Chemical Processing Systems and Equipment

Abstract

Described embodiments relate to a chemical processing instrument configured to receive one or more sample cartridges for processing one or more corresponding fluid samples, the chemical processing instrument comprising a reagent dispenser configured to dispense one or more fluid reagents into the reagent containers through an open top of the reagent container, and a pneumatic module configured to connect to a primary pneumatic port of the primary reaction container and selectively adjust pressure in the primary reaction container when the lid is closed to draw fluid from the reagent containers through the primary reagent channel into the primary reaction container.

Description

[Technical field]

[0001] CROSS-REFERENCE TO RELATED APPLICATIONS This application claims priority to the following provisional applications: U.S. Provisional Patent Application No. 63 / 130,450, filed December 24, 2020; U.S. Provisional Patent Application No. 63 / 241,167, filed September 7, 2021; and U.S. Provisional Patent Application No. 63 / 292,314, filed December 21, 2021, the entire contents of which are incorporated by reference into this specification.

[0002] SUMMARY OF THE DISCLOSURE Embodiments relate generally to systems, apparatus, methods, and computer readable media for performing operations on samples, such as nucleic acid extraction operations, and sample cartridges for use in chemical processing instruments. [Background technology]

[0003] State-of-the-art automated machines and instruments for performing nucleic acid extraction procedures and the like tend to be capable of receiving and processing small sample inputs, usually less than 1 ml, typically around 200 ul, however, it may be desirable to extract nucleic acid from much larger input samples in order to output sufficient genetic material for downstream processing.

[0004] Furthermore, in a typical high throughput laboratory using well plates and large automated liquid handling robots, large volumes of samples typically need to be aliquoted into smaller volumes for automated processing, which is an inefficient use of the machine. A typical machine may have many channels, each capable of taking a small sample, but aliquoting reduces the number of patients that occupy machine uptime.

[0005] A further common problem with known automated machines is contamination: this risk increases whenever containers containing patient-derived material are opened within the machine, when moving pipettors are used, and / or when materials that have come into contact with patient-derived material are stored within the instrument (such as pipette tips).

[0006] A further problem with known automated machines is the difficulty of achieving sufficient control of the end-to-end process to ensure the highest quality.

[0007] A further problem is achieving adequately concentrated and / or quantified nucleic acids from the extraction workflow that are directly input to downstream assays. Applications such as MRD typically require highly concentrated DNA (about 500 ng / μL), which is rarely achieved using available instrumentation for nucleic acid extraction. In addition, most existing systems aimed at automating cell-free DNA (cfDNA) extraction do not select for nucleic acids of a specific size. cfDNA is typically about 150 bp, and downstream assays are adversely affected by the presence of genomic DNA (gDNA) contamination in cfDNA samples.

[0008] It is desirable to provide systems, apparatus, methods, and computer-readable media for performing operations on a sample that address or ameliorate one or more of the shortcomings or disadvantages associated with the prior art, or at least provide a useful alternative thereto.

[0009] Discussion of documents, acts, materials, devices, articles or the like which has been included in this specification should not be deemed to be an admission that any or all of such matters formed part of the prior art base or were general general knowledge in the field relevant to this disclosure as if they existed prior to the priority date of each of the appended claims. Summary of the Invention [Means for solving the problem]

[0010] Some embodiments relate to a sample cartridge for a chemical processing instrument, the sample cartridge comprising: a primary reaction vessel configured to contain a fluid sample for processing, the primary reaction vessel configured to receive a lid to close the open top of the primary reaction vessel; a reagent vessel configured to receive one or more fluid reagents through the open top of the reagent vessel, the reagent vessel connected to the primary reaction vessel via a primary reagent channel with a primary reagent valve disposed in the primary reagent channel to control fluid flow through the primary reagent channel; and a pneumatic port in fluid communication with the primary reaction vessel, the pneumatic port configured to connect to a pneumatic module to selectively adjust pressure within the primary reaction vessel when the lid is closed to draw fluid contents of the reagent vessel into the primary reaction vessel.

[0011] The sample cartridge may further comprise a primary pneumatic channel extending between the primary pneumatic port and the primary reaction vessel, the opening of the primary pneumatic channel into the primary reaction vessel being located halfway up a sidewall of the primary reaction vessel. The opening of the primary pneumatic port into the primary reaction vessel being located closer to a top of the primary reaction vessel than to a bottom of the primary reaction vessel. In some embodiments, the opening of the primary reagent channel into the primary reaction vessel is located halfway up a sidewall of the primary reaction vessel. In some embodiments, the opening of the primary reagent channel into the primary reaction vessel being closer to a top of the primary reaction vessel than to a bottom of the primary reaction vessel.

[0012] In some embodiments, the sample cartridge may further comprise a liquid trap configured to restrict the passage of liquid out of the sample cartridge. The liquid trap may be disposed, for example, in or at one end of the primary pneumatic channel. The liquid trap may be disposed at or at the base of the sample cartridge. The liquid trap may comprise a gas permeable membrane. The liquid trap may include a hydrophobic polymeric material that can act as a gas permeable or semi-permeable membrane. The liquid trap may be configured to accommodate a minimum amount of liquid before being blocked or overflowing. The minimum liquid volume of the liquid trap may be, for example, in the range of 1 μL to 1000 μL, 10 μL to 100 μL, 40 μL to 80 μL, or 50 μL to 60 μL.

[0013] In some embodiments, the sample cartridge further comprises an output bin configured to receive a final output fluid from the primary reaction bin via the final output channel. The sample cartridge may further comprise an output bin pneumatic port in communication with the output bin via the output bin pneumatic channel, the output bin pneumatic port may be configured to be connected to a pneumatic module to selectively adjust the pressure in the output bin to draw the final output fluid from the primary reaction bin via the final output channel into the output bin. The sample cartridge may further comprise a temporary lid configured to close the output bin during processing, the temporary lid may be connected to and define an opening for the output bin pneumatic channel to the final output channel and the output bin.

[0014] In some embodiments, the sample cartridge further comprises a quality control vessel configured to receive an aliquot of the output fluid for quality control analysis, a quality control channel extending between the quality control vessel and a quality control junction with the final output channel, and a quality control pneumatic port in fluid communication with the quality control vessel and configured to be connected to a pneumatic module to selectively adjust pressure in the quality control vessel to draw an aliquot of the final output fluid from the final output channel, through the quality control channel, and into the quality control vessel. The quality control vessel may be pre-loaded with a dye to be mixed with the aliquot of the final output fluid for quality control analysis.

[0015] The sample cartridge may further comprise a buffer container configured to receive buffer through an open top of the buffer container for mixing with the final output fluid for quality control analysis, a buffer channel extending between the buffer channel and a buffer junction with the final output channel between the quality control junction and the primary reaction container, and a buffer channel valve disposed in the buffer channel to control the flow of buffer through the buffer channel.

[0016] The sample cartridge may further comprise an intermediate outlet from the final output channel between the quality control junction and the output container, a sealed chamber into which the intermediate outlet opens, an air permeable liquid barrier membrane covering the outlet, and an intermediate outlet air pressure port in fluid communication with the sealed chamber and configured to be connected to an air module to selectively adjust pressure within the sealed chamber to draw air from the final output channel through the air permeable membrane.

[0017] In some embodiments, the sample cartridge further comprises a sealed waste container configured to receive waste fluid from the primary reaction container via the waste channel, and a waste pneumatic port in fluid communication with the waste container and configured to be connected to a pneumatic module to selectively adjust the pressure in the waste container to draw fluid from the primary reaction container through the waste channel and into the waste container.

[0018] In some embodiments, the sample cartridge further comprises a secondary reaction vessel configured to receive a primary output fluid from the primary reaction vessel via a primary output channel fluidically connecting the primary reaction vessel to the secondary reaction vessel and configured to receive one or more fluidic reagents from a reagent vessel via a secondary reagent channel fluidically connecting the reagent vessel to the secondary reaction vessel, a primary outlet valve disposed in the primary outlet channel to control flow through the primary outlet channel, and a secondary reagent valve disposed in the secondary reagent channel to control flow through the secondary reagent channel. The secondary reaction vessel may be sealed, and in some embodiments, the sample cartridge further comprises a secondary pneumatic port in fluid communication with the secondary reaction vessel and configured to be connected to a pneumatic module to selectively adjust pressure in the secondary reaction vessel to draw fluid from the primary outlet channel or the secondary reagent channel into the secondary reaction vessel. The sample cartridge may further comprise a secondary pneumatic channel extending between the secondary pneumatic port and the secondary reaction vessel, the opening of the secondary pneumatic channel to the secondary reaction vessel being located halfway up a sidewall of the secondary reaction vessel closer to a top of the secondary reaction vessel than to a bottom of the secondary reaction vessel. One or more inlets of the primary output channel and the secondary reagent channel may open into the secondary reaction vessel, closer to the top of the secondary reaction vessel than to the bottom of the secondary reaction vessel, and halfway up a sidewall of the secondary reaction vessel.

[0019] Some embodiments relate to a chemical processing instrument configured to receive a sample cartridge according to any of the described embodiments, the instrument comprising: a reagent dispenser configured to dispense one or more fluid reagents into the reagent vessels through an open top of the reagent vessels; and a pneumatic module configured to connect to a primary pneumatic port of the primary reaction vessel and selectively adjust pressure in the primary reaction vessel when the lid is closed to draw fluid from the reagent vessels through the primary reagent channel into the primary reaction vessel.

[0020] The reagent dispenser may include a reagent cartridge including multiple reagent reservoirs, each containing a volume of reagent in fluid communication with a dispense pump via one or more valves. The instrument may be configured to operate the one or more valves to connect a selected one of the reagent reservoirs to the pump and to operate the pump to dispense a selected amount of reagent from the selected reagent reservoir into a reagent container of the sample cartridge. The reagent cartridge may be removable from the dispense pump and the instrument to facilitate refilling or replacement of the reagent reservoirs.

[0021] In some embodiments, the instrument further comprises a heater mounted to the carriage assembly, the carriage assembly configured to selectively move the heater relatively close to a primary reaction vessel of the sample cartridge to heat the fluid sample in the primary reaction vessel, and to move the heater relatively farther away from the sample cartridge when heating is not required.

[0022] The heater may comprise a radiator configured to pass through a slot or hole in the sample cartridge and partially surround the primary reaction vessel.

[0023] In some embodiments, the instrument further comprises a magnet mounted to the carriage and configured to be moved relatively closer to a primary reaction vessel of the sample cartridge to apply a magnetic field to the fluid sample in the primary reaction vessel, and moved relatively farther away from the sample cartridge when a magnetic field is not needed.

[0024] The carriage can be configured to allow independent movement of the heater relative to the magnet to heat the fluid sample without the application of a magnetic field.

[0025] The heater may be mounted to the carriage via a spring-loaded rod that biases the heater away from the carriage to a disengaged position and to a first heater engagement position and allows the heater to move relatively closer to the carriage and magnet when the carriage is moved to the magnet engagement position.

[0026] In some embodiments, the pneumatic module is configured to connect to a plurality of different pneumatic ports on each sample cartridge and to apply a selected pressure level to each pneumatic port independently at a selected time.

[0027] In some embodiments, the instrument further comprises an optical module configured to detect light transmitted from the fluid sample to determine a property of the fluid sample.

[0028] The pneumatic module may be further configured to connect to the output vessel pneumatic port and selectively adjust the pressure in the output vessel to draw final output fluid from the primary reaction vessel through the final output channel into the output vessel. The pneumatic module may be further configured to connect to the quality control pneumatic port and selectively adjust the pressure in the quality control vessel to draw an aliquot of final output fluid from the final output channel through the quality control channel into the quality control vessel. The reagent module may be configured to dispense buffer into the buffer vessel. The pneumatic module may be further configured to connect to the intermediate outlet pneumatic port and selectively adjust the pressure in the sealed chamber to draw air from the final output channel through the air permeable membrane. The pneumatic module may be further configured to connect to the waste pneumatic port and selectively adjust the pressure in the waste vessel to draw fluid from the primary reaction vessel through the waste channel into the waste vessel. The pneumatic module may be further configured to connect to the secondary pneumatic port and selectively adjust the pressure in the secondary reaction vessel to draw fluid from the primary outlet channel or the secondary reagent channel into the secondary reaction vessel.

[0029] The pneumatic module may be configured to detect a change in pressure and / or flow rate to determine when a liquid transfer operation is complete. For example, when pressure is adjusted to draw liquid from one chamber to another, once all the liquid has been drawn through the transfer channel, air is drawn in following the liquid, which requires less pressure differential and thus has a higher flow rate. This change in pressure and / or flow rate may be detected by the pneumatic module and used as a signal to stop pressure actuation when the transfer process is complete.

[0030] The pneumatic module may be configured to use positive or negative pressure to move liquid between various reservoirs of the cartridge, i.e., to apply positive pressure (above atmospheric pressure) to one reservoir to push liquid through a transfer channel into another reservoir, or to apply negative pressure (below atmospheric pressure) to one reservoir to draw liquid through a transfer channel into another reservoir.

[0031] In some embodiments, the pneumatic module may be configured to operate using a single pressure level selectively applied to the various pneumatic ports at different times to affect different operations. In some embodiments, the pneumatic module may be configured to operate using only two pressure levels selectively applied to the various pneumatic ports at different times to affect different operations.

[0032] In some embodiments, the instrument may further comprise an optical module configured to measure a characteristic of the aliquot of the output fluid contained in the quality control vessel.

[0033] The instrument may be configured to receive a plurality of sample cartridges of the sample cartridges. The pneumatic module may be configured to connect to all of the pneumatic ports of the plurality of sample cartridges and selectively apply pressure to selected ones of the pneumatic ports at selected times. The reagent module is configured to dispense reagent to each of the plurality of sample cartridges at selected times.

[0034] In some embodiments, the instrument further comprises mechanisms and actuators configured to move the reagent module to various positions within the instrument, each position corresponding to a respective one of a plurality of sample cartridges, enabling the reagent module to dispense one or more reagents to a respective sample cartridge.

[0035] Some embodiments provide a chemical processing instrument configured to receive one or more sample cartridges each containing a fluid sample for processing, each sample cartridge defining a primary reaction vessel configured to contain the fluid sample for processing, the primary reaction vessel configured to receive a lid to close the open top of the primary reaction vessel, a reagent vessel configured to receive one or more fluid reagents through the open top of the reagent vessel, the reagent vessel connected to the primary reaction vessel through a primary reagent channel with a reagent valve disposed in the reagent channel to control fluid flow through the primary reagent channel, and a pneumatic port in fluid communication with the primary reaction vessel, the chemical processing instrument including: a reagent dispenser configured to dispense the one or more fluid reagents into the reagent vessel through the open top of the reagent vessel; a pneumatic module configured to connect to a primary pneumatic port of the primary reaction vessel and to selectively adjust pressure within the primary reaction vessel to draw fluid contents into the primary reaction vessel when the lid is closed.

[0036] Some embodiments relate to an instrument including one or more stationary sample cartridge sockets, each configured to receive a sample cartridge including a fluid sample in a reaction vessel for processing, the instrument further including a heater mounted on a carriage assembly configured to selectively move the heater relatively close to the reaction vessel of the sample cartridge to heat the fluid sample in the reaction vessel and to move the heater relatively farther away from the sample cartridge when heating is not required.

[0037] The heater may comprise a radiator configured to pass through a slot or hole in the sample cartridge and partially surround the reaction vessel.

[0038] In some embodiments, the instrument further comprises a magnet mounted to the carriage and configured to be moved relatively closer to the reaction vessel of the sample cartridge to apply a magnetic field to the fluid sample in the reaction vessel and to be moved relatively farther away from the sample cartridge when the magnetic field is not needed.

[0039] The carriage can be configured to allow independent movement of the heater relative to the magnet to heat the fluid sample without the application of a magnetic field.

[0040] The heater may be mounted to the carriage via a spring-loaded rod that biases the heater away from the carriage to a disengaged position and to a first heater engagement position and allows the heater to move relatively closer to the carriage and magnet when the carriage is moved to the magnet engagement position.

[0041] Some embodiments relate to a chemical processing system comprising an instrument according to any one of the described embodiments and one or more of the sample cartridges according to any one of the described embodiments.

[0042] Some embodiments relate to a chemical processing system comprising one or more sample cartridges defining a primary reaction vessel configured to contain a fluid sample for processing, the primary reaction vessel configured to receive a lid to close the open top of the primary reaction vessel, a reagent vessel configured to receive one or more fluid reagents through the open top of the reagent vessel, the reagent vessel connected to the primary reaction vessel through a primary reagent channel with a reagent valve disposed in the reagent channel to control fluid flow through the primary reagent channel, and a pneumatic port in fluid communication with the primary reaction vessel, wherein the chemical processing instrument comprises a reagent dispenser configured to dispense one or more fluid reagents into the reagent vessel through the open top of the reagent vessel, and a pneumatic module configured to connect to the pneumatic port of the primary reaction vessel and selectively adjust pressure in the primary reaction vessel when the lid is closed to draw fluid contents of the reagent vessel into the primary reaction vessel.

[0043] Some embodiments relate to a method of operating a chemical processing instrument system according to any one of the described embodiments, comprising receiving one or more of the sample cartridges according to any one of the described embodiments, each including a fluid sample in a primary reaction vessel, the method comprising connecting a pneumatic module to a primary pneumatic port of the or each sample cartridge, operating a reagent module to dispense one or more reagents into the reagent vessel of the or each sample cartridge, and operating the pneumatic module to reduce pressure in the primary reaction vessel of the or each sample cartridge and draw fluid contents of the corresponding reagent vessel into the primary reaction vessel of the or each sample cartridge through the or each primary reagent channel.

[0044] The method may further include operating a shaker of the instrument to facilitate mixing of fluid in the primary reaction vessel of the or each sample cartridge.The method may further include operating a heater of the instrument to heat the primary reaction vessel of the or each sample cartridge to a predetermined temperature for a predetermined period of time.

[0045] In some embodiments, the reagents in the primary reaction vessel of the or each sample cartridge include functionalized magnetic beads, and the method further includes manipulating or moving a magnet to retain the magnetic beads at a selected location in the primary reaction vessel.

[0046] The method may further include connecting a pneumatic module to a waste pneumatic port of the or each sample cartridge and reducing pressure in the waste container to draw fluid from the primary reaction container through the waste channel and into the waste container.The method may further include connecting a pneumatic module to a secondary pneumatic port of the or each sample cartridge and reducing pressure in the secondary reaction container to draw fluid from the primary outlet channel into the secondary reaction container.The method may further include connecting a pneumatic module to a secondary pneumatic port of the or each sample cartridge and reducing pressure in the secondary reaction container to draw fluid from the secondary reagent channel into the secondary reaction container.

[0047] The method may further include operating a shaker of the instrument to facilitate mixing of fluid in the secondary reaction vessel of the or each sample cartridge.The method may further include operating a heater of the instrument to heat the secondary reaction vessel of the or each sample cartridge to a predetermined temperature for a predetermined period of time.

[0048] In some embodiments, the reagent in the or each sample cartridge secondary reaction vessel comprises functionalized magnetic beads, and the method further comprises manipulating or moving a magnet to retain the magnetic beads at a selected location in the secondary reaction vessel.

[0049] The method may further include connecting a pneumatic module to a waste pneumatic port of the or each sample cartridge and reducing pressure in the waste container to draw fluid from the secondary reaction container and into the waste container via a secondary waste channel extending between the secondary reaction container and the waste container. The method may further include connecting a pneumatic module to a pneumatic port of an output container of the or each sample cartridge and reducing pressure in the output container to draw processed fluid from the primary reaction container and into the output container via a final output channel.

[0050] In some embodiments, treated fluid drawn from the primary reaction vessel of the or each sample cartridge is drawn into a secondary reaction vessel and treated with further reagents before being drawn into a final output vessel via a final output channel.

[0051] The method may further include connecting a pneumatic module to a quality control pneumatic port of the or each sample cartridge, and reducing the pressure in the quality control vessel to draw an aliquot of the processed fluid from the final output channel through the quality control channel into the quality control vessel before reducing the pressure in the output vessel to draw the processed fluid into the output vessel.

[0052] The method may further include operating a reagent module to dispense buffer into a buffer reservoir of the or each sample cartridge, and opening a buffer channel valve of the or each sample cartridge before reducing the pressure in the quality control reservoir of the or each sample cartridge to draw buffer from the buffer reservoir through the evacuation channel and into the quality control reservoir along with an aliquot of treated fluid through the final output channel and the quality control channel.

[0053] The method may further include connecting a pneumatic module to an intermediate outlet pneumatic port of the or each sample cartridge, and reducing pressure in the outlet chamber of the or each sample cartridge to draw air from a final output channel through an air permeable membrane prior to reducing pressure in the quality control vessel.

[0054] The method may further include operating the optical module or measuring a characteristic of the aliquot of processed fluid contained in the quality control receptacle of each sample cartridge.

[0055] In some embodiments, operating the reagent module to dispense reagent into the reagent container further includes operating mechanisms and actuators to move the reagent module to various positions within the instrument, each position corresponding to one or more of the sample cartridges.

[0056] Some embodiments relate to a computer-readable medium having stored thereon instructions that, when executed by a computer, cause the computer to perform any one of the methods described herein.

[0057] Some embodiments relate to a method of using the system of any one of the described embodiments, comprising depositing a fluid sample in a primary reaction vessel of the or each sample cartridge, applying a lid to sealingly close an open top of the primary reaction vessel of the or each sample cartridge, inserting the or each sample cartridge into a corresponding cartridge slot in an instrument, and operating the instrument to process the fluid sample.

[0058] Some embodiments relate to a method of using the system of any one of the described embodiments, comprising depositing a fluid sample in a primary reaction vessel of the or each sample cartridge, applying a lid to sealingly close an open top of the primary reaction vessel of the or each sample cartridge, inserting the or each sample cartridge into a corresponding cartridge slot in an instrument, and operating the instrument to process the fluid sample.

[0059] The method may further include removing the or each sample cartridge from the instrument once the fluid sample has been processed. The method may further include removing an output container containing the processed fluid sample from the sample cartridge. The method may further include removing a temporary lid from the output container.

[0060] Some embodiments include a sample cartridge for use with a fluid analysis instrument, the sample cartridge including a sample container configured to receive a fluid sample for analysis, a buffer container configured to receive a buffer, an analysis container configured to receive a mixed fluid including an aliquot of the fluid sample mixed with at least a portion of the buffer for analysis, a sample channel extending between the sample container and a first junction, a sample channel valve disposed in the sample channel to control flow of the sample through the sample channel, a buffer channel extending between the buffer container and the first junction, and a buffer chuck. the sample cartridge comprising: a buffer channel valve disposed in the buffer channel to control flow of buffer through the channel; a metering channel in fluid communication with the buffer channel and the sample channel, the metering channel extending between a first junction and a second junction; an analysis vessel channel in fluid communication with the metering channel and extending between the second junction and an analysis vessel; and an analysis vessel pneumatic port in communication with the analysis vessel and configured to be connected to a pneumatic module to selectively adjust pressure in the analysis vessel to draw fluid into the analysis vessel via the analysis vessel channel.

[0061] In some embodiments, at least one of the sample channel valve and the buffer channel valve comprises an active valve that can be selectively opened and closed to draw an aliquot of the fluid sample into the metering channel and then cause a buffer to be drawn along with the aliquot of the fluid sample for analysis through the buffer channel and through the metering channel and the analysis reservoir channel into the analysis reservoir. The analysis reservoir can be preloaded with a dye configured to mix with the buffer and the fluid sample to facilitate analysis.

[0062] The sample cartridge may further comprise an intermediate outlet in fluid communication with the metering channel through the second junction, an outlet chamber into which the intermediate outlet opens, an air permeable liquid barrier membrane covering the outlet, an intermediate outlet pneumatic port in fluid communication with the outlet chamber and configured to be connected to a pneumatic module to selectively adjust pressure in the outlet chamber to draw air from the metering channel through the air permeable membrane, the intermediate outlet being positioned to allow liquid drawn from the sample channel or the buffer channel into the metering channel to fill the metering channel but not pass to the analysis reservoir channel. The intermediate outlet may be located at the second junction.

[0063] In some embodiments, the sample cartridge further comprises an outlet channel extending between the second junction and the outlet, such that liquid drawn from the sample channel or the buffer channel into the metering channel fills the metering channel and allows it to proceed to the outlet channel but not to the analysis reservoir channel.

[0064] The sample channel may further include an output bin in fluid communication with the metering channel through the second junction and through the output channel, and an output bin pneumatic port in communication with the output bin and configured to connect to a pneumatic module to selectively adjust pressure in the output bin to draw fluid from the metering channel through the second junction and the output channel to the output bin. The output channel may extend from the second junction to the output bin. The output channel may extend between the intermediate outlet and the output bin.

[0065] In some embodiments, a pressure-actuated valve is provided that includes a buffer channel valve pneumatic port connected to the pneumatic module and configured to selectively open and close the buffer channel valve.

[0066] Some embodiments relate to a fluid analysis instrument configured to receive a sample cartridge of any one of the described embodiments, comprising: a pneumatic module configured to connect to an analysis vessel pneumatic port and selectively adjust the pressure in the analysis vessel to draw fluid into the analysis vessel via the analysis vessel channel; and an analysis module configured to measure properties of the fluid in the analysis vessel.

[0067] Some embodiments relate to a fluid analysis instrument comprising a sample cartridge of any one of the described embodiments, the fluid analysis instrument comprising: a pneumatic module configured to connect to an analysis vessel pneumatic port and selectively adjust the pressure in the analysis vessel to draw fluid into the analysis vessel via the analysis vessel channel; and an analytical module configured to measure properties of the fluid in the analysis vessel.

[0068] The analysis module may comprise a light source configured to illuminate the fluid in the analysis vessel and an optical detector configured to detect or measure light transmitted from the fluid in the analysis vessel.

[0069] In some embodiments, the pneumatic module may be further connected to the intermediate outlet pneumatic port or configured to connect to the intermediate outlet pneumatic port and configured to selectively adjust the pressure in the outlet chamber to draw air from the metering channel through the air permeable membrane. The pneumatic module may be further connected to the output reservoir pneumatic port or configured to connect to the output reservoir pneumatic port and configured to selectively adjust the pressure in the output reservoir to draw fluid from the metering channel into the output reservoir via the second junction and the output channel. The pneumatic module may be further connected to the buffer channel valve pneumatic port or configured to connect to the buffer channel pneumatic port to selectively open and close the buffer channel valve.

[0070] In some embodiments, the instrument is configured to receive a plurality of sample cartridges of any one of the described embodiments that contain a fluid sample.

[0071] The instrument may further comprise mechanisms and actuators configured to move the analysis module to various positions corresponding to ones of the sample cartridges for analysis of the fluid in the analysis reservoir of each sample cartridge.

[0072] Some embodiments relate to a fluid analysis system comprising any one or more of the instruments of the described embodiments and one or more of the sample cartridges of any one of the described embodiments.

[0073] Some embodiments relate to a method of operating the fluid analysis instrument of any one of the described embodiments containing a fluid sample in a sample vessel, the method comprising: operating the pneumatic module to draw sample fluid from the sample vessel through the sample channel and into the metering channel to a second junction without the sample fluid passing into the analysis vessel channel; and operating the pneumatic module to draw fluid from the buffer vessel, along with an aliquot of sample fluid from the metering channel, through the buffer channel, the metering channel, and the analysis channel into the analysis vessel.

[0074] The method may further include operating the pneumatic module to reduce pressure in the analytical vessel for a predetermined period of time to draw sample fluid from the sample vessel through the sample channel and into the metering channel to the second junction without the sample fluid passing into the analytical vessel channel, and operating the pneumatic module to reduce pressure in the analytical vessel after the predetermined period of time to draw fluid from the buffer vessel through the buffer channel, the metering channel, and the analytical channel into the analytical vessel along with an aliquot of sample fluid from the metering channel.

[0075] In some embodiments, the method may further include operating the pneumatic module to reduce the pressure in the intermediate outlet to draw sample fluid from the sample vessel through the sample channel and into the metering channel until the sample fluid fills the air permeable barrier, and then operating the pneumatic module to reduce the pressure in the analysis vessel to draw fluid from the buffer vessel through the buffer channel, the metering channel, and the analysis channel into the analysis vessel, and operating the pneumatic module with an aliquot of sample fluid from the metering channel.

[0076] The method may further include operating the pneumatic module to reduce pressure in the output vessel for a predetermined period of time to draw sample fluid from the sample vessel through the sample channel and into the metering channel to a second junction without sample fluid traveling into the analysis vessel channel, and operating the pneumatic module to reduce pressure in the analysis vessel after the predetermined period of time to draw fluid through the buffer channel, the metering channel, and the analysis channel into the buffer vessel along with an aliquot of sample fluid from the metering channel. In some embodiments, operating the pneumatic module to draw fluid from the buffer vessel through the buffer channel continues until the metering channel is filled with air. The method may then further include operating the pneumatic module to reduce pressure in the output vessel and draw sample fluid from the sample vessel into the output vessel.

[0077] In some embodiments, the method further includes operating the pneumatics module to maintain the buffer valve in a closed state during the period in which fluid is drawn into the sample container, and then operating the pneumatics module to maintain the buffer valve in an open state to allow fluid to be drawn from the buffer container.

[0078] Some embodiments relate to a method of operating a fluid analysis instrument of any one of the described embodiments housing one or more of the sample cartridges of any one of the described embodiments containing a fluid sample in a sample reservoir of each sample cartridge, comprising: operating a pneumatic module to draw sample fluid from a sample reservoir of the or each sample cartridge through the sample channel and into a metering channel to a second junction without the sample fluid traveling into the analysis reservoir channel; and then operating the pneumatic module to draw fluid from a buffer reservoir of the or each sample cartridge through the buffer channel, the metering channel, and the analysis channel to the analysis reservoir, along with an aliquot of sample fluid from the metering channel.

[0079] In some embodiments, the method further includes connecting a pneumatic module to the analytical reservoir pneumatic port of the or each sample cartridge; operating the pneumatic module to reduce pressure in the analytical reservoir of the or each sample cartridge for a predetermined period of time to draw fluid from the sample reservoir through the sample channel and into the metering channel to the second junction without sample fluid traveling into the analytical reservoir channel; and operating the pneumatic module to reduce pressure in the analytical reservoir of the or each sample cartridge after a predetermined period of time to draw fluid from the buffer reservoir through the buffer channel, the metering channel, and into the analytical reservoir along with an aliquot of sample fluid from the metering channel.

[0080] The method may further include connecting a pneumatic module to the analysis reservoir pneumatic port and the intermediate outlet pneumatic port of the or each sample cartridge; operating the pneumatic module to reduce pressure in the intermediate outlet of the or each sample cartridge to draw sample fluid from the sample reservoir through the sample channel and into the metering channel until the sample fluid reaches an air permeable barrier; and then operating the pneumatic module to reduce pressure in the analysis reservoir of the or each sample cartridge to draw fluid from the buffer reservoir through the buffer channel, the metering channel, and the analysis channel into the analysis reservoir along with an aliquot of sample fluid from the metering channel.

[0081] The method may further include connecting a pneumatic module to the analytical reservoir pneumatic port and the output reservoir pneumatic port of the or each sample cartridge; operating the pneumatic module to reduce pressure in the output reservoir of the or each sample cartridge to draw sample fluid from the sample reservoir through the sample channel and into the metering channel to a second junction without the sample fluid traveling into the analytical reservoir channel; and operating the pneumatic module to reduce pressure in the analytical reservoir of the or each sample cartridge after a predetermined time to draw fluid from the buffer reservoir through the buffer channel, the metering channel, and the analytical channel into the analytical reservoir along with an aliquot of sample fluid from the metering channel.

[0082] Operation of the pneumatic module to draw fluid from the buffer reservoir through the buffer channel may continue until the metering channel of the or each sample cartridge is filled with air.

[0083] In some embodiments, the method may further include connecting a pneumatic module to an output reservoir pneumatic port of the or each sample cartridge and then operating the pneumatic module to reduce pressure in the output reservoir of the or each sample cartridge and draw sample from the sample reservoir into the output reservoir to draw buffer into an analysis reservoir. The method may further include connecting a pneumatic module to a buffer valve pneumatic port of the or each sample cartridge and operating the pneumatic module to maintain the buffer valve of the or each sample cartridge closed during a period of time that fluid is drawn from the sample reservoir, and then operating the pneumatic module to maintain the buffer valve of the or each sample cartridge open to allow fluid to be drawn from the buffer reservoir.

[0084] The method may then further include operating the analysis module to measure a property of the fluid in the analysis vessel.

[0085] The method may further include transmitting data related to the measured characteristic to an external computing device.

[0086] Some embodiments relate to a computer-readable medium having stored thereon instructions that, when executed by a computer, cause the computer to perform any one of the methods described herein.

[0087] Some embodiments relate to a method of using any one of the described systems, comprising depositing a fluid sample in a sample vessel of the or each sample cartridge, inserting the or each sample cartridge into a corresponding cartridge slot in an instrument, and operating the instrument to analyze the fluid sample. The method may further include removing the or each sample cartridge from the instrument once the fluid sample has been processed.

[0088] Some embodiments include a sample cartridge for use with a fluid analysis instrument, the sample cartridge comprising: a sample vessel configured to receive a fluid sample for analysis; a buffer vessel configured to receive a buffer; a sealed analysis vessel configured to receive a mixed fluid including an aliquot of the fluid sample mixed with at least a portion of the buffer for analysis; a first channel extending between the sample vessel and the analysis vessel; a second channel extending from the buffer vessel to a junction with the first channel; a first valve disposed in the first channel between the sample vessel and the junction; and a second channel extending between the buffer vessel and the junction. a second valve disposed within the first channel and a pneumatic port communicating with the analysis container and configured to be connected to a vacuum pump to draw fluid from the first channel into the analysis container, at least one of the first and second valves comprising an active valve that is selectively opened and closed to allow an aliquot of a fluid sample to be drawn past the junction into the first channel and thereafter allow a buffer solution to be drawn through the second channel, past the junction into the first channel, to transport and mix the aliquot of the fluid sample before it flows into the analysis container for analysis.

[0089] Some embodiments relate to a chemical processing instrument configured to receive a sample cartridge containing a fluid sample of at least 0.2 mL volume, the instrument configured to be operated according to instructions stored on a computer readable storage medium that causes the sample to perform any two or more of the following processing steps: processing the sample while keeping it isolated to avoid contamination of the instrument or cross-contamination with other samples; selecting nucleic acids using specific chemistry, incubation conditions, bead selection, and elution parameters; selecting a desired range of single-stranded or double-stranded nucleic acid sizes in the processed fluid product and discarding undesirable material outside the desired range; increasing the concentration of the selected nucleic acid product; and quantifying an aliquot of the processed fluid product, mixing it with a specific fluorochrome for the selected nucleic acid, and quantifying a characteristic of the product, such as against a standard or calibration reference curve.

[0090] Throughout this specification the term "comprise" or variations such as "comprises" or "comprising" will be understood to imply the inclusion of a stated element, integer, or step, or group of elements, integers, or steps, but not the exclusion of any other element, integer, or step, or group of elements, integers, or steps. [Brief description of the drawings]

[0091] The various figures of the accompanying drawings merely depict exemplary embodiments of the present disclosure and are not to be considered as limiting its scope.

[0092] [Figure 1A] FIG. 1 is a schematic diagram of an instrument configured to receive one or more sample cartridges, each containing a sample for processing, according to some embodiments. [Figure 1B] FIG. 1B is a perspective view of the device of FIG. 1A according to some embodiments. [Figure 1C] FIG. 1B is a cutaway perspective view showing some of the internal components of the device of FIG. 1A, according to some embodiments. [Figure 2A] FIG. 1 is a perspective view of a sample cartridge for use with the instrument according to some embodiments. [Figure 2B] FIG. 2B is a top view of the sample cartridge of FIG. 2A. [Figure 2C] FIG. 2B is a side view of the sample cartridge of FIG. 2A. [Figure 2D] FIG. 2B is a bottom view of the sample cartridge of FIG. 2A. [Figure 2E] FIG. 2B is a bottom view of the sample cartridge of FIG. 2A showing further detail. [Figure 2F] 2B is a bottom view of a fluid metering arrangement according to some embodiments that may form part of the sample cartridge of FIG. 2A. [Figure 2G] FIG. 2B is a circuit diagram of the sample cartridge of FIG. 2A according to some embodiments. [Figure 2H] FIG. 2B is a perspective view showing an alternative channel arrangement of the sample cartridge of FIG. 2A according to some embodiments. [Figure 2I] FIG. 2B is a perspective view showing an alternative channel arrangement of the sample cartridge of FIG. 2A according to some embodiments. [Figure 2J] 2B illustrates an alternative valve for the sample cartridge of FIG. 2A according to some embodiments. [Figure 2K] 2B illustrates an alternative valve for the sample cartridge of FIG. 2A according to some embodiments. [Figure 2L] 2B illustrates an alternative valve for the sample cartridge of FIG. 2A according to some embodiments. [Figure 2M] 2B illustrates an alternative valve for the sample cartridge of FIG. 2A according to some embodiments. [Figure 2N] 2B illustrates an alternative valve for the sample cartridge of FIG. 2A according to some embodiments. [Figure 2O] FIG. 13 is a close-up perspective view of an intermediate outlet of a sample cartridge according to some embodiments. [Figure 3A] FIG. 1C is a perspective view of a reagent module of the instrument of FIGS. 1A-1C according to some embodiments. [Figure 3B] FIG. 3B is a perspective view of a reagent cartridge of the reagent module of FIG. 3A. [Figure 4A] FIG. 1C is a schematic diagram of an optical module of the apparatus of FIGS. 1A-1C, according to some embodiments. [Figure 4B] FIG. 1C is a schematic diagram of an optical module of the apparatus of FIGS. 1A-1C, according to some embodiments. [Figure 5A] FIG. 1C is a schematic diagram of the device of FIGS. 1A-1C showing a portion of a pneumatic module, a thermal module, a magnetic module, a mixing module, and a kinetic module, according to some embodiments. [Figure 5B] FIG. 1D is a side view of the device of FIGS. 1A-1C showing a portion of the thermal module, magnetic module, mixing module, and kinetic module, according to some embodiments. [Figure 6] FIG. 1C is a schematic diagram of a control module of the device of FIGS. 1A-1C, according to some embodiments. [Figure 7A] FIG. 1 is a perspective view of a chemical processing apparatus according to some embodiments. [Figure 7B] FIG. 7B is a perspective view of the device of FIG. 7A with some features omitted. [Figure 7C] 7B shows a portion of the reagent module and kinetic module of the apparatus of FIG. 7A. [Figure 7D] FIG. 7B is another view of the reagent module, also showing the location of the optical module of the instrument of FIG. 7A. [Figure 7E] FIG. 2 is a diagram of a motion module and a motion module. [Figure 7F] FIG. 7B is a further view of the movement module of the apparatus of FIG. 7A. [Figure 8A] FIG. 7B is a fluid layout diagram of the reagent module of the instrument of FIG. 7A. [Figure 8B] 1 is a close-up of the reagent cartridge layout of the reagent module. [Figure 8C] 1 is an enlarged view of the layout of the pump portion of the reagent module. [Figure 8D]1 is an enlarged view of the layout of the dispensing section of the reagent module. [Figure 8E] FIG. 2 is a perspective view of a reagent module and a disconnected reagent cartridge. [Figure 8F] FIG. 1 is an internal perspective view of the reagent cartridge, omitting the outer housing. [Figure 8G] FIG. 2 is a perspective view of a reagent storage support and clamping mechanism in an unclamped configuration. [Figure 8H] FIG. 8H is an enlarged perspective view of the reagent cartridge clamp of FIG. 8G. [Figure 8I] FIG. 2 is a perspective view of a pump portion of the reagent module. [Figure 8J] FIG. 2 is a perspective view of a dispensing portion of a reagent module. [Figure 9A] FIG. 7B is a perspective view of the pneumatic module and core unit of the instrument of FIG. 7A. [Figure 9B] FIG. 13 is a further view of the pneumatic module. [Figure 9C] FIG. 2 is a perspective view of a manifold of the pneumatic module. [Figure 9D] FIG. 9D is a cross-sectional perspective view of the manifold of FIG. 9C. [Figure 9E] FIG. 13 is a perspective view of a pinch valve of the pneumatic module in an open configuration. [Figure 9F] FIG. 9F is a cross-sectional perspective view of the pinch valve of FIG. 9E in an open configuration. [Figure 9G] FIG. 9F is a perspective view of the pinch valve of FIG. 9E in a closed configuration. [Figure 9H] FIG. 9F is a cross-sectional perspective view of the pinch valve of FIG. 9E in a closed configuration. [Figure 9I] FIG. 9B is a pneumatic circuit diagram of the pneumatic module of FIG. 9A. [Figure 9J] FIG. 2 is a pneumatic circuit diagram of a first manifold of the pneumatic module. [Figure 9K] FIG. 13 is a pneumatic circuit diagram of a second manifold of the pneumatic module. [Figure 9L] FIG. 1 is a pneumatic circuit diagram of the pneumatic interface plate of the pneumatic module. [Figure 10A]FIG. 7B is a perspective view of a core unit of the device of FIG. 7A. [Figure 10B] FIG. 10B is an enlarged perspective view of the pneumatic interface plate of FIG. 9L in the core unit of FIG. 10A. [Figure 10C] 10B shows the internal components of the core unit of FIG. 10A with other components omitted for clarity. [Figure 10D] FIG. 10B is a perspective view of a heating assembly of the core unit of FIG. 10A. [Figure 10E] FIG. 13 is a cross-sectional perspective view of a heating assembly mounted on a motion carriage along with a magnet. [Figure 10F] 12A installed in a socket of the core unit of FIG. 10A and a heating assembly engaged with the sample cartridge. FIG. [Figure 10G] 12B is a perspective view of the sample cartridge of FIG. 12A installed in a socket of the core unit of FIG. 10A with a heating assembly and magnet engaged with the sample cartridge. [Figure 10H] 10B is a force diagram of the orbital shaker of the instrument of FIG. 7A and the core unit of FIG. 10A. [Figure 10I] FIG. 2 is a perspective view of an orbital shaker with certain components omitted for clarity. [Figure 10J] FIG. 2 is an enlarged cross-sectional perspective view of an orbital shaker. [Figure 10K] FIG. 13 is a further perspective view showing the internal components of the orbital shaker including the stopping mechanism. [Figure 10L] FIG. [Figure 10M] FIG. 2 is a perspective view of a magnet holder and magnets of a magnetic module according to some embodiments. [Figure 10N] FIG. 10M is a cross-sectional view of the top of the magnet holder. [Figure 11] FIG. 7E is a cross-sectional perspective view of the optical module of FIG. 7D. [Figure 12A] FIG. 2 is a bottom perspective view of a sample cartridge according to some embodiments. [Figure 12B]FIG. 12B is an exploded top perspective view of the sample cartridge of FIG. 12A. [Figure 13] FIG. 7B is a schematic diagram of the control module and associated software components of the device of FIG. 7A. [Figure 14A] FIG. 7B is an electrical layout diagram of the device of FIG. 7A. [Figure 14B] 7B shows the electrical layout of a controller unit forming part of the control module of the device of FIG. 7A. [Figure 14C] 7B shows the electrical layout of the power subassembly of the device of FIG. 7A. [Figure 14D] 7B shows the electrical layout of a portion of the exercise module of the apparatus of FIG. 7A. [Figure 14E] FIG. 7B shows the electrical layout of the pneumatic module of the instrument of FIG. 7A. [Figure 14F] FIG. 7B shows the electrical layout of the core unit of the device of FIG. 7A. [Figure 14G] FIG. 7B shows a first expanded view of the electrical layout of the core unit of the device of FIG. 7A. [Figure 14H] FIG. 7B shows a second expanded view of the electrical layout of the core unit of the device of FIG. 7A. [Figure 14I] FIG. 7B shows a third enlarged view of the electrical layout of the core unit of the instrument of FIG. 7A for controlling movement of the core carriage. [Figure 14J] FIG. 7B shows a fourth enlarged view of the electrical layout of the core unit of the instrument of FIG. 7A for controlling movement of the core carriage. [Figure 14K] FIG. 7B shows a fifth enlarged view of the electrical layout of the core unit of the instrument of FIG. 7A for controlling the orbital shaker. DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

[0093] SUMMARY OF THE DISCLOSURE The embodiments relate generally to systems, devices, methods, and computer readable media for performing operations on samples, such as nucleic acid extraction operations.

[0094] Conventionally, there are many chemical process workflows that include several steps that require the transfer of a fluid sample to different containers and / or different instruments, with each transfer step having the potential for sample spillage, contamination of the instrument by the sample, and potential cross-contamination with other samples for processing.

[0095] Some embodiments relate to a sample cartridge for a chemical processing instrument that facilitates a workflow process to separate samples and mitigate cross-contamination. The sample cartridge includes a primary reaction vessel arranged to receive a lid and a reagent vessel. The primary reaction vessel and the reagent vessel are connected or in fluid communication via a primary reagent channel. The primary reagent channel may have a primary reagent valve disposed therein to control fluid flow through the primary reagent channel. A primary pneumatic port is in fluid communication with the primary reaction vessel and is configured to be connected to a pneumatic module. The pneumatic module can be used to selectively adjust the pressure in the primary reaction vessel when the lid is closed to draw fluid contents of the reagent vessel into the primary reaction vessel.

[0096] The sample cartridge may further include a primary pneumatic channel extending between the primary pneumatic port and the primary reaction vessel, with the opening of the primary pneumatic channel into the primary reaction vessel located halfway up a sidewall of the primary reaction vessel. The opening of the primary pneumatic port into the primary reaction vessel is located closer to a top of the primary reaction vessel than to a bottom of the primary reaction vessel. This may reduce the possibility of liquid specimen being drawn into the pneumatic module and potentially contaminating the instrument.

[0097] In some embodiments, the opening of the primary reagent channel into the primary reaction vessel is located halfway into the sidewall of the primary reaction vessel. In some embodiments, the opening of the primary reagent channel into the primary reaction vessel is located closer to the top of the primary reaction vessel than to the bottom of the primary reaction vessel. This may reduce the possibility of liquid sample entering the reagent channel and subsequently into the reagent vessel, which may lead to cross-contamination within the instrument.

[0098] According to some embodiments, various other features are described below that further mitigate cross-contamination, including sealed containers for processing samples, separate open containers for receiving reagents, one-way valves, and a pneumatic system for driving fluid flow that allows sealing of the reaction containers.

[0099] There are also many chemical processing workflows that require the quantification of an aliquot of a fluid sample for analysis or measurement of one or more properties of the fluid sample, such as for quality control.

[0100] Some embodiments relate to an arrangement of channels and valves that allows for accurate fluid measurement to separate aliquots of known volume for analysis or quality control, as described below in connection with Figures 2E-2G, which may be included in a sample cartridge for use with an instrument, or even included in a dedicated fluid analysis instrument.

[0101] 1A-1C, an instrument 100 according to some embodiments is shown. The instrument 100 may be configured to accept one or more sample cartridges 200, each containing a sample for processing. The instrument 100 may be configured to perform one or more operations on the sample, such as a chemical processing step, heating, cooling, incubation, mixing, analysis, or measurement. The instrument 100 may be configured to perform multiple operations on the sample that may traditionally be performed in a separate instrument or manually in a laboratory.

[0102] In some embodiments, the instrument 100 can be configured to perform one or more nucleic acid extraction operations on a sample, such as extracting nucleic acids (e.g., DNA or RNA) from a patient sample and providing an output fluid containing concentrated, and optionally quantified, nucleic acids from the sample.

[0103] The instrument 100 may comprise a variety of different modules configured to perform operations on a sample. These may include any one or more selected from a reagent module 300, an optical module 400, a pneumatic module 500, a thermal module 600, a magnetic module 700, a mixing module 800, a motion module 900, and a control module 101 to control the operations performed by the instrument 100. The instrument 100 may also have a power source 102 or may be connected to a power source 102 to provide power to the various modules.

[0104] The reagent module 300 may be configured to dispense selected reagents into the sample cartridge 200. For example, the reagent module 300 may include multiple reservoirs each containing a corresponding number of reagents for use in the operation of the instrument workflow. The reagent module 300 may include one or more pumps, channels, and dispense nozzles to selectively dispense controlled amounts of reagents into selected sample cartridges 200 at selected times as part of one or more of the instrument workflows.

[0105] For example, the reagent module 300 may include a syringe pump configured to control the dispensing of a reagent. The reagent module may include two dispensing nozzles, each configured to dispense a different reagent at a different time. The previous reagent may be flushed from the nozzle before dispensing a subsequent reagent into the cartridge. In some embodiments, the instrument may include a waste receptacle, and the reagent module may be configured to dispense some reagents into the waste receptacle to flush the previous reagent from the nozzle before dispensing into the cartridge.

[0106] In some embodiments, the reagent module 300 may include a sensor configured to detect the presence or absence of liquid in a portion of the reagent module. For example, a sensor may be configured to monitor a dispense outlet or dispense outlet tube to indicate or confirm when reagent is being dispensed through the output tube. In some embodiments, multiple sensors may be configured to monitor multiple different fluid lines and / or fluid levels in reagent reservoirs within the reagent module.

[0107] The or each sensor may comprise an optical sensor, such as a light source and a photodetector positioned to detect light from the light source passing through (or reflected from) a translucent or transparent wall of the fluid line or reservoir.

[0108] One or more sensors in the reagent module may be connected to a user interface or indicator LEDs, for example, to verify priming of the reagent lines, to verify when a reagent is being dispensed, or to indicate when a reagent has been drained or will soon be drained and needs to be replaced.

[0109] The tubing used for the reagent lines in the reagent module may comprise any suitable material, such as, for example, silicone tubing or PTFE tubing. Any suitable dimensions of the tubing may be selected depending on the liquid to be dispensed for a particular application. For example, the inner diameter may be about 0.3 mm and the outer diameter may be about 1.6 mm.

[0110] The optical module 400 may comprise an optical sensor or detector for optical inspection of the material or fluid contained within the sample cartridge 200. The optical module 400 may further comprise one or more light sources for illuminating the material or fluid contained within the sample cartridge 200 for inspection. The optical module 400 may be configured to detect and / or measure particular frequencies and / or intensities of light within the optical or near-optical spectrum to determine a particular property of the material or fluid contained within the sample cartridge, such as, for example, concentration or density.

[0111] For example, the optical module may include an epifluorescence system that includes a UV LED light source that transmits light through a bandpass filter, exciting fluorescence in a dye in the cartridge, causing an emission from the dye that is detected by a photodiode.

[0112] The pneumatic module 500 may be configured to apply a pressure differential across particular flow paths of the sample cartridge 200 or instrument 100 to drive fluid flow along those flow paths.

[0113] The pneumatic module may be configured to move liquid between various reservoirs of the cartridge using positive or negative pressure, i.e., applying a positive pressure (above atmospheric pressure) to one reservoir to push liquid through a transfer channel into another reservoir, or applying a negative pressure (below atmospheric pressure) to one reservoir to pull liquid from another reservoir through a transfer channel.

[0114] In some embodiments, the pneumatic module may be configured to operate using a single pressure level selectively applied to the various pneumatic ports at different times to affect different operations. In some embodiments, the pneumatic module may be configured to operate using only two pressure levels selectively applied to the various pneumatic ports at different times to affect different operations.

[0115] For example, if the cartridge includes a pressure-activated valve that requires a higher pressure than the actuation pressure to move liquid through a channel, two pressure levels may be required.

[0116] Any suitable pressure differential (e.g., vacuum pressure) may be used to drive flow within the cartridge, but it should be noted that too little pressure can result in particularly long liquid transfer times, and too much pressure gradient can result in splashing or sputtering, which may be undesirable in certain applications, or high shear rates of liquid flow, which may potentially damage certain molecules, such as nucleic acids. Suitable vacuum pressures also depend on the viscosity or range of viscosities of the liquid used in a given application. In some embodiments, the driving vacuum pressure can be, for example, in the range of 50 mBar to 500 mBar, 80 mBar to 300 mBar, 100 mBar to 200 mBar, 100 mBar to 120 mBar, about 100 mBar, or about 120 mBar.

[0117] The thermal module 600 may comprise one or more heating or cooling elements configured to control and / or adjust the temperature of the sample cartridge 200 and materials contained therein during different operations of the instrument workflow, such as incubation for a culture.

[0118] The magnetic module 700 may comprise one or more permanent magnets or electromagnets configured to control the movement of magnetic beads within the sample cartridge 200. For example, magnetic beads may be used within a primary reaction vessel 210 (FIG. 2A) for sample components to bind during a particular operation of the instrument workflow. The magnetic module 700 may be configured to hold the magnetic beads in place while liquid is drained away from the magnetic beads.

[0119] Alternatively, non-magnetic functionalized beads may be used for binding and a filter may be used to restrict the beads from leaving the reaction vessel. Another alternative is to use a porous material such as a frit with a functionalized surface for binding, and liquids can be drawn through the frit to achieve the desired reaction.

[0120] In other embodiments, the chemical catalyst or reactant may be provided as a coating on the surface of a solid structure, such as a bead or porous solid, for reacting with the liquid in the reaction vessel.

[0121] The mixing module 800 may be configured to facilitate mixing of fluids within the primary and / or secondary reaction vessels 210, 220 (FIG. 2A) during a particular operation of the instrument workflow. For example, the mixing module 800 may include an orbital shaker, such as an eccentric weight configured to be rotated by a motor.

[0122] The motion module 900 may comprise one or more motors or actuators configured to move a particular module to different positions corresponding to the cartridge slots 120 to perform operations on the corresponding cartridges 200 (and / or samples therein) at different times. For example, the reagent module 300 and the optics module 400 may be moved to different cartridge positions to perform operations on the corresponding cartridges 200 at those positions.

[0123] The control module 101 may include electronics hardware for communicating with other modules of the instrument 100 and software configured to control the operation of the instrument modules according to a selected instrument workflow.

[0124] Each of the modules, according to some embodiments, is further described below.

[0125] The instrument 100 may be configured to connect to an external computer system, such as a laboratory information system 103. The instrument 100 may be configured to transmit data, such as analytical or measurement data associated with the sample in the sample cartridge 200, to the external laboratory information system 103. In some embodiments, the instrument 100 may be configured to receive information, such as data associated with the sample, reference data for comparison, or instructions for controlling the operation of the instrument 100, from the external laboratory information system.

[0126] In some embodiments, the instrument 100 may include a user interface 105. The user interface 105 may include a display on the instrument 100 itself or an external display in communication with the instrument 100. The user interface 105 may be configured to allow a user to select a workflow program to run on the samples in the sample cartridge 200. The workflow program may be selected from a list of different programs that include different workflow operations configured to accomplish different processes.

[0127] For example, the list of workflow programs may include extraction, isolation, enrichment, concentration, or quantification of natural or non-natural nucleic acids, including, for example, DNA (genomic DNA, rearranged immunoglobulin or TCR DNA, cDNA, cfDNA, etc.) and RNA (mRNA, primary RNA transcripts, transcribed RNA, or microRNA, etc.). Non-natural nucleic acids to be isolated include glycolic nucleic acids, threose nucleic acids, locked nucleic acids, and peptide nucleic acids. Other workflow programs may include preparation of nucleic acids for amplification (e.g., PCR library preparation) or any other type of manipulation or analysis, such as insertion into a vector for applications such as sequencing or in vitro transcription and / or translation.

[0128] The user interface 105 may also display information related to the sample and / or an indication of which workflow program or a particular step of a workflow program is currently in progress.

[0129] The instrument 100 may include a chassis or housing 110 to house some or all of the modules. In some embodiments, the housing 110 may be configured to be stackable with other instruments of the instrument 100, e.g., so that multiple instruments of the instrument 100 can be stacked vertically or placed side-by-side in a laboratory.

[0130] The instrument 100 may include multiple cartridge slots or sockets 120, each configured to receive a corresponding sample cartridge 200. In this manner, multiple samples may be processed simultaneously. The cartridge slots 120 may be defined at least in part by an exterior opening in the housing 110 configured to receive the sample cartridge 200.

[0131] Some of the modules may have dedicated components for each cartridge socket 120. Some of the modules may simultaneously service all of the cartridges 200 in the cartridge slots 120. Some of the modules may be configured to service different cartridges 200 in the cartridge slots 120 at different times.

[0132] 1C, a cutaway view of the instrument 100 is shown showing a portion of the motion module 900, according to some embodiments. Shown are a number of sample cartridges 200 disposed in a corresponding number of cartridge slots 120. The cartridges 200 and cartridge slots 120 are arranged side-by-side and extend across a portion of the instrument 100.

[0133] The motion module 900 may include a track 910 that extends across the multiple cartridge slots 120 and a carriage 920 configured to move along the track 910. The carriage 920 may be configured to carry one or more of the modules, such as the reagent module 300 and the optics module 400, and move them to different cartridge positions to perform operations on the sample cartridge 200. An actuator, such as a motor operated by the control module 101, may be configured to move the carriage 920 between a rest position and the various cartridge positions.

[0134] In some embodiments, the motion module 900 may comprise multiple carriages 920 and corresponding tracks 910 configured to carry different modules, such as, for example, a reagent module 300 and an optical module 400, respectively.

[0135] The track 910 may include a motion stage 912, which may include markings or other indicia, to identify a number of carriage positions corresponding to cartridge positions that properly align the carriage module with the cartridge slot 120 and corresponding sample cartridge 200 to enable the module to perform an operation on a selected sample cartridge 200. The motion module 900 may include one or more sensors disposed on the carriage 920 configured to detect an indicator signal for the carriage 920 to stop at a selected carriage position. Alternatively, a known actuator state (e.g., stepper motor angle) corresponding to a particular carriage position may be selected to move the carriage to the selected carriage position.

[0136] 2A-2N, a sample cartridge 200 is shown according to some embodiments. The sample cartridge 200 includes a base 202, a primary reaction vessel 210, a reagent vessel 230, and an output vessel 250. The sample cartridge 200 may include different features for different applications depending on the operations to be performed on the sample.

[0137] In some embodiments, the sample cartridge 200 may further comprise an optional secondary reaction vessel 220, as shown in FIG. 2A and further described below.

[0138] In some embodiments, the sample cartridge 200 may further comprise an optional waste container 240, as shown in FIG. 2A and further described below.

[0139] In some embodiments, the sample cartridge 200 may further comprise an optional quality control module 260, as shown in FIG. 2A and further described below.

[0140] The sample cartridge 200 defines channels connecting various vessels (primary reaction vessel 210, reagent vessel 230, and output vessel 250, as well as, in some embodiments, optional secondary reaction vessel 220, optional waste vessel 240, optional quality control module 260) that are in fluid communication and allow fluids (including liquids and potentially liquid slurries containing solids) to be exchanged between the vessels. The sample cartridge 200 may include valves that selectively allow or disallow flow through the channels, allowing control of fluid exchange between the vessels. The network of valves and channels, according to some embodiments, is further described below.

[0141] In some embodiments, the containers (including primary reaction container 210, reagent container 230, output container 250, and optional secondary reaction container 220, waste container 240, and quality control module 260) may be integrally formed with base 202.

[0142] In some embodiments, the output container 250 may comprise a separate, removable component, such as, for example, an Eppendorf tube, allowing for easy removal of the final output liquid from the cartridge 200 within the sealed container 250 for further processing or use elsewhere.

[0143] The sample cartridge 200 may define an output receptacle holder or seat 254, which may be integrally formed with the base 202. The output receptacle 250 may be seated in the seat 254 during processing in the instrument 100. Once a selected instrument workflow is completed and the output fluid has been deposited in the output receptacle 250, the output receptacle 250 may be sealed and removed from the seat 254, and the remainder of the sample cartridge 200 may be discarded.

[0144] 2G, a flow schematic of a sample cartridge 200, along with optional additional features, according to some embodiments, is shown. The channel and valve network of the sample cartridge 200 is described with reference to a simple workflow, but it will be understood that many different workflows can be implemented on or within the cartridge 200.

[0145] A liquid sample may be introduced into the primary reaction vessel 210, and a lid 211 may be used to seal the sample in the primary reaction vessel 210. The lid 211 may be integrally formed with the primary reaction vessel 210, for example, as shown in FIG. 2A.

[0146] One or more reagents may be dispensed (e.g., from a reagent module 300) into the open top of the reagent vessel 230. A primary reagent channel 231 extends between the reagent vessel 230 and the primary reaction vessel 210. Reagents may be delivered from the reagent vessel 230 to the primary reaction vessel 210 via the primary reagent channel 231.

[0147] A primary reagent valve 235 may be disposed within the primary reagent channel 231 to control flow through the primary reagent channel 231. The primary reagent valve 235 may include an active valve (examples of which are discussed below) or a passive valve. For example, the primary reagent valve 235 may include a low pressure valve that has a relatively low break pressure compared to certain other valves in the network. That is, the valve may restrict flow until a relatively low threshold pressure differential exists across the valve, at which point the primary reagent valve 235 opens to allow fluid to flow from the reagent vessel 230 to the primary reaction vessel 210 through the primary reagent channel 231.

[0148] The driving pressure gradient may be created using a pneumatic module 500. The cartridge 200 may include a primary pneumatic channel 212 extending between a primary reaction vessel 211 and a primary pneumatic port 213. The primary pneumatic port 213, along with other pneumatic ports described below, may be defined by an opening on an exterior surface of the sample cartridge 200, such as the bottom or side of the base 202, and may be configured to engage a pneumatic connector 510 of the instrument 100 to connect the pneumatic port 213 to the pneumatic module 500.

[0149] The pneumatic module 500 may include a plate defining a number of pneumatic ports connected by pneumatic lines to a pressure control manifold. Each pneumatic port may include a seal and may be configured to connect to a corresponding port on the underside of the cartridge base 202. The plate may be configured to be moved upward by the kinematic module to meet the cartridge when the cartridge is installed in the instrument, and the corresponding ports may be connected to connect the pneumatic module to channels in the cartridge such that they are in fluid communication.

[0150] With the lid 211 sealed, when the pneumatic module 500 applies negative or vacuum pressure (negative relative to atmospheric or ambient pressure) to the pneumatic port 213, a pressure gradient is created between the primary reaction vessel 210 and the reagent vessel 230, allowing reagent to be drawn from the reagent vessel 230 through the primary reagent channel 231 into the primary reaction vessel 210 and the sample contained therein.

[0151] The primary reagent valve 235 may remain closed to restrict flow in the primary reagent channel 231 until it is actuated to open or until a threshold crack pressure is overcome by pressure applied to the pneumatic port 213 by the pneumatic module 500. The primary reagent valve 235 may include a check valve configured to restrict or prevent backflow to avoid a portion of the fluid sample in the primary reaction chamber 210 flowing into the reagent container 230.

[0152] To avoid a portion of the contents of the primary reaction vessel 210 being sucked into the primary air pressure channel 212, the opening of the primary air pressure channel 212 into the primary reaction vessel 210 may be defined halfway into the sidewall of the primary reaction vessel 210, or at or near the top of the primary reaction vessel 210, as shown in Figure 2A. The primary air pressure channel 212 may be defined in a structure extending up the side of the primary reaction vessel 210, either in the sidewall of the primary reaction vessel 210, or in line with the sidewall of the primary reaction vessel 210, as shown in Figure 2A.

[0153] 2A, the primary reagent channel 231 may also extend upward along the sidewall and open into the primary reaction vessel 210 at or near the top of the primary reaction vessel 210. This may further reduce the possibility of part of the fluid sample flowing from the primary reaction vessel 210 into the primary reagent channel 231 or reagent vessel 230.

[0154] Alternative designs for incorporating the pneumatic and input channels of either of the reaction vessels 210, 230 into the sample cartridge 200 are shown in Figures 2H and 2I. For example, the channels can be formed as open channels in the base 202 and in the flat vertical web 203, as shown in Figure 2H. Alternatively, the channels can be formed as open channels in a side structure 204 that runs along the side of the reaction vessels 210, 230, as shown in Figure I. The channels can then be closed by covering them with a foil or film that can be adhesively bonded or welded to the base 202 and web 203 or side structure 204.

[0155] If the instrument workflow includes operations requiring removal of waste fluid from the primary reaction vessels 210, the sample cartridge 200 may include a waste vessel 240. Alternatively, the instrument 100 may include a waste receptacle or waste channel for external disposal of waste fluid.

[0156] The sample cartridge 200 may include a primary waste channel 214 extending between the primary reaction vessel 210 and a waste vessel 240 (or other waste channel or receptacle). A primary waste valve 215 may be disposed within the primary waste channel 214 to control when fluid is removed from the primary reaction vessel 210 through the primary waste channel 214. For example, the primary waste valve 215 may include a low pressure valve having a relatively low break pressure.

[0157] The sample cartridge 200 may further include a waste pneumatic channel 242 extending between the waste container 240 and a waste pneumatic port 243. The waste pneumatic channel 242 may also open into the waste container 240 at or near the top of the waste container 240 to avoid drawing waste fluid into the waste pneumatic channel 242. The top of the waste container 240 may be sealed, for example, with a lid or foil.

[0158] In some embodiments, some splashing will occur depending on what liquid needs to be transferred between the containers 210, 220, 230, 240 and small amounts of liquid may splash into the pneumatic channels 212, 222, 242. If liquids are aspirated through the pneumatic channels, they may pass out of the cartridge and into the pneumatic module 500, thereby contaminating the instrument.

[0159] To mitigate this scenario, the cartridge may include a liquid trap associated with one or more (or each) of the pneumatic channels to prevent or limit liquid leaving the cartridge via the pneumatic channel. For example, the liquid trap may include a gas permeable membrane that allows the passage of air but limits or stops the passage of liquid. The gas permeable membrane may be located anywhere along the pneumatic channels 212, 222, 242, such as at an opening, or at the end of each pneumatic channel at the base of the cartridge.

[0160] In some embodiments, the gas permeable membrane may be disposed over a relatively large area (larger than the cross-section of the corresponding channel) to increase the volume of trapped liquid that may be present before blocking the flow of gas through the membrane. The instrument may be configured to detect a pressure change due to either the channel or the liquid trap being blocked and then trigger, for example, an end of the workflow operation and an indication that the process has failed.

[0161] The sample cartridge 200 may further define a primary output channel 216 to allow for the discharge of output fluid from the primary reaction chamber 210. In some embodiments, if only one reaction vessel is required, the primary output channel 216 may lead directly to the output vessel 250. In some embodiments, if a secondary reaction vessel is required, the primary output channel 216 may extend between the primary reaction vessel 210 and the secondary reaction vessel 220.

[0162] A primary outlet valve 217 may be disposed within the primary outlet channel 216 to control the exit of the output fluid through the primary output channel 216. For example, the primary outlet valve 217 may include an active pressure actuated valve that is actuated by applying pressure to a corresponding primary outlet valve pneumatic port 218.

[0163] In embodiments in which the sample cartridge 200 includes a secondary reaction vessel 220 , the sample cartridge 200 may include a secondary reagent channel 232 extending between the reagent vessel 230 and the secondary reaction vessel 220 .

[0164] The secondary reagent valve 236 may be disposed in the secondary reagent channel 232 to control the flow of reagent through the secondary reagent channel 232. For example, the secondary reagent valve 236 may include a high-pressure valve having a relatively high cracking pressure as compared to other valves in the sample cartridge 200.

[0165] The sample cartridge 200 may include a secondary air pressure channel 222 extending between the secondary reaction vessel 220 and a secondary air pressure port 223. The secondary air pressure channel 222 may open into the secondary reaction vessel 220 at or near the top of the secondary reaction vessel 220. The top of the waste vessel 240 may be sealed, for example, with a lid or foil.

[0166] Reagent may be drawn from the reagent vessel 230 into the secondary reaction vessel 220 via the secondary reagent channel 232 by applying a negative vacuum pressure to the secondary air pressure port 223 to create a pressure differential across the secondary reagent valve 236 sufficient to overcome the relatively high crack pressure. During this flow, the primary output valve 217 may be closed to avoid flow through the primary outlet output 216.

[0167] On the other hand, when output fluid flow is required from the primary reaction vessel 210 to the secondary reaction vessel 220, the primary output valve 217 may be opened and a vacuum pressure may be applied to the secondary pneumatic port 223, creating a pressure differential sufficient to drive flow through the primary output channel 216, but not sufficient to overcome the relatively high breach pressure of the secondary reagent valve 236. The primary output channel 216 may open into the secondary reaction vessel 220 at or near the top of the secondary reaction vessel 220.

[0168] The sample cartridge 200 may include a secondary waste channel 224 extending between the secondary reaction vessel 220 and a waste vessel 240 (or other waste channel or receptacle). A secondary waste valve 225 may be disposed within the secondary waste channel 224 to control when fluid is removed from the secondary reaction vessel 220 through the secondary waste channel 224. For example, the secondary waste valve 225 may include a low pressure valve having a relatively low break pressure. In some embodiments, the secondary waste channel 224 may not be needed, i.e., when there is no waste fluid to be removed from the secondary reaction vessel 220.

[0169] The sample cartridge 200 may further define a secondary output channel 226 to allow for the discharge of output fluid from the secondary reaction chamber 220. In some embodiments, if quality control is not required, the secondary output channel 226 may lead directly to the output vessel 250. In some embodiments, if quality control is required, the secondary output channel 226 may extend between the secondary reaction vessel 220 and a quality control module 260.

[0170] A secondary output channel 226 can extend between the secondary reaction vessel 220 and a buffer junction 228. A secondary outlet valve 227 can be disposed within the secondary outlet channel 226 to control the discharge of the output fluid through the secondary output channel 226. For example, the secondary outlet valve 227 can include a high-pressure valve having a relatively high crack pressure.

[0171] The quality control (QC) module 260 comprises a quality control QC vessel 261 configured to receive a volume of output fluid from the secondary reaction vessel 220 (or the primary reaction vessel 210 if no secondary vessel is present) for analysis. The sample cartridge 200 may further comprise a QC pneumatic channel 262 and a QC pneumatic port 263 to which a vacuum pressure may be applied to draw output fluid from the secondary output channel 226 into the QC vessel 261. The top of the QC vessel 261 may be sealed, for example, with a lid or foil.

[0172] In some embodiments, the QC container 261 may be pre-loaded with dye (optionally dry dye) to facilitate optical analysis by the optical module 400 .

[0173] In some embodiments, the output fluid may be mixed with a quality control buffer prior to optical analysis. The QC buffer may be held in a QC buffer container 265 prior to being transferred with the output fluid into the QC container 261. For example, the QC buffer container 265 may define an open top such that a buffer may be dispensed into the QC buffer container 265 by the reagent module 300.

[0174] The sample cartridge 200 may include a QC buffer channel 266 extending from the QC buffer reservoir 261 to the secondary output channel 226 (or to the primary output channel 216 if no secondary reservoir is present) at the buffer junction 228. A QC buffer valve 267 may be disposed within the QC buffer channel 266 to control the flow of buffer through the QC buffer channel 266. For example, the QC buffer valve 267 may include an actuated valve, such as a pressure actuated valve that is actuated by applying positive or negative pressure to a corresponding QC buffer pneumatic port 268.

[0175] The sample cartridge 200 may further include a metering channel 299 in fluid communication with the secondary output channel 226 and the buffer channel 266 and extending from the buffer junction 228 to the quality control junction 229 .

[0176] Sample cartridge 200 may further include a QC channel 269 extending between QC junction 229 and QC vessel 261. Sample cartridge 200 may further include a QC vessel valve 264 disposed in QC channel 269 to control the flow of fluid through QC channel 269 and into QC vessel 261. QC vessel valve 264 may include a low pressure valve having a relatively low crack pressure.

[0177] While the QC buffer valve 267 is closed, vacuum pressure may be applied to the QC vessel air pressure port 263, creating a relatively high pressure differential that briefly overcomes the threshold of the secondary output valve 227 to draw a portion of the output fluid from the secondary reaction vessel 220 through the buffer junction 228 into the secondary output channel 226 and into the metering channel 299 up to the QC junction 229, after which the pressure difference may be neutralized to stop the flow. The metering channel 299 may define a known volume (e.g., 1 μL) such that the metering channel 299 may be filled from the buffer junction 228 to the QC junction 229 to define a precise aliquot of output fluid.

[0178] QC buffer valve 267 can then be opened by applying an appropriate actuation pressure to QC buffer air pressure port 268 and a vacuum pressure to QC reservoir air pressure port 263, creating a pressure differential high enough to open low pressure QC reservoir valve 264, but below the threshold of high pressure secondary output valve 227. This allows QC buffer, along with an aliquot of output fluid from measurement channel 299, to flow through QC buffer channel 266 and through measurement channel 299 and QC channel 269 into QC reservoir 261.

[0179] The mixed fluid may then be mixed with pre-loaded dye in a QC container 261 for analysis.

[0180] In some embodiments, the sample cartridge 200 may further comprise one or more QC reference containers 271, each with a corresponding QC reference air pressure channel 272 and QC reference air pressure port 273, each of which may be preloaded with a given amount of dried dye. Each QC reference container 271 may also have a corresponding QC buffer container 275 configured to receive a specific required amount of QC buffer that is drawn into the QC reference container 271 by applying a vacuum pressure to the corresponding QC reference air pressure port 273.

[0181] The contents of the QC vessel 261 can then be compared to the contents of the QC reference vessel 271 using the optical module 400 to determine a property of the output fluid, such as the concentration of a particular component.

[0182] Sample cartridge 200 further includes a final output channel 256 that branches off from secondary output channel 226 at QC junction 229 and connects secondary output channel 226 to output reservoir 250. Final output valve 257 is disposed within final output channel 256 and controls flow through final output channel 256. Final output valve 257 can include, for example, a low pressure check valve.

[0183] The sample cartridge 200 further comprises an output bin pneumatic channel 252 extending between the output bin 250 and an output bin pneumatic port 253. A vacuum pressure can be applied to the output bin pneumatic port 253 to draw the output fluid through a final output channel 256 into the output bin 250.

[0184] The final output channel 256 and the output bin pneumatic channel 252 may be connected to a temporary, removable lid 259 (shown in FIGS. 2F and 2G) that is used to seal the output bin 250 closed during the instrument workflow. Once the sample has been processed and the sample cartridge 200 has been removed from the instrument 100, the temporary lid 259 may be removed from the output bin 250 and the output bin 250 may be closed with the main output bin lid 251. For example, the output bin lid 251 may be a hinged lid formed integrally with the output bin 250, as shown in FIG. 2A.

[0185] To measure an accurate aliquot of output fluid for QC analysis, vacuum pressure can be applied for a predetermined period of time until the output fluid fills the metering channel 299 between the QC junction 229 and the buffer junction 228 and enters the final output channel 256. The length of the metering channel 299 can be designed to define a specific known volume (e.g., 1 μL). Flow through the final output channel 256 can then be stopped by returning the pressure at the output reservoir pneumatic port 253 to ambient pressure.

[0186] The QC buffer valve 267 may then be opened and vacuum pressure may be applied to the QC pneumatic port 263, drawing buffer from the QC buffer reservoir 265 through the metering channel 299 and the QC channel 269, past the combined QC and buffer junctions 228, 229, carrying an aliquot of output fluid to be drawn into the QC reservoir 261. In this way, a precise aliquot volume is defined between the QC and buffer junctions 228, 229, which travels as a slug in the QC reservoir to be mixed with the buffer.

[0187] The entire contents of the QC buffer reservoir 265 may be drawn into the QC reservoir 261 such that no buffer (or only a small amount) remains in the channels between the QC and buffer junctions 228, 229. This ensures that a known volume (or very close to a known volume) of buffer has been drawn into the QC reservoir 261. It also reduces or minimizes the amount of buffer that may remain in the channels, diluting the output fluid, which may be advantageous if a highly concentrated output fluid is required.

[0188] In some embodiments, the sample cartridge 200 may include a waste channel 279 to discard excess fluids into waste container 240, as shown in Figure 2G. However, in some embodiments, this may not be necessary as precise volumes of output fluids and buffers can be measured and drawn into the QC container 261 so that there is no excess fluid.

[0189] In some embodiments, sample cartridge 200 may further include an intermediate outlet 280 from final output channel 256 between final output valve 257 and output reservoir 250. Outlet 280 may be sealed with an air permeable membrane 281 that is permeable to gases but not liquids. On the other side of membrane 281 (opposite channel 256), intermediate outlet pneumatic channel 282 connects outlet 280 to intermediate outlet pneumatic port 283. Air can be drawn through air permeable membrane 281 by applying a vacuum pressure to intermediate outlet pneumatic port 283.

[0190] When this occurs, liquid output fluid is drawn along final output channel 256 but stops when it reaches air permeable membrane 281. This results in an increase in a pressure gradient that can be detected by pneumatic module 500, indicating that channel 256 has filled up to intermediate outlet 280. This signal can be used to trigger the next step in the workflow, such as flowing buffer through measurement channel 299 and QC channel 269.

[0191] The sealed reaction vessels 210, 220, QC vessel 261, QC reference vessel 271, output vessel 250, and waste vessel 240 allow for the processing of fluid samples without cross-contamination or instrument contamination from splashing of fluid samples out of these vessels. This is accomplished by providing separate vessels (e.g., reagent vessel 230 and buffer vessels 265, 275) to receive reagents from the reagent module and, if necessary, transferring the reagents to the sealed vessels for processing using a pneumatic module and corresponding pneumatic ports to create a pressure gradient to drive flow. Locating the openings of the inlet and pneumatic channels at or near the top of the sealed vessels also reduces the chance of backflow of sample fluid into the inlet channel or aspirating sample fluid into the pneumatic module, which could contaminate the instrument.

[0192] Referring to Figure 2E, a bottom view of the sample cartridge 200 is shown, showing the cartridge's network of channels and valves in further detail. A close-up view of the quality control module 260 is shown in Figure 2F. Like elements are designated with like reference numbers.

[0193] In some embodiments, the QC module 260 may be included as part of a larger sample cartridge, such as sample cartridge 200, or other sample cartridge that may require QC analysis or precise fluid metering. In some embodiments, the QC module 260 may be included as part of a measurement or analytical instrument.

[0194] 2F, according to some embodiments, the QC module 260 may be considered independently as a separate sample cartridge 290. Some embodiments relate to a separate sample cartridge 290 that includes only the QC module 260, as shown in FIG.

[0195] The sample cartridge 290 may be configured for use with, for example, a fluid analysis instrument. The cartridge 290 includes a sample vessel 220 configured to contain a fluid sample for analysis. The sample vessel 220 may correspond to a secondary reaction vessel 220 of the sample cartridge 200 or may correspond to a primary reaction vessel 210 in a sample cartridge 200 that does not include a secondary reaction vessel 220.

[0196] Cartridge 290 includes a buffer reservoir 265 (similar to sample cartridge 200) configured to receive a buffer solution. Cartridge 290 includes a sealed analysis reservoir 261 (corresponding to QC reservoir 261) configured to receive a mixed fluid that includes an aliquot of a fluid sample mixed with at least some buffer solution for analysis.

[0197] Cartridge 290 includes a sample channel 226 (corresponding to secondary output channel 226) extending between sample reservoir 220 and a first interface 228 (corresponding to buffer interface 228).

[0198] Cartridge 290 includes a sample channel valve 227 (corresponding to secondary output valve 227 ) disposed within sample channel 226 to control the flow of sample through sample channel 226 .

[0199] The cartridge 290 includes a buffer channel 266 extending between the buffer reservoir 265 and the first junction 288. A buffer channel valve 267 is disposed within the buffer channel 266 and controls the flow of buffer through the buffer channel 266.

[0200] The cartridge 290 includes a metering channel 299 in fluid communication with the buffer channel 266 and the sample channel 226, the metering channel 299 extending between a first junction 228 and a second junction 229 (corresponding to the QC junction 229).

[0201] The cartridge 290 includes an analysis vessel channel 269 (corresponding to the QC channel 269) in fluid communication with the measurement channel 299 and extending between the second junction 229 and the analysis vessel 261. The cartridge 290 includes an analysis vessel pneumatic port 263 (corresponding to the QC pneumatic port 263) in communication with the analysis vessel 261 and configured to be connected to a pneumatic module to selectively adjust the pressure in the analysis vessel 261 to draw fluid into the analysis vessel 261 via the analysis vessel channel 269.

[0202] At least one of the sample channel valve 227 and the buffer channel valve 267 may comprise an active valve that is selectively opened and closed to allow an aliquot of the fluid sample to be drawn into the metering channel 299 and then a buffer solution, along with an aliquot of the fluid sample for analysis, through the buffer channel 266 and through the metering channel 299 and the analysis reservoir channel 269 to the analysis reservoir 261. For example, the buffer channel valve 267 may include an active valve and the sample channel valve 227 may include a relatively high pressure check valve.

[0203] The analysis reservoir 261 may be pre-loaded with buffers and dyes configured to mix with the fluid sample to facilitate analysis.

[0204] Sample cartridge 290 or 200 may further include an intermediate outlet 280 in fluid communication with metering channel 299 via second junction 229. Intermediate outlet 280 may be similar to the intermediate outlet of sample cartridge 200, both of which may include any of the features described below.

[0205] Referring to FIG. 2O (adjacent FIG. 2F), an enlarged top perspective view of outlet 280 is shown, according to some embodiments.

[0206] In some embodiments, the outlet 280 can be located at the second junction 229. In some embodiments, the outlet 280 can be located away from the second junction 229 and connected to the second junction 229 via an outlet channel 285.

[0207] The sample cartridge 290 or 200 may include an outlet chamber 284 into which the intermediate outlet 280 opens. An air permeable liquid barrier membrane 281 may cover the outlet 280.

[0208] The sample cartridge 290 or 200 may include an intermediate outlet pneumatic port 283 in fluid communication with the outlet chamber 284 and connected to a pneumatic module configured to selectively adjust the pressure within the outlet chamber 284 and draw air from the metering channel 299 through the air permeable membrane 281.

[0209] Sample cartridge 290 or 200 may include an intermediate outlet pneumatic channel 282 extending between an intermediate outlet pneumatic port 283 and an outlet chamber 284. The outlet chamber 284 may be sealed at only two fluid openings, namely, the outlet 280 and the opening of the intermediate outlet pneumatic channel 282. The top of the outlet chamber 284 may be sealed, for example, with foil.

[0210] The intermediate outlet 280 may be positioned to allow liquid drawn from the sample channel 226 or the buffer channel 266 into the metering channel 299 to fill the metering channel 299 but not to allow it to enter the analysis reservoir channel 269.

[0211] The sample cartridge 290 or 200 may include an outlet channel 285 extending between the second junction 229 and the outlet 280, allowing liquid drawn from the sample channel 226 or the buffer channel 266 into the metering channel 299 to fill the metering channel 299 and proceed to the outlet channel 285, but not to enter the analysis reservoir channel 269.

[0212] The sample cartridge 290 or 200 may include an output bin 250 in fluid communication with the metering channel 299 via a second junction 229 and via an output channel 256. The output channel 256 may extend from the second junction 229 to the output bin 250. Alternatively or additionally, the output channel may extend between the intermediate outlet 280 and the output bin 250.

[0213] The sample cartridge 290 or 200 may include an output container pneumatic port 253 in communication with the output container 250 and configured to be connected to a pneumatic module to selectively adjust the pressure within the output container 250 to draw fluid from the metering channel 299 through the second junction 229 and the output channel 256 to the output container 250.

[0214] The capacity of the metering channels can be precisely defined, allowing precise quantification of aliquots of sample fluid (or processed fluid) through the arrangement of channels, valves, reservoirs, and outlets of sample cartridge 290 and QC module 260. The above arrangement can be used to precisely meter fluid for quantification in any application where precise quantification is required.

[0215] Sample cartridge 290 may further include one or more reference reservoirs 271 and associated buffer reservoirs 275 , pneumatic channels 272 , and pneumatic ports 273 as described in connection with sample cartridge 200 .

[0216] Output channel 256 and output bin pneumatic channel 252 may be connected to a temporary lid 259 that defines an opening of output channel 256 and output bin pneumatic channel 252 into output bin 250 and may be configured to seal output bin 250. Temporary lid 259 may be removed to allow output bin 250 to be removed from base 202 of sample cartridge 290, and output bin 250 may be sealed with output bin lid 251.

[0217] The sample cartridge 200 or 290 may be formed of any suitable plastic material for a given application, for example, for handling biological materials, polypropylene may be used.

[0218] The sample cartridge 200 or 290 may be formed by injection molding. For example, the sample cartridge 200 or 290 may be formed with some or all of the channels, chambers, and vessels having open tops or sides, and some of the openings may be sealed with welding foils, for example, as needed to form the sealed channels, chambers, and vessels described above.

[0219] The channels in the base may be covered with a polypropylene membrane that may be heat welded to the base, and the channels in the sidewalls communicating with the container may be covered with a polypropylene membrane that is similarly heat welded to the body, for example, the heat welding may include laser welding, and tractor welding around each channel may secure the membrane to the body to define each channel.

[0220] The valves may include any suitable active or passive valves depending on the arrangement and application. Suitable valves may include check valves with different relative break pressures (e.g., as shown in FIG. 2J), duckbill valves (e.g., as shown in FIG. 2L), umbrella valves (e.g., as shown in FIG. 2M), microfluidic or capillary valves with different break pressures depending on surface tension and capillary action, pressure-activated switch valves (e.g., as shown in FIG. 2K), electronically-activated switch valves (e.g., solenoid valves), or mechanically-activated switch valves such as Prodger valves (e.g., as shown in FIG. 2N). A combination of different valve types may be used to achieve the required flow within the sample cartridge 200.

[0221] 3A and 3B, a reagent module 300 is shown, according to some embodiments. The reagent module 300 includes a plurality of reagent cartridges 320 removably mounted to a frame 350. The frame 350 also supports a pump 360 configured to control the dispensing of reagents from the reagent cartridges 320.

[0222] Reagent cartridges 320 are shown in isolation in Figure 3B. Each reagent cartridge 320 includes a reservoir 322, a flexible dispense tube 323, and a reagent cartridge frame 325 configured to support the reservoir 322 and configured to engage a reagent module frame 350 to mount the reagent cartridge 320 to the frame 350.

[0223] Pump 360 may include a peristaltic pump. For example, pump 360 may include one or more motors 362, each configured to drive rotation of a pump shaft 363 and a pump cam (not shown) mounted on pump shaft 363. The pump cam may be generally circular with protrusions, such as, for example, a round toothed gear.

[0224] When mounted on the reagent module frame 350, the reagent cartridge frame 325 may support the dispense tube 323 such that a portion of the tube 323 extends at least partially around the circumference of the pump cam, and when the pump cam is rotated by a corresponding motor 362, a protrusion on the pump cam may contact and compress a portion of the dispense tube 323, thereby forcing fluid through the dispense tube 323 as the pump cam rotates. The dispense tube 323 may be positioned such that an opening dispenses reagent into a desired container (reagent container or QC buffer container) of the sample cartridge 200 when the reagent module 300 is aligned with the sample cartridge 200.

[0225] Dispense tube 323 may be made of any suitable material, and in some cases may be made of different materials depending on their compatibility with respective reagents. For example, dispense tube 323 may be made of silicone, viton, or Chem-Durance Bio tubing.

[0226] Each reagent cartridge 320 may be engaged by a respective pump cam driven by a corresponding one of the motors 362. In some embodiments, a single pump cam, or a single pump shaft 363 configured to drive rotation of multiple pump cams, may be configured to engage more than one of the reagent cartridges 320 to control dispensing. For example, when dispensing multiple reagents simultaneously in similar amounts, corresponding reagent cartridges 320 may be engaged simultaneously by a single pump system to dispense reagents into the sample cartridge 200.

[0227] Pump 360 may include independent motors 362 and drive shafts 363 to independently control the dispensing of reagents from different reagent cartridges 320 .

[0228] The reservoirs 322 of different reagent cartridges 320 may define different volumes in proportion to the expected rate of consumption of the different reagents contained therein. For example, if a first reagent is typically dispensed at twice the volume of a second reagent, the reservoir 322 for the first reagent may be twice the volume of the reservoir 322 for the second reagent.

[0229] The reservoirs 322 may contain a sufficient volume of reagent to run a certain number of instrument workflows. When the reagent reservoirs 322 are empty, the reagent module 300 slides partially out of the instrument housing 110, as shown in FIG. 1B, allowing the reagent reservoirs 322 to be refilled or the empty reagent cartridge 320 to be removed completely and replaced with a filled reagent cartridge 320.

[0230] In some embodiments, the reagent module frame 350 may include or be mounted to a carriage 920 of a motion module 900. The reagent module 300 may be moved (by the motion module 900) along an axis of movement 903 across multiple sample cartridges 200 in the cartridge slots 120 and may dispense reagents to the sample cartridges 200 at selected points during the instrument workflow.

[0231] The reagent module 300 may be moved to a selected carriage position at a selected time corresponding to a selected one of the sample cartridges 200. The pump 360 may then be operated to dispense one or more reagents from the corresponding reagent cartridge 320 into a selected reservoir within the sample cartridge 200, such as, for example, a reagent reservoir 230 or a quality control buffer reservoir.

[0232] 4A and 4B, a diagram of an optical module 400 is shown, according to some embodiments. The optical module 400 comprises a light source 410 and a detector 420. The light source 410 is configured to illuminate a quality control (QC) sample 404, which may include the output liquid in the QC container 261 or a reference liquid in one of the QC reference containers 271. The detector 420 is configured to detect and measure light transmitted from the QC sample 404.

[0233] For example, light source 410 may include an LED or a laser. Detector 420 may include a photodiode or any other suitable photodetector. Light source 410 and detector 420 may be configured to operate in any suitable frequency range depending on the application and the property being measured, including the visible, near-visible, infrared, and ultraviolet ranges.

[0234] The optical module 400 may be configured to measure any one or more of the scattered, refracted, or reflected light transmitted from the QC sample 404.

[0235] In some embodiments, the optical module 400 may include one or more lenses, filters, and / or other optical devices. For example, the optical module 400 may include a source lens 412 for focusing (e.g., into a parallel line) light from the light source 410, a beam splitter 414 for redirecting the light from the light source 410 towards the QC sample 404, a sample lens 402 for focusing the source light onto the QC sample 404 and refocusing (e.g., into a parallel line) the light transmitted from the QC sample 404, a detector lens 422 for focusing the light transmitted from the QC sample 404 onto a detector 420, and one or more filters 430 disposed in the detector path and / or the source path for filtering out specific frequencies of light.

[0236] The optical module 400 may be mounted on a carriage 920 of the motion module 900 (either the same carriage as the reagent module 300 or an independent carriage 920) and may be aligned with a selected one of the sample cartridges 200 in the cartridge slots 120 to enable optical analysis of a QC sample 404 disposed in the sample cartridge 200.

[0237] 2A includes one QC container 261 and three QC reference containers 271 for comparison. The QC container 261 and the three QC reference containers 271 may be positioned along a lateral axis of the sample cartridge 200 parallel to the axis of movement 904 of the optical module 404, allowing the optical module 400 ready access to the QC samples 404. The carriage 920 may be moved by the motion module 900 to different carriage positions corresponding to the positions of the QC container 261 and the three QC reference containers 271.

[0238] The QC container 261 and the three QC reference containers 271 may include transparent windows (at the top, bottom, or sides) that allow light to pass from the light source 410 into the QC sample 404 contained therein and from the QC sample 404 to the photodetector 420. The windows may have an SPI A-1 grade surface finish to minimize scattering. The window thickness may be 3 mm or less.

[0239] The motion module 900 may be positioned with the optical module 400 such that the QC sample 404 is within 2 mm of the optical focal plane of the optical module 400, and optionally within a lateral positional tolerance of 1.25 mm. Depending on the characteristics of the optical module 400 and the sample cartridge 200, different tolerances may be suitable for different applications.

[0240] A pneumatic module 500, according to some embodiments, is shown in FIG. 1C. The pneumatic module 500 may include a pressure regulator and a compressor, a vacuum generator, or a vacuum pump. Alternatively, the pneumatic module 500 may be configured to be connected to an external pressure source or vacuum line, for example.

[0241] The pneumatic module 500 may comprise a network of pneumatic lines and valves with connectors adjacent the cartridge slot 120 configured to connect to pneumatic ports of the sample cartridge 200. The pneumatic module 500 may be configured to selectively deliver positive and / or negative pressure (relative to atmospheric pressure) to selected pneumatic ports of the sample cartridge 200 at selected times during the instrument workflow.

[0242] In some embodiments, the pneumatics module 500 may be configured to deliver relative pressure differentials of different magnitudes to different pneumatic ports of the sample cartridge 200. In some embodiments, the pneumatics module 500 may be configured to deliver relative pressure differentials of different magnitudes to selected pneumatic ports of the sample cartridge 200 at different times. In some embodiments, the pneumatics module 500 may be configured to deliver only negative pressure to pneumatic ports of the sample cartridge 200.

[0243] In some embodiments, the pneumatic module 500 may include sets of pneumatic lines, each set configured to simultaneously deliver a selected pressure to all corresponding pneumatic ports of multiple sample cartridges 200 in a cartridge slot 120, such as to simultaneously apply a particular negative pressure to all of the primary pneumatic ports 213.

[0244] In some embodiments, each pneumatic port of the sample cartridge 200 may have a single selected pressure or range of pressure delivered to it at a selected time without pressure fluctuations.

[0245] The pneumatic module 500 may comprise any suitable valve system for selectively delivering the required pressure to the required pneumatic port at a selected point in the instrument workflow, such as an array of solenoid valves electronically operated by the control module 101, or a manifold valve system, or a rotary valve system.

[0246] 5A and 5B, a portion of a pneumatic module 500, a thermal module 600, a magnetic module 700, a mixing module 800, and a kinetic module 900 are shown according to some embodiments.

[0247] The pneumatic connector 510 is shown below the cartridge slot 120, which is supported by a pneumatic support frame 505. The support frame 505 is connected to a pneumatic module actuator 905, which may form part of the motion module 900. The pneumatic module actuator 905 may include a motor or a linear actuator configured to raise and lower the pneumatic connector 510. The pneumatic connector 510 may be in a lower position to load (or remove) a sample cartridge 200 into (or from) the cartridge slot 120. When a sample cartridge 200 is received in the cartridge slot 120, the pneumatic module actuator 905 is operated to raise the pneumatic support frame 505 and the pneumatic connector 510 such that the pneumatic connector 510 engages an air port in the sample cartridge 200, fluidly connecting the pneumatic module 500 to the channels of the sample cartridge 200.

[0248] In some embodiments, the motion module 900 may further comprise a vertical movement platform 950 configured to raise and lower other components of the apparatus 100 within the housing 110. Movement of the platform 950 may be driven by a platform actuator 955, which may include, for example, a linear actuator with a motor 957 and a lead screw 959 or a lead screw actuator, as shown in FIG.

[0249] The vertical movement platform 950 may be configured to raise and lower components of, for example, the thermal module 600 and / or the magnetic module 700, as well as any other components of the instrument that may need to be raised and lowered. In some embodiments, the pneumatic support frame 505 and connectors 510 may be mounted to a similar vertical movement platform 950. In some embodiments, the kinematic module 900 may include multiple vertical movement platforms 950 configured to be independently operated to independently raise and lower different components or groups of components. For example, the thermal module and the magnetic module may be mounted to a single vertical movement platform, which may have additional vertical movement platforms mounted thereto to raise and lower the thermal module independently of the magnetic module.

[0250] In some embodiments, the instrument 100 may not include a vertical movement platform 950 .

[0251] The thermal module 600 may include one or more thermal control devices 610, which may include heating and / or cooling elements, thermoelectric devices, Peltier elements, resistive heaters, heat lamps, heat exchangers, and / or fans. When heating (or other thermal control) is needed during one of the instrument workflows (e.g., for incubation), the platform 950 may be raised to bring the thermal control device 610 (e.g., a heater) closer to the sample cartridge 200 in the cartridge slot, and the thermal control device 610 may be activated.

[0252] In some embodiments, the thermal module 600 may include a conductive member coupled to a heating element to facilitate heating of the reaction vessel. For example, the conductive member may include a plate or jacket that may define complementary surfaces configured to partially surround the reaction vessel.

[0253] The thermal module 600 may include a cooling fan disposed below the heating element and conductive members and configured to direct ambient air around the heating element and conductive members to cool them as needed.

[0254] The cartridge may define an opening in the base 202 around the bottom of the primary reaction vessel 210 and / or secondary reaction vessel 220 configured to allow passage of one or more conductive members and / or magnets for positioning adjacent to the reaction vessels 210, 220.

[0255] In some embodiments, the thermal module 600 is fixed in position adjacent to the cartridge slot 120 and aligned with the primary and / or secondary reaction vessels 210, 220 and can be simply switched from heating to cooling or anything in between depending on the thermal regulation required for a particular workflow operation.

[0256] The magnetic module 700 may comprise one or more magnets 710 arranged to control the movement of magnetic beads in the primary and / or secondary reaction vessels 210, 220. The magnets 710 may comprise permanent magnets and / or electromagnets and may be mounted on a vertical movement platform 950 so that they are elevated close to the primary and / or secondary reaction vessels 210, 220 when the magnetic beads are at rest and lowered further away from the primary and / or secondary reaction vessels 210, 220 so that the magnets 710 have less effect on the magnetic beads. The magnets 710 may be disposed on either side of the primary and / or secondary reaction vessels 210, 220 to hold the beads away from the exhaust outlet to avoid blocking or narrowing the exhaust flow into the channel.

[0257] In some embodiments, for example when the magnet 710 comprises an electromagnet, the magnet 710 can be fixed in position adjacent to the cartridge slot 120, aligned with the primary and / or secondary reaction vessels 210, 220, and simply switched on or off depending on the conditions required for a particular workflow operation.

[0258] In some embodiments, the instrument may not include a magnetic module 700 and the functionalized beads in the primary and / or secondary reaction vessels may be kept away from the output channel by a physical barrier or restriction, such as a filter.

[0259] The mixing module 800 may include any suitable device for enhancing mixing of the fluids within the sample cartridges 200. For example, the mixing module 800 may include a shaker 810. The shaker 810 may include an orbital shaker, such as an eccentric cam or offset weights configured to be rotated by a motor to induce vibrations within the instrument 100. Alternatively, other conventional mixing devices may be used to facilitate mixing of the fluids within the sample cartridges 200. In some embodiments, the mixing module 800 includes a single shaker 810 configured to shake all of the sample cartridges 200 simultaneously.

[0260] The orbital shaker may include a number of weights and counterweights configured to vibrate the cartridge without tipping the instrument. A suitable power, frequency, and amplitude of vibration may be selected to suit the required application. For processing relatively fragile molecules (e.g., nucleic acids), frequencies below 2000 rpm may be suitable, such as about 1100 rpm.

[0261] 6, a schematic diagram of the control module 101 is shown, according to some embodiments. The control module 101 comprises electronics and software configured to control operations performed by the instrument 100, which may include control of the reagent module 300, the optical module 400, the pneumatic module 500, the thermal module 600, the magnetic module 700, the mixing module 800, and the motion module 900.

[0262] The control module 101 may also include one or more sensors for monitoring the operation of the module. The sensors may include, for example, position sensors, accelerometers, proximity sensors, angle sensors (e.g., shaft angle or speed sensors), Hall sensors, and pressure sensors.

[0263] 7A-14K, there is shown an instrument 1000, according to some embodiments. The instrument 1000 may include any of the features described in connection with the instrument 100 with reference to Figures 1-6, and like features are indicated with like reference numerals.

[0264] Instrument 1000 may be configured to accept one or more sample cartridges 200 or 1200 (see, e.g., FIGS. 12A and 12B), each containing a sample for processing. Instrument 1000 may be configured to perform one or more operations on the sample, such as a chemical processing step, heating, cooling, incubation, mixing, analysis or measurement, or nucleic acid extraction, as described in connection with instrument 100.

[0265] The instrument 1000 may include similar modules as described above configured to perform operations on a sample. These may include a reagent module 300, an optical module 400, a pneumatic module 500, a thermal module 600, a magnetic module 700, a mixing module 800, a kinetic module 900, and / or a control module 101 for controlling the operations performed by the instrument 100. The instrument 1000 may have or be connected to a power source 102, as shown in FIG. 1A, for powering the various modules.

[0266] 7A, the various modules of the instrument 1000 may be supported by a frame or chassis 1010. The frame 1010 may include a viewing window 1011 to allow viewing of the instrument operation. In some embodiments, the instrument 1000 may include an opaque exterior housing that covers most or all of the instrument modules during operation. The following figures show certain portions of the instrument 1000 with other portions (e.g., the frame 1010) omitted for clarity.

[0267] Figures 7A and 7B show the general arrangement of a reagent module 300, a pneumatic module 500, a motion module 900, and a control module 101, according to some embodiments. An optical module 400 may be mounted on a carriage below the reagent module 300 and is not visible in Figures 7A and 7B, but is visible in Figures 7C-7F.

[0268] The instrument 1000 may include one or more core units 1100, for example, two core units 1100 are shown in the instrument 1000 of Figures 7A and 7B. Each core unit 1100 is configured to engage multiple sample cartridges 200, 1200, for example, four cartridges at a time. Each core unit 1100 may include an independent thermal module 600, magnetic module 700, and / or mixing module 800, and the reagent module 300, pneumatic module 500, kinematic module 900, and / or control module 101 may be shared between the core units 1100 and are configured to perform operations on the cartridges 200, 1200 of each core unit 1100.

[0269] In some embodiments, each core unit 1100 may include other of the modules 300, 400, 500, 600, 700, 800, 900, which may be independent of other modules in other core units 1100. In some embodiments, other of the modules 300, 400, 500, 600, 700, 800, 900 may be shared among multiple core units 1100.

[0270] 7C-7F show portions of the reagent module 300, the optical module 400, and the kinetic module 900 in greater detail, according to some embodiments.

[0271] The exercise module 900 comprises a track 910 extending across the apparatus 1000 supported by a frame 1010, and a carriage 920 (FIG. 7E) configured to move along the track 910. In some embodiments, as shown, the track 910 includes rails, e.g., two rails 912, and the carriage 920 includes corresponding sliders 922, e.g., two corresponding sliders 922, configured to engage and slide along the rails 912 while supporting the carriage 920.

[0272] A suitable rail and carriage assembly is for example the Linear rail-L1010.15.790 and Linear carriage L1010.C15 from Automotion components.

[0273] The motion module 900 includes a drive motor 926 mounted to a carriage 920 and configured to rotate a lead screw nut 928 about a lead screw 918. The lead screw 918 may be fixed to the frame 1010 so as to be generally parallel to the track 910. The lead screw nut 928 may be rotatably mounted to the carriage 920 such that as the lead screw nut 928 rotates, it advances along the lead screw 918, moving the carriage 920 along the track 910.

[0274] A suitable lead screw and lead screw nut assembly is Leadscrew M18x24mm pitch (e.g. Igus-DST-LS-18x24-R-ES) and Leadscrew nut M18x24mm pitch (e.g. Igus-DST-JFRM-2835DS18x24). The lead screw nut 928 may be mounted to the carriage via a Roller bearing-ID3 0OD42×7 (e.g. Simply Bearings S61806-2RS) and the rotation of the lead screw nut 928 may be driven by a Stepper Motor-PKP266D14A2-NEMA 24+LC2B06E cable from Oriental Motors via, for example, a Pulley-T5 14 Teeth 10mm belt width with boss (14 T5-15-14) and a Belt T5 / 245 49 Teeth-10mm width (BT5 / 245 / 10) from HPC Gears.

[0275] The optical module 400 is mounted to a lower bracket of the carriage 920 and in some embodiments is configured to be positioned below the cartridges 200, 1200 for quality control operations.

[0276] The reagent module 300 may be mounted on top of the carriage 920 with the outlet nozzle positioned below the carriage for dispensing reagents into the cartridges 200, 1200, as described in more detail below.

[0277] In some embodiments, the motor 926, the reagent module 300, and the optical module 400 are all connected to the control module 101 and the power supply 102 via cables housed in a cable chain 121 (Figure 7C), thereby enabling the motor 926, the reagent module 300, and the optical module 400 to move along the track 910 together with the carriage 920 while the control module 101 is fixed to the frame 1010.

[0278] 8A-8J, a reagent module 300 is shown in further detail, according to some embodiments. The reagent module 300 includes a reagent cartridge 1320, a pump portion 1360, and a dispense portion 1390. A schematic diagram of the reagent module 300 is shown in FIG. 8A, with enlarged views of each portion shown in FIG. 8B, 8C, and 8D, respectively. Perspective views of the reagent cartridge 1320 are shown in FIG. 8E and 8F, the connection between the reagent cartridge 1320 and the pump portion 1360 is shown in FIG. 8G and 8H, a perspective view of the pump portion 1360 is shown in FIG. 81, and the dispense portion 1390 is shown in FIG. 8J.

[0279] The reagent cartridge 1320 may include a removable reagent storage that can be removed from the instrument 1000 so that the reagents can be replaced or refilled when depleted. The reagent cartridge 1320 may be configured to be received in a reagent storage support 1340 that is mounted to the carriage 920 along with the pump portion 1360.

[0280] The reagent cartridge 1320 may include multiple reagent reservoirs 1322 configured to accommodate various reagents to be dispensed into the sample cartridge 200, 1200 for processing. Any suitable number of reagent reservoirs 1322 may be provided depending on the number of different reagents required for a given process. The illustrated reagent cartridge 1320 includes, for example, 16 reagent reservoirs 1322. Each reagent reservoir 1322 may have any suitable capacity for a given application. Different ones of the reagent reservoirs 1322 may have different volumetric capacities to account for different reagents being consumed at different rates in the instrument process.

[0281] The reagent reservoirs 1322 may have any suitable form in any suitable arrangement within the reagent cartridge 1320. The reagent cartridge 1320 shown in FIG. 8F includes flexible bag reagent reservoirs 1322 arranged to hang from a support frame 1324 disposed near a top of the reagent cartridge 1320. The support frame 1324 defines a plurality of hooks configured to engage a top of each of the reagent reservoirs 1322 to hang within the interior volume of the reagent cartridge 1320.

[0282] The reagent cartridge 1320 may be generally rectangular (but may define other shapes) and includes end walls 1326 and, in some embodiments, an outer casing 1328 (FIG. 8E) that covers the top and sides of the reagent cartridge 1320.

[0283] The reagent cartridge 1320 may include a cartridge connection block 1330 or manifold configured to fluidly connect the reagent reservoirs 1322 to the pump portion 1360. The cartridge connection block 1330 defines a flat surface 1331 that defines a number of connection ports 1332 corresponding to each of the reagent reservoirs 1322. The reagent reservoirs 1322 may be fluidly connected to the connection ports 1332 by channels or tubes 1334. (Note: for clarity, portions of the tubes 1334 are omitted from FIG. 8F.)

[0284] The cartridge connection block 1330 may define locating slots or recesses 1337 , 1339 configured to receive corresponding locating pins 1357 , 1359 to facilitate connection to the pump portion 1360 .

[0285] 8E and 8G, the reagent storage support 1340 may include a support rail 1342 configured to support the reagent cartridge 1320. The reagent storage support 1340 may include a housing 1344 configured to enclose a portion of the reagent cartridge 1320. The reagent cartridge 1320 may be placed in the reagent storage support 1340 by sliding the reagent cartridge 1320 into the housing 1344 on the rail 1342.

[0286] The reagent storage support 1340 further comprises a spring loaded retaining clip 1346 biased to a retaining position such that when the reagent cartridge 1320 is installed in the reagent storage support 1340, the clip 1346 is depressed by a portion of the reagent cartridge 1320 and then returns to the retaining position when the reagent cartridge 1340 is fully installed to limit removal of the reagent cartridge 1320. The retaining clip 1346 may also be manually depressed by a side tab to allow removal of the reagent cartridge 1320. Alternatively, an automatic or electronically actuated retention mechanism may be used to hold the reagent cartridge 1320 in place.

[0287] The reagent storage support 1340 may further include a sensor 1348 coupled to the control module 101, such as an optical sensor, to indicate when the reagent cartridge 1320 is properly attached to the reagent storage support 1340, for example with the retaining clip 1346 engaged.

[0288] The pump portion 1360 includes a pump connector block 1350 or manifold configured to connect with a cartridge connection block 1330 to fluidly connect the reagent cartridge 1320 with the pump portion 1360 .

[0289] The pump connector block 1350 defines a flat surface 1331 that defines a number of connection ports 1352 that correspond to the connection ports 1332 of the cartridge connection block 1330, as shown in FIG. 8H.

[0290] The reagent module 300 includes a connector clamping mechanism 1354. The connector clamping mechanism 1354 may be mounted to the reagent storage support 1340 and configured to clamp the pump connector block 1350 and the cartridge connector block 1330 with the connection ports 1332, 1352 aligned to fluidly connect each corresponding pair of connection ports 1332, 1352. One or both of the connector blocks 1330, 1350 may include a gasket 1333 configured to seal around the connection between each corresponding pair of connection ports 1332, 1352. For example, the gasket 1333 may include an O-ring set in a gasket seat around each of the connection ports 1332 of the cartridge connector block 1330, as shown in FIG. 8F.

[0291] The clamping mechanism 1354 may include a stationary block 1355 and a mechanical linkage 1356 rotatably coupled to the stationary block 1355. The mechanical linkage 1356 may also include a handle for manipulating the clamping mechanism 1354. Alternatively, the clamping mechanism may be electronically controlled by an actuator, such as a motor, which may be operated automatically or via a user interface to fluidly connect the reagent cartridge 1320 to the pump portion 1360 when the reagent cartridge 1320 is installed.

[0292] In some embodiments, the clamping mechanism 1354 may further include two protrusions 1357 extending away from the stationary block 1355 and through holes in the pump connector block 1350 such that the pump connector block 1350 can slide along the protrusions 1357. A mechanical linkage 1356 may be slidably coupled to side pins 1353 extending from either side of the pump connector block 1350 such that as the mechanical linkage 1356 rotates relative to the stationary block 1355, the pump connector block 1350 slides up and down along the protrusions 1357.

[0293] This movement can be seen when comparing FIG. 8G, which shows the clamp mechanism 1354 and pump connection block 1350 in a raised or disconnected configuration, and FIG. 8H, which shows the clamp mechanism 1354 and pump connection block 1350 in a lowered configuration for connection to the cartridge connection block 1330.

[0294] The protrusions 1357 of the clamping mechanism 1354 may also function as locating pins that are received in locating slots 1337 of the cartridge connector block 1330 when the reagent cartridge 1320 is installed on the reagent storage support 1340. Each of the protrusions 1357 may include a head 1358 that is relatively wider in diameter than a portion of the locating slots 1337 such that the cartridge connector block 1330 is clamped between the protrusion heads 1358 and the pump connector block 1350 when the clamping mechanism 1354 is operated to clamp the connector blocks 1330, 1350 together.

[0295] The pump connector block 1350 may further include one or more surface alignment pins 1359 configured to be vertically received in corresponding alignment recesses 1339 in the surface 1331 of the cartridge connector block 1330 and assist in aligning corresponding pairs of connection ports 1332, 1352.

[0296] The pump connector block 1350 defines a number of tube outlets 1362 for fluidly connecting the connection ports 1352 to corresponding tubes 1364 of the pump section 1360 .

[0297] 8C and 8I , pump portion 1360 comprises a system of one or more pumps 1366 and one or more valves 1368 configured to enable dispensing of a selected reagent from reagent cartridge 1320. Any suitable arrangement of pumps and valves may be used for a given application. In the illustrated embodiment, tubing 1364 connects connection port 1352 of pump connector block 1350 to two dispense tubes 1394 (optionally, three or more dispense tubes) via two 12-way valves 1368 and pump 1366.

[0298] For example, the pump 1366 and valve 1368 may include two Tecan Centris pumps (CG CM 30063057 or 30039102) with Tecan 12-way ceramic valves (12+1 / 4-28CM 30038192 or 30077366) and Tecan Ball end Syringes (1.0ml 20728662). The first syringe pump 1368a is configured to operate only as a valve, and the second syringe pump 1368b is configured to operate as a combination valve and pump. The syringe pump 1366 includes a syringe 1371 and a linear actuator 1372 connected to the control module 101 and configured to move the plunger of the syringe 1371 to draw precise amounts of reagent into the syringe and then pump them out again to dispense the reagent into the sample cartridge 200, 1200. The control module 101 is also configured to operate the valve 1368 to connect any two of the valve ports.

[0299] 8C, nine of the connecting tubes 1364 (P-10 through P-18) connect the connecting port 1352 from the pump connector block 1350 to the first valve 1368a, the remaining seven connecting tubes 1364 (P-19 through P-25) connect the connecting port 1352 from the pump connector block 1350 to the second valve 1368b, and an additional connecting tube P-4 connects the first valve 1368a to the second valve 1368b. Two dispensing tubes 1394 (P-1, P-2, and optionally P-3) connect the second valve 1368b to a dispensing nozzle 1392 in dispensing portion 1390.

[0300] This arrangement allows for the selection of any of the reagents in the reagent reservoirs 1322 by operating the valve 1368 to select a corresponding connection tube 1364, which is connected to the reagent reservoir 1322 via a corresponding reagent cartridge tube 1334 and corresponding connection ports 1332, 1352. The syringe pump 1366 can then be operated to draw a precise amount of reagent into the syringe in accordance with operational instructions from the control module 101. A second valve 1368b can then be adjusted to connect the pump 1366 to a selected one of the dispensing nozzles 1392, and the pump 1366 can be operated to dispense the reagent through the selected dispensing nozzle 1392.

[0301] Dispensing nozzle 1392 is shown in Figures 8D and 8J. Nozzle 1392 may include, for example, a Preci-tip nozzle (IDMSPREC30-PB-EN) connected to dispensing tubing 1394 via a 1 / 4"-28 straight adapter and a 1 / 4"-28 luer fitting.

[0302] The nozzle 1392 is connected to the carriage 920 by a nozzle clamp 1396 and can be positioned below (or to the side of) the reagent storage support 1340 so that the carriage 920 can be moved to position the nozzle 1392 above the reagent container 230 of the sample cartridge 200, 1200 for reagent dispensing.

[0303] In an exemplary embodiment, one of the nozzles 1392 may be configured to dispense a reagent into the reagent container 230, and the other nozzle 1392 may be configured to dispense a buffer solution into the QC buffer container 265 and the three QC reference buffer containers 275.

[0304] The dispensing portion 1390 may further include a fluid sensor 1391 associated with each of the nozzles 1392. The fluid sensor 1391 may be connected to the control module 101 and configured to indicate when fluid (or air bubbles) are present in the dispensing tube 1394 adjacent to the nozzle 1392. This may be useful as a signal to the control module 101 that dispensing of a particular reagent has begun or is complete. The fluid sensor 1391 may comprise an optical sensor with a light source disposed on one side of the tube 1394 and a photodetector disposed on the opposite side of the tube 1394, such that the presence of fluid in the tube 1394 reduces the intensity of light detected by the photodetector. For example, one suitable optical sensor for this purpose is the Optek Technology Optical Sensor Liquid 0.125" (3.18 mm) Phototransistor Module (OPB350W125Z).

[0305] The illustrated embodiment includes two nozzles 1392 with an optional third nozzle 1392 for applications requiring it. In other embodiments, only one dispense nozzle 1392 may be required, or three, four, five, six or more additional nozzles 1392 may be included, depending on the application. In some embodiments, different dispense nozzles may be used for different reagents dispensed into a single reagent vessel on the cartridge 200, 1200, or different dispense nozzles 1392 may be arranged to dispense reagents into multiple different vessels on the sample cartridge.

[0306] The reagent reservoirs 1322 and connecting tubes 1334, 1364, 1394 may be formed of any suitable material for the reagents being used, such as, for example, polytetrafluoroethylene (PTFE) or silicone, or other suitable polymers. In some embodiments, different materials and / or tube sizes may be required for different reagents in the system. For example, some reagents may require specific non-reactive materials or have a particular viscosity that requires a specific inner diameter to avoid leaving residue or to reduce flow resistance. Exemplary embodiment materials and tube dimensions are shown in the table below for illustrative purposes only.

[0307] [Table 1]

[0308] 8J, the instrument 1000 may further include a reagent waste receptacle 1397. For example, the waste receptacle 1397 may include a drip tray secured to the instrument frame 1010 and positioned below the rest position of the dispense nozzle 1392 (for when no dispense operation is occurring) to capture any droplets from the dispense nozzle 1392.

[0309] The waste receptacle 1397 may further comprise a gutter 1398 configured to catch droplets from the dispense nozzle 1392 and direct the reagent to a bottle or other container 1399 in a drip tray, where waste reagents can be discarded periodically removed by the user. This may also be useful to rinse reagents from the dispense tubes 1394 and nozzles 1392 with a buffer solution, for example, to avoid contamination of subsequent reagents.

[0310] 9A-9L, the pneumatic module 500 is shown in further detail. The pneumatic module 500 includes one or more compressors or vacuum pumps and a network of pneumatic lines (or tubes) and valves configured to connect the one or more compressors to the sample cartridge 200, 1200 to regulate pressure within different channels and reservoirs of the sample cartridge 200, 1200 to control fluid flow therein.

[0311] Different numbers of tubes may be required for different embodiments depending on the number of cartridges 200, 1200 that the instrument 1000 is configured to accommodate, as well as the layout of the cartridges 200, 1200, and the number of pneumatic ports requiring pressure control.

[0312] The illustrated embodiment of the instrument 1000 includes two core units 1100 each configured to receive four sample cartridges 1200, each defining ten pneumatic ports configured to be connected to a pneumatic module 500 for controlling fluid movement within the cartridge 1200. (See FIGS. 12A and 10B.)

[0313] This corresponds to 80 pneumatic lines or tubes that may be divided into 8 groups of 10 rows for each cartridge 1200, as shown diagrammatically in Figures 9I-9L, where again, in the perspective views, some of the tubes have been omitted for clarity.

[0314] In some embodiments, if only one pressure differential is required at any one time, all of the pneumatic lines may be connected to a single compressor. For example, if the driving pressure is high enough to overcome the cracking pressure of the valve, a passive valve may be used. For processing of nucleic acids, or other proteins, or biological materials, it may be necessary to avoid high shear rates in the fluid flow within the cartridge 1200, so the pressure differential may be relatively low. In this application and some others, it may be necessary to include an active valve so that relatively high cracking pressures are not required, in which case a pressure-activated valve may be used.

[0315] In the illustrated embodiment of the instrument 1000 configured to perform operations on the illustrated sample cartridge 1200, two different pressure levels are required so that the driving pressure to move fluid through channels in the cartridge 1200 does not interfere with the control of pressure-actuated valves in the cartridge 1200 in the situation where two pressures are acting in competition. Thus, pneumatic lines are connected to two compressors via two manifolds and multiple valves, as shown in Figures 9I-9L.

[0316] 9A and 9B, the compressors, valves, and pneumatic lines are located behind the two core units 1100. The pneumatic module 500 includes a first compressor 511 and a second compressor 512. The compressors 511, 512 may also be referred to as vacuum pumps or pressure pumps and are configured to draw air from the pneumatic lines to selectively reduce pressure in specific channels or reservoirs of the cartridge 1200.

[0317] The compressors 512, 512 may be sized appropriately for a particular application and configured to produce any suitable selected pressure differential depending on the application, including positive pressure (above atmospheric or ambient pressure) or negative pressure (below atmospheric or ambient pressure).

[0318] For example, the first compressor 511 may be configured to provide a relatively high magnitude negative pressure in the range of 180 mBar to 500 mBar, 190 mBar to 350 mBar, or about 200 mBar, and the second compressor 512 may be configured to provide a relatively low magnitude negative pressure in the range of 50 mBar to 200 mBar, 80 mBar to 150 mBar, 100 mBar to 120 mBar, or about 120 mBar. The difference between the two pressure levels may be, for example, in the range of 20 mBar to 200 mBar, 50 mBar to 100 mBar, at least 20 mBar, at least 50 mBar, or at least 100 mBar. Any suitable compressors 511, 512 may be used, such as, for example, Diaphragm pumps (4.3 l / min-600 mb)-(1410-VD-0-D-24V-BLDC-4600-15-EEE-PAA part number 14100217) from Garner Denver Thomas GMBH. Other pumps with higher or lower pressure supplies may be used for other applications, as needed. In some embodiments, the pressure module 500 may include one or more variable pressure compressors configured to selectively draw different operating pressures for different operations during processing. In some embodiments, the compressors may be configured to alternate between negative and positive pressures at different times. For example, positive pressure may be provided to close valves in the cartridge or to maintain them in a closed position against channel pressure gradients that may cause leakage through the valves.

[0319] The first compressor 511 is connected to a first manifold 521 as shown in Figures 9I, 9J, and 9K, and the second compressor 512 is connected to a second manifold 522, for example, by a pneumatic line or tube 515. The manifolds 521, 522 are shown in perspective view in Figure 9C and in partial cross-section in Figure 9D. The pneumatic line 515 has been omitted from Figures 9C-9H for clarity.

[0320] Manifolds 521, 522 define a number of barbed connectors 530 configured to connect to pneumatic lines 515 (e.g., silicone tubing) to fluidly connect various components of pneumatic module 500, as shown in Figures 9I-9L.

[0321] The first manifold 521 includes two compressor connectors 531 for connecting to the first compressor 511 via pneumatic lines 515. The connectors 531 are in fluid communication with control valves V11 and V12, respectively, which, depending on the valves V11, V12, control the pressure (either positive or negative) delivered by the compressor 511 to the remainder of the first manifold 521 and selectively vent through corresponding vents 532 to allow the pressure in the manifold 521 to equalize and return it to ambient pressure.

[0322] Valves V11 and V12 are also configured to selectively allow fluid communication between the first compressor 511 and a first group of valves V1, V2, V3, V4, V5, which are configured to selectively allow fluid communication with corresponding pneumatic ports in the sample cartridge 1200 to create a pressure differential to drive flow in the cartridge 1200 or to control flow by opening and closing valves in the cartridge 1200.

[0323] The first manifold 521 may also define a sensor connector 535 fluidly connected to all of the first group of valves V1, V2, V3, V4, V5 and control valves V11 and V12 and configured to connect to a first pressure sensor 551 configured to measure the pressure within the first manifold 521.

[0324] The second manifold 522 includes one compressor connector 536 for connecting to the second compressor 512 via pneumatic line 515. The connector 536 is in fluid communication with a second group of valves V6, V7, V8, V9, V10 configured to selectively allow fluid communication with corresponding pneumatic ports in the sample cartridge 1200 to create a pressure differential to drive flow in the cartridge 1200 or control flow by opening and closing valves in the cartridge 1200.

[0325] The second manifold 522 may also define a sensor connector 538 in fluid communication with all of the second group of valves V6, V7, V8, V9, V10 and configured to connect to a second pressure sensor 552 configured to measure the pressure within the second manifold 522. The valves of the second manifold 522 and the second compressor 512 are also configured to selectively vent or release pressure through vents 537. In some embodiments, some of the vents 537, for example the vents 537 corresponding to valves V6 and V7, may be closed with plugs as shown in FIG. 9K. In some embodiments, the second manifold 522 may be configured similarly to the first manifold 521 with two additional valves to select positive or negative pressure from the compressor (according to V11 and V12 on the first manifold 521).

[0326] Any suitable pneumatic valve may be used for valves V1, V2, V3, V4, V5, V6, V7, V8, V9, V10, V11, V12, such as, for example, the Genvi Solenoid Valve Assembly (LEE PRODUCTS LIMITED - LFKX0503050A).

[0327] Any suitable pressure sensor may be used, including, for example, a Honeywell Piezoresistive Pressure Sensor (SSCDANN015PD2A5).

[0328] The first and second manifolds 521, 522 may each include a number of connectors 530 in fluid communication with each valve V1, V2, V3, V4, V5, V6, V7, V8, V9, V10 to fluidly connect to corresponding pneumatic ports in the multiple cartridges 1200. For example, Figures 9I, 9J, and 9K show connections for eight cartridges 1200. The first and second manifolds 521, 522 shown in Figure 9C include 16 connectors 530 for each valve to provide connections to 16 cartridges 1200. Some of the connectors 530 may be blocked if not needed.

[0329] The connectors 530 are arranged in pairs in rows corresponding to each valve. Connectors 530 in rows 501a and 501b are in fluid communication with valve V1. Connectors 530 in rows 502a and 502b are in fluid communication with valve V2. Connectors 530 in rows 503a and 503b are in fluid communication with valve V3. Connectors 530 in rows 504a and 504b are in fluid communication with valve V4. Connectors 530 in rows 505a and 505b are in fluid communication with valve V5. Connectors 530 in rows 506a and 506b are in fluid communication with valve V6. Connectors 530 in rows 507a and 507b are in fluid communication with valve V7. Connectors 530 in rows 508a and 508b are in fluid communication with valve V8. Connectors 530 in rows 509a and 509b are in fluid communication with valve V9. Connectors 530 in rows 510a and 510b are in fluid communication with valve V10.

[0330] Each pair of rows is connected to a corresponding valve by a sub-manifold within the first or second manifold 511, 522. For example, Figure 9D shows a partial cross-sectional view of a portion of a first sub-manifold 541 in fluid communication with the connectors 530 and valve V1 of rows 501a and 501b, and a second sub-manifold in fluid communication with the connectors 530 and valve V2 of rows 502a and 502b.

[0331] A number of pneumatic lines 515 extend off the first and second manifolds 511, 512 to connectors 530 to the cartridges 1200. As noted above, although eighty connection lines 515 are shown corresponding to eight cartridges 1200, any suitable number may be provided depending on the number of cartridges and the number of pneumatic ports for each cartridge.

[0332] The 80 pneumatic lines 515 are arranged in 10 bundles, with each bundle including one pneumatic line 515 for each of the pneumatic ports of the cartridges 1200 corresponding to each of the valves V1, V2, V3, V4, V5, V6, V7, V8, V9, V10. In some embodiments, the pneumatic lines 515 may directly connect the manifolds 511, 512 to the core unit 1100. In other embodiments, the pneumatic module 500 may include an intermediate shutoff valve 560 configured to selectively block a portion of the pneumatic lines 515. Each bundle of pneumatic lines 515 associated with a corresponding cartridge 1200 may be selectively opened or closed depending on operational requirements, such as when one or more of the cartridge slots 120 are not in use and others are in use, or when an operation is required to be performed for one or more particular cartridges 1200 but not others.

[0333] The illustrated embodiment includes pinch valves or tube clamps 560 configured to selectively block each bundle of ten tubes associated with a corresponding cartridge 1200. One of the pinch valves 560 is shown in more detail in Figures 9E-9H.

[0334] Pinch valve 560 includes a base plate 561 with fins 562 projecting away from the base plate 561 to define channels 563 between adjacent fins 562, and a cover plate 564 for at least partially covering channels 563. Channels 563 are configured to receive pneumatic line tubing 515. Tubes 515 are omitted from Figures 9E-9H, but can be seen in channel 563 in Figure 9B.

[0335] Pinch valve 560 further comprises a pinch bar 565 extending across channel 563 and configured to be moved toward and away from base plate 561 to compress and block tubes 515 contained in channel 563. Cover plate 564 and fins 562 include an opening for receiving pinch bar 565.

[0336] Any suitable mechanism for moving the pinch bar 565 relative to the base plate 561 may be provided. In the illustrated embodiment, the pinch valve 560 comprises a lever 566 rotatably coupled to the base plate 561 via an axle 567 at one end of the lever 566. The other end of the lever 566 is coupled to a shaft 568 of a linear actuator 569 configured to raise and lower the lever 566, thereby raising and lowering the pinch bar 565 to selectively compress and block the tube 515. This movement can be seen by comparing Figures 9E and 9F (showing an open configuration) and Figures 9G and 9H (showing a closed configuration).

[0337] Any suitable actuator may be used to operate the pinch valve 560, such as, for example, an RS PRO Linear Solenoid, 24V, 40x24x29mm, Male (177-0117).

[0338] Another alternative to the above mechanism is, for example, a motor-driven cam to provide a clamping force to tube 515 with a mechanical advantage.

[0339] The compressors 511, 512 and the valves 560, V1, V2, V3, V4, V5, V6, V7, V8, V9, V10 may be electrically connected to and controlled by the pneumatic module controller 150 forming part of the control module 101. The pressure sensors 551, 552 may also be connected to the pneumatic module controller 150 to indicate pressure changes. For example, a sudden change in pressure may indicate that liquid has been completely aspirated through a channel in the cartridge 1200 or may confirm that a valve is open or closed. A particular signal from the pressure sensors 551, 552 may be used to trigger a particular action in the equipment process, for example.

[0340] Pneumatic lines 515 then continue from pinch valve 560 to pneumatic ports in the core unit 1100. In the illustrated embodiment, tubing 515 connects via a direct connect bulkhead 570 to corresponding tubing 515 connected to the core unit 1100, allowing the core unit 1100 to be assembled separately and then installed in the instrument 1000 and connected to the pneumatic module 500. The instrument frame 1010 also includes brackets 1015 to hold the tubes 515 in place.

[0341] 10A and 10B, one of the core units 1100 is shown in greater detail, illustrating the connection of pneumatic lines 515 to the core unit 1100, according to some embodiments. The core unit 1100 defines cartridge slots or sockets 120, each configured to receive a cartridge 1200. Each cartridge socket 120 has an associated pneumatic interface plate 1500 configured to engage and mate the cartridge 1200 to the pneumatic module 500.

[0342] The pneumatic plate 1500 defines pneumatic plate ports 1501, 1502, 1503, 1504, 1505, 1506, 1507, 1508, 1509, 1510 that are in fluid communication with corresponding valves V1, V2, V3, V4, V5, V6, V7, V8, V9, V10 via pneumatic lines 515. The pneumatic plate ports are in turn configured to connect with corresponding cartridge pneumatic ports 1201, 1202, 1203, 1204, 1205, 1206, 1207, 1208, 1209, 1210 in the cartridge 1200. The arrangement and connections between the corresponding pneumatic plate ports and the cartridge pneumatic ports on the underside of the sample cartridge 1200 can be understood by comparing Figures 9L, 10B and 12A (pages 35 and 37). Cartridge port 1201 is configured to connect to pneumatic plate port 1501 and valve V1. Cartridge port 1202 is configured to connect to pneumatic plate port 1502 and valve V2. Cartridge port 1203 is configured to connect to pneumatic plate port 1503 and valve V3. Cartridge port 1204 is configured to connect to pneumatic plate port 1504 and valve V4. Cartridge port 1205 is configured to connect to pneumatic plate port 1505 and valve V5. Cartridge port 1206 is configured to connect to pneumatic plate port 1506 and valve V6. Cartridge port 1207 is configured to connect to pneumatic plate port 1507 and valve V7. Cartridge port 1208 is configured to connect to pneumatic plate port 1508 and valve V8. Cartridge port 1209 is configured to connect to pneumatic plate port 1509 and valve V9. Cartridge port 1210 is configured to connect to pneumatic plate port 1510 and valve V10.

[0343] The socket 120 includes parallel rails 1120 defining grooves configured to slidably receive edges of the cartridge base 202 when inserted into the socket 120. The rails 1120 may include recesses 1122 configured to receive resilient clips 1222 integrally formed with the cartridge base 202. The rails 1120 are secured to the core unit frame 1110.

[0344] In some embodiments, the instrument 1000 may include a sensor or switch associated with each of the sockets 120 and configured to indicate when the sample cartridge 1200 is properly installed in the socket 120 .

[0345] In some embodiments, the pneumatic interface plate 1500 is positioned below the socket 120 and is spring biased into an engaged position. The core unit 1100 may include a core carriage 1190 configured to move up and down a pair of lead screws 1191 operated by a motor 1192 forming part of the kinematic module 900. The core carriage 1190 can be seen in FIG. 10C, which omits some of the components of the core unit 1100 to better visualize the internal components. Suitable motors 1192 include, for example, NANOTEC's STEPPER MOTOR-NEMA 17 (ST4118M1206-B).

[0346] In some embodiments, the pneumatic plate 1500 is connected to a retraction rod 1520 that passes through the core carriage 1190 such that the retraction rod 1520 can slide up and down, the lower end of the retraction rod 1520 comprising a stop 1522 positioned below the core carriage 1190. When the core carriage 1190 is relatively lowered beyond engagement with the stop 1522, the retraction rod 1520 and pneumatic interface plate 1500 are lowered with the core carriage 1190 relative to the core unit frame 1110.

[0347] Retraction of the interface plate 1500 allows insertion of the cartridge 1200 into the socket 120. The kinematic module 900 can be operated to raise the core carriage 1190 to cause the springs to raise the interface plate 1500 and press it against the base 202 of the cartridge 1200, clamping it between the interface plate 1500 and the rail 1120. The pneumatic interface plate 1500 can include gaskets or sealing portions 1530 surrounding each of the pneumatic plate ports 1501, 1502, 1503, 1504, 1505, 1506, 1507, 1508, 1509, 1510 configured to be compressed and deformed between the pneumatic plate 1500 and the cartridge 1200 to provide a seal around the connection between the corresponding pneumatic ports 1501, 1201. The gaskets 1530 can be formed of any suitable elastomeric material, such as, for example, rubber, silicone, or other polymers.

[0348] The magnetic module 700 may comprise a permanent magnet 710 mounted on the carriage 1190 and configured to move with the carriage 1190 and engage with the primary and secondary reaction vessels 210, 220 for each cartridge 1200 when raised to a position adjacent the reaction vessels 210, 220.

[0349] The thermal module 600 includes a separate thermal subassembly 660 corresponding to each cartridge socket 120. Referring to Figures 10D and 10E, each thermal subassembly 660 includes an elongated heating element 661 connected at one end to a radiator 662 and at the opposite end to a cooling fan 663, such as a Thorlabs cartridge heater (HT15W).

[0350] In some embodiments, each thermal subassembly 660 is mounted to a carriage 1190 and configured to move with the carriage 1190. To enable heating of the primary reaction vessel 210 without engagement of the magnetic module 700, each thermal subassembly 660 may be mounted to the carriage 1190 via a spring connecting rod 668 that is slidably mounted to the carriage 1190 and biased to an extended position by a compression spring 669, as shown in FIG.

[0351] When the core carriage 1190 rises relative to the core unit frame 1110 to engage the extended heat subassembly 660 with the cartridge 1200, the magnet 710 is positioned down and out of the way, as shown in Figure 10F. When the core carriage 1190 rises further to engage the magnet 710 with the reaction vessel 210, 220, the heat subassembly 660 is compressed into a stored state closer to the magnet 710, as shown in Figure 10G, allowing simultaneous heating and magnetic engagement.

[0352] In some embodiments, the radiator 662 and magnet 710 define slits, as shown in Figures 10C and 10D, allowing them to extend through holes 1230 in the base of the cartridge 1200, as shown in Figure 12A, allowing for greater proximity between the radiator 662, magnet 710, and reaction vessels 210, 220.

[0353] A magnet 710 associated with the primary reaction vessel 210, according to some embodiments, is shown in more detail in FIGS. 10M and 10N. The magnet 710 may comprise a magnet holder 710 configured to support a plurality of magnets 717 arranged at various angles such that the axis of each magnet 717 is oriented toward the primary reaction vessel 210. For example, the magnets 717 may be arranged with the north pole of each magnet 717 oriented toward the primary reaction vessel 210. The angle of the magnets 717 within the magnet holder 715 is shown in cross section in FIG. 10N. In some embodiments, the magnets 717 may be arranged in a stack within the magnet holder 715, for example, four stacks of two magnets 717. The magnets 717 may include cylindrical neodymium magnets, which may have, for example, a diameter of 3 mm and a length of 4 mm. The magnet holder 715 may be formed of, for example, ASLS, or any other suitable material. The magnets 717 may be adhesively bonded or otherwise fastened to the magnet holder 715.

[0354] 10H-10L, a mixing module 800 is shown according to some embodiments. The mixing module 800 includes an orbital shaker 810 positioned at the base of each core unit 1100.

[0355] 10A, the orbital shaker 810 may include an upper mounting plate 812, a base 813, and a lower housing 814. The upper mounting plate 812 may support a core unit frame 1110 secured to the mounting plate 812.

[0356] As shown in FIG. 10H, the mounting plate 812, core frame 1110, and attached components (including the core carriage 1190, motor 1192, thermal module 600, magnetic module 700, pneumatic plate 1500, and sample cartridge 1200 housed in socket 120) together define a core mass m1.

[0357] The orbital shaker 810 comprises a motor 801 configured to rotate a shaft 804 and an eccentric shaft extension 806, described below, which is configured to move an upper mounting plate 812 and attached components, including the cartridge 1200 and reaction vessels 210, 220, in an orbital motion, thereby mixing liquid reagents and samples within the primary or secondary reaction vessels 210, 220, depending on the processing step.

[0358] The orbital motion of the top plate 812 creates significant unbalanced forces that are balanced, at least in part, by the counterweights, as described below.

[0359] 10H is a force diagram illustrating a simplified view of the core unit 1100 and the orbital shaker 810. The orbital shaker 810 comprises a first counterweight 802 and a second counterweight 803 coupled to a shaft 804. The center of mass of each of the first and second counterweights 802, 803 is offset from the central axis of rotation 805 of the shaft 804.

[0360] The motor 801 and shaft 804 are positioned such that the center of mass m1 is radially offset from the axis 805 by a first radius r1. The center of mass m2 of the first counterweight 802 is radially offset from the axis 805 by a second radius r2 and is spaced apart by a first distance d 12 The center of mass m3 of the second counterweight 803 is radially offset from the axis 805 by a third radius r3 and is spaced apart from the axis 805 by a second distance d 23 is axially offset from the center of mass m2 by

[0361] When the motor 804 is operated to rotate the counterweights 802, 803 at a given angular velocity ω, centrifugal forces F1, F2, and F3 act on the masses m1, m2, and m3, respectively, as shown in FIG. 10H (where F n =M n r n ω).

[0362] Considering only masses m1, m2, and m3, the static balance of centrifugal forces is m1r1 + m3r3 = m2r2.

[0363] And the zero moment dynamic balance is m1r1d 12 =m3r3d 23 It becomes.

[0364] Using these equations, for a given core mass m1, an orbital shaker can be designed with a counterweight and offset distance to balance the equations to avoid unstable vibrations during operation.

[0365] For example, in the illustrated embodiment, the orbit radius r1 is 1.6 mm, 2000 rpm (ω), m1=4200 g, r1=1.6 mm, d 12 = 94mm, m2 = 582g, r2 = 27.3mm, m3 = 484g, r3 = 19mm. Any other suitable parameters may be selected in accordance with the equations shown above. However, it is not essential that the counterweights 802, 803 are precisely balanced.

[0366] In practice, there may be small imbalances that can cause undesirable vibrations. Therefore, the orbital shaker 810 may include bearing features to provide a restoring force. For example, the bearing balls 807 exert a restoring force F on the mounting plate 812 in the event of dynamic imbalance (which would cause the core mass m1 to rotate in a direction away from the axis 805). R , and ball bearings 808, 809 may be positioned directly beneath the upper mounting plate 812 to provide support for the shaft 804 and exert a restoring force F on the shaft 804 in the event of static imbalance (which creates a moment on the shaft 804 in a direction away from the axis 805). R The signal processing unit may be configured to provide:

[0367] 10I-10K, an orbital shaker 810 is shown in further detail, according to some embodiments. The upper mounting plate 812 and lower housing 814 are omitted from FIG. 10I to better visualize the internal components of the shaker 810.

[0368] The lower housing 814 may be connected to the base 813 by multiple, for example four, vibration isolation mounts or dampeners 815 to dampen vibrations transmitted to the base 813. For example, the dampeners 815 may include a Round M6 Anti Vibration Mount 53364145 19mm diameter (255-3118) from RS.

[0369] Motor 801 includes a stator 801a mechanically fastened to a lower housing 814 and a rotor 801b connected to a shaft 804 and configured to rotate with the shaft 804 about an axis 805. For example, one suitable motor is the BRUSHLESS DC MOTOR (EXTERNAL ROTOR) from NANOTEC (DFA90S024027-A).

[0370] The first counterweight 802 may be positioned above the motor 801 and connected to the shaft 805 by a first clamp 832, which itself forms part of the first counterweight 802. The second counterweight 803 may be positioned below the motor 801 and connected to the rotor 801b by a second clamp 833, which itself forms part of the second counterweight 803.

[0371] A first ball bearing 808 may be positioned on the shaft 805 between the motor 801 and the first clamp 832. The first ball bearing 808 may be housed in and supported by the lower housing 814, allowing the shaft 805 to rotate within the housing 814.

[0372] A second ball bearing 809 may be positioned on the shaft extension 806 (connected to the shaft 805) between the first clamp 832 and the upper mounting plate 812. The second ball bearing 809 may be contained within and supported by the mounting plate 812 to allow the shaft extension 806 and shaft 805 to rotate within the mounting plate 812.

[0373] The shaft extension 806 may be off-center (or eccentric) such that the central axis of the outer cylindrical surface of the shaft extension 806 is radially offset from the central axis of the inner cylindrical surface of the shaft extension 806 (which is concentrically connected to the shaft 805 and centered on the axis 805). The radial offset of the shaft extension 806 may be, for example, in the range of 0.5 mm to 5 mm, 0.7 mm to 3 mm, 1 mm to 2 mm, about 1 mm, or about 1.6 mm. In other embodiments, the shaft extension 806 may include any suitable radial offset for a given application. Suitable orbital motion characteristics for particular mixing requirements are discussed at www.qinstruments.com / knowledge / .

[0374] The upper mounting plate 812 may be coupled to the lower housing 814, for example, via a connecting rod 820 and a coupling plate 822. The lower housing 814 may be mechanically fastened to the coupling plate 822, which surrounds the motor 801 but may not contact the motor 801. The connecting rod 820 may include multiple connecting rods 820, such as three connecting rods 820, which may be equally spaced (and / or equiaxially) spaced about the axis 805.

[0375] The connecting rod 820 may be coupled to the coupling plate 822 and the upper mounting plate 812 by a spherical bearing 823, such as, for example, an EGLM-05 from Igus. The spherical bearing 823 allows the connecting rod 820 to support the upper mounting plate 812 while allowing the upper mounting plate 812 to move within a small orbit in the horizontal plane.

[0376] The mechanical connection may have some flexibility to allow for small out-of-plane movements of the upper mounting plate 812. To mitigate this, the orbital shaker 810 may include multiple bearing balls 807 (e.g., three, four, or more) disposed about the periphery of the motor 801 and counterweights 802, 803. For example, the bearing balls 807 may include three bearing balls 807 equally (and / or equiaxially) spaced about the axis 805. Each bearing ball 807 may be equally spaced between two of the connecting rods 820.

[0377] Each bearing ball 807 may be received in a cavity 817 defined by the lower housing 814, as shown in FIG. 10J, and may be sandwiched between an upper bearing disk 837 coupled to the upper mounting plate 812 and a lower bearing disk 838 coupled to the lower housing 814. Suitable bearing balls include 25 mm Diameter Delrin (Acetal) Plastic Balls.

[0378] The orbital shaker 810 may include a stop mechanism 880, as shown, for example, in Figures 10K and 10L. The first counterweight clamp 832 may include an outer annular ring 834 defining a notch 835 configured to receive a locking member 885 of the stop mechanism 880. The stop mechanism 880 may be coupled to the lower housing 814 and configured to move the locking member 885 into the notch 835 to stop rotation of the counterweights 802, 803 or move away from the notch 835 to allow rotation of the counterweights 802, 803. For example, the locking member 885 may be disposed substantially radially relative to the axis 805 and configured to move in and out of the notch 835.

[0379] The stop mechanism 880 may include a spring 888 for biasing the locking member 885 to the unlocked position and an actuator 889 for selectively moving the locking member 885 to the locked position within the notch 835. For example, the actuator 889 may include a linear solenoid actuator.

[0380] Ring 834 may define a lead-in portion 836 adjacent notch 835 to allow locking members 885 to begin moving radially inward (upon actuation of locking mechanism 880) before being aligned with notch 835. Lead-in portion 836 may have a smaller radial extent than the remainder of ring 834, as shown opposite notch 835.

[0381] The core unit 1100 may also include a circuit board 890 secured to the base 813 and connected to the control module 101 to control the operation of the orbital shaker motor 804 and the core carriage motor 1192, both of which may be connected to the circuit board 890 via, for example, flexible cables, allowing relative movement between the orbital shaker 810, the core frame 1110, and the base 813. The cables are not shown in the perspective views, but motor connection terminals 894 are shown in Figure 10J and various electrical connections are shown in Figures 14A-14K.

[0382] 11, an optical module 400 is shown in further detail, according to some embodiments. As described in connection with FIGS. 4A and 4B, the optical module 400 includes a source lens 412 for focusing light from a source 410, a beam splitter 414 for redirecting the light from the source 410 towards the QC sample 404, a sample lens 402 for focusing the source light onto the QC sample 404 and refocusing the light transmitted from the QC sample 404, a detector lens 422 for focusing the light transmitted from the QC sample 404 onto a detector 420, and one or more filters 430 disposed in the detector path and / or the source path for filtering out light of specific frequencies.

[0383] These components are mounted in a housing 450, as shown in cross section in Figure 11, and a circuit board 451 is mounted to the exterior of the housing 450 to position the power source 410 and detector 420 in alignment with the optical components. In some embodiments, the positions of the power source and detector may be swapped.

[0384] In some embodiments, the optical module 400 may optionally include a second light source 411 and corresponding lens 412, beam splitter 414, and filter 430, as shown in Figure 11. The second light source 411 may be configured to generate light at a different wavelength than that of the first light source 410, suitable for example for analyzing concentrations of different dyes. The second light source 411 and beam splitter 414 may be configured for use with the same detector 420 or different detectors, for example.

[0385] For example, any suitable optical components may be used: The power source 410 can be an Inolux-6868 high power UV LED. Lenses 402, 412, 422 can be 12.5mm Dia.x25mm EFL, UV-VIS Coated, Near UV Achromatic Lenses from Edmund Optics. The source filter 430 may be a Shemrock-BrightLine-FF01-433 / 530-13x13. The beam splitter 414 can be a Shemrock-BrightLine-FF414-Di01-20x20. The detector filter 430 can be a Shemrock-BrightLine-Hg01-365-13x13. The detector 420 may be a Hamamatsu photodiode S1223.

[0386] The optical module 400 is configured to analyze the sample and reference fluids at the target location 401, and the optical module 400 is moved along the instrument 1000 below the QC container 261 and the reference container 271 to sequentially analyze and measure the signal intensity (e.g., fluorescence intensity) from each container that corresponds to a particular characteristic of the sample, such as the concentration of a particular component in the liquid, e.g., a target nucleic acid (NA).

[0387] A measurement of a property of interest (e.g., concentration) of the sample may be determined by interpolating or extrapolating corresponding measurements of reference containers with known concentrations, for example using linear or quadratic regression, or another technique suitable for the relationship between the measured signal and the property of interest. The concentration (or other property) of the undiluted output fluid may then be determined as follows:

[0388] 12B, a sample cartridge 1200 is shown in further detail, according to some embodiments. Cartridge 1200 includes similar features to those described with respect to sample cartridge 200, and similar features are designated with similar reference numbers.

[0389] As discussed with respect to cartridge socket 120, cartridge 1200 may include a resilient clip 1222 configured to engage a recess 1122 in rail 1120 of socket 120 to properly position cartridge 1200 within socket 120 such that the pneumatic ports are aligned with pneumatic interface plate 1500. Clip 1222 may be integrally formed with an edge of base 202 of cartridge 1200, for example.

[0390] The cartridge 1200 includes a pneumatic channel plate 1250 that defines a number of cartridge pneumatic ports 1201, 1202, 1203, 1204, 1205, 1206, 1207, 1208, 1209, 1210 and includes pneumatic channels that connect various portions of the cartridge 1200 to operate the valves. The base 202 also defines fluid channels and several pneumatic channels. A polypropylene membrane 1290 may be sandwiched between the base 202 and the pneumatic channel plate 1250 as shown and described in connection with FIG. 2K to provide a flexible membrane to separate several channels of the other two layers and / or to form valves in cooperation with other layers.

[0391] Pneumatic channel plate 1250 defines a QC hole 1261 aligned with QC receptacle 261, and a plurality, e.g., three QC reference holes 1271 aligned with QC reference receptacle 271. Polypropylene membrane 1290 forms the bottom of each of QC receptacle 261 and reference receptacle 271 and may provide a transparent observation window allowing optical access of an optical module to analyze the contents of QC receptacle 261 and reference receptacle 271 through QC hole 1261 and QC reference hole 1271.

[0392] In some embodiments, the cartridge 1200 may include an indicia 1295, such as, for example, a bar code, to identify the sample stored therein. The cartridge 1200 may be provided with an output receptacle 250, which may include a corresponding indicia 1296 or bar code that may be identical to the indicia 1295 or may be associated with the indicia 1295. Alternatively, the cartridge 1200 may include one or more peel-off labels with corresponding indicia 1296 that may be removed from the cartridge 1200 and applied to a suitable output receptacle 250 in which the output fluid will be received once the sample has been processed.

[0393] The indicia 1295, 1296 may be scanned so as to be associated with data generated by the instrument 1000 when processing the sample, or the data may be otherwise entered into a laboratory information system or the like.

[0394] 13, the control module 101 may comprise one or more processors 1300 and memory 1302. The processor 1300 may comprise integrated electronic circuits for performing calculations, such as, for example, a microprocessor, a graphic processing unit, etc. The memory 1302 may comprise both volatile and non-volatile memory for storing executable program code or data. The memory 1302 includes program code that, when executed by the processor 1300, provides the functionality of the control module 101.

[0395] The block diagram of FIG. 13 illustrates some of the software modules or components stored in memory 1302 that, when executed by processor 1300, perform the functions of control module 101, as described.

[0396] As shown, memory 1302 may include pneumatic components 1304 configured to, when executed by processor 1300, cause pneumatic module 500 to perform the functionality described. For example, pneumatic components 1304 may be configured to cooperate with or control pumps, valves, and / or pressure sensors of the instrument.

[0397] The memory 1302 may include a dispense control component 1306 configured, when executed by the processor 1300, to cause the reagent module 300 and / or the optical module 400 to perform the described functions. For example, the dispense control component 1306 may be configured to cooperate with or control the reagent module 300 and / or the optical module 400.

[0398] The memory 1302 may include a core device management component 1308 configured, when executed by the processor 1300, to cooperate with or control the thermal module 600, the magnetic module 700, the mixing module 800, and / or the motion module 900.

[0399] The memory 1302 may include an extraction process component 1310 configured to, when executed by the processor 1300, cause the instrument 100 to function according to described embodiments. For example, the extraction process component 1310 may communicate with the pneumatics component 1304, the dispense control component 1306, and the core device management component 1308 to cause each component to perform operations to cause the instrument 100 to function according to described embodiments. In some embodiments, the extraction process component 1310 may include computer code for executing a workflow program from a list of workflow programs.

[0400] 14A-14K show the electrical layout of device 1000, according to some embodiments.

[0401] Example 1 For illustrative purposes only, example instrument workflows are described here: In some embodiments, instrument 100 may be configured to perform, for example, a nucleic acid extraction workflow.

[0402] Before the instrument workflow begins, a user may pipette a fluid sample, such as a biological sample, into the primary reaction vessel 210 of the sample cartridge 200. For example, 0.2-5 mL of blood or bone marrow drawn from a patient.

[0403] The user may then close the lid 211 of the primary reaction vessel 210 and then record or scan the serial number or other indicia of the sample cartridge 200 and record the corresponding patient details, for example from a vial that previously contained a sample. This information may be recorded, for example, in a LIMS system or laboratory information system.

[0404] The user may then insert the cartridge 200 into one of the cartridge slots 120 in the instrument 100 .

[0405] The user can then use the user interface to select an instrument workflow program. The instrument workflow can then be initiated by the instrument functions controlled by the control module 101 under instructions recorded on the computer readable storage medium, such as the nucleic acid extraction workflow described below.

[0406] The motion module is operated to cause the pneumatic module to engage the pneumatic port on the sample cartridge, clamping the cartridge and restricting removal of the cartridge 200 from the cartridge slot 120 .

[0407] Next, the motion module is operated to move the reagent module to a position above the sample cartridge, and the reagent module is operated to dispense proteinase K into the reagent container 230. For example, the amount of proteinase K is in the range of 50 to 100 μg per mL volume of the sample.

[0408] The pneumatic module is operated to transfer reagents along with the sample to the primary reaction vessel 210 .

[0409] The orbital shaker of the mixing module is operated to promote mixing of the reagents and sample in the primary reaction vessel.

[0410] The kinetic and thermal modules are operated to turn on and ramp up the heater to heat the primary reaction vessel and incubate at 62 C for 10 minutes to digest the proteins in the blood. The heater can then be turned down and stopped.

[0411] The kinetic and reagent modules are then operated to dispense lysis buffer (eg, 5 M guanadinium HCl, 0.25% Tween-20) into reagent reservoir 230.

[0412] The pneumatic module is then operated to transfer the lysis buffer into the primary reaction vessel.

[0413] The kinetic and reagent modules are then operated to dispense functionalized magnetic beads (eg, carboxyl COOH magnetic beads) into the reagent vessels.

[0414] Any suitable type of functionalized bead may be used, including, for example, solid phase reversible immobilization (SPRI) functionalized beads, carboxylated beads, or other magnetically functionalized beads.

[0415] The pneumatic module is then operated to transfer the beads to a primary reaction vessel.

[0416] The orbital shaker is operated to facilitate mixing of the contents of the primary reaction vessel.

[0417] The kinetic and thermal modules are operated to heat the primary reaction vessel and incubate the contents at 62 C for 15 minutes to lyse the blood and bind the nucleic acids (NA) to the beads.

[0418] The heater is then turned off and the cooling fan is turned on to cool the primary reaction vessel 210 .

[0419] The motor and magnetic modules are operated to engage magnets 710 and retain magnetic beads to one or more sides of the primary reaction vessel.

[0420] Operate the pneumatic module to hold the beads in place for 1-5 minutes while the liquid contents of the primary reaction vessel, including the lysate, are transferred to the waste vessel 240.

[0421] The magnet 710 is then disengaged from the primary reaction vessel.

[0422] The kinetic and reagent modules are then operated to dispense Wash 1 buffer into the reagent vessel (eg, 3M guanadinium HCl, 30% ethanol).

[0423] The pneumatic module is then operated to transfer Wash 1 solution to the primary reaction vessel.

[0424] The orbital shaker is operated to facilitate mixing of the contents of the primary reaction vessel.

[0425] The motor and magnetic modules are operated to engage magnets 710 and retain magnetic beads to one or more sides of the primary reaction vessel.

[0426] The beads are held in place for 1-5 minutes while the pneumatic module is operated to transfer the liquid contents of the primary reaction vessel to a waste vessel 240.

[0427] The magnet 710 is then disengaged from the primary reaction vessel.

[0428] The kinetic and reagent modules are then operated to dispense Wash 2 buffer into the reagent vessel (eg, 20 mM glycine HCl (pH 3.0) 80% ethanol).

[0429] The pneumatic module is then operated to transfer Wash 2 solution to the primary reaction vessel.

[0430] The orbital shaker is operated to facilitate mixing of the contents of the primary reaction vessel.

[0431] The motor and magnetic modules are operated to engage magnets 710 and retain magnetic beads to one or more sides of the primary reaction vessel.

[0432] The beads are held in place for 1-5 minutes while the pneumatic module is operated to transfer the liquid contents of the primary reaction vessel to a waste vessel 240.

[0433] The magnet 710 is then disengaged from the primary reaction vessel.

[0434] The kinetic and reagent modules are then operated to dispense Wash 3 buffer into the reagent vessel (eg, 20 mM glycine HCl (pH 3.0) + 0.1% Tween 20).

[0435] The pneumatic module is then operated to transfer Wash 3 solution to the primary reaction vessel.

[0436] The orbital shaker is operated to facilitate mixing of the contents of the primary reaction vessel.

[0437] The motor and magnetic modules are operated to engage magnets 710 and retain magnetic beads to one or more sides of the primary reaction vessel.

[0438] The beads are held in place for 1-5 minutes while the pneumatic module is operated to transfer the liquid contents of the primary reaction vessel to a waste vessel 240.

[0439] The magnet 710 is then disengaged from the primary reaction vessel.

[0440] The kinetic and reagent modules are then operated to dispense Wash 4 buffer into the reagent vessel (eg, 20 mM glycine HCl (pH 3.0) + 0.1% Tween 20).

[0441] The pneumatic module is then operated to transfer Wash 4 solution to the primary reaction vessel.

[0442] The orbital shaker is operated to facilitate mixing of the contents of the primary reaction vessel.

[0443] The motor and magnetic modules are operated to engage magnets 710 and retain magnetic beads to one or more sides of the primary reaction vessel.

[0444] The beads are held in place for 1-5 minutes while the pneumatic module is operated to transfer the liquid contents of the primary reaction vessel to a waste vessel 240.

[0445] The magnet 710 is then disengaged from the primary reaction vessel.

[0446] The kinetic and reagent modules are then operated to dispense elution buffer into the reagent vessel (eg, 1xTE, pH 8.0).

[0447] The pneumatic module is then operated to transfer the elution buffer to the primary reaction vessel.

[0448] The orbital shaker is operated to facilitate mixing of the contents of the primary reaction vessel.

[0449] The heater is turned up and on, heating the primary reaction vessel to 74 C for 15 minutes, releasing the DNA from the beads into the elution buffer.

[0450] The motor and magnetic modules are operated to engage magnets 710 and retain magnetic beads to one or more sides of the primary reaction vessel.

[0451] The beads are held in place for 1-5 while the pneumatic module is operated to transfer the liquid contents of the primary reaction vessel (eluate) to the secondary reaction vessel 220.

[0452] The magnet 710 is then disengaged from the primary reaction vessel.

[0453] Next, the motor module and the reagent module are operated to dispense the COOH (carboxyl) beads into the reagent solution along with a binding buffer (eg, 0.8 M NaCl + 11% PEG8000).

[0454] The pneumatic module is then operated to transfer the contents of the reagent vessel to a secondary reaction vessel.

[0455] Operate the orbital shaker to facilitate mixing of the contents of the secondary reaction vessel and binding of the extracted DNA to the COOH beads.

[0456] The motor and magnetic modules are operated to engage magnets 710 and retain magnetic beads to one or more sides of the secondary reaction vessel.

[0457] The beads are held in place for 1-5 minutes while the pneumatic module is operated to transfer the liquid contents of the secondary reaction vessel to the waste vessel 240.

[0458] The magnet 710 is then disengaged from the primary reaction vessel.

[0459] Next, operate the kinetic module and the reagent module to dispense COOH Beads Wash 1 into the reagent container (e.g., 85% ethanol).

[0460] The pneumatic module is then operated to transfer the contents of the reagent vessel to a secondary reaction vessel.

[0461] The contents of the secondary reaction vessel are then incubated for 30 seconds.

[0462] The motor and magnetic modules are operated to engage magnets 710 and retain magnetic beads to one or more sides of the secondary reaction vessel.

[0463] The beads are held in place for 1-5 minutes while the pneumatic module is operated to transfer the liquid contents of the secondary reaction vessel to the waste vessel 240.

[0464] The magnet 710 is then disengaged from the primary reaction vessel.

[0465] Next, operate the kinetic module and the reagent module to dispense COOH Beads Wash 2 into the reagent container (e.g., 85% ethanol).

[0466] The pneumatic module is then operated to transfer the contents of the reagent vessel to a secondary reaction vessel.

[0467] The contents of the secondary reaction vessel are then incubated for 30 seconds.

[0468] The motor and magnetic modules are operated to engage magnets 710 and retain magnetic beads to one or more sides of the secondary reaction vessel.

[0469] The beads are held in place for 1-5 minutes while the pneumatic module is operated to transfer the liquid contents of the secondary reaction vessel to waste vessel 240. The magnet 710 is then disengaged from the primary reaction vessel.

[0470] The kinetic and reagent modules are then operated to dispense COOH elution buffer (eg, 10 mM Tris, pH 8.0) into the reagent vessel.

[0471] The pneumatic module is then operated to transfer the elution buffer to a second reaction vessel.

[0472] Operate the orbital shaker to facilitate mixing of the contents of the secondary reaction vessel and release the DNA from the COOH beads into the elution buffer.

[0473] The motor and magnetic modules are operated to engage magnets 710 and retain magnetic beads to one or more sides of the secondary reaction vessel.

[0474] The pneumatic module is then operated to draw the liquid contents of the secondary reaction vessel (eluate) up into the air permeable membrane, filling the metering channel.

[0475] The kinetic and reagent modules are then operated to dispense the neutral buffer into the QC buffer reservoir 265 and the three QC reference buffer reservoirs 275 .

[0476] The pneumatic module is then operated to draw buffer from the QC buffer reservoir through the metering channel into the QC reservoir along with an aliquot (e.g., 1 μL) of eluate from the metering channel, and transfer buffer from the QC reference buffer reservoir 275 to the corresponding QC reference reservoir 271.

[0477] The pneumatic module is then operated to transfer the remainder of the eluate from the secondary reaction vessel to the output vessel 250 .

[0478] The orbital shaker is operated to facilitate mixing of the contents of the QC vessel 261 and the QC reference vessel 271, and resuspension of the preloaded dye and reference nucleic acid (NA) in the QC reference vessel.

[0479] The motion module is operated to move the optical module to a position corresponding to a QC receptacle containing an aliquot of eluate along with a sample cartridge and buffer, and the optical module is operated to perform a fluorescence measurement on the contents of the QC receptacle.

[0480] The motion module is further operated to move the optical module to three positions corresponding to the three QC reference vessels, and the optical module is operated to perform a fluorescence measurement on the contents of each of the QC reference vessels.

[0481] Data from the fluorescence measurements are then used to determine the DNA concentration of the final eluate. The resulting data provides quantification and can be transmitted to a LIMS system for recording and / or capture.

[0482] Finally, the pneumatic module may be lowered and disengaged from the sample cartridge, which may include the termination of the workflow program according to some embodiments.

[0483] The sample cartridge 200 may then be removed from the instrument 100 by the user. The temporary lid 259 may be removed from the output receptacle 250 and the primary lid may be closed to seal the output receptacle 250.

[0484] The output bin 250 may then be removed from the output bin sheet 254 and the remainder of the sample cartridge 200 may be discarded.

[0485] Example 2 Another example workflow is shown below, according to some embodiments. The chemistry and operational parameters are suitable for gDNA extraction from a 0.5 mL sample of whole blood. The details of the instrument operation may also be suitable for other applications and processes.

[0486] For example, any suitable reagent may be used, including the following substitutions, by way of example only: Proteinase K Proteinase K supporting buffer (4.93 M G-HCl, 67 mM maleic acid, 30% Tween-20 (v / v), pH 6) Binding buffer (0.8M Guanidine HCl; 10mM Tris pH 8; 50% IPA; 2mM EDTA; 1.2M NaCl; 0.25% Tween) or (5M Guanidine HCl + 0.25% Tween 20) Beads (Silica-coated paramagnetic beads) (Siemens Versant 50 μL, or alternatively, Magtivo Magsi-DNAmf MD020001) Wash 1 (5.61M G.HCl, 0.28M LiCl, 1.12%Tw-20, 25.24%EtOH) Alternatively, (3M Guanidine.HCl pH3.0+30%EtOH) Wash 2 (19 mM Tris, 80% EtOH) alternatively, (20 mM citric acid pH 3.0, 80% ethanol) Wash 3 (20 mM Hepes, pH 6.5) alternatively (20 mM Glycine.HCl pH 3.0, 0.1% Tw-20) Elution buffer (1xTE, pH8.0)

[0487] Incubation times and temperatures may be adjusted to suit a particular application, for example, incubation temperatures may range from 21°C to 72°C.

[0488] Before the instrument workflow is initiated, a user may pipette a fluid sample, such as a biological sample, into the primary reaction vessel 210 of the sample cartridge 200. For example, 0.5 mL of blood drawn from a patient.

[0489] The user may then close the lid 211 of the primary reaction vessel 210 and then record or scan the serial number or other indicia of the sample cartridge 200 and record the corresponding patient details, for example from a vial that previously contained a sample. This information may be recorded, for example, in a LIMS system or laboratory information system.

[0490] The user may then insert the cartridge 200 into one of the cartridge slots 120 in the instrument 100 .

[0491] The user can then use the user interface to select an instrument workflow program. The instrument workflow can then be initiated by the instrument functions controlled by the control module 101 under instructions recorded on the computer readable storage medium. For example, a nucleic acid extraction workflow is described below.

[0492] The motion module is operated to cause the pneumatic module to engage the pneumatic port on the sample cartridge, clamping the cartridge and restricting removal of the cartridge 200 from the cartridge slot 120 .

[0493] The motor module is then operated to move the reagent module into position above the sample cartridge and the reagent module is operated to dispense 50 μL of Proteinase K (Qiagen as received from supplier) into reagent container 230 .

[0494] The pneumatic module is operated to transfer reagents along with the sample to the primary reaction vessel 210 .

[0495] The reagent module is then operated to dispense 120 μL of commercial supporting buffer AL into the reagent vessel 230 and the pneumatics module is operated to transfer the reagent along with the sample to the primary reaction vessel 210 .

[0496] Alternatively, proteinase K and buffer may be dispensed, either together or one at a time, into the reagent vessel 230 and then transferred together to the primary reaction vessel 210 in a single transfer step.

[0497] Operation of the pneumatic module may include, for example, applying a vacuum or negative pressure (relative to ambient pressure) in the range of 100 mBar to 120 mBar.

[0498] The orbital shaker of the mixing module is operated at 1100 rpm for 10 seconds to facilitate mixing of the reagents and sample in the primary reaction vessel.

[0499] The kinetic and thermal modules are operated to heat the primary reaction vessel by turning on and ramping up the heater and incubating at 25° C. for 10 minutes to digest proteins in the blood. The heater may then be turned down and stopped.

[0500] Alternatively, if the ambient temperature is close to 25° C., a heater may not be needed for this step.

[0501] The kinetic and reagent modules are then operated to dispense 825 μL of lysis buffer (0.8 M g. HCl, 0.01 M Tris pH 8, 50% 2-propanol, 1.2 M NaCl, 2 mM EDTA, 0.25% Tween-20) into reagent reservoir 230.

[0502] The pneumatic module is then operated to transfer the lysis buffer into the primary reaction vessel.

[0503] The kinetic and reagent modules are then operated to dispense functionalized magnetic beads (Siemens Versant 50 μL) into the reagent vessel.

[0504] The pneumatic module is then operated to transfer the beads to a primary reaction vessel.

[0505] To avoid or reduce the time available for beads to precipitate or settle in the reagent vessels (which may lead to blockages), the pneumatic module may be operated to transfer beads to the primary reaction vessel before dispensing of the beads into the reagent vessels is completed. For example, the transfer may be initiated during dispensing or midway through dispensing, and may be done in stages. Dispensing may also be done in stages in some embodiments.

[0506] Alternatively or additionally, a portion of the lysis buffer (e.g., two-thirds) may be dammed and dispensed into the reagent chamber after dispensing and transferring the beads to wash away any beads remaining in the reagent vessel or to transfer the channel into the primary reaction vessel.

[0507] The orbital shaker is operated to facilitate mixing of the contents of the primary reaction vessel at 1100 rpm for 10 seconds.

[0508] The kinetic and thermal modules are operated to heat the primary reaction vessel and incubate the contents at approximately 62° C. for 15 minutes to lyse the blood and bind the nucleic acids (NA) to the beads. An orbital shaker may also be operated at 1100 rpm during the incubation period to facilitate mixing.

[0509] The heater is then stopped and the cooling fan is operated to cool the primary reaction vessel 210 back to ambient temperature. For example, the cooling operation may have a duration ranging from 1 minute to 5 minutes, 2 minutes to 3 minutes, or about 2 minutes, depending on the cooling rate. In some embodiments, it may be necessary to cool the reaction vessel to prevent the beads from drying out. In other embodiments, this step may be omitted if drying is not an issue.

[0510] The motor and magnetic modules are operated to engage magnets 710 and retain magnetic beads to one or more sides of the primary reaction vessel.

[0511] The magnets may be engaged during the cooling operation.

[0512] The beads are held in place for 1-5 minutes while the pneumatic module is operated to transfer the liquid contents of the primary reaction vessel, including the lysate, to the waste vessel 240. A magnet may be applied to engage the beads for about 1 minute prior to the transfer of the liquid, to move the beads toward the magnet so that they are held against the vessel wall with sufficient strength to resist flowing with the liquid during the transfer process. The length of time required may depend on the strength of the magnetic attraction between the beads and the magnet and the viscosity of the fluid. In some embodiments, shorter settling times (less than 1 minute) may be sufficient, or longer settling times (e.g., more than 1 minute, more than 2 minutes, more than 3 minutes, or more than 4 minutes) may be required.

[0513] The magnet 710 is then disengaged from the primary reaction vessel.

[0514] Next, operate the kinetic and reagent modules to dispense 850 μL of Wash 1 buffer into the reagent vessel (eg, 3 M guanadinium HCl (gHCl), 30% ethanol).

[0515] The pneumatic module is then operated to transfer Wash 1 solution to the primary reaction vessel.

[0516] The orbital shaker is operated at 1100 rpm for 10 seconds to facilitate mixing of the contents of the primary reaction vessel.

[0517] The motor and magnetic modules are operated to engage magnets 710 and retain magnetic beads to one or more sides of the primary reaction vessel.

[0518] The beads are held in place for 1-5 minutes while the pneumatic module is operated to transfer the liquid contents of the primary reaction vessel to a waste vessel 240. A magnet may be applied to engage the beads for approximately 1 minute prior to transferring the liquid.

[0519] The magnet 710 is then disengaged from the primary reaction vessel.

[0520] In some embodiments, only one washing process may be required, while in other embodiments, additional washing steps may be required, as described below.

[0521] The kinetic and reagent modules are then operated to dispense 450 μL of Wash 2 buffer (eg, 80% ethanol, 0.1 M sodium citrate buffer, pH 3) into the reagent vessel.

[0522] The pneumatic module is then operated to transfer Wash 2 solution to the primary reaction vessel.

[0523] The orbital shaker is operated at 1100 rpm for 10 seconds to facilitate mixing of the contents of the primary reaction vessel.

[0524] The motor and magnetic modules are operated to engage magnets 710 and retain magnetic beads to one or more sides of the primary reaction vessel.

[0525] The beads are held in place for 1-5 minutes while the pneumatic module is operated to transfer the liquid contents of the primary reaction vessel to a waste vessel 240. A magnet may be applied to engage the beads for approximately 1 minute prior to transferring the liquid.

[0526] The magnet 710 is then disengaged from the primary reaction vessel.

[0527] The kinetic and reagent modules are then operated to dispense 450 μL of Wash 3 buffer into the reagent vessel (eg, 20 mM glycine HCl, 0.1% Tw-20, pH 3).

[0528] The pneumatic module is then operated to transfer Wash 3 solution to the primary reaction vessel.

[0529] The orbital shaker is operated at 1100 rpm for 10 seconds to facilitate mixing of the contents of the primary reaction vessel.

[0530] The motor and magnetic modules are operated to engage magnets 710 and retain magnetic beads to one or more sides of the primary reaction vessel.

[0531] The beads are held in place for 1-5 minutes while the pneumatic module is operated to transfer the liquid contents of the primary reaction vessel to a waste vessel 240. A magnet may be applied to engage the beads for approximately 1 minute prior to transferring the liquid.

[0532] The magnet 710 is then disengaged from the primary reaction vessel.

[0533] The kinetic and reagent modules are then operated to dispense 450 μL of Wash 4 buffer (eg, 20 mM glycine HCl, 0.1% Tw-20, pH 3) into the reagent vessel.

[0534] Wash 4 is completed using the same buffer as Wash 3 to flush out any contaminants in the dispense system from the previous step. This step may be repeated more than once as necessary to ensure purity or to further reduce the possibility of contaminants appearing in the solution. Alternatively, this step may be omitted if contaminants are not a concern or if the dispense system includes independent channels that avoid potential contamination.

[0535] The pneumatic module is then operated to transfer Wash 4 solution to the primary reaction vessel.

[0536] The orbital shaker is operated at 1100 rpm for 10 seconds to facilitate mixing of the contents of the primary reaction vessel.

[0537] The motor and magnetic modules are operated to engage magnets 710 and retain magnetic beads to one or more sides of the primary reaction vessel.

[0538] The beads are held in place for 1-5 minutes while the pneumatic module is operated to transfer the liquid contents of the primary reaction vessel to a waste vessel 240. A magnet may be applied to engage the beads for approximately 1 minute prior to transferring the liquid.

[0539] The magnet 710 is then disengaged from the primary reaction vessel.

[0540] The kinetic and reagent modules are then operated to dispense 165 μL of elution buffer into the reagent vessel (eg, 1×TE, pH 8.0).

[0541] The pneumatic module is then operated to transfer the elution buffer to the primary reaction vessel.

[0542] The heater is turned up and on to heat the primary reaction vessel to approximately 62° C. for 10 minutes, releasing the DNA from the beads into the elution buffer. An orbital shaker can be operated at 1100 rpm during the 10 minute incubation period to facilitate mixing of the contents of the primary reaction vessel.

[0543] The motor and magnetic modules are then manipulated to engage magnets 710 and retain the magnetic beads to one or more sides of the primary reaction vessel.

[0544] The beads are held in place for 1-5 minutes while the pneumatic module is operated to transfer the liquid contents of the primary reaction vessel (eluate) to the secondary reaction vessel 220. A magnet may be applied to engage the beads for approximately 1 minute before transferring the liquid. The used beads then remain in the primary reaction vessel until the end of the process (during further processing of the eluate in the secondary reaction vessel) or when the cartridge is discarded.

[0545] The magnet 710 is then disengaged from the primary reaction vessel.

[0546] Next, the kinetic and reagent modules are operated to dispense COOH (carboxyl) beads into the reagent container along with binding buffer (e.g., 470 μL of master mix, 1.24 M NaCl, 13.95% PEG8000, 0.78% w / v ratio (MFY0002 Bangslab beads)).

[0547] The pneumatic module is then operated to transfer the contents of the reagent vessel to a secondary reaction vessel.

[0548] The orbital shaker is operated at 1100 rpm for 10 seconds to facilitate mixing of the contents of the primary reaction vessel.

[0549] The motor and magnetic modules are operated to engage magnets 710 and retain magnetic beads to one or more sides of the primary reaction vessel.

[0550] The beads are held in place for 1-5 minutes while the pneumatic module is operated to transfer the liquid contents of the primary reaction vessel to a waste vessel 240. A magnet may be applied to engage the beads for approximately 1 minute prior to transferring the liquid.

[0551] In this example, the beads in the secondary reaction vessel beads have a weaker magnetic attraction to the magnet and are in a more viscous solution. Therefore, a longer settling time (e.g., 2 minutes) may be necessary. However, longer or shorter settling times may be used if sufficient, from less than 1 minute to more than 2 minutes, more than 3 minutes, or more than 4 minutes.

[0552] In some embodiments, the magnet may remain engaged during subsequent washing steps: for example, if the beads have relatively weak binding kinetics, as in this case, holding the beads in place with a magnet may mitigate premature washing of DNA from the beads.

[0553] Next, operate the kinetic module and the reagent module to dispense 200 μL of COOH Beads Wash 1 into the reagent container (e.g., 85% ethanol).

[0554] The pneumatic module is then operated to transfer the contents of the reagent vessel to a secondary reaction vessel.

[0555] The contents of the secondary reaction vessel are then incubated at room temperature for 30 seconds.

[0556] The pneumatic module is then operated to transfer the liquid contents of the secondary reaction vessel to waste vessel 240 while the magnet (still engaged) holds the beads in place.

[0557] Next, operate the kinetic module and the reagent module to dispense 200 μL of COOH Beads Wash 2 into the reagent container (e.g., 85% ethanol).

[0558] COOH Beads Wash 2 is completed using the same buffer as COOH Beads Wash 1 to wash away any contaminants in the dispense system from the previous step. This step can be repeated two or more times as necessary to ensure purity or to further reduce the possibility of contaminants appearing in the solution. Alternatively, this step can be omitted if contaminants are not a concern or if the dispense system includes independent channels that avoid potential contamination.

[0559] The pneumatic module is then operated to transfer the contents of the reagent vessel to a secondary reaction vessel.

[0560] The contents of the secondary reaction vessel are then incubated at room temperature for 30 seconds.

[0561] The pneumatic module is then operated to transfer the liquid contents of the secondary reaction vessel to waste vessel 240 while the magnet (still engaged) holds the beads in place.

[0562] The magnet 710 is then disengaged from the primary reaction vessel.

[0563] Next, operate the kinetic and reagent modules to dispense 30 μL of COOH elution buffer (eg, 1× TE buffer pH 8) into the reagent vessel.

[0564] The pneumatic module is then operated to transfer the elution buffer to a second reaction vessel.

[0565] Operate the orbital shaker at 1100 rpm for 10 seconds to facilitate mixing of the contents of the secondary reaction vessel and release the DNA from the COOH beads into the elution buffer.

[0566] The kinematic and magnetic modules are operated to engage magnets 710 and hold the magnetic beads to one or more sides of the secondary reaction vessel. A settling time of about 1 minute may be allowed before the next step.

[0567] The pneumatic module is then operated to draw the liquid contents of the secondary reaction vessel (eluate) up into the air permeable membrane, filling the metering channel.

[0568] The kinetic and reagent modules are then operated to dispense a neutral buffer (e.g., 199 μL of 1× TE buffer pH 8) into the QC buffer reservoir 265 and into the three QC reference buffer reservoirs 275 (e.g., 200 μL of 1× TE buffer pH 8).

[0569] The pneumatic module is then operated to draw buffer from the QC buffer reservoir through the metering channel and into the QC reservoir 265 along with an aliquot (e.g., 1 μL) of eluate from the metering channel until air fills the channel. The pneumatic module is also operated to transfer buffer from the QC reference buffer reservoir 275 to the corresponding QC reference reservoir 271.

[0570] QC container 265 and QC reference buffer container 275 each contain a similar amount (e.g., 0.2 μg) of dried DNA dye, and QC reference buffer containers 275 each contain a different reference amount of gDNA for comparison (e.g., 4 ng gDNA, 60 ng gDNA, and 500 ng gDNA, respectively).

[0571] The pneumatic module is then operated to transfer the remainder of the eluate from the secondary reaction vessel to the output vessel 250 .

[0572] The orbital shaker is operated at 1100 rpm for 10 seconds to facilitate mixing of the contents of the QC vessel 261 and the QC reference vessel 271, and resuspension of the preloaded dye and reference nucleic acid (NA) in the QC reference vessel.

[0573] The motion module is operated to move the optical module to a position corresponding to a QC receptacle containing an aliquot of eluate along with a sample cartridge and buffer, and the optical module is operated to perform a fluorescence measurement on the contents of the QC receptacle.

[0574] The motion module is further operated to move the optical module to three positions corresponding to the three QC reference vessels, and the optical module is operated to perform a fluorescence measurement on the contents of each of the QC reference vessels.

[0575] The data from the fluorescence measurements is then used to determine the DNA concentration of the final eluate by curve fitting between measurements from three reference vessels with known concentrations and interpolating (or extrapolating) to determine the concentration of the eluate. The resulting data can be transmitted to a LIMS system for recording and / or capture.

[0576] Finally, the pneumatic module may be lowered and disengaged from the sample cartridge, which may include the termination of the workflow program according to some embodiments.

[0577] The sample cartridge 200 may then be removed from the instrument 100 by the user. The temporary lid 259 may be removed from the output receptacle 250 and the primary lid may be closed to seal the output receptacle 250.

[0578] The output bin 250 may then be removed from the output bin sheet 254 and the remainder of the sample cartridge 200 may be discarded.

[0579] It will be understood by those skilled in the art that numerous variations and / or modifications may be made to the above-described embodiments without departing from the broad general scope of the present disclosure, and the present embodiments are therefore to be considered in all respects as illustrative and not restrictive.

Claims

1. 1. A chemical processing instrument configured to receive one or more sample cartridges each containing a fluid sample for processing, each sample cartridge comprising: a primary reaction vessel configured to contain a fluid sample for processing, the primary reaction vessel configured to receive a lid for closing an open top of the primary reaction vessel; a reagent vessel configured to receive one or more fluid reagents through an open top of the reagent vessel, the reagent vessel being connected to the primary reaction vessel through a primary reagent channel with a reagent valve disposed within the reagent channel to control fluid flow through the primary reagent channel; a pneumatic port in fluid communication with said primary reaction vessel; The chemical processing tool comprises: a reagent dispenser configured to dispense one or more fluid reagents into the reagent container through the open top of the reagent container; a pneumatic module connected in fluid communication with the primary pneumatic port of the primary reaction vessel and configured to selectively adjust pressure in the primary reaction vessel to draw fluid from the reagent vessel through the primary reagent channel and into the primary reaction vessel when the lid is closed.

2. the reagent dispenser includes a reagent cartridge including a plurality of reagent reservoirs, each reagent reservoir containing a quantity of reagent in fluid communication with a dispense pump via one or more valves; 2. The instrument of claim 1, wherein the instrument is configured to operate the one or more valves to connect a selected one of the reagent reservoirs to the pump and to operate the pump to dispense a selected amount of reagent from the selected reagent reservoir into the reagent container of the sample cartridge.

3. The instrument of claim 2 , wherein the reagent cartridge is removable from the dispense pump and instrument to facilitate refilling or replacement of the reagent reservoir.

4. 4. The instrument of claim 1, further comprising a heater mounted to a carriage assembly configured to selectively move the heater relatively close to the primary reaction vessel of the sample cartridge to heat a fluid sample in the primary reaction vessel and to move the heater relatively farther away from the sample cartridge when heating is not required.

5. 5. The instrument of claim 4, wherein the heater comprises a radiator configured to pass through a slot or hole in the sample cartridge and partially surround the primary reaction vessel.

6. 6. The apparatus of claim 4 or 5, further comprising a magnet mounted to the carriage and configured to be moved relatively closer to the primary reaction vessel of the sample cartridge to apply a magnetic field to the fluid sample in the primary reaction vessel and to be moved relatively farther away from the sample cartridge when the magnetic field is not needed.

7. The apparatus of claim 6 , wherein the carriage is configured to permit independent movement of the heater relative to the magnet to heat the fluid sample without application of the magnetic field.

8. 8. The apparatus of claim 7, wherein the heater is mounted to the carriage via a spring-loaded rod that biases the heater away from the carriage to a disengaged position and to a first heater-engaged position and allows the heater to move relatively closer to the carriage and the magnet when the carriage is moved to a magnet-engaged position.

9. 9. An apparatus according to any one of claims 1 to 8, wherein the pneumatic module is configured to connect to a plurality of different pneumatic ports on each sample cartridge and to apply a selected pressure level to each pneumatic port independently at a selected time.

10. The apparatus of any one of claims 1 to 9, further comprising an optical module configured to detect light transmitted from the fluid sample to determine a property of the fluid sample.

11. 1. A chemical processing system comprising: one or more sample cartridges, each sample cartridge comprising: a primary reaction vessel configured to contain a fluid sample for processing, the primary reaction vessel configured to receive a lid for closing an open top of the primary reaction vessel; a reagent vessel configured to receive one or more fluid reagents through an open top of the reagent vessel, the reagent vessel being connected to the primary reaction vessel through a primary reagent channel with a reagent valve disposed in the reagent channel to control fluid flow through the primary reagent channel; and one or more sample cartridges defining a pneumatic port in fluid communication with the primary reaction vessel; A system comprising: a chemical treatment tool according to any one of claims 1 to 10.

12. the sample cartridge further comprising a removable output vessel configured to receive a final output fluid from the primary reaction vessel via a final output channel; the sample cartridge further comprises an output bin pneumatic port in communication with the output bin pneumatic channel and configured to be connected to a pneumatic module to selectively adjust the pressure in the output bin to draw the final output fluid from the primary reaction bin through the final output channel and into the output bin; 12. The system of claim 11 , wherein the pneumatic module is further configured to connect to the output basin pneumatic port and selectively adjust the pressure in the output basin to draw the final output fluid from the primary reaction vessel into the output basin via the final output channel.

13. 13. The system of claim 12, wherein the sample cartridge further comprises a temporary lid configured to close the output bin during processing, the temporary lid being connected to and defining an opening for the final output channel and an output bin pneumatic channel to the output bin.

14. the device is configured to receive a plurality of the sample cartridges; 14. The system of claim 11, wherein the pneumatic module is configured to connect to all of the pneumatic ports of the plurality of sample cartridges and selectively apply pressure to selected ones of the pneumatic ports at selected times.

15. 15. A method of operating a chemical processing system according to any one of claims 11 to 14, comprising one or more sample cartridges, each containing a fluid sample in said primary reaction vessel, comprising: connecting the pneumatic module to the primary pneumatic port of the or each sample cartridge; operating a reagent module to dispense one or more reagents into the reagent vessels of the or each sample cartridge; and operating the pneumatic module to reduce the pressure in the primary reaction vessel of the or each sample cartridge and draw the fluid contents of the corresponding reagent vessel through the or each primary reagent channel and into the primary reaction vessel of the or each sample cartridge.

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