Chemical processing systems, instruments, and sample cartridges

Abstract

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, and a reagent vessel configured to receive one or more fluid reagents via the open top of the reagent vessel. The reagent vessel is 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. The sample cartridge further comprises a primary pneumatic port in fluid communication with the primary reaction vessel, the primary pneumatic port configured to be connected to a pneumatic module to selectively adjust pressure within the primary reaction vessel when the lid is closed to draw fluid contents within the reagent vessel into the primary reaction vessel.

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; U.S. Provisional Patent Application No. 63 / 292,314, filed December 21, 2021; and U.S. Design Patent Application No. 29 / 820,394, 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 (~500ng / 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 around 150bp, 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

[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 in the range of, for example, 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 may be provided without an output bin and may further comprise a final output channel configured to convey a final output fluid from the primary reaction bin to a removable output bin. The cartridge may further comprise an output bin pneumatic port configured to be in fluid communication with the output bin via the output bin pneumatic channel, which 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 through the final output channel and into the output bin. The sample cartridge may further comprise a temporary lid configured to close the output bin during processing, which may be configured to fluidly connect the final output channel and the output bin pneumatic channel to the output bin.

[0015] 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.

[0016] 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.

[0017] 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.

[0018] 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.

[0019] 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 said 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 into 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 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.

[0020] In some embodiments, at the quality control junction, the quality control channel forms an obtuse angle with a portion of the final output channel that extends between the quality control junction and the buffer junction.

[0021] In some embodiments, at the buffer junction, the buffer channel forms an obtuse angle with a portion of the final output channel that extends between the quality control junction and the buffer junction.

[0022] In some embodiments, at the buffer junction, the buffer pre-junction of the final output channel forms an obtuse angle with a portion of the final output channel that extends between the quality control junction and the buffer junction.

[0023] In some embodiments, at the quality control junction, the post-QC junction of the final output channel forms an obtuse angle with the portion of the final output channel that extends between the quality control junction and the buffer junction.

[0024] 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.

[0025] 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.

[0026] 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.

[0027] The pneumatic module may be configured to move liquid between various reservoirs of the cartridge using positive or negative pressure, i.e., applying positive pressure (above atmospheric pressure) to one reservoir to push liquid through a transfer channel into another reservoir, or applying negative pressure (below atmospheric pressure) to one reservoir to draw liquid through a transfer channel into another reservoir.

[0028] 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.

[0029] 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.

[0030] 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.

[0031] 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.

[0032] 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.

[0033] 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.

[0034] 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.

[0035] 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 further 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.

[0036] 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.

[0037] 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.

[0038] 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.

[0039] 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.

[0040] 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.

[0041] 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.

[0042] 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.

[0043] 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.

[0044] The method may further include operating the 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 ebb channel, and through the final output channel and the quality control channel into the quality control reservoir along with an aliquot of treated fluid.

[0045] 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.

[0046] 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.

[0047] 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.

[0048] 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.

[0049] 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.

[0050] 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.

[0051] 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.

[0052] 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 the flow of the sample through the sample channel, a buffer channel extending between the buffer container and the first junction, and a buffer. The present invention relates to a sample cartridge comprising: a buffer channel valve disposed in the buffer channel for controlling a 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.

[0053] 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.

[0054] 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.

[0055] 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.

[0056] 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.

[0057] 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.

[0058] 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.

[0059] 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.

[0060] 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.

[0061] 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.

[0062] 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.

[0063] 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.

[0064] 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.

[0065] 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.

[0066] 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.

[0067] 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 subsequently 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.

[0068] The method may further include operating the pneumatics module to reduce pressure in the output reservoir for a predetermined period of time to draw sample fluid from the sample reservoir through the sample channel and into the metering channel to the second junction without sample fluid traveling into the analysis reservoir channel, and operating the pneumatics module to reduce pressure in the analysis reservoir after the predetermined period of time to draw fluid through the buffer channel, the metering channel, and the analysis channel into the buffer reservoir along with an aliquot of sample fluid from the metering channel. In some embodiments, operating the pneumatics module to draw fluid from the buffer reservoir through the buffer channel continues until the metering channel is filled with air. The method may further include subsequently operating the pneumatics module to reduce pressure in the output reservoir and draw sample fluid from the sample reservoir into the output reservoir.

[0069] 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 subsequently operating the pneumatics module to maintain the buffer valve in an open state to allow fluid to be drawn from the buffer container.

[0070] 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 subsequently 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.

[0071] 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.

[0072] 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 into the analysis reservoir along with an aliquot of sample fluid from the metering channel.

[0073] 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.

[0074] 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.

[0075] 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 in which fluid is drawn from the sample reservoir, and subsequently 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.

[0076] The method may then further include operating the analytical module to measure a property of the fluid in the analytical vessel.

[0077] The method may further include transmitting data related to the measured characteristic to an external computing device.

[0078] 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.

[0079] 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.

[0080] Some embodiments provide 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 valve disposed between the buffer vessel and the junction. the second valve disposed within the first channel; and a pneumatic port communicating with an 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 valve and the second valve including 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.

[0081] Some embodiments relate to a chemical processing instrument configured to accept 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 instrument 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 chemistries, 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 undesired material that does not fall within 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 standard curve.

[0082] Some embodiments relate to a kit including a sample cartridge according to any one of the described embodiments and a temporary lid configured to close the output vessel during processing, the temporary lid configured to fluidly connect the final output channel and the output vessel pneumatic channel to the output vessel. The kit may further include an output vessel, such as, for example, an Eppendorf tube.

[0083] The temporary lid may be configured to be mechanically coupled to the cartridge by a resiliently flexible body. The body may be integrally formed with the temporary lid. The body may be configured to press the output receptacle against the cartridge upon connection. The body may define a channel fluidly connecting the final output channel and the output receptacle pneumatic channel to the output receptacle.

[0084] 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]

[0085] 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.

[0086] [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 5C]FIG. 1 illustrates a perspective view of a core unit of the instrument according to some embodiments. [Figure 5D] FIG. 5D is an enlarged perspective view of the pneumatic interface plate of the core unit of FIG. 5C. [Figure 5E] 1 shows the internal components of the core unit, with other components omitted for clarity. [Figure 5F] 7B is a perspective view of the sample cartridge of FIG. 7A installed in a socket of the core unit of FIG. 5C and a heating assembly engaged with the sample cartridge. [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 sample cartridge according to some embodiments. [Figure 7B] FIG. 7B is a bottom perspective view of the sample cartridge of FIG. 7A. [Figure 7C] FIG. 7B is an exploded view of the sample cartridge of FIG. 7A. [Figure 7D] FIG. 7B is an enlarged exploded view of the base and pneumatic channel plate of the sample cartridge of FIG. 7A. [Figure 7E] FIG. 7B is a bottom perspective view of the base and pneumatic channel plate of the sample cartridge of FIG. 7A. [Figure 7F] FIG. 7B is a bottom cross-sectional view of the top of the base of the sample cartridge of FIG. 7A. [Figure 7G] FIG. 7B is a bottom view of the base of the sample cartridge of FIG. 7A. [Figure 7H] FIG. 7B is a bottom view of the base membrane of the sample cartridge of FIG. 7A. [Figure 7I] FIG. 7B is a bottom view of the PSA layer of the sample cartridge of FIG. 7A. [Figure 7J] FIG. 7B is a bottom cross-sectional view of the upper portion of the pneumatic channel plate of the sample cartridge of FIG. 7A. [Figure 7K] FIG. 7B is a bottom view of the pneumatic channel plate of the sample cartridge of FIG. 7A. [Figure 7L] This is a superposition of Figures 7H and 7J. [Figure 7M] FIG. 7B is a vertical cross-sectional view of the sample cartridge of FIG. 7A. [Figure 7N] FIG. 7B is a cross-sectional view of the bottom of the primary reaction vessel of the sample cartridge of FIG. 7A. [Figure 7O] FIG. 7B is an enlarged perspective cross-sectional view of the top of a primary reaction vessel of the sample cartridge of FIG. 7A. [Figure 7P] FIG. 7B is a cross-sectional view of the lid of the primary reaction vessel of the sample cartridge of FIG. 7A. [Figure 7Q] FIG. 7B is a close-up view of the secondary reaction vessel shown in FIG. 7M. [Figure 7R] FIG. 13 is an alternative top perspective view of the secondary reaction vessel. [Figure 7S] FIG. 7B is an enlarged assembly view of the sample cartridge of FIG. 7A. [Figure 7T] FIG. 7B is a perspective view of the waste trap and primary fluid trap of the sample cartridge of FIG. 7A. [Figure 7U] FIG. 7B is a perspective view of a secondary fluid trap of the sample cartridge of FIG. 7A. [Figure 7V] FIG. 7B is an enlarged assembly view of another portion of the sample cartridge of FIG. 7A. [Figure 7W] FIG. 7B is an enlarged assembly view of the intermediate outlet and gas permeable membrane of the sample cartridge of FIG. 7A. [Figure 7X] FIG. 7B is a perspective cross-sectional view of the assembled intermediate outlet and gas permeable membrane of the sample cartridge of FIG. 7A. [Figure 7Y] FIG. 7B is a bottom view of the weld pattern of the base membrane of the sample cartridge of FIG. 7A. [Figure 7Z] FIG. 7B is a close-up bottom view of the metering channels and microfluidic junctions of the sample cartridge of FIG. 7A. [Figure 8A] 1 is a perspective view of a fluid transfer device according to some embodiments. [Figure 8B] FIG. 8B is a perspective view of the fluid transfer device of FIG. 8A installed in the sample cartridge of FIG. 7A. [Figure 8C] FIG. 13 is an enlarged cross-sectional perspective view of the connection between the fluid transfer device and the sample cartridge. DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

[0087] 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.

[0088] 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.

[0089] 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.

[0090] 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.

[0091] 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.

[0092] 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.

[0093] 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.

[0094] 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.

[0095] 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.

[0096] 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.

[0097] 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.

[0098] 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.

[0099] 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.

[0100] 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.

[0101] 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.

[0102] 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.

[0103] 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.

[0104] 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.

[0105] 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 emission from the dye that is detected by a photodiode.

[0106] 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.

[0107] 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.

[0108] 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.

[0109] 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.

[0110] 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.

[0111] 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.

[0112] 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.

[0113] 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.

[0114] 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.

[0115] 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.

[0116] 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.

[0117] 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.

[0118] Each of the modules, according to some embodiments, is further described below.

[0119] 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.

[0120] 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.

[0121] 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.

[0122] 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.

[0123] 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.

[0124] 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.

[0125] 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.

[0126] 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.

[0127] 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.

[0128] 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.

[0129] 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.

[0130] 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.

[0131] 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.

[0132] In some embodiments, the sample cartridge 200 may further comprise an optional waste container 240, as shown in FIG. 2A and further described below.

[0133] 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.

[0134] 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.

[0135] 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.

[0136] 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.

[0137] 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.

[0138] 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.

[0139] 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.

[0140] 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.

[0141] 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.

[0142] 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.

[0143] 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.

[0144] 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.

[0145] 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.

[0146] 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.

[0147] 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.

[0148] 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.

[0149] 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.

[0150] 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.

[0151] 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.

[0152] 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.

[0153] 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.

[0154] 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 prior to 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 subsequently trigger, for example, an end of the workflow operation and an indication that the process has failed.

[0155] 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.

[0156] 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.

[0157] 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 .

[0158] 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.

[0159] 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.

[0160] 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.

[0161] 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.

[0162] 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.

[0163] 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.

[0164] 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.

[0165] 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.

[0166] 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 .

[0167] 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.

[0168] 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.

[0169] 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 .

[0170] 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.

[0171] 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.

[0172] 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.

[0173] The mixed fluid may then be mixed with pre-loaded dye in a QC container 261 for analysis.

[0174] 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.

[0175] 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.

[0176] 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.

[0177] 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.

[0178] 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.

[0179] 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.

[0180] 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.

[0181] 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.

[0182] 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.

[0183] 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.

[0184] 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.

[0185] 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.

[0186] 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.

[0187] 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.

[0188] 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.

[0189] 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.

[0190] 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.

[0191] 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).

[0192] 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 .

[0193] 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.

[0194] 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).

[0195] 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.

[0196] 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 comprise an active valve and the sample channel valve 227 may comprise a relatively high pressure check valve.

[0197] The analysis reservoir 261 may be pre-loaded with buffers and dyes configured to mix with the fluid sample to facilitate analysis.

[0198] 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.

[0199] Referring to FIG. 2O (adjacent FIG. 2F), an enlarged top perspective view of outlet 280 is shown, according to some embodiments.

[0200] 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.

[0201] 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.

[0202] 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.

[0203] 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.

[0204] 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.

[0205] 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.

[0206] 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.

[0207] 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.

[0208] 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.

[0209] 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 .

[0210] 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.

[0211] 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.

[0212] 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.

[0213] 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.

[0214] 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.

[0215] 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.

[0216] 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.

[0217] 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.

[0218] 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.

[0219] 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.

[0220] 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.

[0221] Pump 360 may include independent motors 362 and drive shafts 363 to independently control the dispensing of reagents from different reagent cartridges 320 .

[0222] 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.

[0223] 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.

[0224] 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.

[0225] 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.

[0226] 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.

[0227] 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.

[0228] 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.

[0229] 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.

[0230] 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.

[0231] 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.

[0232] 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.

[0233] 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.

[0234] 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.

[0235] 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.

[0236] 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.

[0237] 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.

[0238] 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.

[0239] 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.

[0240] 5A and 5B, in some embodiments, a portion of the pneumatic module 500, thermal module 600, magnetic module 700, mixing module 800, and kinematic module 900 are shown housed within a chassis or housing 110 to form a core unit 1100 that cooperates to define a cartridge slot or socket 120.

[0241] 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.

[0242] 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.

[0243] 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.

[0244] In some embodiments, the instrument 100 may not include a vertical movement platform 950 .

[0245] 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.

[0246] 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.

[0247] 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.

[0248] 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.

[0249] 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.

[0250] 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.

[0251] 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.

[0252] 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.

[0253] 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.

[0254] 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.

[0255] 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.

[0256] 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.

[0257] 5C-5F, further details of the core unit 1100 are shown in accordance with some embodiments, which may be configured to receive the sample cartridge 200 (or the sample cartridge 1000 shown in FIG. 7A), as described further below.

[0258] The core unit 1100 may at least partially define cartridge slots or sockets 120 each configured to receive a cartridge 1000. Each cartridge socket 120 may have an associated pneumatic interface plate 1500 (FIG. 5D) configured to engage and mate the cartridge 1000 to the pneumatic module 500 via pneumatic lines 515.

[0259] The pneumatic plate 1500 may define pneumatic plate ports 1501, 1502, 1503, 1504, 1505, 1506, 1507, 1508, 1509, 1510 in fluid communication with the pneumatic line 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 1000 (FIG. 7B). The pneumatic plate ports may be arranged differently or in different numbers to suit other different sample cartridges. The arrangement and connections between the corresponding pneumatic plate ports and the cartridge pneumatic ports on the underside of the sample cartridge 1000 can be understood by comparing FIGS. 5D and 7B. The cartridge port 1201 is configured to connect to the pneumatic plate port 1501 . The cartridge port 1202 is configured to connect to the pneumatic plate port 1502 . The cartridge port 1203 is configured to connect to the pneumatic plate port 1503 . The cartridge port 1204 is configured to connect to the pneumatic plate port 1504 . The cartridge port 1205 is configured to connect to the pneumatic plate port 1505 . The cartridge port 1206 is configured to connect to the pneumatic plate port 1506 . The cartridge port 1207 is configured to connect to the pneumatic plate port 1507 . The cartridge port 1208 is configured to connect to the pneumatic plate port 1508 . The cartridge port 1209 is configured to connect to the pneumatic plate port 1509 . The cartridge port 1210 is configured to connect to the pneumatic plate port 1510 .

[0260] The pneumatic module 500 may be configured to independently and selectively adjust the pressure in each pneumatic line 515 to drive liquid flow in channels of the cartridge 1000 and / or operate valves in the cartridge 1000.

[0261] In some embodiments, the sample cartridge may be configured for a positive operating pressure (above ambient pressure) in some or all of the pneumatic lines 515. In an exemplary embodiment, the sample cartridge 1000 is configured for a negative operating pressure (below ambient pressure) in all of the pneumatic lines 515.

[0262] In some embodiments, the sample cartridge may be configured for an operating pressure at a single pressure level. In an exemplary embodiment, the sample cartridge 1000 is configured for two operating pressure levels. The first operating pressure may be, for example, a relatively high magnitude negative pressure in the range of 180 mBar to 500 mBar, 190 mBar to 350 mBar, or about 200 mBar. The second operating pressure may be, for example, 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. The cartridge pneumatic ports 1201, 1202, 1203, 1204, 1205 may be configured for a relatively high first operating pressure. The cartridge pneumatic ports 1206, 1207, 1208, 1209, 1210 can be configured for a second, relatively low operating pressure.

[0263] The socket 120 may include parallel rails 1120 defining grooves configured to slidably receive edges 1220 of the cartridge base 202 upon insertion into the socket 120. The rails 1120 may include recesses 1122 configured to receive resilient clips 1222 integrally formed with the cartridge base 202 (FIG. 7F).

[0264] The pneumatic interface plate 1500 may be positioned below the socket 120 and biased into an engaged position by a spring. 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 that forms part of the kinematic module 900. The core carriage 1190 can be seen in FIG. 5E, where some of the components of the core unit 1100 have been omitted to better visualize the internal components.

[0265] The pneumatic plate 1500 may be connected to a retraction rod 1520 that passes through the core cartridge 1190 such that the core cartridge 1190 can slide up and down the retraction rod 1520, the lower end of which includes a stop 1522 positioned below the core cartridge 1190. When the core carriage 1190 is lowered past engagement with the stop 1522, the retraction rod 1520 and pneumatic interface plate 1500 are lowered with the core carriage 1190.

[0266] Retraction of the interface plate 1500 allows insertion of the cartridge 1000 into the socket 120. The motion module 900 can be operated to raise the core carriage 1190 causing the springs to raise the interface plate 1500 and press it against the base 202 of the cartridge 1000, clamping it between the interface plate 1500 and the rail 1120.

[0267] The pneumatic interface plate 1500 may include a gasket or sealing portion 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 1000 to provide a seal around the connection between the corresponding pneumatic ports 1501, 1201. The gasket 1530 may be formed of any suitable elastomeric material, such as, for example, rubber, silicone, or other polymers. The gasket 1530 may define a frustoconical shape, for example, or any other suitable shape for providing a seal between the opposing flat surfaces of the pneumatic interface plate 1500 and the bottom of the cartridge 1000.

[0268] The thermal module 600 may comprise a heater 610 including a radiator 662 at one end and a cooling fan 663 at the opposite end (FIG. 5F), which may be mounted to the core carriage 1190 or a separate motion stage.

[0269] The radiator 662 and magnet 710 may define slits, as shown in Figures 5D and 5E, allowing them to extend through holes 1230 in the base of the cartridge 1000, as shown in Figures 7B and 5F, allowing for greater proximity between the radiator 662, magnet 710, and reaction vessels 210, 220.

[0270] 7A-7Z, a sample cartridge 1000 is shown in further detail, according to some embodiments. Sample cartridge 1000 includes similar features as those described with respect to sample cartridge 200, and similar features are designated with similar reference numbers.

[0271] Referring to FIG. 7C, the sample cartridge 1000 is shown in an exploded perspective view showing the various components that combine to form the sample cartridge 1000.

[0272] The sample cartridge 1000 comprises a body 1001 that defines a base 202, a primary reaction vessel 210, a secondary reaction vessel 220, a reagent vessel 230, and a waste vessel 240. The body 1001 also defines other features that are described in more detail below.

[0273] The body 1001 may be formed by any suitable means of any material suitable for a particular application. Some applications may require a non-reactive material suitable for the samples and reagents being processed. The body 1001 may be injection molded and formed from a non-reactive polymeric material such as polycarbonate or polypropylene, for example.

[0274] The body 1001 defines a plurality of channels, as described with respect to the sample cartridge 200 and further described below with respect to the cartridge 1000. Some of the channels defined in the body 1001 are partially open to facilitate manufacture by injection molding. A portion of the vessel defined by the body 1001 may be formed with an opening to facilitate manufacture. The cartridge 1000 may include a plurality of membranes connected to the body 1001 to cover and seal a portion of the vessel opening, cover the open channels, and cooperate to define the channels.

[0275] The membrane may be formed of any suitable material, such as, for example, polypropylene, and may have a thickness, for example, in the range 20 μm to 200 μm, 50 μm to 150 μm, or about 100 μm.

[0276] The membrane may be secured to the body 1001 by, for example, adhesive bonding and / or welding, such as heat welding or laser welding.

[0277] The cartridge 1000 is a base membrane 1402 covering the channels defined in the base 202; a waste top membrane 1440 for covering and sealing the top of the waste container 240; a waste side membrane 1442 covering a portion of the waste air pressure channel 242; a primary pneumatic side membrane 1412 covering a portion of the primary pneumatic channel 212; a primary reagent side membrane 1431 covering a portion of the primary reagent channel 231; a secondary upper membrane 1420 for covering and sealing the upper portion of the secondary reagent container 220; a secondary membrane 1422 covering a portion of the secondary air pressure channel 222 and the secondary reagent channel 232; an intermediate outlet membrane 1480 for covering and sealing the top of the intermediate outlet chamber 284T; a QC top membrane 1461 for covering and sealing the top of the QC container 261 and the QC reference container 271; and a QC side membrane 1462 covering a portion of the QC air pressure channel 262 and the QC reference air pressure channel 272.

[0278] The cartridge 1000 may further comprise a pneumatic channel plate 1602 defining cartridge pneumatic ports 1201, 1202, 1203, 1204, 1205, 1206, 1207, 1208, 1209, 1210, and a plurality of pneumatic channels connecting the pneumatic ports to corresponding pneumatic ports and pneumatic channels in the base 202 to drive fluid flow through fluid channels in the base and operate the cartridge valves. The pneumatic channel plate 1602 may also define valve recesses that cooperate with valve ports defined in the base 202 and the base membrane 1402 to define valves, as further described below in connection with Figures 7J and 7N.

[0279] The pneumatic channel plate 1602 may be bonded to the base 202 with the base membrane 1402 sandwiched therebetween. The pneumatic channel plate 1602 may be adhesively bonded to the base membrane 1402 and / or the base 202 by adhesive bonding, such as a pressure sensitive adhesive (PSA), e.g., 3M 300LSE adhesive. The adhesive may be formulated as a PSA layer 1606, which defines openings corresponding to certain portions of the base 202 that do not require bonding, such as valves and pneumatic ports.

[0280] The cartridge 1000 may further comprise a gas permeable membrane configured to allow the passage of air but resist or prevent the passage of liquid. As discussed with respect to the sample cartridge 200, a gas permeable membrane may be used to limit liquid that may inadvertently enter the pneumatic channels in the cartridge 100 from escaping the cartridge 1000 during processing and potentially contaminating the instrument 100.

[0281] The gas permeable membrane may be formed of any suitable material for a given application, taking into account the sample and reagents involved, such as a hydrophobic gas permeable membrane, e.g., PTFE or PP. The gas permeable membrane may have a thickness in the range of, for example, 20 μm to 200 μm, 50 μm to 150 μm, or about 110 μm.

[0282] The cartridge 1000 is a primary permeable membrane 1415 associated with the primary air pressure channel 212 (and optionally also with the QCQC air pressure channel 262 and the QC reference air pressure channel 272); a secondary permeable membrane 1425 associated with the secondary air pressure channel 222; a waste permeable membrane 1445 associated with the waste pneumatic channel 242; and an intermediate outlet permeable membrane 281 associated with the intermediate outlet 280.

[0283] 7D and 7E show the top and bottom surfaces of base 202, base membrane 1402, PSA layer 1606, and pneumatic channel plate 1602, illustrating how the components are aligned to connect together during stacking of the layers.

[0284] The base 202 defines a plurality of channels recessed into the bottom surface of the base 202 which is covered with a base membrane 1402 to define the channels. The base membrane 1402 and PSA layer 1606 define a simple sheet with through-thickness holes corresponding to the various ports, valves and holes in the base 202 and the pneumatic channel plate 1602. The pneumatic channel plate 1602 defines a plurality of pneumatic channels, valve recesses in the top surface of the pneumatic channel plate 1602, and cartridge pneumatic ports 1201, 1202, 1203, 1204, 1205, 1206, 1207, 1208, 1209, 1210 are defined in the bottom surface of the pneumatic channel plate 1602.

[0285] Figures 7F-7K show cross sections through each layer as viewed from underneath cartridge 1000 to show the pathways and connections of the reservoirs, channels, valves, and ports to facilitate comparison between layers. Figure 7L shows the channels and valves of base 202 (Figure 7G) superimposed on the channels, valve recesses, and pneumatic ports of pneumatic channel plate 1602 (Figure 7J) for direct comparison and to see the alignment of corresponding features.

[0286] 7F shows the top layer of the base 202 immediately above the base channel. Shown are the edges 1220 and resilient clips 1222 of the base 202 that are configured to engage with the rails 1120 and clip recesses 1122 of the cartridge socket 120.

[0287] The base may also define a recess 1230 surrounding the reagent container 230 that has a reduced thickness to reduce warping due to material shrinkage after injection molding. For example, the base 202 may have a thickness of about 2.5 mm elsewhere and taper to about 1.5 mm at the recess 1230.

[0288] Figure 7G shows channels formed on the bottom surface of base 202. With reference to Figures 7F and 7G, these channels are described corresponding to the flow schematic of Figure 2G for illustrative purposes only. The channels and valves may be arranged differently in other embodiments, which may include different channels and valves associated with different combinations of containers.

[0289] A primary waste channel 214 extends between an outlet at the bottom of primary reaction vessel 210 and an inlet at the bottom of waste vessel 240 through a primary waste valve 215, shown as a gap between the two valve ports in FIG. 7G.

[0290] A secondary waste channel 224 extends between an outlet at the bottom of the secondary reaction vessel 220 and an inlet at the bottom of the waste vessel 240 through a secondary waste valve 225, shown as a gap between the two valve ports in FIG. 7G.

[0291] A primary reagent channel 231 extends between an outlet at the bottom of the reagent vessel 230 and an inlet of the primary reaction vessel 210 (FIG. 7M) through a primary reagent valve 235, shown as a gap between two valve ports in FIG. 7G.

[0292] As discussed above, the inlet of the primary reagent channel 231 may open into the primary reaction vessel 210 near the top of the primary reaction vessel 210, as shown in FIG. 7M, and in more detail in FIG.

[0293] In some embodiments, the primary reaction vessel 210 may define an inlet recess 1231 to reduce splashing of liquid reagents entering the primary reaction vessel 210. The primary reagent channel 231 may open into a first sidewall 1231a of the inlet recess 1231 opposite a second sidewall 1231b opposite the inlet recess 1231. The inlet recess 1231 may be defined in part by a convex surface 1231c between the first and second sidewalls 1231a, 1231b. Liquid reagents entering the inlet recess 1231 at a relatively high velocity may impact the second sidewall 1231b and then flow down the convex surface 1231c and down the sidewall of the primary reaction vessel 210. The convex surface 1231c may provide a smooth transition between the inlet recess 1231 and the sidewall of the primary reaction vessel 210. These features may reduce or mitigate splashing of reagents within the primary reaction vessel 210 that might otherwise result in residual fluid remaining on the side walls or potentially being sucked into the pneumatic channels 212.

[0294] The primary reaction vessel 210 may define a similar recess at the opening of the primary air pressure channel 212 to reduce the likelihood of liquid being drawn into the primary air pressure channel 212.

[0295] A secondary reagent channel 232 extends between an outlet at the bottom of the reagent vessel 230 and an inlet of the secondary reaction vessel 220 (FIG. 7M) through a secondary reagent valve 236, shown as a gap between the two valve ports in FIG. 7G.

[0296] As discussed above, the inlet of the secondary reagent channel 232 may open into the secondary reaction vessel 220 near the top of the secondary reaction vessel 220, as shown in Figure 7M, and in more detail in Figure 7Q.

[0297] In some embodiments, the secondary reaction vessel 230 may define an inlet recess similar to the inlet recess 1231 of the primary reaction vessel 210. In some embodiments, the secondary reagent channel 232 may open directly into the secondary reaction vessel 220. In some embodiments, the secondary reaction vessel 220 may define a recess 1232c leading from the secondary reagent channel 232 to the secondary reaction vessel 220. The recess 1232c may provide a smooth transition between the secondary reagent channel 232 and a sidewall of the secondary reaction vessel 220.

[0298] 7O and 7P, the lid 211 of the primary reaction vessel 210 may be integrally formed with the body 1001 and connected to the primary reaction vessel 210 via a flexible hinge portion 211a. The lid 211 may include a resiliently deformable annular flange 1211 configured to engage the top rim of the primary reaction vessel 210 in a press-fit, snap-fit, or interference fit connection, for example, to seal the primary reaction vessel 210.

[0299] It will be understood that references herein to sealed containers, chambers, or channels are intended to mean sealed other than at defined inlets and outlets to the various ports and channels. In some cases, a fluid-tight or gas-tight seal may be formed. However, depending on the application, a perfect seal may not be required and there may be some degree of fluid leakage.

[0300] The secondary reagent channels 232 and the secondary air pressure channels 222 may be partially defined in a top surface 1223 surrounding the upper portion of the secondary reaction vessel 230 and may open relatively closely into the secondary reaction vessel 230, as shown in FIG. 7Q.

[0301] In some embodiments, the opening of the secondary reagent channel 232 into the secondary reaction vessel 230 may be relatively far from the opening of the secondary pneumatic channel 222 into the secondary reaction vessel 230. For example, the openings may be separated by a distance in the range of 2 mm to 20 mm, 3 mm to 10 mm, 5 mm to 8 mm, or at least 2 mm, at least 3 mm, at least 5 mm, or at least 10 mm.

[0302] The secondary reagent channel 232 may extend partially around the circumference of the secondary reaction vessel 230 in the top surface 1223 to achieve separation between the openings, for example as shown in FIG. 7R. Alternatively or additionally, the primary air pressure channel 222 may extend partially around the circumference of the secondary reaction vessel 230 in the top surface 1223.

[0303] This configuration may mitigate or reduce the likelihood that reagent entering the secondary reaction vessel 220 from the secondary reagent channel 232 will be inadvertently drawn into the secondary air pressure channel 222 .

[0304] Primary output channel 216 extends from an outlet at the bottom of primary reaction vessel 210 and joins secondary reagent channel 232 through primary output valve 217, shown as a gap between two valve ports in FIG. 7G.

[0305] A secondary output channel 226 extends from an outlet at the bottom of secondary reaction vessel 220 to buffer junction 228 through a secondary output valve 227, shown as the gap between the two valve ports in FIG. 7G.

[0306] From the buffer junction 228, the volumetric metering and QC module 260 may include channels and valves similar to those described in connection with the close-up of FIG. 2F, although these may be arranged differently, as shown in FIG. 7G.

[0307] In particular, base 202 defines reference buffer channels 1275 extending from the bottom outlets of each of QC reference buffer containers 275 to the corresponding QC reference containers 271 via reference buffer valves 1277. This allows QC air pressure channel 262 and QC reference air pressure channel 272 to be connected to a single air pressure line 515 while allowing QC reference air pressure channel 272 to be blocked by closing reference buffer valve 1277.

[0308] The final output channel 256 terminates in a fluid connection port 1256 adjacent the output vessel pneumatic port 253 and a mechanical clip 1280 configured to connect to the fluid transfer device 880 shown in Figures 8A-8C, thus providing fluid communication between the final output channel 256, the output vessel pneumatic port 253 and the output vessel 250.

[0309] A portion of the waste pneumatic channel 242 is shown extending up the side of the waste container 240, as shown in Figure 7S, and extending down to connect to the waste trap 1640, as shown in Figure 7J. The waste trap 1640 comprises a chamber defined by the base membrane 1402 and a recess 1642 in the pneumatic channel plate 1602.

[0310] The recess 1642 defines an annular projection 1643 set at a height above a lower surface 1644 of the recess 1642. The waste pneumatic channel 242 extends through a portion of the pneumatic channel plate 1602 to be in fluid communication with the recess 1642 connecting through a sidewall of the recess 1642 above the height of the projection 1643, as shown in Figures 7J and 7T. The lower surface 1644 defines an aperture which forms the cartridge pneumatic port 1205.

[0311] The waste permeable membrane 1445 is secured (e.g., by adhesive or heat welding) to the protrusion 1643 to separate the cartridge pneumatic port 1205 from the waste pneumatic channel 242, thereby allowing any fluid inadvertently aspirated into the waste pneumatic channel 242 to be captured in the drain trap 1640 and restricted from passing through the waste permeable membrane 1445 to the cartridge pneumatic port 1205.

[0312] The waste trap 1640 may further include a spacer protrusion 1645 extending from the lower surface 1644 to the height of the protrusion 1643 for supporting the waste permeable membrane 1445 .

[0313] Portions of the primary and secondary pneumatic channels 212, 222 are shown extending upwardly down the sides of the primary and secondary reaction vessels 210, 220 in Figure 7F and downwardly towards the pneumatic channel plate 1602 in Figure 7G. The QC pneumatic channel 262 and the QC reference pneumatic channel 272 are shown extending upwardly down the sides of the QC vessel 261 and the QC reference vessel 271 in Figure 7F and downwardly towards the pneumatic channel plate 1602 via the channels shown in Figure 7G.

[0314] The primary and secondary pneumatic channels 212, 222 connect to primary and secondary fluid traps 1611, 1620, respectively, as well as the waste trap 1640. The QC pneumatic channel 262 and the QC reference pneumatic channel 272 also connect to the primary fluid trap 1611, as shown in Figure 7J.

[0315] The primary fluid trap 1611 comprises a chamber defined by the base membrane 1402 and a recess 1612 in the pneumatic channel plate 1602 .

[0316] The recess 1612 defines an annular projection 1613 set at a height above a lower surface 1614 of the recess 1612. The primary pneumatic channel 210 extends through a portion of the pneumatic channel plate 1602 to be in fluid communication with the recess 1612 connecting through a sidewall of the recess 1612 above the height of the projection 1613, as shown in Figures 7J and 7T. The lower surface 1614 defines an aperture which forms the cartridge pneumatic port 1206.

[0317] The primary permeable membrane 1415 is secured (e.g., by adhesive or heat welding) to the protrusion 1613 to isolate the cartridge pneumatic port 1206 from the primary pneumatic channel 210 such that any fluid inadvertently aspirated into the primary pneumatic channel 210 is captured in the primary fluid trap 1611 and restricted from passing through the primary permeable membrane 1415 to the cartridge pneumatic port 1206.

[0318] Similarly, QC pneumatic channel 262 and QC reference pneumatic channel 272 both connect to a common QC pneumatic channel 1660 in pneumatic channel plate 1602 which connects through the sidewall of recess 1612 above the level of protrusion 1613, as shown in Figures 7J and 7T. Any fluid inadvertently aspirated into QC pneumatic channel 262 or QC reference pneumatic channel 272 will be trapped in primary fluid trap 1611 and restricted from passing through primary permeable membrane 1415 to cartridge pneumatic port 1206.

[0319] The primary fluid trap 1611 may further comprise a spacer protrusion 1615 extending from the lower surface 1614 to the height of the protrusion 1613 for supporting the primary permeable membrane 1415 .

[0320] Similar to the waste and primary fluid traps 1640 , 1611 , the secondary fluid trap 1620 comprises a chamber defined by the base membrane 1402 and a recess 1622 in the pneumatic channel plate 1602 .

[0321] The recess 1622 defines an annular projection 1623 set at a height above a lower surface 1624 of the recess 1622. The secondary pneumatic channel 220 extends through a portion of the pneumatic channel plate 1602 to be in fluid communication with the recess 1622 connecting through a sidewall of the recess 1622 above the height of the projection 1623, as shown in Figures 7J and 7U. The lower surface 1624 defines an aperture which forms the cartridge pneumatic port 1208.

[0322] The secondary permeable membrane 1425 is secured (e.g., by adhesive or heat welding) to the protrusion 1623 to separate the cartridge pneumatic port 1208 from the secondary pneumatic channel 220 such that any fluid inadvertently drawn into the secondary pneumatic channel 220 is trapped in the secondary fluid trap 1620 and restricted from passing through the secondary permeable membrane 1425 to the cartridge pneumatic port 1208.

[0323] The secondary fluid trap 1620 may further comprise a spacer protrusion 1625 spaced from the lower surface 1624 and extending to the height of the protrusion 1623 for supporting the secondary permeable membrane 1425 .

[0324] The shape, depth, diameter, and volume of the fluid traps 1611, 1620, 1640 (as well as the exposed area of ​​the gas permeable membranes 1415, 1425, 1445) can be tailored for different applications depending on the amount of liquid that may be inadvertently drawn into the pneumatic channel. The volume of the fluid trap above the membrane may range, for example, from 10 μL to 1 mL, 50 μL to 500 μL, or about 100 μL, and the surface area of ​​the membrane may be, for example, 50 mm 2 ~500mm 2 , 100mm 2 ~300mm 2 or about 200 mm 2 may be also possible.

[0325] Alternatively, in some embodiments, other types of fluid traps may be employed, such as microfluidic or gravity type fluid traps, hi some embodiments, the fluid trap may be omitted entirely.

[0326] 7S, a portion of the waste pneumatic channel 242 may be defined in an exterior side of the waste container 240 and may be sealed by a waste side membrane 1442. The top of the waste container 240 may be sealed by a waste top membrane 1440.

[0327] As shown in Figure 7S, a portion of each of the primary pneumatic channel 212, the primary reagent channel 231, the secondary pneumatic channel 222, and the secondary reagent channel 232 may be defined in an outer side of the support web 203 (extending between the waste receptacle 240, the primary reaction vessel 210, the reagent vessel 230, and the secondary reaction vessel 220) and may be sealed by a corresponding side membrane 1412, 1431, 1422. Other portions of the channels 212, 231, 222, 232 may be completely defined by the body 1001, e.g., near the base 202 and / or near the tops of the reaction vessels 210, 220, as shown in Figures 7M and 7Q.

[0328] A portion of the secondary air pressure channels 222 and the secondary reagent channels 232 may be defined in the upper surface 1223 and may be sealed by a secondary upper membrane 1420, as shown in Figures 7Q and 7R.

[0329] The sealing membrane may comprise a breakaway portion 1401 for ease of assembly, which may be removed once the corresponding sealing membrane is secured to the body 1001 .

[0330] 7V, portions of the QC pneumatic channel 262 and the QC reference pneumatic channel 272 may be defined on the outer sides of the QC container 261 and the QC reference container 271 and sealed by a QC side membrane 1462. A QC top membrane 1461 may be provided to cover and seal the tops of the QC container 261 and the QC reference container 271.

[0331] An intermediate outlet membrane 1480 may be secured to the upper surface of the base 202 to cover and seal the top of the intermediate outlet chamber 284. This is shown in more detail in Figures 7W and 7X.

[0332] Intermediate outlet chamber 284 may be defined by a recess in the top surface of base 202. The bottom surface of outlet chamber 284 may define intermediate outlet 280 and an opening to intermediate outlet pneumatic channel 282. Intermediate outlet permeable membrane 281 may be secured (adhesive or heat welded) to the bottom surface of intermediate outlet chamber 284 such that it covers intermediate outlet 280, but not intermediate outlet pneumatic channel 282. The top opening of intermediate outlet chamber 284 may be sealed by intermediate outlet membrane 1480.

[0333] When the pneumatic module 500 is operated to reduce the pressure in the intermediate outlet pneumatic channel 282, air may be drawn from the metering channel 299 (and / or outlet channel 285) through the permeable membrane 281, which may cause liquid in the metering channel to be drawn up to the membrane 281 without passing toward the chamber 284.

[0334] 7J, the pneumatic channel plate 1602 also defines a number of pneumatic channels connecting other pneumatic ports to the valve recesses to enable operation of the cartridge valves, which include switch valves configured as shown in FIG.

[0335] For example, a vertical cross section of primary waste valve 215 is shown in Figure 7N. Primary waste channel 214 may be defined in base 202 that extends from an outlet at the bottom of primary reaction vessel 210 toward waste vessel 240. Breaks may occur in valve 215 that separate primary waste channel 214 into two sections that terminate at first and second valve ports 214a and 214b.

[0336] Valve ports 214a, 214b may be closed in the static configuration by base membrane 1402 (which also closes all corresponding valve ports of other cartridge valves in the static configuration). On the other side of base membrane 1402, opposite valve ports 214a, 214b, there is provided a primary waste valve recess 1615 defined by pneumatic channel plate 1602 and extending between (opposite side of base membrane 1402) valve ports 214a, 214b.

[0337] The primary waste valve recess 1615 may be connected to the cartridge pneumatic port 1204 such that the pneumatic module 500 can be operated to reduce pressure in the primary waste valve recess 1615, causing the base membrane 1402 to bend toward the primary waste valve recess 1615, opening the primary waste valve 215 and allowing fluid communication between the first and second valve ports 214a, 214b. In some embodiments, positive pressure can be applied to the valve recess 1615 (and others) to ensure that the valve remains closed, for example, during operations that might pressure the valve open.

[0338] Similarly, other cartridge valves may include valve ports and corresponding valve recesses connected to cartridge pneumatic ports by pneumatic channels to enable actuation of the valves by pneumatic module 500 .

[0339] Pneumatic channel plate 1602 defines a primary waste valve recess 1615 which corresponds to primary waste valve 215 and is connected to cartridge pneumatic port 1204 via pneumatic channel 1604 .

[0340] Pneumatic channel plate 1602 defines a secondary reagent valve recess 1636 which corresponds to secondary reagent valve 236 and is connected to cartridge pneumatic port 1204 via pneumatic channel 1604 .

[0341] Pneumatic channel plate 1602 defines a primary output valve recess 1617 which corresponds to primary output valve 217 and is connected to cartridge pneumatic port 1207 via pneumatic channel 1607 .

[0342] Pneumatic channel plate 1602 defines a primary reagent valve recess 1635 which corresponds to primary reagent valve 235 and is connected to cartridge pneumatic port 1203 via pneumatic channel 1603 .

[0343] Pneumatic channel plate 1602 defines a secondary waste valve recess 1625 which accommodates secondary waste valve 225 and is connected to cartridge pneumatic port 1203 via pneumatic channel 1603 .

[0344] Pneumatic channel plate 1602 defines a secondary outlet valve recess 1627 which corresponds to secondary outlet valve 227 and is connected to cartridge pneumatic port 1209 via pneumatic channel 1609 .

[0345] Pneumatic channel plate 1602 defines a final output valve recess 1657 which corresponds to the final output valve 257 and is connected to the cartridge pneumatic port 1209 via a pneumatic channel 1609 .

[0346] Pneumatic channel plate 1602 defines three reference buffer valve recesses 1677 which correspond to the three reference buffer valves 1277 and are connected to cartridge pneumatic ports 1209 via pneumatic channels 1609 .

[0347] Pneumatic channel plate 1602 defines a QC receptacle valve recess 1664 which corresponds to QC receptacle valve 264 and is connected to cartridge pneumatic port 1210 via pneumatic channel 1610 .

[0348] The pneumatic channel plate 1602 defines a QC buffer valve recess 1667 which corresponds to the QC buffer valve 267 and is connected to the cartridge pneumatic port 1210 via a pneumatic channel 1610 .

[0349] The valve recess may have any suitable size, shape, and proportions for a particular application. For example, the valve recess may be generally rectangular with rounded corners as shown in the drawings. The valve recesses in the illustrated embodiment are all similar in dimensions, for example having a length of about 6 mm, a width of about 2 mm, and a depth of about 0.5 mm.

[0350] The pneumatic channels defined in the pneumatic channel plate 1602 are approximately 0.5 mm deep and approximately 1 mm wide.

[0351] Similarly, a fluid channel may have a depth of about 0.5 mm and a width of about 1 mm, however, some of the fluid channels may have smaller dimensions, such as for a volumetric metering section, where a smaller channel cross-section allows for more precise control of the volumetric flow rate and volume of liquid within the channel.

[0352] For example, channels 226, 256, 266, 269, 299, 285 may have widths of less than 0.5 mm, less than 0.3 mm, or about 0.25 mm, and depths of less than 1 mm, less than 0.5 mm, less than 0.3 mm, or about 0.2 mm. These channels may widen to form valve ports for each valve, for example, to a width of about 1 mm, as shown in FIG. 7X.

[0353] In some embodiments, all of the valve ports may radiate from the corresponding channels, as shown in FIG. 7Y, which illustrates a weld pattern for welding the base membrane 1402 to the base 202 (e.g., by heat or laser welding). Some suitable dimensions are provided in the enlarged view of FIG. 7Y for different valves in the cartridge 1000 for illustrative purposes only. The corresponding valve recesses in the pneumatic channel plate 1602 may, for example, substantially conform to the shape and dimensions shown in FIG. 7Y.

[0354] The weld pattern may include an inner weld line 1403 that runs along the edge of the channel and connects the valve ports to form the valve. In some embodiments, the weld pattern may also include an outer weld line 1404 that provides a second barrier around the channel for redundancy.

[0355] 7Z, metering channel 299, according to some embodiments, is shown in further detail with a close-up view of buffer junction 228 and quality control junction 229. The shape of the channel and junctions may include any suitable shape for a given application. For example, in FIG. 2F, junctions 228, 229 are shown as vertical T-junctions. Alternatively, junctions 228, 229 may comprise, for example, angled Y-junctions, or curved Y-junctions as shown in FIG. 7Z, or any other suitable geometric shape.

[0356] At the quality control junction 229 , the quality control channel 269 may form an obtuse angle α with the metering channel 299 .

[0357] At the buffer junction 228 , the buffer channel 266 may form an obtuse angle β with the metering channel 299 .

[0358] Similarly, at the quality control junction 229 , the output channel 285 may form an obtuse angle γ with the metering channel 299 .

[0359] At the buffer junction 228 , the secondary output channel 226 (or alternatively, the primary output channel 216 ) may form an obtuse angle δ with the metering channel 299 .

[0360] Each of the joint angles α, β, γ, and δ can be, for example, in the range of 90° to 180°, 100° to 170°, 110° to 160°, 120° to 150°, 130° to 140°, approximately 135°, or approximately 137°.

[0361] The metering channel 299 may widen at each junction 228 , 229 and may define curved edges that transition into the connecting channels 226 , 266 , 269 , 285 .

[0362] At the quality control junction 229, the quality control channel 269 and the output channel 285 may form an acute angle ε and an inflection point 229a.

[0363] At the buffer junction 228, the buffer channel 266 and the secondary output channel 226 (or alternatively, the primary output channel 216) may form an acute angle ζ and an inflection point 228a.

[0364] Each of the acute angles ε and ζ can be, for example, in the range of 10° to 90°, 30° to 60°, about 45°, or about 40°.

[0365] The radius of curvature of inflection points 228a and 229a can be, for example, in the range of 0.1 mm to 0.5 mm, less than 0.5 mm, less than 0.4 mm, less than 0.3 mm, less than 0.2 mm, or about 0.2 mm.

[0366] 7H, the base membrane 1402 defines through openings allowing fluid communication through the base membrane 1402 between corresponding portions of the ports, the channels 242, 212, 222, 253, 283, 262, 272 in the base 202, and the pneumatic channel plate 1602. The base membrane 1402 also includes openings 1230 to allow passage of radiators and magnets.

[0367] In the QC and metering portion of the cartridge 1000, the intermediate outlet 280 is connected to the cartridge pneumatic port 1202 via an intermediate outlet pneumatic channel 282 defined in the pneumatic channel plate 1602, as shown in Figures 7J and 7X.

[0368] The output bin pneumatic port 253 is connected to the cartridge pneumatic port 1201 via an output bin pneumatic channel 252 which may be defined in a pneumatic channel plate 1602 as shown in FIG. 7J.

[0369] The pneumatic channel plate 1602 defines a QC hole 1261 aligned with the QC well 261, and three QC reference holes 1271 aligned with the QC reference wells 271. A polypropylene membrane 1402 forms the bottom of each of the QC wells 261 and the reference wells 271, and may provide a transparent observation window that allows optical access for an optical module to analyze the contents of the QC wells 261 and the reference wells 271 through the QC holes 1261 and the QC reference holes 1271.

[0370] In some embodiments, the pneumatic channel plate 1602 (or alternatively, another portion of the cartridge 1000) may define a switch recess 1690 configured to engage with a switch or microswitch on the instrument 100 to indicate that the cartridge 1000 is properly installed in the socket 120.

[0371] 7I shows PSA layer 1606 in more detail, showing holes corresponding to areas that do not require adhesive bonding, which essentially correspond to all of the holes in base membrane 1402 and recesses in the top surface of pneumatic channel plate 1602, including valve recesses, fluid traps, QC holes 1261, and QC reference holes 1271. PSA layer 1606 does not necessarily need to define holes for the pneumatic channels in the pneumatic channel plate, since adhesive may not affect the function of the channels.

[0372] 8A and 8B, there is shown in more detail a fluid transfer device 880. The device 880 comprises a temporary and removable lid 259 that is used to seal the output container 250 closed during the workflow of the instrument, as described in relation to Figures 2F and 2G.

[0373] The apparatus 880 further comprises a transfer pneumatic channel 882 configured to fluidly connect the output container 250 to the output container pneumatic channel 252, and a liquid transfer channel 886 configured to transport liquid from the final output channel 256 to the output container 250 via an outlet in the temporary lid 259.

[0374] Channels 882, 886 are defined in a body 888 (eg, injection molded polypropylene) and are covered and sealed with a transfer device membrane 840 (eg, heat welded polypropylene membrane), as shown in FIG. 7C.

[0375] The body 888 also defines a connector 889 configured to connect the transfer pneumatic channel 882 to the output reservoir pneumatic channel 252 and the liquid delivery channel 886 to the final output channel 256 by being mechanically coupled to a corresponding connector 1289 on the top surface of the base 202 near the output reservoir sheet 254, as shown in FIG. 8C.

[0376] The body 888 may be resiliently flexible and, when bent into a twisted connection configuration to fluidly and mechanically couple the output receptacle 250 to the cartridge 1000, as shown in FIG. 7A, the body 888 may be configured to press and secure the output receptacle 250 toward the cartridge 1000 (e.g., into the seat 254) during operation of the instrument, such as mixing with an orbital shaker.

[0377] The fluid transfer device 880 may be provided, for example, with the cartridge 1000 (and optionally the output receptacle 250) in a kit.

[0378] Alternatively, the temporary lid 259 may simply be connected to the channels 256 , 252 via tubing rather than the fluid transfer device 880 .

[0379] The cartridge 1000 may include an indicia 1295, such as, for example, a bar code, to identify the samples stored therein (FIG. 7A). The cartridge 1000 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 related to the indicia 1295. Alternatively, the cartridge 1000 may be provided with one or more peel-off labels with corresponding indicia 1296 that may be removed from the cartridge 1000 and, once the samples have been processed, applied to the appropriate output receptacle 250 in which the output fluid is to be received.

[0380] 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.

[0381] 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.

[0382] 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, 0.2-5 mL of blood or bone marrow drawn from a patient.

[0383] 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.

[0384] The user may then insert the cartridge 200 into one of the cartridge slots 120 in the instrument 100 .

[0385] 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.

[0386] 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 .

[0387] 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.

[0388] The pneumatic module is operated to transfer reagents along with the sample to the primary reaction vessel 210 .

[0389] The orbital shaker of the mixing module is operated to promote mixing of the reagents and sample in the primary reaction vessel.

[0390] 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.

[0391] 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.

[0392] The pneumatic module is then operated to transfer the lysis buffer into the primary reaction vessel.

[0393] The kinetic and reagent modules are then operated to dispense functionalized magnetic beads (eg, carboxyl COOH magnetic beads) into the reagent vessels.

[0394] 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.

[0395] The pneumatic module is then operated to transfer the beads to a primary reaction vessel.

[0396] The orbital shaker is operated to facilitate mixing of the contents of the primary reaction vessel.

[0397] 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.

[0398] The heater is then turned off and the cooling fan is turned on to cool the primary reaction vessel 210 .

[0399] 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.

[0400] 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.

[0401] The magnet 710 is then disengaged from the primary reaction vessel.

[0402] The kinetic and reagent modules are then operated to dispense Wash 1 buffer into the reagent vessel (eg, 3M guanadinium HCl, 30% ethanol).

[0403] The pneumatic module is then operated to transfer Wash 1 solution to the primary reaction vessel.

[0404] The orbital shaker is operated to facilitate mixing of the contents of the primary reaction vessel.

[0405] 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.

[0406] 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.

[0407] The magnet 710 is then disengaged from the primary reaction vessel.

[0408] 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).

[0409] The pneumatic module is then operated to transfer Wash 2 solution to the primary reaction vessel.

[0410] The orbital shaker is operated to facilitate mixing of the contents of the primary reaction vessel.

[0411] 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.

[0412] 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.

[0413] The magnet 710 is then disengaged from the primary reaction vessel.

[0414] 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).

[0415] The pneumatic module is then operated to transfer Wash 3 solution to the primary reaction vessel.

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

[0417] 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.

[0418] 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.

[0419] The magnet 710 is then disengaged from the primary reaction vessel.

[0420] 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).

[0421] The pneumatic module is then operated to transfer Wash 4 solution to the primary reaction vessel.

[0422] The orbital shaker is operated to facilitate mixing of the contents of the primary reaction vessel.

[0423] 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.

[0424] 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.

[0425] The magnet 710 is then disengaged from the primary reaction vessel.

[0426] The kinetic and reagent modules are then operated to dispense elution buffer into the reagent vessel (eg, 1xTE, pH 8.0).

[0427] The pneumatic module is then operated to transfer the elution buffer to the primary reaction vessel.

[0428] The orbital shaker is operated to facilitate mixing of the contents of the primary reaction vessel.

[0429] 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.

[0430] 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.

[0431] 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.

[0432] The magnet 710 is then disengaged from the primary reaction vessel.

[0433] 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).

[0434] The pneumatic module is then operated to transfer the contents of the reagent vessel to a secondary reaction vessel.

[0435] 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.

[0436] 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.

[0437] 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.

[0438] The magnet 710 is then disengaged from the primary reaction vessel.

[0439] Next, operate the kinetic module and the reagent module to dispense COOH Beads Wash 1 into the reagent container (e.g., 85% ethanol).

[0440] The pneumatic module is then operated to transfer the contents of the reagent vessel to a secondary reaction vessel.

[0441] The contents of the secondary reaction vessel are then incubated for 30 seconds.

[0442] 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.

[0443] 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.

[0444] The magnet 710 is then disengaged from the primary reaction vessel.

[0445] Next, operate the kinetic module and the reagent module to dispense COOH Beads Wash 2 into the reagent container (e.g., 85% ethanol).

[0446] The pneumatic module is then operated to transfer the contents of the reagent vessel to a secondary reaction vessel.

[0447] The contents of the secondary reaction vessel are then incubated for 30 seconds.

[0448] 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.

[0449] 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.

[0450] The kinetic and reagent modules are then operated to dispense COOH elution buffer (eg, 10 mM Tris, pH 8.0) into the reagent vessel.

[0451] The pneumatic module is then operated to transfer the elution buffer to a second reaction vessel.

[0452] 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.

[0453] 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.

[0454] 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.

[0455] 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 .

[0456] 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.

[0457] The pneumatic module is then operated to transfer the remainder of the eluate from the secondary reaction vessel to the output vessel 250 .

[0458] 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.

[0459] 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.

[0460] 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.

[0461] 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.

[0462] 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.

[0463] 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.

[0464] 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.

[0465] 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.

[0466] 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.

[0467] 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.

[0468] The user may then insert the cartridge 200 into one of the cartridge slots 120 in the instrument 100 .

[0469] 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.

[0470] 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 .

[0471] 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 .

[0472] The pneumatic module is operated to transfer reagents along with the sample to the primary reaction vessel 210 .

[0473] 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 .

[0474] 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.

[0475] 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.

[0476] 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.

[0477] 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.

[0478] Alternatively, if the ambient temperature is close to 25° C., a heater may not be needed for this step.

[0479] 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.

[0480] The pneumatic module is then operated to transfer the lysis buffer into the primary reaction vessel.

[0481] The kinetic and reagent modules are then operated to dispense functionalized magnetic beads (Siemens Versant 50 μL) into the reagent vessel.

[0482] The pneumatic module is then operated to transfer the beads to a primary reaction vessel.

[0483] 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.

[0484] 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.

[0485] The orbital shaker is operated to facilitate mixing of the contents of the primary reaction vessel at 1100 rpm for 10 seconds.

[0486] 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.

[0487] 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.

[0488] 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.

[0489] The magnets may be engaged during the cooling operation.

[0490] 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.

[0491] The magnet 710 is then disengaged from the primary reaction vessel.

[0492] 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).

[0493] The pneumatic module is then operated to transfer Wash 1 solution to the primary reaction vessel.

[0494] The orbital shaker is operated at 1100 rpm for 10 seconds to facilitate mixing of the contents of the primary reaction vessel.

[0495] 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.

[0496] 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.

[0497] The magnet 710 is then disengaged from the primary reaction vessel.

[0498] 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.

[0499] The pneumatic module is then operated to transfer Wash 2 solution to the primary reaction vessel.

[0500] The orbital shaker is operated at 1100 rpm for 10 seconds to facilitate mixing of the contents of the primary reaction vessel.

[0501] 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.

[0502] 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.

[0503] The magnet 710 is then disengaged from the primary reaction vessel.

[0504] The kinetic and reagent modules are then operated to dispense 450 μL of Wash 3 buffer (eg, 20 mM glycine HCl, 0.1% Tw-20, pH 3) into the reagent vessel.

[0505] The pneumatic module is then operated to transfer Wash 3 solution to the primary reaction vessel.

[0506] The orbital shaker is operated at 1100 rpm for 10 seconds to facilitate mixing of the contents of the primary reaction vessel.

[0507] 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.

[0508] 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.

[0509] The magnet 710 is then disengaged from the primary reaction vessel.

[0510] 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.

[0511] 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 two or more times 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.

[0512] The pneumatic module is then operated to transfer Wash 4 solution to the primary reaction vessel.

[0513] The orbital shaker is operated at 1100 rpm for 10 seconds to facilitate mixing of the contents of the primary reaction vessel.

[0514] 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.

[0515] 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.

[0516] The magnet 710 is then disengaged from the primary reaction vessel.

[0517] 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).

[0518] The pneumatic module is then operated to transfer the elution buffer to the primary reaction vessel.

[0519] 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.

[0520] 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.

[0521] 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. 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.

[0522] The magnet 710 is then disengaged from the primary reaction vessel.

[0523] 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)).

[0524] The pneumatic module is then operated to transfer the contents of the reagent vessel to a secondary reaction vessel.

[0525] The orbital shaker is operated at 1100 rpm for 10 seconds to facilitate mixing of the contents of the primary reaction vessel.

[0526] 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.

[0527] 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.

[0528] 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.

[0529] 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.

[0530] 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).

[0531] The pneumatic module is then operated to transfer the contents of the reagent vessel to a secondary reaction vessel.

[0532] The contents of the secondary reaction vessel are then incubated at room temperature for 30 seconds.

[0533] 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.

[0534] 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).

[0535] COOH Beads Wash 2 is completed using the same buffer as COOH Beads Wash 1 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.

[0536] The pneumatic module is then operated to transfer the contents of the reagent vessel to a secondary reaction vessel.

[0537] The contents of the secondary reaction vessel are then incubated at room temperature for 30 seconds.

[0538] 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.

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

[0540] 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.

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

[0542] 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.

[0543] 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.

[0544] 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.

[0545] 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).

[0546] 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.

[0547] 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).

[0548] The pneumatic module is then operated to transfer the remainder of the eluate from the secondary reaction vessel to the output vessel 250 .

[0549] 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.

[0550] 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.

[0551] 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.

[0552] 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.

[0553] 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.

[0554] 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.

[0555] 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.

[0556] 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 sample cartridge for a chemical processing instrument, 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 primary reagent valve disposed within the primary reagent channel to control fluid flow through the primary reagent channel; a primary pneumatic port in fluid communication with the primary reaction vessel and configured to be fluidly connected 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.

2. a primary air pressure channel extending between the primary air pressure port and the primary reaction vessel; 2. The sample cartridge of claim 1, wherein the opening of the primary pneumatic channel into the primary reaction vessel is located halfway up a side wall of the primary reaction vessel.

3. 3. The sample cartridge of claim 1, wherein the opening of the primary reagent channel into the primary reaction vessel is located halfway up a side wall of the primary reaction vessel.

4. The sample cartridge of any one of claims 1 to 3, further comprising a final output channel configured to convey a final output fluid from the primary reaction vessel to a removable output vessel.

5. 5. The sample cartridge of claim 4, further comprising an output vessel pneumatic port configured to be in fluid communication with an output vessel via an output vessel pneumatic channel, the output vessel pneumatic port configured to be connected to a pneumatic module to selectively adjust the pressure in the output vessel to draw the final output fluid from the primary reaction vessel through the final output channel and into the output vessel.

6. 6. The sample cartridge of claim 5, further comprising a temporary lid configured to close the output bin during processing, the temporary lid configured to fluidly connect the final output channel and the output bin pneumatic channel to the output bin.

7. a sealed quality control container 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; 7. The sample cartridge of claim 4, further comprising 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 the 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.

8. 8. The sample cartridge of claim 7, wherein the quality control reservoir is preloaded with a dye that is mixed with an aliquot of the final output fluid for quality control analysis.

9. a buffer container configured to receive a buffer solution 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 quality control junction and the final output channel buffer junction between the primary reaction vessel; 9. The sample cartridge of claim 7 or 8, further comprising a buffer channel valve disposed in the buffer channel to control the flow of the buffer solution through the buffer channel.

10. an intermediate outlet from the final output channel between the quality control interface and the output bin; a sealed chamber into which the intermediate outlet opens; an air permeable liquid barrier membrane covering the outlet; 10. The sample cartridge of claim 7, further comprising an intermediate outlet pneumatic port in fluid communication with the sealed chamber and configured to be connected to a pneumatic module to selectively adjust the pressure within the sealed chamber to draw air from the final output channel through the air permeable membrane.

11. a sealed waste container configured to receive waste liquid from the primary reaction container via a waste channel; 11. The sample cartridge of any one of claims 1 to 10, further comprising a waste pneumatic port in fluid communication with the waste container and configured to be connected to a pneumatic module to selectively adjust pressure in the waste container to draw fluid from the primary reaction container through the waste channel and into the waste container.

12. 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 fluid reagents from the reagent vessel via secondary reagent channels 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; A sample cartridge according to any preceding claim, further comprising a secondary reagent valve disposed within the secondary reagent channel to control flow through the secondary reagent channel.

13. The secondary reaction vessel is sealed; 13. The sample cartridge of claim 12, further comprising a secondary pneumatic port in fluid communication with the secondary reaction vessel and configured to be connected to a pneumatic module to 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.

14. a secondary air pressure channel extending between the secondary air pressure port and the secondary reaction vessel; 14. The sample cartridge of claim 13, wherein the opening of the secondary pneumatic channel into the secondary reaction vessel is closer to the top of the secondary reaction vessel than to the bottom of the secondary reaction vessel and is located halfway up a side wall of the secondary reaction vessel.

15. 15. A method of using a sample cartridge according to any one of claims 1 to 14, comprising operating an instrument to effect extraction, isolation, enrichment, concentration or quantification of nucleic acid from a sample in said sample cartridge, or preparation of nucleic acid for manipulation, analysis, amplification, sequencing, PCR library preparation or insertion into a vector. (1) Claims 1 and 15 have been amended. (2) Claims 3, 5, 17 to 68, 70, and 71 have been deleted. (3) The dependent relationships of the claims have been amended. (4) There are no other changes.

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