Rotary carousels and rotary valves for analysis systems

Abstract

Rotary carousels and rotary valve devices are described for use in cartridges designed to be inserted into automated fluid sample analysis systems. The rotary carousels and rotary valve devices include one or more reservoirs and can be used in various automated protocols including polymerase chain reactions and solid-phase reversible immobilization.

Description

ROTARY CAROUSELS AND ROTARY VALVES FOR ANALYSIS SYSTEMSRELATED APPLICATIONS

[0001] This application is entitled to the benefit of the filing date of United States provisional application 63 / 516,973 filed on August 1, 2023, the entire contents of which are hereby incorporated by reference.TECHNICAL FIELD

[0002] The present disclosure relates generally to rotary carousel devices and rotary valve devices for use in automated analysis systems. The systems can be used, for example, for automated assay protocols, e.g., automated polymerase chain reaction (PCR) protocols and solidphase reversible immobilization (SPRI) bead and other reagent cleanup protocols (SPRI®, Beckman Coulter).BACKGROUND

[0003] Automated analysis systems, e.g., for PCR, require the use of a variety of reagents in different volumes. In some analysis systems, these different reagents must be added to the system manually, which requires a skilled technician and a stockpile of the required reagents. Manual addition of various regents to the systems can potentially result in errors in volumes, concentrations, and materials. Furthermore, many automated analysis systems have relatively long channels that can create “dead” space that must be fdled, often with larger volumes of expensive reagents than required for a given assay. In some cases, analysis systems can receive cartridges that provide the required reagents. The cartridges can be replaceable to run repeated assays.

[0004] PCR is a method to produce large amounts (e.g., millions to billions) of copies of a nucleic acid, e.g., DNA, sample rapidly, e.g., by amplifying a small sample of DNA to a large enough amount to study in detail.

[0005] Solid-phase reversible immobilization (SPRI) cleanup protocols utilize SPRI reagents (e.g., SPRI beads) that selectively bind nucleic acids, e.g., by type and size. SPRI cleanup protocols can be used to isolate, purify, and clean samples to target a desired fragment type and fragment size.SUMMARY

[0006] The present disclosure provides rotary carousels and rotary valves for use in cartridges that are used in various automated analysis systems, e.g., systems that can provide automated assay protocols, such as PCR and SPRI bead cleanup protocols. The rotary carousels and rotary valves can rotate to provide easy, selective access to a large number of different low-volume samples, reagents, buffers, etc., used during PCR or other assay protocols. Automated rotation of such carousels or valves provides automated access to different samples, reagents, buffers, etc. as required for a variety of automated assay protocols, such as automated PCR and automated SPRI bead cleanup, as described herein.

[0007] In one aspect, the disclosure provides rotary carousels that include a base having a channel with an opening arranged on a surface of the base, a carousel including a plurality of reservoirs and rotatably mounted on the surface of the base, wherein each reservoir is configured to store liquid, wherein the carousel and the base are configured to be rotatable relative to one another, wherein each reservoir has an opening, such that when an opening in a reservoir aligns with the opening of the channel, the reservoir is fluidly connected to the opening of the channel and the liquid stored in the reservoir is accessible via the channel, and wherein when an opening of a reservoir is not aligned with the channel, the opening of the reservoir is sealed.

[0008] Embodiments can include one or any combination of two or more of the following features.

[0009] When the opening of the reservoir is not aligned with the channel, the opening of the reservoir is sealed by a seal arranged between the base and a bottom of the reservoir. The seal can be watertight. The base can further include an air vent, wherein the opening of the channel is arranged at a first radial distance from a center of the base and the air vent is arranged at a second radial distance from the center of the base, wherein the second radial distance is different than the first radial distance.

[0010] At least one of the reservoirs can have two openings, such that when the actuator rotates a first opening of the two openings to align with the opening of the channel, a second opening of the two openings is aligned with the air vent. In other embodiments, at least one of the reservoirs includes first and second openings, wherein the first opening and the second opening arearranged at different distances from a center of the rotary carousel. For example, the reservoir with the first and second openings can be arranged and controlled as a polymerase chain reaction chamber.

[0011] The rotary carousel can include at least one foil cover over one or more, or all, of the plurality of reservoirs. The rotary carousel can include a receiver for an actuator to rotate the carousel relative to the base.

[0012] The rotary carousel can be configured for use with an analysis system including an actuator and a controller configured to cause the actuator to engage the receiver to rotate the carousel automatically so that an opening in a specific reservoir aligns with the opening of the channel.

[0013] In some embodiments, the receiver includes an opening into which the actuator fits. The receiver can include teeth to engage an actuator comprising a sprocket wheel. In some embodiments, at least one reservoir contains a reagent. For example, each reservoir can have a volume between 1-100 milliliters.

[0014] In certain embodiments, the rotary carousel is configured for use with an analysis system that includes a syringe pump configured to pump liquid into and / or out of a selected reservoir when the selected reservoir is fluidly connected to the channel. In some embodiments, the rotary carousel is provided in a cartridge.

[0015] In another aspect, the disclosure provides automated methods of solid phase reversible immobilization cleanup including automatically rotating the rotary carousels described herein to fluidly connect a pump to reservoirs of the rotary carousel, transferring a sample from a sample reservoir of the rotary carousel to a mixing reservoir of the rotary carousel, transferring a paramagnetic bead reagent from a reagent reservoir of the rotary carousel into the mixing reservoir, such that the paramagnetic bead reagent mixes with the sample, triturating the paramagnetic bead reagent and the sample within the mixing reservoir, engaging and disengaging a magnet to form pellets from the paramagnetic bead reagent, transferring a supernatant from the mixing reservoir into a waste reservoir of the rotary carousel, transferring a washing fluid from a washing fluid reservoir of the rotary carousel into the mixing reservoir, such that the washing fluid contacts the paramagnetic bead reagent, transferring the washing fluid from the mixing reservoir into a waste reservoir, transferring an elution buffer from anelution buffer reservoir of the rotary carousel into the mixing reservoir, such that the elution buffer contacts the paramagnetic bead reagent, and extracting the elution buffer.

[0016] In another aspect, the disclosure features automated methods of conducting polymerase chain reaction (PCR) including automatically rotating the rotary carousels described herein to transfer liquid between reservoirs of the rotary carousel, transferring a sample from a sample reservoir of the rotary carousel into the polymerase chain reaction chamber of the rotary carousel, denaturing the nucleic acid sample in the reservoir by heating the polymerase chain reaction chamber to a first temperature sufficient to denature the nucleic acid sample, annealing primers to the nucleic acid sample in the polymerase chain reaction chamber by heating the polymerase chain reaction chamber to a second temperature sufficient to anneal the primers, extending the primers along the nucleic acid sample in the polymerase chain reaction chamber by heating the polymerase chain reaction chamber to a third temperature sufficient to extend the primers, and transferring the nucleic acid sample from the polymerase chain reaction chamber into a mixing reservoir of the rotary carousel, wherein the mixing reservoir is one of the plurality of reservoirs.

[0017] Embodiments can include one or any combination of two or more of the following features.

[0018] The first temperature can be within a range of 94 to 98°C. The second temperature can be within a range of 55 to 65°C. The third temperature can be within a range of 70 to 75°C.

[0019] The methods can include transferring a paramagnetic bead reagent from a reagent reservoir into the mixing reservoir, such that the paramagnetic bead reagent mixes with the nucleic acid sample, wherein the reagent reservoir is one of the plurality of reservoirs of the rotary carousel.

[0020] In another aspect, the disclosure provides rotary valve devices that include a base, a plurality of reservoirs mounted on the base, wherein each reservoir is configured to store liquid, and a rotary valve rotatably mounted to the base and comprising a channel with an opening, wherein each reservoir has an opening, such that when the opening of the channel aligns with an opening in a reservoir, the reservoir is fluidly connected to the opening of the channel and the liquid stored in the reservoir is accessible via the channel, and wherein when an opening of a reservoir is not aligned with the channel, the opening of the reservoir is sealed.

[0021] Embodiments can include one or any combination of two or more of the following features.

[0022] In some embodiments, when the opening of the reservoir is not aligned with the channel, the opening of the reservoir can be sealed by a seal arranged between the base and a bottom of the reservoir. The seal can be watertight. In some embodiments, the rotary valve can further include an air vent.

[0023] In certain embodiments, at least one of the reservoirs can have two openings, such that when the actuator rotates the opening of the channel to align with a first opening of the two openings, the air vent is aligned with a second opening of the two openings. In some embodiments, at least one of the reservoirs includes first and second openings, wherein the first opening and the second opening are arranged at different distances from a center of the rotary valve. For example, the reservoir with the first and second openings can be arranged and controlled as a polymerase chain reaction chamber. The rotary valve device can include at least one foil cover over one or more, or all, of the plurality of reservoirs.

[0024] In some embodiments, the rotary valve device includes a receiver for an actuator to rotate the rotary valve with respect to the base. The rotary valve device can be configured for use with an analysis system comprising an actuator and a controller configured to cause the actuator to engage the receiver to rotate the rotary valve automatically so that the opening of the channel aligns with an opening in a specific reservoir.

[0025] In certain embodiments, the receiver includes an opening into which the actuator fits. In some embodiments, the receiver includes teeth to engage an actuator comprising a sprocket wheel. For example, at least one reservoir can contain a reagent. Each reservoir can have a volume from about 1.0 microliter to about 100 milliliters.

[0026] In some embodiments, the rotary valve device is configured for use with an analysis system that includes a syringe pump configured to pump liquid into and / or out of a selected reservoir when the selected reservoir is fluidly connected to the channel. In some embodiments, the rotary valve device is provided on a cartridge.

[0027] In another aspect, the disclosure provides automated methods of solid phase reversible immobilization cleanup that include automatically rotating the rotary valve device described herein, transferring a sample from a sample reservoir of the rotary valve device to a mixing reservoir of the rotary valve device, transferring a paramagnetic bead reagent from a reagentreservoir of the rotary valve device into the mixing reservoir, such that the paramagnetic bead reagent mixes with the of sample, triturating the paramagnetic bead reagent and the sample within the mixing reservoir, engaging and disengaging a magnet to form a pellet from the paramagnetic bead reagent, transferring a supernatant from the mixing reservoir into a waste reservoir of the rotary valve device, transferring a washing fluid from a washing fluid reservoir of the rotary valve device into the mixing reservoir, such that the washing fluid contacts the pellet, transferring the washing fluid from the mixing reservoir into the waste reservoir, transferring an elution buffer from an elution buffer reservoir of the rotary valve device into mixing reservoir, such that the elution buffer contacts the pellet, and extracting the elution buffer.

[0028] In another aspect, the disclosure features automated methods of conducting polymerase chain reaction (PCR) that include automatically rotating the rotary valve device described above to transfer liquid between reservoirs of the rotary valve device, transferring a sample from a sample reservoir of the rotary valve device into a polymerase chain reaction chamber of the rotary valve device, denaturing the nucleic acid sample in the polymerase chain reaction chamber by heating the polymerase chain reaction chamber to a first temperature sufficient to denature the nucleic acid sample, annealing primers to the nucleic acid sample in the polymerase chain reaction chamber by heating the polymerase chain reaction chamber to a second temperature sufficient to anneal the primers, extending the primers along the nucleic acid sample in the polymerase chain reaction chamber by heating the polymerase chain reaction chamber to a third temperature sufficient to extend the primers, and transferring the nucleic acid sample from the polymerase chain reaction chamber into a mixing reservoir of the rotary valve device, wherein the mixing reservoir is one of the plurality of reservoirs.

[0029] Embodiments can include one or any combination of two or more of the following features.

[0030] In some embodiments, the first temperature is within a range of 94 to 98°C. The second temperature can be within a range of 55 to 65°C. The third temperature can be within a range of 70 to 75°C.

[0031] The methods can include transferring a paramagnetic bead reagent from a reagent reservoir into the mixing reservoir, such that the paramagnetic bead reagent mixes with thenucleic acid sample, wherein the reagent reservoir is one of the plurality of reservoirs of the rotary carousel.

[0032] In certain embodiments, denaturing the sample within the polymerase chain reaction chamber occurs while the channel and the air vent are not fluidly connected with the polymerase chain reaction chamber.

[0033] In some embodiments, the polymerase chain reaction chamber is a first polymerase chain reaction chamber, and the methods include transferring the sample from the polymerase chain reaction chamber into the rotary valve, and transferring the sample into a second polymerase chain reaction chamber, wherein the second polymerase chain reaction chamber has a different volume than the first polymerase chain reaction chamber.

[0034] The methods can include transferring the sample from the rotary valve device into a mixing reservoir, transferring paramagnetic bead reagent from a reagent reservoir into the rotary valve device, transferring the paramagnetic bead reagent into the mixing reservoir to mix the paramagnetic bead reagent with the sample, engaging a magnet with the mixing reservoir to pull the paramagnetic bead reagent to a wall of the mixing reservoir, and transferring the sample from the mixing reservoir into the rotary valve device.

[0035] The systems disclosed herein are advantageous in that the liquids can be stored in an easily accessible fashion, allowing automated access to the stored liquids during the assay protocols. An automated process reduces the hands-on time and manual labor required to run the assay protocols, such as PCR. For example, the systems described herein allow for the repeated steps of PCR followed by SPRI® bead cleanup by providing a single accessible reservoir of SPRI® beads to be used at each step and an addressable set of PCR reaction chambers provided on the cartridge. The present systems also hermetically seal, e.g., with a water-tight seal, a PCR chamber during PCR amplification to provide sample containment and prevent sample runaway and evaporation at the elevated temperatures required for PCR (e.g., close to the boiling point of the sample).

[0036] Additionally, the systems disclosed herein are advantageous in that the fluids (e.g., reagents, buffers, etc.) can be stored in a variety of volumes, including low volumes. Being able to store fluids in a range of volumes is advantageous, for example, as assays can require reagent volumes ranging from several microliters to many milliliters. Other advantages include providing the fluids in an easily accessible fashion, allowing automated access for experimentation, e.g.,SPRI® bead cleanup, with the stored fluids. Additionally, the present rotary carousel reduces “dead” space in the system, by omitting many of the channels found in convention microfluidic devices. A minimized swept volume can be achieved by locating a reservoir outlet directly above the location where the fluid is required. Typically, small volume reagents are expensive, and reducing swept volume directly reduces cost. Therefore, the present systems provide efficient storage of fluids, can be implemented easily in automated experimentation, and provide savings in reagent volumes, manual labor, and costs.

[0037] Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, suitable methods and materials are described below. All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety. In case of conflict, the present specification, including definitions, will control. In addition, the materials, methods, and examples are illustrative only and not intended to be limiting.

[0038] Various embodiments of the features of this disclosure are described herein. However, it should be understood that such embodiments are provided merely by way of example, and numerous variations, changes, and substitutions can occur to those skilled in the art without departing from the scope of this disclosure. It should also be understood that various alternatives to the specific embodiments described herein are also within the scope of this disclosure.

[0039] Other features and advantages of the invention will be apparent from the following detailed description, and from the claims.DESCRIPTION OF DRAWINGS

[0040] FIG. l is a top view of an example of a rotary carousel with eight reservoirs that is used as part of a cartridge designed for insertion into an analysis system.

[0041] FIG. 2 is a cross-sectional view of the example of the rotary carousel of FIG. 1.

[0042] FIG. 3 is a schematic diagram of an example of a rotary carousel with six regular reservoirs and two reservoirs in the form of PCR chambers, wherein the rotary carousel is rotated into a position in which one reservoir is accessing a channel and no reservoir is accessing an air vent.

[0043] FIG. 4 is a schematic diagram of the example of the rotary carousel of FIG. 3 rotated into a position in which the two openings of one of the PCR chambers are aligned with an air vent and a channel, respectively, in the base of the rotary carousel.

[0044] FIG. 5 is a schematic diagram of an example of a rotary valve device, arranged for use in an SPRI cleanup protocol.

[0045] FIGS. 6A-6F are schematic diagrams of movements of a rotary valve device during a PCR process.

[0046] FIG. 7 is a flowchart of an automated SPRI cleanup protocol.

[0047] FIG. 8 is a flowchart of an automated PCR protocol.DETAILED DESCRIPTION

[0048] The present disclosure provides new rotary carousel and rotary valve devices for use in cartridges that are used in automated analysis systems. These devices and systems can be used to carry out automated assay protocols that require easy access to different samples, reagents, buffers, etc., for example, as required for various automated assay protocols, such as automated PCR protocols and automated SPRI® bead cleanup protocols.Rotary Carousels for Automated Analysis Systems

[0049] FIG. 1 shows an example of a rotary carousel 100 that is used as a part of a cartridge used, for example, for automated assay protocols as described herein. For example, the rotary carousel 100 can be used in automated SPRI® cleanup protocols, as will be discussed further below. The rotary carousel 100 includes a base 102 and a carousel 104 rotatably mounted on the base 102. For example, an actuator of an automated analysis system can cause the carousel 104 to rotate on top of the base 102 by actuating an actuator (which can be part of the analysis system) to engage an actuator receiver 120. In some implementations, the actuator receiver can be implemented along the outer perimeter of the carousel 104, e.g., as one or more slots or teeth along a track along the outer perimeter to be engaged by a sprocket wheel driven by a motor that is part of the analysis system. The base 102 has a channel 106 that allows fluid to flow into and out of a selected one of the fluid reservoirs 108a, 108b, 108c, 108d, 108e, 108f, 108g, 108h of the carousel 104, when an end of the channel is aligned with an opening 110a, 110b, 110c, 1 lOd, 1 lOe, 11 Of, 110g, and 11 Oh of a respective fluid reservoir. When the carousel 104 is rotated sothat one of the fluid reservoirs is aligned with the end of the channel 106, fluid can flow into and / or out of that fluid reservoir through the respective opening of the reservoir.

[0050] FIG. 2 shows a cross-section of the rotary carousel 100. Fluid reservoirs 108a, 108e are shown in the cross-section view. In the shown position, the opening 110a of the fluid reservoir 108a is aligned with the end of channel 106, e.g., such that fluid can be drawn (e.g., by a syringe pump) from the fluid reservoir 108a. In some implementations, the channel 106 extends through a seal 124 arranged between the carousel 104 and the base 102. For example, the seal 124 can include a rubber gasket, an O-ring, etc., and can be a water-tight, air-tight, and / or a hermetic seal. In some implementations, the seal 124 includes multiple seals. For example, in some implementations each fluid reservoir has a respective O-ring creating a sealed connection between the fluid reservoir and the base 102. The seal 124 prevents leakage from the fluid reservoirs when the fluid reservoirs are not aligned with the channel 106 (e.g., during rotation of the carousel 104). Alternatively, the seal can be one piece, e.g., a rubber sheet or gasket, covering the base under the carousel, and having one opening aligned with the end of the channel.

[0051] In some implementations, foil covers 122a, 122e cover the fluid reservoirs 108a, 108e. For example, the foil covers 122a, 122e can seal the fluid reservoirs 108a, 108e and protect the fluids from the atmosphere. In some cases, the fluids need to be covered to maintain freshness. Before or during use of the rotary carousel 100, the foil covers can be punctured to prevent vacuums forming in the fluid reservoirs 108a, 108e (e.g., when the fluid is pulled from the fluid reservoir). Although they are not shown, foil covers also cover the other fluid reservoirs 108b, 108c, 108d, 108f, 108g, and 108h. In some implementations, a single large foil cover can cover all of the fluid reservoirs.

[0052] The fluid reservoirs 108a, 108b, 108c, 108d, 108e, 108f, 108g, and 108h can vary in different implementations of the rotary carousel. For example, the geometries, sizes, etc. of the fluid reservoirs can vary. In some implementations, the fluid reservoirs can include microtubes, wells, etc. In some implementations, the volumes of the reservoirs can range from 1.0 microliter to about 100 milliliters. In some implementations, the fluid reservoirs are identical; in other implementations, one or more of the fluid reservoirs can be different in size, depth, area, volume, and / or shape than other fluid reservoirs. In some implementations, the rotary carousel can include fewer or more fluid reservoirs (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more reservoirs, morethan five reservoirs, fewer than 10 reservoirs, more than 10 reservoirs, etc.). In some implementations, the fluid reservoirs can be separate, e.g., pre-filled, containers that can be inserted into the carousel 104.

[0053] FIG. 3 shows an example of another embodiment of a rotary carousel 300 that can be used, for example, to automate assay protocols as described herein. For example, the rotary carousel 300 can be used to automate a PCR protocol, as will be discussed further below. The rotary carousel 300 includes a base 302 and a carousel 304 rotatably mounted on the base 302. For example, an actuator of a system can cause the carousel 304 to rotate on top of the base 302 by actuating an actuator “key” or receiver 320. The base 302 has a channel 306 that allows fluid to flow into and out of a selected one of fluid reservoirs 308a, 308b, 308c, 308d, 308e, 308f of the carousel 304, when properly aligned with an opening 310a, 310b, 310c, 3 lOd, 3 lOe, 3 lOf of a respective fluid reservoir. When the carousel 304 is rotated so that one of the fluid reservoirs is aligned with the channel 306, fluid can flow into and / or out of that fluid reservoir.

[0054] The carousel 304 also includes two reservoirs in the form of PCR chambers 312a, 312b. Similar to the other fluid reservoirs, the PCR chambers each have a first opening 314a, 314b that can align with and fluidly connect to the end of channel 306 when the respective PCR chamber opening is aligned with the channel. Additionally, the PCR chambers each have a second opening 316a, 316b that can align with and fluidly connect to an air vent 318 when the respective PCR chamber is aligned with the channel 306. The air vent 318 vents the PCR chamber, for example, while that PCR chamber is being filled with fluid from the channel 306.

[0055] During use, a PCR chamber receives fragments of DNA and / or RNA to be amplified, primers, enzymes, other reagents / catalysts (e.g., Mg++), etc. In some implementations, a thermal cycler is coupled to the rotary carousel and can heat the PCR chambers as necessary to complete a PCR cycle. In some implementations, a single thermal cycler is large enough to heat both PCR chambers. Alternatively, multiple thermal cyclers can be used. In some implementations, the thermal cycler can be separate from the cartridge that houses the rotary carousel, and the PCR chambers can be rotated to be positioned sufficiently near or in or contacting the thermal cycler to run a PCR cycle within the PCR chambers. In some implementations, a heater (e.g., a resistance heater) may be provided in the carousel 304 or in the cartridge in which the carousel is arranged.

[0056] The first openings 314a, 314b and the second openings 316a, 316b of the PCR chambers 312a, 312b can be positioned at different radial distances relative to a center of the carousel 304. In the shown implementation, the second openings 316a, 316b are positioned farther from the center of the carousel 304 than the first openings 314a, 314b. The air vent 318 and the channel 306 also can have ends that open at different radial distances relative to the center of the carousel. The channel 306 can be positioned at a first radial distance such that only the first openings 314a, 314b of the PCR chambers, and the openings in the other reservoirs, can align with and fluidly connect to the channel 306 (i.e., the second openings 316a, 316b cannot fluidly connect to the channel 306). The air vent can be positioned at a second radial distance, different from the first radial distance, such that only the second openings 316a, 316b can align with and fluidly connect to the air vent 318 (i.e., the first openings 314a, 314b cannot fluidly connect to the air vent 318).

[0057] The first openings 314a, 314b and the second openings 316a, 316b can be positioned such that when a first opening is aligned with the channel, the respective second opening is aligned with the air vent. For example, when the first opening 314a of the first PCR chamber 312a is aligned with the channel, the second opening 316a of the first PCR chamber 312a is aligned with the air vent. The same can be true for the second PCR chamber 312b. For example, FIG. 4 shows a position of the carousel 304 in which first opening 314a of the first PCR chamber 312a is aligned with the channel 306 and the second opening 316a of the first PCR chamber 312a is aligned with the air vent 318.

[0058] Because the openings 310a, 310b, 310c, 310d, 310e, 310f of the fluid reservoirs 308a, 308b, 308c, 308d, 308e, 308f are positioned to align with and fluidly connect to the channel 306, the openings 310a, 310b, 310c, 31 Od, 31 Oe, 31 Of do not align with and connect to the air vent (e.g., due to the different radial distances from the center of the carousel). In some implementations, positioning the channel opening and the air vent at different radial distances can be advantageous, e.g., because the air vent 318 does not interfere with the openings 310a, 310b, 310c, 3 lOd, 3 lOe, 3 lOf fluid cannot exit the fluid reservoirs 308a, 308b, 308c, 308d, 308e, 308f when they pass over the air vent 318 during rotation of the carousel 304.

[0059] The PCR chambers 312a, 312b can vary in different implementations of the rotary carousel. For example, the geometries, sizes, volumes, etc. of the PCR chambers can vary. For example, in some implementations, the rotary carousel can include more or fewer PCR chambers(e g., one PCR chamber, two PCR chambers, three PCR chambers, four PCR chambers, or five or more PCR chambers). Having a greater number of PCR chambers allows more PCR processes to be run simultaneously. In some implementations, the PCR chambers can be identical; in other implementations, the PCR chambers can be different from each other, e.g., in size, shape, volume, etc.

[0060] The cross-section of the rotary carousel 300 can be similar to the cross-section of the rotary carousel 100 of FIG. 1. For example, the rotary carousel 300 can include a seal that prevents leakage from the fluid reservoirs when the fluid reservoirs are not aligned with the channel and / or air vent, and foil covers that protect the fluid reservoirs and PCR chambers from the atmosphere.

[0061] In some implementations, the carousel 104 of FIG. 1 can be used on the base 302 of FIG. 3. For example, the openings 110a, 110b, 110c, 1 lOd, 1 lOe, 1 lOf, 110g, and 1 lOh can align with the channel 306 of the base 302, and the air vent 318 would not align or interfere with any of the openings 110a, 110b, 110c, HOd, I lOe, I lOf, 110g, and HOh. This can allow a user to change which carousel is being used on the base 302, e.g., depending on the desired assay protocols, reagents, etc. For example, a user can execute an assay protocol using the carousel 304 and the base 302, and swap the carousel to run a second assay protocol using the carousel 104 on the base 302.Rotary Valve Devices for Automated Analysis Systems

[0062] FIG. 5 shows a rotary valve device 500 that can be used in automated analysis systems to carry out a variety of assay protocols. For example, the rotary valve device 500 can be used in addition to, or alternatively to, the rotary carousel 100 of FIG. 1 to run an SPRI® protocol. The rotary valve device 500 can include a rotary valve 502 connected to a syringe pump 504 operable to draw fluid into a channel 512 of the rotary valve 502 and push fluid out of the channel 512 of the rotary valve 502. The rotary valve 502 can be connected to reservoirs 514a, 514b, 514c, 514d, 514e, and 514f, and can selectively rotate the channel 512 to fluidly connect to one of the reservoirs 514a, 514b, 514c, 514d, 514e, and 514f. While the channel 512 is fluidly connected to one of the reservoirs, the syringe pump 504 can draw fluid into the channel 512 from the respective reservoir and / or push fluid out of the channel 512 into the respective reservoir. The rotary valve device 500 can move fluid from a first reservoir to a second reservoir by drawingfluid into the channel 512 from the first reservoir, rotating the channel 512 to fluidly connect with the second reservoir, and pushing fluid out of the channel 512 into the second reservoir. The rotary valve device 500 can be programmed to move desired amounts of fluid between reservoirs automatically, e.g., to automate assay protocols, such as SPRI® cleanup protocols.

[0063] The syringe pump 504 can be connected to a selector valve 506 that allows the syringe pump to draw, for example, wash buffer from a wash buffer reservoir 508 into the syringe pump 504 and / or air from an air reservoir 510 into the syringe pump. In some implementations, the wash buffer reservoir 508 and / or the air reservoir 510 can be utilized to draw fluid from one of reservoirs into the rotary valve 502 and push fluid out of the rotary valve 502. For example, the syringe pump 504 can push air into the air reservoir 510 to empty the syringe pump 504. Then, the syringe pump 504 can draw fluid from one of the reservoirs 514a, 514b, 514c, 514d, 514e, and 514f into the channel by creating a vacuum in the channel 512. In some implementations, the wash buffer 508 and / or the air 510 can be used to clean the channel 512 of the rotary valve 502, e.g., to rinse out leftover waste.

[0064] A magnet 516 can be operable to engage and disengage the reservoir 514f, e.g., provide a magnetic field within the reservoir 514f In some implementations, the reservoir 514f can act as a mixing reservoir. When the magnet introduces a magnetic field within the reservoir 514f, magnetic elements (e.g., magnetic or paramagnetic beads, such as SPRI® beads) are influenced by the magnetic field. For example, the magnet 516 can engage the reservoir 514f to pull SPRI® beads, e.g., magnetic and / or paramagnetic beads, to a wall of the reservoir 514f. The magnet 516 can disengage the reservoir 514f to release the SPRI® beads from the wall of the reservoir 514f. SPRI® cleanup protocols will be discussed below.

[0065] FIGS. 6A-6F show a rotary valve device 600 that can be used to automate assay protocols. For example, the rotary valve device 600 can be used in addition or alternatively to the rotary carousel 100 of FIG. 1 to run automated assay protocols such as SPRI® protocols, PCR protocols, etc. The rotary valve device 600 can include a rotor 602 connected to a syringe pump 604 operable to draw fluid into a channel 606 provided on the rotor 602 and push fluid out of the channel 606. The rotor 602 is operable to rotate to fluidly connect the channel 606 with one of a number of fluid reservoirs 608a, 608b, 608c, 608d, and 608e. The rotor 602 can rotate to fluidly connect the channel 606 with a fluid reservoir, and then the syringe pump 604 draws fluid into the channel 606 from the fluid reservoir and / or pushes fluid out of the channel 606 into the fluidreservoir. In this fashion, the rotary valve device 600 can selectively move fluids into or out of reservoirs or PCR chambers, mix fluids, etc. to automate desired assay protocols.

[0066] PCR chambers 610a, 610b, 610c, and 610d can also fluidly connect to the rotor 602 so that the rotary valve can draw fluid into the channel 606 from one of the PCR chambers and / or push fluid out of the channel 606 into the PCR chamber. During use, a PCR chamber can receive fragments of DNA and / or RNA to be amplified, primers, enzymes, and other reagents / catalysts (e.g., Mg++). A thermal cycler, e.g., that may be part of the analysis system, can be used to heat the PCR chambers as necessary to complete a PCR cycle. In some implementations, a single thermal cycler can be large enough to heat all of the PCR chambers; alternatively, multiple thermal cyclers can be used.

[0067] FIG. 6B shows a stator 620 of the rotary valve device 600 (with the rotor 602 removed). The stator 620 provides the various openings that interact with the rotor 602. The rotor 602 rotates relative to the stator 620 to connect the channel 606 with the openings provided in the stator 620.

[0068] Each of the PCR chambers 610a, 610b, 610c, and 610d can include a first opening 612a, 612b, 612c, and 612d and a second opening 614a, 614b, 614c, and 614d provided in the stator 620. The first openings 612a, 612b, 612c, and 612d, and the second openings 614a, 614b, 614c, and 614d of the PCR chambers 610a, 610b, 610c, and 610d can be positioned at different radial distances relative to a center of the rotary valve device 600. For example, the second openings 614a, 614b, 614c, and 614d can be positioned closer to the center of the rotary valve 602 than the first openings 612a, 612b, 612c, and 612d. An air vent 616 of the rotary valve 602 can be positioned at a first radial distance from the center of the rotary valve 602 so that when the rotary valve 602 rotates, the air vent 616 can fluidly connect to the second openings 614a, 614b, 614c, and 614d (i.e., the first openings 612a, 612b, 612c, and 612d cannot fluidly connect to the air vent 616). An end of the channel 606 of the rotary valve 602 can be positioned at a second radial distance from the center of the rotary valve 602 so that when the rotary valve 602 rotates, the channel 606 can fluidly connect to the first openings 612a, 612b, 612c, and 612d (and the second openings 614a, 614b, 614c, 614d cannot fluidly connect to the channel 606).

[0069] The first openings 612a, 612b, 612c, 612d and the second openings 614a, 614b, 614c, 614d can be positioned such that when a first opening is aligned with the channel, the respective second opening is aligned with the air vent. For example, when the first opening 612a of the firstPCR chamber 610a is aligned with the channel 606, the second opening 614a of the first PCR chamber 610a is aligned with the air vent 616. The same can be true for the second PCR chamber 610b, the third PCR chamber 610c, and the fourth PCR chamber 610d. For example, FIG. 6C shows a position of the rotary valve 602 in which first opening 612a of the first PCR chamber 610a is aligned with the channel 606 and the second opening 614a of the first PCR chamber 610a is aligned with the air vent 616. This arrangement allows the first PCR chamber 610a to be filled with liquid and subsequently hermetically sealed by rotating the valve to a position that disconnects the air vent 616 from the second opening 614a and channel 606 from the first opening 612a (as indicated in Figure 6D). The sealing of the first PCR chamber 610a limits air bubbles from forming and expanding, displacing the liquid inside the first PCR chamber 610a during thermocycling, during which temperatures can get close to the boiling point of water.

[0070] Because the openings 618a, 618b, 618c, 618d, and 618e of the fluid reservoirs 608a, 608b, 608c, 608d, and 608e can be positioned to align with and fluidly connect to the channel 606, the openings 618a, 618b, 618c, and 618e do not align with and connect to the air vent (e.g., due to the different radial distances from the center of the rotary valve to the air vent and to the channel).

[0071] Depending on the assay protocol, the rotary valve device can be operated to access a variety of fluids (samples, reagents, buffers, etc.) provided in the fluid reservoirs (e.g., the fluid reservoirs 608a-e) connected to the rotary valve. For example, during a PCR protocol, the rotary valve can access a sample of DNA, RNA, etc. that will be amplified during the PCR protocol as well as reagents required for the protocol. The rotary valve can also contain a variety of primers that define the portions of the sample to be amplified. The rotary valve can contain a variety of buffers that provide a suitable chemical environment for PCR amplification. The rotary valve can contain a polymerase (e.g., Taq polymerase) that amplifies the desired sample sequences.

[0072] The fluid reservoirs 608a, 608b, 608c, 608d, and 608e can vary in different implementations of the rotary valve device. For example, the geometries, sizes, etc. of the fluid reservoirs can vary. For example, in some implementations, the fluid reservoirs can include microtubes, wells, etc. In some implementations, the fluid reservoirs are identical; in other implementations, one or more of the fluid reservoirs can be different than other fluid reservoirs.In some implementations, the rotary valve device can include fewer or more fluid reservoirs than shown in the figures (e.g., more than 2, 3, 6, 5, 6, 7, 8, 9, or 10 reservoirs).

[0073] The PCR chambers 610a, 610b, 610c, 61 Od can vary in different implementations of the rotary valve. For example, the geometries, sizes, etc. of the PCR chambers can vary. For example, in some implementations, the rotary valve can include more or fewer PCR chambers (e.g., three PCR chambers, two PCR chambers, one PCR chamber, etc.). Having a greater number of PCR chambers allows more PCR processes to be run simultaneously and / or in sequence. Different accessible PCR chambers allow for assays in which a sample is processed starting with a small reaction volume in a first PCR process followed by a larger reaction volume in a subsequent PCR reaction, for example, as typical in library preparation for sequencing. Providing separate PCR chambers allows for dried (‘spotted’) reagents in each chamber that are unique to a particular PCR reaction in the assay. In this embodiment, during manufacturing of the rotary valve device to be used in a cartridge, reagents can be applied (e.g., by spotting) in liquid form and then dried. Providing reagents directly in the PCR chambers may eliminate the need for additional reagent reservoirs, channels, and valve ports, thus reducing overall complexity and cost of the system. In some implementations, the PCR chambers can be identical; in other implementations, the PCR chambers can be different from each other.Methods of Use

[0074] The rotary carousels and / or rotary valve devices can be used to store reagents required for a variety of cartridge-based assays and protocols, such as SPRI® bead cleanup protocols and the PCR protocols described herein. For example, samples are provided in reservoirs in either the rotary carousels or the rotary valve devices, which are arranged within a cartridge, and which are accessible by the rotary carousel and / or the rotary valve. The rotary carousel and / or rotary valve can be automatically rotated to fluidly connect reservoirs in the carousel or rotary valve device to the cartridge reservoirs within a cartridge and / or within an automated analysis system into which the cartridges containing the rotary carousel and / or a rotary valve device are inserted. The rotary carousel and / or rotary valve can transfer reagents between reservoirs, e.g., using a syringe pump, as described herein. By selectively accessing individual reagents and reservoirs and selectively transferring reagents between reservoirs, the rotary carousel and / or rotary valve device can be used to automate various assay protocols (e.g., SPRI® bead protocols, PCR protocols, etc.). Forexample, the rotary carousel and / or rotary valve can access a sample contained within a reservoir, and can move the sample to a mixing reservoir. The rotary carousel and / or rotary valve can then selectively add and remove reagents and other fluids from the mixing reservoir to automate a desired assay protocol. The rotary carousel and / or rotary valve can selectively add and remove reagents from the mixing reservoir by automatically rotating to fluidly connect reservoirs in the carousel or rotary valve device to cartridge reservoirs within a cartridge. Some examples of protocols are discussed further below. The carousels and / or rotary valves described herein are generally applicable to implementing a wide range of bio / chemical assays in an automated cartridge as the carousel and / or rotary valves provide means for reagent storage, reagent access, sample intake, fluid handling and mixing / reaction chambers.Automated SPRI Cleanup Protocols

[0075] SPRI cleanup is an example of a protocol that the rotary carousels and / or rotary valve devices described herein can be used to automate. SPRI cleanup is a technique applied in isolation, purification, and cleanup procedures. The process uses SPRI® beads (Beckman Coulter) to bind selectively to specific nucleic acids (e.g., DNA and / or RNA). For example, the surfaces of the SPRI® beads can include carbonyl molecules that facilitate DNA binding. After the nucleic acids bind to the surfaces of the SPRI® beads, a magnetic field causes the beads to form a pellet on the wall of the reservoir.

[0076] The SPRI® beads can be rinsed with a washing fluid (e g., with alcohol such as ethanol, organic solvents, alcohols, phenols, and chloroform) to remove excess DNA that is not bound to the SPRI® beads. A selective buffer elutes the bound DNA from the SPRI® beads. For example, the SPRI® beads can interact with polyethylene glycol and salt to reverse the binding process. Then, the desired fragments of DNA can be extracted for analysis and further testing.

[0077] In an SPRI protocol, the rotary carousel can contain a sample of DNA, RNA, etc. For example, SPRI protocols can be run in addition to PCR protocols to clean samples so that the resulting sample contains only a desired range of fragment sizes. The rotary carousel can contain an SPRI® bead solution (e.g., containing micron-sized SPRI® beads with desired surface properties) that is mixed with the sample to clean the sample. The rotary carousel can also include a washing fluid (e.g., an 80% ethanol solution), which is mixed with the SPRI® beadsduring the cleaning process, as discussed further below. The rotary carousel can also contain other samples, reagents, buffers, primers, etc.

[0078] One example of an SPRI cleanup protocol 700 as shown in Fig. 7, includes providing a sample to a reservoir of a cartridge (702). The cartridge is inserted into an analysis system capable of executing an SPRI cleanup protocol (e.g., an automated analysis system) with the provided cartridge (704). In the described implementation, the cartridge can include the rotary valve device 600 described above. In other implementations, the cartridge can include a carousel, e.g., similar to the carousel 100 or carousel 300 described above, or other rotary valve devices, e.g., similar to the rotary valve device 500 described above. The rotary valve 602 can be automatically rotated to fluidly connect a pump of the instrument to reservoirs of the rotary carousel (706). The protocol can include transferring a desired volume of a sample (e.g., DNA, RNA, etc.) into a mixing reservoir in the rotary valve device (708). The rotary valve 602 and the connected syringe pump 604 can draw a sample from a first fluid reservoir 608a (i.e., a sample reservoir) into the channel 606. The rotary valve 602 can rotate to fluidly connect the channel 606 to a second fluid reservoir 608e (i.e., a mixing reservoir) and transfer the sample from the channel 606 into the mixing reservoir 608e. The rotary valve 602 can rotate to fluidly connect the channel 606 to a third fluid reservoir 608d (i.e., an SPRI® reagent reservoir) containing an SPRI® reagent and draw the SPRI® reagent into the channel 606. The rotary valve 602 can rotate to fluidly connect the channel 606 to the mixing reservoir 608e and transfers the SPRI® reagent from the channel 606 into the mixing reservoir 608e (710). In this fashion, the SPRI® reagent mixes with the sample in the mixing reservoir 608e.

[0079] In some implementations, the mixture of the SPRI® reagent and the sample can be triturated by repeatedly drawing the mixture into the channel 606 and pushing the mixture out of the channel 606 and back into the mixing reservoir, to make the mixture more homogenous (712). As the SPRI® beads mix with the sample, fragments of the sample bind to the suspended SPRI® beads. The mixture of SPRI® beads and sample can be left for an incubation time sufficient (e.g., several minutes) to increase the number of sample fragments that bind to the bead surfaces.

[0080] After the SPRI® reagent and the sample are sufficiently mixed, a magnet (e.g., a magnet 516 as shown in FIG. 5) can be used to pull the SPRI® beads to a wall of the mixing reservoir (714). For example, the SPRI® beads can be pulled to a wall or to a bottom of a reservoir toform a pellet. The rotary valve 602 and the syringe pump 604 can draw the supernatant (e.g., the liquid minus the SPRI® beads) from the mixing reservoir 608e and into the channel 606. Here, the pellet is not pulled into the channel 606, because the magnet is engaged. The rotary valve 602 can rotate to fluidly connect the channel 606 with a waste reservoir (not shown) and transfer the supernatant into the waste reservoir (716), for example.

[0081] The rotary valve 602 can rotate to fluidly connect the channel 606 to a fourth reservoir 608c (e.g., a washing fluid reservoir) and the syringe pump 604 can draw washing fluid (e.g., 80% ethanol) into the channel 606. The rotary valve 602 can rotate to fluidly connect the channel 606 to the mixing reservoir 608e and the syringe pump can transfer the washing fluid from the channel 606 into the mixing reservoir 608e (718). In this fashion, the washing fluid can mix with the pellet. After a predetermined period of time (e.g., several minutes), the rotary valve 602 and the syringe pump 604 can draw the washing fluid into the channel 606. Here, the SPRI® pellet is not pulled into the channel 606, because the magnet is engaged. The rotary valve 602 can rotate to fluidly connect the channel 606 with the waste reservoir, and the syringe pump 604 can transfer the used washing fluid into the waste reservoir (720). The magnet can then be disengaged so that the SPRI® beads are not pulled towards the wall of the reservoir (722). The pellet can be left in the mixing reservoir 608e for a predetermined period of time (e.g., 10 minutes) so that the pellet dries.

[0082] After the pellet is dry, the rotary valve 602 can rotate to fluidly connect with a fluid reservoir 608b (i.e., an elution buffer reservoir), and the syringe pump 604 can draw elution buffer (e.g., sodium chloride) into the channel 606. The rotary valve 602 can rotate to fluidly connect the channel 606 to the mixing reservoir 608e, and the syringe pump 604 can transfer the elution buffer out of the channel 606 and into the mixing reservoir 608e (724). The SPRI® beads re-suspend in the elution buffer when the magnet is disengaged. The elution buffer pulls the desired fragment sizes of sample from the SPRI® bead surfaces. The mixture of the elution buffer and the desired fragment sizes is the resulting product of the SPRI® cleanup protocol. The magnet can be engaged again to pull the SPRI® beads to a wall of the mixing reservoir (726) to form a pellet. The syringe pump 604 can pull the mixture of the elution buffer and the desired fragment sizes into the channel 606 to extract the supernatant elution buffer (728). Further assay protocols, e.g., PCR protocols, can utilize the desired fragment sizes suspended in the elution buffer.Automated PCR Protocols

[0083] PCR is another example of a protocol that the rotary carousels and / or rotary valve devices described herein can be used to automate. PCR is a biochemical process capable of amplifying a single DNA molecule (or RNA molecule) into millions of copies in a short time. For example, a method 800 of automated PCR, as shown in Fig. 8, can include automatically rotating a portion of a cartridge to transfer liquid between reservoirs of the cartridge (802). For example, the portion of the cartridge can be a rotary carousel, e.g., similar to the rotary carousel 300 described above, or the portion of the cartridge can be a rotary valve device, e.g., similar to the rotary valve device 600 described above. A sample can be transferred into a reservoir that is capable of conducting PCR (e.g., a PCR chamber) (804). Double-stranded DNA strands can be heated to a first temperature to separate the strands through denaturation (806). At a second temperature, primers can bind to the flanking regions of target DNA to be replicated (808). For example, the primers can bookend the desired sequence of DNA that is to be replicated. Then, polymerase (e.g., Taq polymerase, Pfu polymerase, etc.) can extend the primer along the desired sequence of DNA at a third temperature (810). This process can be cycled (e.g., 25-35 times) to produce an exponential number of exact copies of the target DNA.

[0084] A thermal cycler can be used to automate temperature cycling and incubation times required for PCR. For example, denaturing DNA strands can require a specific temperature and incubation time. In some implementations, denaturation occurs at 94-98°C for about 1-3 minutes. The time and temperature can vary depending on the nature of the target DNA and the salt concentration of the buffer. In some implementations, denaturation can occur in about, e.g., 0.2-2 minutes. Annealing the primers to the target DNA can also require specific temperature and incubation times. For example, in some implementations, annealing can occur after an incubation time of, e.g., 0.2-2 minutes at a temperature of about 55-65°C. The temperature can vary depending on the primers. Extending the primer along the desired sequence of DNA (e.g., replicating the DNA) can also require specific temperature and incubation times. For example, temperatures for activating polymerases can be about 70-75°C. The extension time can depend upon the synthesis rate of the polymerase and the length of the target DNA strand. For example, the typical extension time for Taq polymerase is one minute per kilobase (kb), while theextension time for Pfu polymerase is two minutes per kb. In some implementations, the incubation time for extension can fall within a range of about 5-15 minutes.

[0085] The method can begin by placing a sample into a PCR chamber and running a PCR amplification. The method is described as being performed by the rotary valve device 600 described above, but in other implementations, the method is performed by a rotary carousel, e.g., the rotary carousel 300 described above. The rotary valve 602 and the connected syringe pump 604 draw a sample from a sample container 608a into the channel 606. In implementations including an SPRI® cleanup protocol, the rotary valve 602 and the connected syringe pump 604 draw the mixture of elution buffer and desired fragment sizes from a mixing reservoir 608e into the channel 606 (e.g., as described above). FIG. 6A shows the channel 606 of the rotary valve 602 fluidly connected to the third fluid reservoir 608d.

[0086] The rotary valve 602 can rotate to fluidly connect the channel 606 to the first opening 612a of the first PCR chamber 610a. While the channel 606 is aligned with the first opening 612a, the air vent 616 is aligned with the second opening 614a. This allows the first PCR chamber 610a to vent while the syringe pump 604 transfers the sample from the channel 606 into the first PCR chamber 610a. FIG. 6C shows the channel 606 of the rotary valve 602 aligned with the first opening 612a of the first PCR chamber 610a and the air vent 616 of the rotary valve aligned with the second opening 614a of the first chamber 610a.

[0087] The rotary valve 602 rotates away from the first PCR chamber 610a while a thermal cycler can heat the PCR chamber 610a to amplify the sample (e.g., using the method 800 described above). For example, FIG. 6D shows the rotary valve 602 in a position where channel 606 is not aligned with the first opening 612a of the first PCR chamber 610a. In some implementations, the rotary valve can move other liquids between reservoirs (e.g., by aligning the channel 606 with a first reservoir, drawing in fluid, aligning the channel 606 with a second reservoir, and transferring the fluid) while the PCR chamber 610a is cycling.

[0088] After the PCR reaction is complete in the first PCR chamber 610a, the rotary valve 602 can align with the first opening 612a of the PCR chamber 610a to draw the sample into the channel 606 (e.g., using the syringe pump 604). The air vent 616 can be aligned with the second opening 614a while the channel 606 is aligned with the first opening 612a. FIG. 6E shows the channel of the rotary valve 602 aligned with the first opening 612 of the first PCR chamber 610a to draw fluid into the channel 606 from the first PCR chamber 610a.

[0089] The rotary valve 602 can rotate to fluidly connect the channel 606 with the mixing reservoir 608e to transfer the amplified sample into the mixing reservoir 608e. For example, FIG. 6F shows the channel 606 aligned with the mixing reservoir 608e. The amplified sample is the resulting product. In some implementations, the amplified sample can be cleaned, e.g., using an SPRI cleanup protocol as discussed above.

[0090] Although the PCR protocol is described using the first PCR chamber 610a, similar PCR protocols can utilize the PCR chambers 610b, 610c, 610d. In some implementations, multiple PCR protocols can be run simultaneously and / or in series. For example, while a PCR amplification is running in the first PCR chamber 610a, the rotary valve 602 can run a similar PCR protocol utilizing one or more of the other PCR chambers.OTHER EMBODIMENTS

[0091] While this specification contains many specific implementation details, these should not be construed as limitations on the scope of any inventions or of what may be claimed, but rather as descriptions of features specific to particular implementations of particular inventions. Certain features that are described in this specification in the context of separate implementations can also be implemented in combination in a single implementation. Conversely, various features that are described in the context of a single implementation can also be implemented in multiple implementations separately or in any suitable sub-combination. Moreover, although features may be described above as acting in certain combinations and even initially claimed as such, one or more features from a claimed combination can in some cases be excised from the combination, and the claimed combination may be directed to a sub-combination or variation of a subcombination.

[0092] Similarly, while operations are depicted in the drawings in a particular order, this should not be understood as requiring that such operations be performed in the particular order shown or in sequential order, or that all shown operations be performed, to achieve desirable results. Moreover, the separation of various system components in the implementations described above should not be understood as requiring such separation in all implementations, and it should be understood that the described program components and systems can generally be integrated together in a single software product or packaged into multiple software products.

[0093] Thus, particular implementations of the subject matter have been described. Other implementations are within the scope of the following claims. In some cases, the actions recited in the claims can be performed in a different order and still achieve desirable results. In addition, the processes depicted in the accompanying figures do not necessarily require the particular order shown, or sequential order, to achieve desirable results.

Claims

WHAT IS CLAIMED IS:

1. A rotary carousel, comprising: a base having a channel with an opening arranged on a surface of the base; a carousel comprising a plurality of reservoirs and rotatably mounted on the surface of the base, wherein each reservoir is configured to store liquid; wherein the carousel and the base are configured to be rotatable relative to one another; wherein each reservoir has an opening, such that when an opening in a reservoir aligns with the opening of the channel, the reservoir is fluidly connected to the opening of the channel and the liquid stored in the reservoir is accessible via the channel; and wherein when an opening of a reservoir is not aligned with the channel, the opening of the reservoir is sealed.

2. The rotary carousel of claim 1, wherein when the opening of the reservoir is not aligned with the channel, the opening of the reservoir is sealed by a seal arranged between the base and a bottom of the reservoir.

3. The rotary carousel of claim 2, wherein the seal is watertight.

4. The rotary carousel of any one of claims 1 to 3, wherein the base further comprises an air vent, wherein the opening of the channel is arranged at a first radial distance from a center of the base and the air vent is arranged at a second radial distance from the center of the base, wherein the second radial distance is different than the first radial distance.

5. The rotary carousel of claim 4, wherein at least one of the reservoirs comprises first and second openings, such that when the actuator rotates the first opening to align with the opening of the channel, the second opening is aligned with the air vent.

6. The rotary carousel of claim 5, wherein the first opening and the second opening are arranged at different distances from a center of the rotary carousel.

7. The rotary carousel of claim 6, wherein the reservoir with the first and second openings is arranged and controlled as a polymerase chain reaction chamber.

8. The rotary carousel of any one of claims 1 to 7, further comprising at least one foil cover over one or more, or all, of the plurality of reservoirs.

9. The rotary carousel of any one of claims 1 to 8, further comprising a receiver for an actuator to rotate the carousel relative to the base.

10. The rotary carousel of claims 9, configured for use with an analysis system comprising an actuator and a controller configured to cause the actuator to engage the receiver to rotate the carousel automatically so that an opening in a specific reservoir aligns with the opening of the channel.

11. The rotary carousel of claim 9 or claim 10, wherein the receiver comprises an opening into which the actuator fits.

12. The rotary carousel of claim 9 or claim 10, wherein the receiver comprises teeth to engage an actuator comprising a sprocket wheel.

13. The rotary carousel of any one of claims 1 to 12, wherein at least one reservoir contains a reagent.

14. The rotary carousel of any one of claims 1 to 13, wherein each reservoir has a volume between 1-100 milliliters.

15. The rotary carousel of any one of claims 1 to 14, configured for use with an analysis system that comprises a syringe pump configured to pump liquid into and / or out of a selected reservoir when the selected reservoir is fluidly connected to the channel.

16. The rotary carousel of any one of claims 1 to 15, wherein the rotary carousel is provided in a cartridge.

17. An automated method of solid-phase reversible immobilization (SPRI) cleanup, the method comprising: automatically rotating the rotary carousel of any one of claims 1 to 16 to fluidly connect a pump to reservoirs of the rotary carousel; transferring a sample from a sample reservoir of the rotary carousel to a mixing reservoir of the rotary carousel; transferring a paramagnetic bead reagent from a reagent reservoir of the rotary carousel into the mixing reservoir, such that the paramagnetic bead reagent mixes with the sample; triturating the paramagnetic bead reagent and the sample within the mixing reservoir; engaging and disengaging a magnet to form pellets from the paramagnetic bead reagent; transferring a supernatant from the mixing reservoir into a waste reservoir of the rotary carousel; transferring a washing fluid from a washing fluid reservoir of the rotary carousel into the mixing reservoir, such that the washing fluid contacts the paramagnetic bead reagent; transferring the washing fluid from the mixing reservoir into a waste reservoir; transferring an elution buffer from an elution buffer reservoir of the rotary carousel into the mixing reservoir, such that the elution buffer contacts the paramagnetic bead reagent; and extracting the elution buffer.

18. An automated method of conducting polymerase chain reaction (PCR), the method comprising: automatically rotating the rotary carousel of any one of claims 5 to 16 to transfer liquid between reservoirs of the rotary carousel; transferring a sample from a sample reservoir of the rotary carousel into the polymerase chain reaction chamber of the rotary carousel; denaturing the nucleic acid sample in the reservoir by heating the polymerase chain reaction chamber to a first temperature sufficient to denature the nucleic acid sample;annealing primers to the nucleic acid sample in the polymerase chain reaction chamber by heating the polymerase chain reaction chamber to a second temperature sufficient to anneal the primers; extending the primers along the nucleic acid sample in the polymerase chain reaction chamber by heating the polymerase chain reaction chamber to a third temperature sufficient to extend the primers; and transferring the nucleic acid sample from the polymerase chain reaction chamber into a mixing reservoir of the rotary carousel, wherein the mixing reservoir is one of the plurality of reservoirs.

19. The method of claim 18, wherein the first temperature is within a range of 94 to 98°C.

20. The method of claim 18 or claim 19, wherein the second temperature is within a range of 55 to 65°C.

21. The method of any one of claims 18 to 20, wherein the third temperature is within a range of 70 to 75°C.

22. The method of any one of claims 18 to 21, further comprising transferring a paramagnetic bead reagent from a reagent reservoir into the mixing reservoir, such that the paramagnetic bead reagent mixes with the nucleic acid sample, wherein the reagent reservoir is one of the plurality of reservoirs of the rotary carousel.

23. A rotary valve device, comprising: a base; a plurality of reservoirs mounted on the base, wherein each reservoir is configured to store liquid; and a rotary valve rotatably mounted to the base and comprising a channel with an opening; wherein each reservoir has an opening, such that when the opening of the channel aligns with an opening in a reservoir, the reservoir is fluidly connected to the opening of the channel and the liquid stored in the reservoir is accessible via the channel; andwherein when an opening of a reservoir is not aligned with the channel, the opening of the reservoir is sealed.

24. The rotary valve device of claim 23, wherein when the opening of the reservoir is not aligned with the channel, the opening of the reservoir is sealed by a seal arranged between the base and a bottom of the reservoir.

25. The rotary valve device of claim 24, wherein the seal is watertight.

26. The rotary valve device of claim 23, wherein the rotary valve further comprises an air vent.

27. The rotary valve device of claim 26, wherein at least one of the reservoirs has a first opening and a second opening, such that when the actuator rotates the opening of the channel to align with the first opening, the air vent is aligned with the second opening.

28. The rotary valve device of claim 27, wherein the first opening and the second opening are arranged at different distances from a center of the rotary valve.

29. The rotary valve device of claim 28, wherein the reservoir with the first and second openings is arranged and controlled as a polymerase chain reaction chamber.

30. The rotary valve device of any one of claims 23 to 29, further comprising at least one foil cover over one or more, or all, of the plurality of reservoirs.

31. The rotary valve device of any one of claims 23 to 30, further comprising a receiver for an actuator to rotate the rotary valve with respect to the base.

32. The rotary valve device of claim 31, configured for use with an analysis system comprising an actuator and a controller configured to cause the actuator to engage the receiver torotate the rotary valve automatically so that the opening of the channel aligns with an opening in a specific reservoir.

33. The rotary valve device of claim 31 or claim 32, wherein the receiver comprises an opening into which the actuator fits.

34. The rotary valve device of claim 31 or claim 32, wherein the receiver comprises teeth to engage an actuator comprising a sprocket wheel.

35. The rotary valve device of any one of claims 23 to 34, wherein at least one reservoir contains a reagent.

36. The rotary valve device of any one of claims 23 to 35, wherein each reservoir has a volume from about 1.0 microliter to about 100 milliliters.

37. The rotary valve device of any one of claims 23 to 36, configured for use with an analysis system that comprises a syringe pump configured to pump liquid into and / or out of a selected reservoir when the selected reservoir is fluidly connected to the channel.

38. The rotary valve device of any one of claims 23 to 37, wherein the rotary valve is provided on a cartridge.

39. An automated method of solid-phase reversible immobilization (SPRI) cleanup, the method comprising: automatically rotating the rotary valve device of any one of claims 23 to 38; transferring a sample from a sample reservoir of the rotary valve device to a mixing reservoir of the rotary valve device; transferring a paramagnetic bead reagent from a reagent reservoir of the rotary valve device into the mixing reservoir, such that the paramagnetic bead reagent mixes with the of sample; triturating the paramagnetic bead reagent and the sample within the mixing reservoir;engaging and disengaging a magnet to form a pellet from the paramagnetic bead reagent; transferring a supernatant from the mixing reservoir into a waste reservoir of the rotary valve device; transferring a washing fluid from a washing fluid reservoir of the rotary valve device into the mixing reservoir, such that the washing fluid contacts the pellet; transferring the washing fluid from the mixing reservoir into the waste reservoir; transferring an elution buffer from an elution buffer reservoir of the rotary valve device into mixing reservoir, such that the elution buffer contacts the pellet; and extracting the elution buffer.

40. An automated method of conducting polymerase chain reaction (PCR), the method comprising: automatically rotating the rotary valve device of any one of claims 23 to 38 to transfer liquid between reservoirs of the rotary valve device; transferring a sample from a sample reservoir of the rotary valve device into a polymerase chain reaction chamber of the rotary valve device; denaturing the nucleic acid sample in the polymerase chain reaction chamber by heating the polymerase chain reaction chamber to a first temperature sufficient to denature the nucleic acid sample; annealing primers to the nucleic acid sample in the polymerase chain reaction chamber by heating the polymerase chain reaction chamber to a second temperature sufficient to anneal the primers; extending the primers along the nucleic acid sample in the polymerase chain reaction chamber by heating the polymerase chain reaction chamber to a third temperature sufficient to extend the primers; and transferring the nucleic acid sample from the polymerase chain reaction chamber into a mixing reservoir of the rotary valve device, wherein the mixing reservoir is one of the plurality of reservoirs.

41. The method of claim 40, wherein the first temperature is within a range of 94 to 98°C.

42. The method of claim 40 or 41 , wherein the second temperature is within a range of 55 to65°C.

43. The method of any one of claims 40 to 42, wherein the third temperature is within a range of 70 to 75°C.

44. The method of any one of claims 40 to 43, further comprising transferring a paramagnetic bead reagent from a reagent reservoir into the mixing reservoir, such that the paramagnetic bead reagent mixes with the nucleic acid sample, wherein the reagent reservoir is one of the plurality of reservoirs of the rotary carousel.

45. The method of any one of claims 40 to 44, wherein denaturing the sample within the polymerase chain reaction chamber occurs while the channel and the air vent are not fluidly connected with the polymerase chain reaction chamber.

46. The method of any one of claims 40 to 45, wherein the polymerase chain reaction chamber is a first polymerase chain reaction chamber, and wherein the method further comprises: transferring the sample from the polymerase chain reaction chamber into the rotary valve; and transferring the sample into a second polymerase chain reaction chamber, wherein the second polymerase chain reaction chamber has a different volume than the first polymerase chain reaction chamber .

47. The method of any one of claims 40 to 46, further comprising: transferring the sample from the rotary valve device into a mixing reservoir; transferring paramagnetic bead reagent from a reagent reservoir into the rotary valve device; transferring the paramagnetic bead reagent into the mixing reservoir to mix the paramagnetic bead reagent with the sample;engaging a magnet with the mixing reservoir to pull the paramagnetic bead reagent to a wall of the mixing reservoir; and transferring the sample from the mixing reservoir into the rotary valve device.

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