XNTP can have two distinct functional regions; namely, a selectively cleavable phosphorami date bond, linking the 5’ a-phosphate to the nucleobase, and a symmetrically synthesized reporter tether (SSRT) that is attached within the nucleoside triphosphoramidate at positions that allow for controlled expansion by cleavage of the phosphoramidate bond. The SSRT can include linkers separated by the selectively cleavable phosphoramidate bond. Each linker attaches to one end of a reporter code.Attorney Docket No.: P37148-WO-1

[0247] Section 1 shows primer-directed Xpandomer synthesis. XNTP 260A is illustrated in the “constrained configuration," characteristic of the XNTP substrates and the daughter strand products of template-dependent polymerization. The constrained configuration of polymerized XNTPs is the precursor to the expanded configuration (XNTP 260B), as found in Xpandomer products. Section 2 illustrates cleaving to expand the Xpandomer. The transition from the constrained configuration to the expanded configuration occurs upon scission of the P-N bond of the phosphorarmdate within the primary backbone of the daughter strand.

[0248] During assembly, the monomeric XNTP substrates (XATP, XCTP, XGTP and XTTP) are polymerized on the extendable terminus of a nascent daughter strand by a process of template-directed polymerization using single-stranded template as a guide. Generally, this process is initiated from a primer and proceeds in the 5’ to 3’ direction. Generally, a DNA polymerase 261 or other polymerase is used to form the daughter strand, and conditions are selected so that a complimentary copy of the template strand is obtained. After the daughter strand is synthesized, the coupled SSRTs form the constrained Xpandomer that further forms the daughter strand. SSRTs in the daughter strand have the “constrained configuration” of the XNTP substrates. The constrained configuration of the SSRT is the precursor to the expanded configuration, as found in the Xpandomer product.

[0249] In this example, once synthesis and expansion are complete, each monomeric XNTP unit 262 in the Xpandomer contains two reporter codes 266a and 266b with a Reporter Code “level” corresponding to the base t pe it encodes, and a Translocation Control Element (TCE) 263. The TCE 263 controls the rate of Xpandomer translocation through a nanopore through a combination of sterics, electrorepulsion, and / or preferential interaction with the nanopore. The resistance of the TCE 263 to the driving force of the ion current when positioned at the pore aperture and the consequent increase in applied voltage (i. e. , the voltage pulse) necessary to overcome the arrest and resume translocation, can be customized by modulating various properties of the TCE 263, (and in some embodiments, the reporter codes and other elements of the SSRT) e.g., the bulk, length, and / or charge density.

[0250] Brancher 264 is the branched structure that terminates the TCE 263 and links to reporter codes 266a and 266b. Enhancers 268a and 268b may aid in polymerase incorporation. Nucleotide 265 is attached to enhancer 268b and may include a cleavable linker 267.Attorney Docket No.: P37148-WO-1Cleavable linker 267 may be a photocleavable linker. Cleavable linker 267 may be cleaved to result in the expansion shown in section 2.

[0251] The Xpandomer as shown in FIG. 54 can be synthesized while bound to the surface 154 of a flow channel of the synthesis flow cell 150 as discussed above and particularly in connection with FIG. 53.

[0252] After the synthesis is complete, the Xpandomer can be cleaved and therefore released from the surface 154 by UV radiation. Referring again to FIG. 53, in step D, UV radiation is delivered via the illumination assembly 1700 to cleave (release) the macromolecule 160 from the surface 154 of the synthesis flow cell 150.

[0253] The cleaved (released) macromolecules can be provided to a sequencing system for determining the nucleotide sequence of the target nucleotide 158 by examining the synthesized macromolecule 160. For instance, in some embodiments, a liquid phase including the cleaved (released) macromolecules can be removed from the collection reservoir 1662 (and, e.g., from the instrument 1002) and conveyed to a sequencing instrument (e.g., instrument 1001) by a transport mechanism. In other embodiments, the cleaved (released) macromolecules can be conveyed directly from the synthesis flow cell 150 and into the sequencing instrument (e.g., instrument 1001) and / or the consumable device therein (e.g., consumable device 400) by the fluid transfer system 1640.

[0254] The controller 1750 is an electronic control system that includes any of the electronic components to produce the desired inputs, outputs, signals or the like to control the operation of the instrument 1002 to perform the synthesis methods described herein. For example, the controller 1750 is configured to control the operation of the illumination assembly 1700 to cleave macromolecules within the synthesis flow cell 150 as described herein. For example, in some embodiments, the controller 1750 can be configured to set one or more of an illumination intensity according to a predetermined profile and an illumination duration in a process of synthesizing the macromolecule from a sample. For instance, the controller 1750 can be configured to deliver UV radiation with a particular illumination intensity for a predetermined duration to cleave cleavable linkers (photocleavable linkers) of capture probes that are configured to bind the macromolecules to the surface 154 (e.g., a surface of a channel of the flow cell 150 or walls of the flow channels of the flow cell 150). The controller 1750 can be configured to deliver the UV radiation with a particularAttorney Docket No.: P37148-WO-1 illumination intensity for a predetermined duration repeatedly in a process of synthesizing the macromolecules.

[0255] The controller 1750 can be configured to control the other components within the instrument 1002 (in addition to the operation of the UV radiation source). For example, the controller 1750 can receive signals from the sensor(s) 1642 and provide signals to the fluid transfer system 1640 to control the flow of fluids into and within the flow cell 150. The controller 1750 can also control the operations to convey the synthesized macromolecule from the instrument 1002 and into the sequencing instrument (e.g., the instrument 1001). In some embodiments, the control 1750 of the synthesis instrument 1002 (or any of the synthesis instruments described herein) can be operably coupled to the electronic control system of the sequencing instrument (e.g., the electronic control system 1900 of the instrument 1001).

[0256] FIG. 55 is a perspective view of an instrument 2002 for synthesizing a macromolecule, according to an embodiment. Portions of the instrument 2002 (e.g., panels) are not shown to provide clarity of the components therein. The instrument 2002 is configured to receive a synthesis flow cell 250 within a mount (or interface) assembly 2620. The instrument 2002 further includes a housing 2600, a fluid transfer system 2640, a synthesis reagent system with vials 2661, an illumination assembly (not identified), an XYZ gantry 2665, and a synthesis controller (not shown). The structure and function of the instrument 2002 is similar to that of the synthesis instrument 1002 and is not described in detail. For example, the interface assembly 2620 can be similar in structure and function to the interface assembly 1620 described herein. The fluid transfer system 2640 can be similar in structure and function to the fluid transfer system 1640 described herein. The housing 2600 contains and / or supports the components of the instrument 2002 and includes a chassis 2601, a set of panels (not identified) and other structure (e.g., fasteners, vents, etc.) to support the operation of the components therein. In some embodiments, the housing 2600 and / or the chassis 2601 can be coupled to a housing or chassis of a sequencing instrument (e.g.. the instrument 1001).

[0257] The synthesis flow cell 250 can be similar to the synthesis flow cell 150 and is a fluidic device within which a synthesized macromolecule is produced from a sample. The sample can include a specimen (e.g.. a nucleotide sample including a nucleotide sequence, e.g., a DNA sample or an RNA sample) for which sequencing is desired. Referring to FIGS. 56A- 56B, the synthesis flow cell 250 includes two inlet ports 270 and two outlet ports 271. The inlet ports 270 are each coupled to (or includes) a transfer tube 274. The synthesis flow cellAttorney Docket No.: P37148-WO-1250 include two flow channels 252 that are fluidically coupled between one inlet port 270 and one outlet port 271. As shown in FIG. 56B. the synthesis flow cell 250 can be constructed from a substrate 251 (which can be, for example, an injection molded component) that is coupled to (or covered by) a thin film 275 (or cover). Thus, substrate 251 includes wall or surfaces 254 that define the flow channels 252. The surfaces 254 are similar to the surface 154 described above and provide the structure that is functionalized to perform the synthesis methods described herein.

[0258] The flow channels 252 can be used to perform reactions involving fluid volumes in the microliter range. For example, in some embodiments, the flow channel 252 can have cross- sectional dimensions that are about 0.6 mm x 0.3 mm, or about 0.8 mm x 0.4 mm, or less than 30 about 1 mm x less than 0.5 mm, or less than 2 mm x less than 1 mm. In some embodiments, the volume of the flow channel 252 can be about 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, 600, 700, 800, 900, or 1000 microliters. The surface area to volume ratio of the flow channel 252 can be about 5, 6, 7, 8. 9, 10, 11, 12. 13. 14. 15, 16, 17, 18, 19, 20, 30, 40, or 50 mm'1. The flow channel 252 can be serpentine, i.e. serpentine-shaped, to increase the flow length and surface area available to carry out the reactions and / or to aid in mixing.

[0259] The thin film 275 can be disposed over the base substrate 251 and flow channels 252 to enclose and complete the formation of the flow channels 252. The thin film 275 can be placed against a thermal block (e.g., the block 1621 as described herein). The thin film 275 can have a low thermal resistance which allows efficient heat transfer from a thermal block to the flow cell 250, which allows the rapid heating and cooling of the flow cell 250 to facilitate the different temperature reactions of the Xpandomer synthesis process. In order to achieve the desired thermal resistance, the thin film 275 can have a thickness between about 100 pm to about 500 pm. The thickness can be less than about 500, 400, 300, 200, or 100 pm, wherein the thickness can be about 100, 200, 300, 400, or 500 pm. The thin film can be made of a cyclic olefin polymer (COP) or a cyclic olefin copolymer (COC). Other types of polymers may also be used to form the thin film, such UV transparent polymers that can be functionalized (i.e., proton abstractable polymers) and bonded to the substrate 251. Other polymers that can be used include but are not limited to polypropylene and polyethylene. The thin film 275 can be bonded to the substrate 251 using a variety of techniques, such as thermal bonding, laser welding, or chemical bonding.Attorney Docket No.: P37148-WO-1

[0260] In some embodiments, the components and systems for synthesizing a macromolecule for sequencing and the components for sequencing the macromolecule can be included in a single housing and / or can share certain components (such as fluid transfer systems or the like). For example, FIG. 57 is a schematic illustration of an end-to-end system for sequencing a target molecule according to an embodiment. The system can include an optional sample preparation system 1003. a synthesis system 1002. and a sequencing system 1001. The sample preparation system 1003 is optional and can include, for example, the reagents, components and systems to receive a biological sample and extract a target nucleic acid therefrom. In other embodiments, the system need not include an integrated sample preparation system 1003, but instead can receive the target nucleic acid sample from an external sample preparation system.

[0261] As described above, the synthesis system 1002 can synthesize a macromolecule for sequencing. As shown, the synthesis system 1002 includes the fluid transfer sy stem 1640 that includes a fluidic circuit 1649 through which the synthesized macromolecule is conveyed from the synthesis system 1002 to the sequencing system 1001. More particularly, the synthesized macromolecule can be conveyed via the fluidic circuit 1649 to a reagent vial 3310 (which functions as a product reservoir). In this embodiment, the synthesis system 1002 and the sequencing system 1001 include a shared electronic control system 1900 that controls the functions of each instrument, as described herein. Specifically, the electronic control system 1900 includes the processor 1922 and the sensor module 1926, as well as any other components or modules as described herein. The sequencing system 1001 receives the consumable device 400 of the types shown and described herein.

[0262] FIG. 58 is an illustration of a system that includes a synthesis system 3002 and a sequencing system 3001 that are cojoined. The synthesis system 3002 can be similar to any of the synthesis systems described herein and the sequencing system 3001 can be similar to any of the sequencing systems described herein. The synthesis system 3002 can produce a synthesized macromolecule and a fluid transfer system (not shown) can convey the synthesized product to the sequencing system 3001. In this manner, the system can provide for end-to-end sequencing.

[0263] Any of the processors described herein can be any suitable processor for performing the methods described herein. In some embodiments, the processor of any of the instruments described herein can be configured to run and / or execute application modules, processes and / orAttorney Docket No.: P37148-WO-1 functions associated with the instrument 1001 or any of the instruments described herein. For example, such processors can be configured to run and / or execute any of the modules described herein, and perform the methods associated therewith. The processor can be, for example, a Field Programmable Gate Array (FPGA), an Application Specific Integrated Circuit (ASIC), a Digital Signal Processor (DSP), and / or the like. The processor can be configured to retrieve data from and / or write data to a memory component.

[0264] The memory component can be, for example, random access memory (RAM), memory7buffers, hard drives, databases, erasable programmable read only memory (EPROMs), electrically erasable programmable read only memory (EEPROMs), read only memory (ROM), flash memory, hard disks, floppy disks, cloud storage, and / or so forth. In some embodiments, the memory component stores instructions to cause the processor to execute modules, processes and / or functions associated with the instrument 1001. For example, the memory component can store instructions to cause the processor to execute any of the application modules described herein, and perform the methods associated therewith.

[0265] The sensor(s) included within the electronic system 1900 of the instrument 1001 can include any number of switches, optical / light input sensors, temperature sensors, contact sensors, and / or any other suitable input device. The sensor(s) can include any of the sensors described herein.

[0266] While various embodiments have been described above, it should be understood that they have been presented by way of example only, and not limitation. Where methods and / or schematics described above indicate certain events and / or flow patterns occurring in certain order, the ordering of certain events and / or operations may be modified. While the embodiments have been particularly shown and described, it will be understood that various changes in form and details may be made.

[0267] Although various embodiments have been described as having particular features and / or combinations of components, other embodiments are possible having a combination of any features and / or components from any of embodiments as discussed above. Aspects have been described in the general context of molecular analyzers, but inventive aspects are not necessarily limited to use in molecular diagnostics and sequencing.

Claims

Attorney Docket No.: P37148-WO-1What is claimed is:1 . An analyzer instrument, comprising: a housing; a piercing tip member movable within the housing, the piercing tip member configured to be moved in response to control signals generated by a processor communicably coupled to the analyzer instrument; at least one sealed container disposed within the housing, the at least one sealed container holding a fluid, wherein a seal of the at least one sealed container is penetrable by the piercing tip member; a fluid transfer system disposed within the housing, the fluid transfer system configured to access and produce a flow of the fluid from the at least one sealed container in response to control signals generated by the processor; and an interface assembly coupled to the housing, the interface assembly configured to receive a chip package containing at least one fluidic lane, the interface assembly configured to fluidically couple the chip package to the fluid transfer system in response to control signals generated by the processor; wherein the fluid transfer system includes an inlet portion for directing fluid flows towards the chip package and an outlet portion for directing fluid flows away from the chip package, and the interface assembly includes an actuator that is movable from a first position to a second position to cause the outlet portion to become fluidically coupled to an aligned fluidic lane from the at least one fluidic lane of the chip package, the actuator being configured to move from the first position to the second position in response to a force applied to the actuator by the piercing tip member.

2. The analyzer instrument of claim 1, wherein: the actuator is coupled to an outlet needle such that each movement of the actuator produces a corresponding movement of the outlet needle, the outlet needle having a lumen in fluidic connection with the outlet portion, and the outlet needle is configured to fluidically engage the aligned fluidic lane from the at least one fluidic lane of the chip package, when the actuator is in theAttorney Docket No.: P37148-WO-1 second position, such that the aligned fluidic lane is fluidically coupled to the outlet portion via the lumen.

3. The analyzer instrument of claim 1, wherein the actuator is further movable from the second position to the first position, the aligned fluidic lane being fluidically isolated from the outlet portion when the actuator is in the first position.

4. The analyzer instrument of claim 3, wherein: the force is a first force, and the actuator is configured to move from the second position to the first position in response to a second force applied by the piercing tip member.

5. The analyzer instrument of claim 4, wherein the second force is applied by the piercing tip member to an actuator pin spaced apart from the actuator.

6. The analyzer instrument of claim 4, wherein: the second force is applied by the piercing tip member to an actuator pin spaced apart from the actuator, the actuator pin being configured to move from a third position to a fourth position in response to the second force. a movement of the actuator pin from the third position to the fourth position is configured to rotate a lift arm contacted by the actuator pin about a pivot disposed between the actuator pin and the actuator, and a rotation of the lift arm about the pivot is configured to lift the actuator from the second position to the first position.

7. The analyzer instrument of claim 1, wherein: the at least one fluidic lane of the chip package comprises a plurality' of fluidic lanes. the actuator that is movable to cause the outlet portion to become fluidically coupled to the aligned fluidic lane is a first actuator, and the interface assembly includes a second actuator that is movable to cause an alignment between a selected fluidic lane from the plurality of fluidic lanes and the outlet portion such that the selected fluidic lane is the aligned fluidic lane, the alignedAttorney Docket No.: P37148-WO-1 fluidic lane being fluidically couplable to the outlet portion based on a movement of the first actuator from the first position to the second position.

8. The analyzer instrument of claim 1, wherein: the at least one fluidic lane of the chip package comprises a plurality' of fluidic lanes that are each capable of being aligned with the outlet portion so as to be fluidically couplable to the outlet portion, the actuator that is movable to cause the outlet portion to become fluidically coupled to an aligned fluidic lane is a first actuator, the interface assembly includes a second actuator that is movable between a plurality of positions, (a) each position from the plurality of positions being associated with (b) a particular fluidic lane or a particular subgroup of fluidic lanes from the plurality of fluidic lanes, and a movement of the second actuator to a position from the plurality of positions is configured to cause the particular fluidic lane or the particular subgroup of fluidic lanes associated the position to be aligned with the outlet portion, such that the particular fluidic lane or the particular subgroup of fluidic lanes serves as the one or more aligned fluidic lanes that are configured to become fluidically coupled to the outlet portion in response to a movement by the first actuator from the first position to the second position.

9. The analyzer instrument of claim 8, wherein: the force is a first force, and the second actuator is configured to move to a given position from the plurality of positions in response to at least a second force applied by the piercing tip member.

10. The analyzer instrument of claim 9, wherein the second force is applied by the piercing tip member to one or more actuator pins associated with the second actuator.

11. The analyzer instrument of claim 10, wherein the one or more actuator pins comprise a set of actuator pins, each actuator pin from the set of actuator pins being configured to move from a respective raised position to a respective lowered position in response to a force applied to that actuator pin by the piercing tip member.Attorney Docket No.: P37148-WO-112. The analyzer instrument of claim 1, wherein the at least one sealed container includes a plurality of sealed containers each having a seal penetrable by the piercing tip member, a first sealed container from the plurality of sealed containers holding a reagent, a second sealed container from the plurality of sealed containers holding a target fluid.

13. The analyzer instrument of claim 12, wherein: the reagent comprises a salt buffer, a protein pore, or a lipid, and the target fluid comprises an Xpandomer.

14. The analyzer instrument of claim 1, wherein the interface assembly includes a cooling assembly with a cap member, the cap member having a plurality of protruding surfaces for making contact with the chip package on a condition that the chip package is inserted into the interface assembly, the plurality of protruding surfaces being spaced apart from one another, each protruding surface from the plurality of protruding surfaces being configured to make contact with the chip package at a different location on the chip package.

15. The analyzer instrument of claim 14, wherein: the plurality of protruding surfaces is arranged in a rectangular configuration, and each protruding surface from the plurality of protruding surfaces is configured to contact the chip package at a location spaced apart from a center of the chip package.

16. The analyzer instrument of claim 14, wherein the cooling assembly includes a thermoelectric cooling element.

17. The analyzer instrument of claim 14, wherein the cooling assembly is coupled to a housing of the interface assembly via a biasing member.

18. The analyzer instrument of claim 14, wherein the interface assembly includes a set of electrical connectors surrounding the cap member of the cooling assembly, the set ofAttorney Docket No.: P37148-WO-1 electrical connectors configured to make contact with the chip package from below on a condition that the chip package is inserted into the interface assembly.

19. The analyzer instrument of claim 1, wherein the interface assembly includes a grounding spring configured to make contact with the chip package upon insertion of the chip package into the interface assembly, the grounding spring configured to dissipate electrostatic charge from the chip package on a condition that the chip package is inserted into the interface assembly.

20. The analyzer instrument of claim 19, wherein: the interface assembly includes an alignment pin configured to be matingly received within an opening defined in a bottom surface of the chip package, and the grounding spring is disposed about the alignment pin.

21. The analyzer instrument of claim 20, wherein: the grounding spring is a first grounding spring from a plurality of grounding springs included in the interface assembly, and the plurality of grounding springs includes a second grounding spring spaced apart from the first grounding spring.

22. The analyzer instrument of claim 21 , wherein: the interface assembly includes a set of electrical connectors disposed betw een the first grounding spring and the second grounding spring, the set of electrical connectors configured to make contact with the chip package on the condition that the chip package is inserted into the interface assembly, and the interface assembly includes a cooling assembly with a cooling interface member, the cooling interface member being surrounded by the set of electrical connectors, the cooling interface member having a plurality of raised surfaces for making contact with the chip package on the condition that the chip package is inserted into the interface assembly, the plurality’ of raised surfaces being spaced apart from one another, each raised surface from the plurality7of raised surfaces being configured to make contact with the chip package at a different location on the chip package.Attorney Docket No.: P37148-WO-123. The analyzer instrument of claim 14, wherein the interface assembly includes a first portion and a second portion that are physically separable from one another, the actuator being located on the first portion, the cooling assembly being located on the second portion.

24. The analyzer instrument of claim 23, wherein: the first portion is a top portion of the interface assembly and the second portion is a bottom portion of the interface assembly, and the interface assembly is configured to house an electronic circuit assembly between the top portion and the bottom portion.

25. The analyzer instrument of claim 1, further comprising a dispensing tip member within the housing, the dispensing tip member being movable within the housing in response to control signals generated by the processor, the dispensing tip member having an outer diameter that is equal to or smaller than an outer diameter of the piercing tip member, and wherein the inlet portion of the fluid transfer system is configured to direct the fluid flows towards the chip package via the dispensing tip member.

26. The analyzer instrument of claim 1, further comprising a dispensing tip member within the housing, the dispensing tip member being movable within the housing in response to control signals generated by the processor, the dispensing tip member being characterized by a cross-sectional area that is equal to or smaller than a cross- sectional area defined by the piercing tip member.

27. An analyzer instrument for performing a sequencing operation, comprising: a housing; a fluid transfer system disposed within the housing, the fluid transfer system configured to access and produce a flow of a fluid associated the sequencing operation; and an interface assembly coupled to the housing, the interface assembly configured to receive a chip package containing at least one fluidic lane, the chip package being fluidically couplable to the fluid transfer system on a condition that the chip package is inserted into the interface assembly;Attorney Docket No.: P37148-WO-1 wherein the fluid transfer system includes an inlet portion configured to direct the flow of the fluid into the chip package and an outlet portion configured to direct the flow out of the chip package, and the interface assembly includes a cooling assembly with a cooling interface member, the cooling interface member having a plurality of protruding surfaces for making contact with the chip package on the condition that the chip package is inserted into the interface assembly, the plurality of protruding surfaces being spaced apart from one another, each protruding surface from the plurality of protruding surfaces being configured to make contact with the chip package at a different location on the chip package.

28. An analyzer instrument for performing a sequencing operation, comprising: a housing; a processor; a fluid transfer system disposed within the housing, the fluid transfer system configured to access and produce a flow of a fluid associated with the sequencing operation in response to control signals generated by the processor; and an interface assembly coupled to the housing, the interface assembly configured to receive a chip package containing at least one fluidic lane, the interface assembly configured to fluidically couple the chip package to the fluid transfer system in response to control signals generated by the processor; wherein the fluid transfer system includes an inlet portion for directing fluid flows towards the chip package and an outlet portion for directing fluid flows away from the chip package, the interface assembly includes at least one electrical connector configured to make contact with the chip package and electronically couple the chip package to the processor on a condition that the chip package is inserted into the interface assembly, and the interface assembly includes at least one grounding spring configured to make contact with the chip package and dissipate electrostatic discharge from the chip package on the condition that the chip package is inserted into the interface assembly.Attorney Docket No.: P37148-WO-129. A system comprising: at least one reservoir containing a fluid; a pierce needle for puncturing a seal of the at least one reservoir; a consumable device having a fluid inlet, at least one fluid outlet, and at least one fluid channel disposed between the fluid inlet and the at least one fluid outlet, wherein the consumable device is configured to receive a flow of the fluid originating from the at least one reservoir, through the fluid inlet, and direct the flow of the fluid, through the at least one fluid channel, towards the at least one fluid outlet; a pump-driven fluidic circuit coupled to the consumable device, wherein the fluidic circuit includes a first circuit segment and a second circuit segment, the first circuit segment configured to direct the flow of the fluid from the at least one reservoir towards the fluid inlet of the consumable device, the second circuit segment configured to direct the flow of the fluid from the at least one fluid outlet of the consumable device towards a waste receptacle; and a docking assembly configured to receive the consumable device, the docking assembly including one or more actuator members configured to produce a fluidic alignment and coupling of the at least one fluid outlet with the second circuit segment in response to a force applied to the one or more actuator members by the pierce needle.

30. The system of claim 29, wherein the first circuit segment and the second circuit segment are external to the consumable device.

31. An apparatus, comprising: a synthesis instrument for producing a synthesized macromolecule, the synthesis instrument including a first fluid transfer system configured to convey the synthesized macromolecule from a synthesis flow cell to a collection reservoir; and a sequencing instrument for performing a sequencing operation, the sequencing instrument including the collection reservoir configured to contain a target fluid comprising the synthesized macromolecule; an interface assembly configured to receive a consumable device, the consumable device having a fluid inlet, at least one fluid outlet, and at least one fluidAttorney Docket No.: P37148-WO-1 channel disposed between the fluid inlet and the at least one fluid outlet, the consumable device being configured to receive a flow of the target fluid from the collection reservoir via the fluid inlet and direct the flow of the target fluid through the at least one fluid channel and towards the at least one fluid outlet; a needle configured to access at least one of the fluid inlet or the fluid outlet of the consumable device; a second fluid transfer system configured to be operably coupled to the consumable device, the second fluid transfer system including a first circuit segment and a second circuit segment, the first circuit segment configured to direct the flow of the target fluid from the collection reservoir into the fluid inlet of the consumable device, the second circuit segment configured to direct the flow of the target fluid from the at least one fluid outlet of the consumable device towards a waste receptacle; and an actuator assembly including an actuator pin, the actuator assembly configured to align and fluidically couple the at least one fluid outlet with the second circuit segment in response to a force applied to the actuator pin by the needle.

32. The apparatus of claim 31, wherein the needle is configured to pierce an inlet seal covering the fluid inlet of the consumable device to access the fluid inlet.

33. The apparatus of claim 32. wherein: the actuator assembly further includes a force transfer link and a positioning bar, the force transfer link transferring movement of the actuator pin along a first axis into movement of the positioning bar along a second axis, the positioning bar being coupled to an outlet needle such that movement of the positioning bar along the second axis produces a corresponding movement of the outlet needle to selectively place the outlet needle in fluidic connection with the at least one fluid outlet of the consumable device.

34. The apparatus of claim 31, wherein: the collection reservoir is within a reagent assembly of the sequencing instrument, the reagent assembly include at least one sealed container containing a reagent; and the needle is configured to pierce a seal of the sealed container.

35. The apparatus of any of claims 31-34, wherein the synthesized macromolecule comprises an Xpandomer.Attorney Docket No.: P37148-WO-136. The apparatus of any of claims 31-34, wherein: the first fluid transfer system includes a pump, a valve, and a fluid transfer circuit, the pump configured to produce a flow of the synthesized macromolecule from the synthesis flow cell into the fluid transfer circuit, the valve configured to selectively place the fluid transfer circuit in fluid communication wi th the collection reservoir.

37. The apparatus of claim 36, wherein: the first fluid transfer system includes a pipetting assembly coupled to the fluid transfer circuit, the pipetting assembly configured to convey the synthesized macromolecule into the collection reservoir.

38. The apparatus of any of claims 31-34, wherein: the first fluid transfer system includes a pipetting assembly configured to convey the synthesized macromolecule into the collection reservoir.

39. The apparatus of any of claims 31-34, wherein: the synthesis instrument and the sequencing instrument are discrete instruments that are operably coupled via the first fluid transfer system.

40. The apparatus of any of claims 31-34, further comprising: a housing, the synthesis instrument and the sequencing instrument each being contained within the housing.

41. An apparatus, comprising: a synthesis instrument for producing a synthesized macromolecule, the synthesis instrument including a first fluid transfer system configured to convey the synthesized macromolecule from a synthesis flow cell to a collection reservoir; and a sequencing instrument for performing a sequencing operation, the sequencing instrument including the collection reservoir configured to contain a target fluid comprising the synthesized macromolecule; an interface assembly configured to receive a consumable device, the consumable device having a fluid inlet, at least one fluid outlet, and at least one fluidAttorney Docket No.: P37148-WO-1 channel disposed between the fluid inlet and the at least one fluid outlet, the consumable device being configured to receive a flow of the target fluid from the collection reservoir via the fluid inlet and direct the flow of the target fluid through the at least one fluid channel and towards the at least one fluid outlet; a second fluid transfer system configured to be operably coupled to the consumable device, the second fluid transfer system including a first circuit segment and a second circuit segment, the first circuit segment configured to direct the flow of the target fluid from the collection reservoir into the fluid inlet of the consumable device, the second circuit segment configured to direct the flow of the target fluid from the at least one fluid outlet of the consumable device towards a waste receptacle; and an actuator assembly configured to align and fluidically couple the at least one fluid outlet with the second circuit segment.

42. An apparatus, comprising: a first interface assembly configured to receive a synthesis flow cell that is configured to receive a sample; an illumination assembly configured to produce an electromagnetic radiation output and guide the electromagnetic radiation output to a portion of the synthesis flow cell to cleave a macromolecule from the sample; a first fluid transfer component configured to convey the macromolecule from the synthesis flow cell to one of a collection reservoir or a consumable device to produce a target fluid; a second interface assembly configured to receive the consumable device, the consumable device having a fluid inlet, at least one fluid outlet, and at least one fluid channel disposed between the fluid inlet and the at least one fluid outlet, the consumable device being configured to receive a flow of the target fluid via the fluid inlet and direct the flow of the target fluid through the at least one fluid channel and towards the at least one fluid outlet; a second fluid transfer component configured to be operably coupled to the consumable device, the second fluid transfer component including a first circuit segment and a second circuit segment, the first circuit segment configured to direct the flow of the target fluid from the fluid inlet and through the consumable device to perform a sequencing operation, the second circuit segment configured to direct the flow of the target fluid from the at least one fluid outlet of the consumable device towards a waste receptacle; andAttorney Docket No.: P37148-WO-1 a controller operably coupled to the illumination assembly, first fluid transfer component and the second transfer component, the controller including at least one processor, the controller being configured to execute a plurality of operations, the plurality of operations including: sending, to the illumination assembly, an illumination control signal to produce the electromagnetic radiation; sending, to the first fluid transfer component, a fluid transfer signal to cause the transfer of the macromolecule from the synthesis flow cell to one of the collection reservoir or the consumable device; sending, to the second fluid transfer component, a flow signal to produce the flow of the target fluid through the consumable device; and receiving, from the consumable device, a plurality of signals associated with the flow of the target fluid through the consumable device, the plurality of signals associated with a sequence of the macromolecule.

43. The apparatus of claim 42. wherein the macromolecule comprises an Xpandomer.

44. The apparatus of any of claims 42-43, wherein: the first fluid transfer component includes a pump, a valve, and a fluid transfer circuit, the pump configured to produce a flow of the macromolecule from the synthesis flow cell into the fluid transfer circuit, the valve configured to selectively place the fluid transfer circuit in fluid communication with one of the collection reservoir or the consumable device.

45. The apparatus of any of claims 42-43, wherein: the first fluid transfer component includes a pipetting assembly, the pipetting assembly configured to convey the macromolecule into the consumable device.

46. A system, comprising: a synthesis instrument for producing a synthesized macromolecule from a sample, the synthesis instrument including a first interface assembly configured to receive at least one synthesis flow cell; and a sequencing instrument coupled to the synthesis instrument and including a second interface assembly configured to receive a consumable device for performing sequencing operations on the synthesized macromolecule,Attorney Docket No.: P37148-WO-1 wherein the system further comprises at least one fluid transfer system operable to transfer the synthesized macromolecule from the at least one synthesis flow cell to the consumable device.

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