Sample preparation device and method of using the same

Abstract

Aspects of the present disclosure include a sample preparation cartridge including a cylindrical structure and one or more covers. The cylindrical structure further includes an upper wall, a lower wall, an annular wall, a plurality of cavities in the annular wall forming chambers with a plurality of open sides of the annular wall, and one or more interconnects providing fluid communication between the plurality of chambers. The one or more covers cover the open sides of the plurality of chambers. A cylindrical housing is also provided that includes one or more magnets. The sample preparation cartridge is removably positioned within or adjacent to the cylindrical housing. Methods of using the sample preparation device are also provided.

Description

Technical Field

[0001] Cross - reference to Related Applications This application claims the benefit of U.S. Provisional Patent Application No. 62 / 955,259, filed December 30, 2019; U.S. Provisional Patent Application No. 63 / 023,659, filed May 12, 2020; U.S. Provisional Patent Application No. 63 / 050,251, filed July 10, 2020; and U.S. Provisional Patent Application No. 63 / 066,683, filed August 17, 2020, which are hereby incorporated by reference in their entirety.

Summary of the Invention

Problems to be Solved by the Invention

[0002] Isolation and purification of nucleic acids are a series of molecular biology techniques used for the extraction of DNA and RNA for use in downstream applications. Isolation and purification methods of nucleic acids include column - based isolation and purification, reagent - based isolation and purification, magnetic bead - based isolation and purification, and other techniques. Reagents, kits, and equipment used for the isolation and purification of nucleic acids are available. Inadequate sample preparation can lead to sub - optimal results in downstream applications, and for this reason, optimized versions of kits have emerged to address variations in sample sources such as blood, plant tissue, fungi, or bacteria.

[0003] The sample preparation process includes the release of target nucleic acids from their native biological sources using chaotropic nucleic acid extraction techniques (e.g., lysis of cells such as patient cells, or lysis of microorganisms such as viruses, bacteria, fungi), binding of nucleic acids to a solid phase (e.g., paramagnetic particles) using silica or iron oxide nucleic acid chemistry, separation of the solid phase from the residual lysate using magnetic separation techniques, washing to remove unwanted substances, and elution or separation of nucleic acids from the solid phase using fluid handling techniques. When the sample preparation protocol is complete, the sample is transferred to the PCR component of the device for nucleic acid detection.

Means for Solving the Problems

[0004] Aspects of the present disclosure include sample preparation cartridges, sample preparation systems, and sample preparation devices for preparing a sample, for example, for concentrating or isolating a target analyte such as nucleic acid present in the sample.

[0005] The sample preparation cartridge includes a cylindrical structure having a plurality of chambers disposed along an annular wall of the structure, and a cover attached onto an outer surface of the annular wall to fluid-tightly cover an opening side surface of the chamber, wherein the annular wall includes a cavity forming the opening side surface of each chamber.

[0006] The sample preparation system includes a sample preparation cartridge and a cylinder housing including one or more magnets. The cartridge is removably disposed within the cylinder housing. In some embodiments, the magnets are external to the cartridge and are used to transfer paramagnetic particles between the chambers of the cartridge.

[0007] The sample preparation device includes a cavity for reversibly engaging a portion of the cartridge. The sample preparation device may include a magnet disposed therein and configured to transfer paramagnetic particles between the chambers of the cartridge. The sample preparation device may include a cavity for reversibly engaging a portion of the cartridge and a surface for attaching the cylinder housing. Some embodiments also provide a sample preparation device that uses a motor to drive the rotation of a cartridge disposed therein. The motor can be automated. The motor can also be controlled by a computer program that, when executed by a processor, causes the motor to rotate the cartridge in a predetermined manner.

[0008] A method of using the sample preparation device is also provided. The method can be semi-automated or fully automated for performing sample preparation. BRIEF DESCRIPTION OF THE DRAWINGS

[0009]

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[0010] Aspects of the present disclosure include a sample preparation cartridge, a sample preparation system, and a sample preparation device for preparing a sample, for example, to concentrate or isolate a target analyte such as nucleic acid present in the sample.

[0011] The sample preparation cartridge includes a cylindrical structure having a plurality of chambers arranged along an annular wall of the structure, and a cover attached onto the outer surface of the annular wall to fluid - seal by covering the opening side surfaces of the chambers. The annular wall has cavities forming the opening side surfaces of each chamber.

[0012] The sample preparation system includes a sample preparation cartridge and a cylinder housing having one or more magnets. The cartridge is removably disposed within the cylinder housing. In some embodiments, the magnets are external to the cartridge and are used to transfer magnetic particles between the chambers of the cartridge.

[0013] The sample preparation device includes a cavity for reversibly engaging a portion of the cartridge. The sample preparation device can include a magnet that is disposed therein and configured to transfer magnetic particles between chambers of the cartridge. The sample preparation device can include a cavity for reversibly engaging a portion of the cartridge and a surface for attaching the cylinder housing. Some embodiments also provide a sample preparation device that uses a motor to drive the rotation of a cartridge disposed therein. The motor can be automated. The motor can also be controlled by a computer program that, when executed by a processor, causes the motor to rotate the cartridge in a predetermined manner.

[0014] A method of using the sample preparation device is also provided. The method can be semi-automated or fully automated for performing sample preparation.

[0015] Before explaining the sample preparation device and method of the present invention in more detail, it is understood that the present disclosure is not limited to the specific embodiments described. It is also understood that the terms used herein are for the purpose of describing particular embodiments only and are not intended to be limiting.

[0016] When a range of values is provided, unless otherwise clearly defined in context to have another meaning, each value that lies within one-tenth of the unit of the lower limit, between the upper and lower limits of the range, and any other stated value or intermediate value within the stated range is understood to be encompassed within the sample preparation cartridge, method, and sample preparation unit of the present invention. The upper and lower limits of these smaller ranges may be independently included in the smaller ranges and are also encompassed within the sample preparation cartridge, method, and sample preparation unit of the present invention and are subject to any specifically excluded limits within the stated range. When the stated range includes one or both of the limits, ranges excluding either or both of these included limits are also included in the sample preparation cartridge, method, and sample preparation unit.

[0017] Certain ranges are presented herein by numerical values preceded by the term "about". The term "about" is used herein to provide literal support for the exact number that it precedes, as well as numbers that are close to or approximate the number that the term precedes. In determining whether a number is close to or approximate the specifically recited number, a number that is not otherwise described as close to or approximate may be a number that provides a substantial equivalent of the specifically recited number in the context in which it is presented.

[0018] 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 disclosure belongs. Any methods and materials similar to or equivalent to those described herein can also be used in the practice or testing of the sample preparation cartridge, method, and sample preparation unit of the present invention, but representative exemplary sample preparation cartridges, methods, and sample preparation units are described herein.

[0019] All publications and patents cited in this specification are hereby incorporated by reference as if each individual publication or patent was specifically and individually indicated to be incorporated by reference, and are incorporated by reference herein to disclose and describe methods and / or materials in connection with the cited publications. The citation of any publication is for its disclosure prior to the filing date and should not be construed as an admission that the present invention has a right to antedate such disclosure by virtue of a prior-filed invention. Further, the provided publication dates may be different from the actual publication dates and may need to be independently verified.

[0020] Note that, as used in this specification and the appended claims, the singular forms "a," "an," and "the" include plural referents unless the context clearly dictates otherwise. Further note that the claims may be drafted to exclude any optional element. Accordingly, this description is intended to serve as a basis for antecedent basis for the use of exclusive terms such as "solely," "only," etc. in connection with the recitation of claim elements or the use of "negative" limitations.

[0021] As will be apparent to those of ordinary skill in the art upon reading this disclosure, each of the individual embodiments described and illustrated herein may have separate components and functional parts that can be easily separated from or combined with any of the functional parts of any of several other embodiments without departing from the scope or spirit of the sample preparation cartridge, method, and sample preparation unit of the present invention. Any of the recited methods can be performed in the order of recited events or in any other order that is logically possible.

[0022] Sample preparation cartridge As summarized above, aspects of the present disclosure include a sample preparation cartridge. According to certain embodiments, the sample preparation cartridge has a substantially cylindrical shape. The sample preparation cartridge includes a cylindrical structure having an upper end, a lower end, and an annular wall extending between the upper end and the lower end. The cylindrical structure includes a plurality of chambers present in the annular wall, one or more channels providing fluid communication between the plurality of chambers, and one or more covers attached over the outer surface of the annular wall to fluidly seal the open side surfaces of the chambers and the depressions. The chambers extend between the outer surface of the annular wall and the interior of the cylindrical structure. The annular wall has cavities forming the open side surfaces of each chamber. The channels are formed by depressions in the annular wall and have open side surfaces.

[0023] Furthermore, in certain embodiments, the sample preparation cartridge may also include a buffer pack, a sealing lid assembly, a protective cover, and a cap. The cartridge may also include a sample input component. The sample preparation cartridge is configured to be used with a cylinder housing having a magnet.

[0024] Each of these components will be described in further detail below.

[0025] Cylindrical structure The term "cylindrical" means that the cylindrical structure can be substantially a right circular cylinder. The cylindrical structure can be rotatable about an axis formed by a line connecting the center of the lower end of the cylindrical structure and the center of the upper end of the cylindrical structure. For example, the cylindrical structure can rotate clockwise or counterclockwise when looking down at the cylindrical structure from above its top. Alternatively, the cylindrical structure can rotate in both clockwise and counterclockwise directions. In some cases, the range of motion of the cylindrical structure can include less than a full rotation around the axis of the cylinder, for example, 3 / 4 rotation, or 1 / 2 rotation, or 1 / 3 rotation. In certain embodiments, the cylindrical structure can rotate a full rotation in the clockwise direction and a full rotation in the counterclockwise direction. In certain embodiments, the cylindrical structure can rotate a full rotation in the clockwise direction and less than a full rotation in the counterclockwise direction, or vice versa. The rotation of the cylindrical structure can be used to mix the contents of one or more chambers, or to arrange magnets present within the cylinder housing adjacent to the chambers to agglomerate magnetic particles present within the chambers and / or transfer the agglomerated magnetic beads from one chamber to another chamber, etc.

[0026] As summarized above, the cylindrical structure includes a plurality of cavities of an annular wall that form a chamber having a plurality of open side surfaces of the annular wall. For example, the plurality of cavities can be recesses of the annular wall that deform a continuous surface of the annular wall. The open side surface means the side surface of the chamber not covered by the annular wall. In one example, the deformed annular wall forms the closed side of the chamber, and the region corresponding to the side surface of the annular wall deformed to form the cavity can form the open side surface of the chamber.

[0027] According to certain embodiments, the opening side surfaces of the plurality of chambers are on the outer surface of the annular wall. For example, the annular wall deforms from the outside inward to form a cavity deformed inward of the annular wall. In such a case, the opening side surface of the chamber can be a region corresponding to the side surface of the annular wall deformed inward to form the cavity. In such a situation, the annular wall deformed inward can form the closed side of the chamber. The volume of the chamber can represent a measurement corresponding to the volume of the recess of the annular wall. The chamber can, in some cases, be 1 cm 3 to about 5 cm 3 , for example, 1 cm 3 to 3 cm 3 or 2 cm 3 to 5 cm 3 and can be any convenient volume within this range. In other cases, the chamber can, in some cases, accommodate any convenient volume of fluid in the range of 1 μL to about 5,000 μL, for example, 1 μL to 100 μL or 1,000 μL to 3,000 μL or 2,000 μL to 5,000 μL. Each chamber of the plurality of chambers can have the same volume or different volumes. The depth of the chamber, measured as the distance from the outer surface of the annular wall to the inside of the chamber, can, in some cases, be any convenient size of 0.1 cm or more, for example 1 cm or 5 cm. Each chamber of the plurality of chambers can have the same depth or different depths.

[0028] According to certain embodiments, the plurality of chambers are disposed proximally to each other on the annular wall. For example, the distance between the lateral boundary of the first chamber and the closest lateral boundary of the second chamber can be about 0.1 cm or more, such as 0.5 cm to 1 cm, for example, 0.5 cm or 0.75 cm or 5 cm. The distance between the side surfaces of a pair of chambers disposed close to each other can be the same or different among the plurality of chambers.

[0029] As summarized above, the sample preparation cartridge includes one or more channels that provide fluid communication between a plurality of chambers. In certain embodiments, the channels are wide enough to pass one or more PMPs, such as aggregates of PMPs. In certain embodiments, one or more of the channels between the chambers are formed by depressions in an annular wall. The depressions in the annular wall mean recesses or cavities in the annular wall that can provide fluid communication between the chambers. In some cases, the depression is formed on the outer surface of the annular wall such that a first chamber and a second chamber having an open side surface on the outer surface of the annular wall are interconnected by such a depression on the outer surface of the annular wall between the first chamber and the second chamber. The depressions in the annular wall can be of any convenient length, width, and depth.

[0030] In certain embodiments, the depression is disposed on the side of the plurality of chambers. The side of the plurality of chambers means the left side or the right side, rather than the upper side or the lower side of the chamber, when the axis of the cylindrical structure formed between the center of the lower end and the center of the upper end of the cylindrical structure is vertically oriented. Disposing the depression on the side of the plurality of chambers means that the depression can interconnect the right side of the first chamber and the left side of the second chamber such that the first chamber and the second chamber are in fluid communication with each other through the depression. The depression between the chambers can be substantially straight between a point on the first chamber and a point on the second chamber. The depression between the first chamber and the second chamber can have substantially the same width and depth in the annular wall over the entire length of the depression or can be different. The depressions between different pairs of chambers can have different dimensions or the same dimensions. The depression is configured in a convenient shape such that PMPs can be transferred therethrough.

[0031] In some embodiments, the depressions are disposed at a substantially constant height above the lower end of the cylindrical structure on the sides of one or more chambers. In these embodiments, the depressions between pairs of chambers can be substantially linear. In these embodiments, the depressions and chambers can be shaped such that there is a straight-line path starting at the leftmost position of the leftmost chamber and passing through each of the plurality of chambers to the rightmost position of the rightmost chamber. This straight line is generally substantially parallel to the lower end of the cylindrical structure. The depressions on the sides of the one or more chambers can be disposed at any convenient height above the lower end of the cylindrical structure. In some of these embodiments, the height above the lower end of the cylindrical structure at which the depressions are disposed corresponds to the vertical midpoint of one or more of the chambers.

[0032] One or more of the plurality of chambers can be substantially cube-shaped, cube-like, oval, or spherical, or combinations thereof, or can have an irregular shape. An irregular shape means that there is no axis of symmetry. A combination of shapes means that one side of one or more chambers can be one shape, for example, a rectangular side, and the remainder of the chamber can have another shape, for example, an oval shape or a spherical shape. Another example of a chamber having a combination of shapes is a cube or cube-like with rounded corners, or an oval or spherical shape with a substantially flat wall. In one example, the sides of one or more chambers formed by the cover and the outer surface of the cylindrical structure are optionally shaped as a square or rectangle with rounded corners, and the remainder of the one or more chambers can have an oval shape. In another embodiment, the chambers can have an oval shape. In some cases, the chambers are arranged such that the axis of symmetry along the shortest part of the oval is parallel to the bottom of the cylindrical structure. In other embodiments, one or more of the plurality of chambers are generally rectangular. A generally rectangular chamber means that the two-dimensional shape of the recess into the annular wall is more elongated than it is wide. The height and width of each chamber can be any convenient height and width. The height and width of each rectangular chamber can be the same or different.

[0033] In certain embodiments, the shape of a chamber connected to another chamber by one or more channels is such that, with respect to the lateral portion of the chamber proximal to the channel, the height of the chamber at each lateral position of the chamber decreases as that position approaches the channel. In some cases, the height of the chamber at each such lateral position decreases linearly to form a tapered region. Such a tapered inlet to the recess may facilitate the transfer of aggregated PMP from the chamber to the channel.

[0034] In certain embodiments, one or more of the chambers comprise a discharge hole. A discharge hole means a hole through which fluid can exit the chamber. For example, fluid can be discharged under the influence of gravity from a discharge hole present at the bottom of the chamber. Alternatively, pressure can be applied to the fluid in the chamber by a plunger to extrude the fluid from the chamber. In one example, only one of the chambers configured to be used as an elution chamber by filling it with an elution buffer has a discharge hole, and the remaining chambers, e.g., the first and second chambers, may not have a discharge hole.

[0035] One or more of the chambers may have an opening configured to vent the chamber and / or fill the chamber with fluid. In one example, the opening may be used to discharge fluid from the chamber.

[0036] In certain embodiments, one or more wells are provided inside a cylindrical structure. A well means one or more enclosures inside the cylindrical structure. The enclosures can be of any convenient dimensions or shape. For example, the enclosures can be substantially cylindrical having a closed lower end, an annular wall, and an open upper end. In these embodiments, the cylindrical structure may further comprise channels within the cylindrical structure that provide fluid communication between such wells and one or more of the plurality of chambers. In some cases, each well is interconnected with a separate chamber via one or more channels.

[0037] In certain embodiments, the plurality of chambers form a first chamber, a second chamber, and a third chamber. In certain embodiments, the first chamber is adjacent to the second chamber, the second chamber is adjacent to the first and third chambers, and the third chamber is adjacent to the second chamber. In certain embodiments, the cylindrical structure further includes a first recess in the annular wall that provides fluid communication between the first chamber and the second chamber, and a second recess in the annular wall that provides fluid communication between the second chamber and the third chamber. In certain embodiments, the first chamber is a lysis chamber, the second chamber is an immiscible phase chamber, and the third chamber is an elution chamber. The lysis chamber refers to a chamber that stores a lysis buffer, such as a fluid that is a lysis buffer, during use of the sample preparation cartridge. The immiscible phase chamber refers to a chamber that stores an immiscible phase, such as a fluid that is immiscible with the aqueous phase, during use of the sample preparation cartridge. In some cases, the immiscible phase is oil. In other cases, the immiscible phase is air. The elution chamber refers to a chamber that stores an elution buffer, such as a fluid that is an elution buffer, during use of the sample preparation device.

[0038] The first chamber may have an opening at the top of the chamber. This opening may be configured as an inlet. The inlet may be configured to introduce a lysis buffer, a sample, and / or a mixture thereof. Thus, the inlet may have a diameter suitable for pipetting, injecting, or pumping a lysis buffer, a sample, and / or a mixture thereof. In some cases, the second chamber may also have an opening at the top of the chamber. This opening may be configured as an inlet for introducing an immiscible phase, such as oil, into the second chamber. In some cases, the third chamber may also have an opening at the top of the chamber. This opening may be configured as an inlet for introducing an elution buffer into the third chamber.

[0039] In some examples, the first chamber may include a compartment disposed at or below the bottom region of the first chamber. The compartment may have an opening that fluidly connects the compartment to the interior of the first chamber. The compartment may store paramagnetic particles (PMPs). The PMPs may be lyophilized. In some embodiments, the first chamber has an opening at the bottom of the chamber, the opening being configured as an inlet for the lysis buffer, and the first chamber has an opening configured as a sample inlet at the top of the first chamber. In some embodiments, the compartment includes an inlet that fluidly connects the compartment to a channel and an outlet that fluidly connects the compartment to the interior of the first chamber.

[0040] Paramagnetic particles (PMPs) and magnetic particles are used interchangeably herein and refer to particles that respond to magnetism. Magnetic-responsive particles include or consist of a magnetic-responsive material. Examples of magnetic-responsive materials include paramagnetic materials, ferromagnetic materials, ferrimagnetic materials, and metamagnetic materials. Examples of suitable paramagnetic materials include iron, nickel, and cobalt, and metal oxides such as Fe 3 O 4 , BaFe 12 O 19 , CoO, NiO, Mn 2 O 3 , Cr 2 O 3 , and CoMnP. The PMPs can be composed of a paramagnetic material encapsulated in a non-magnetic polymer, such as a magnetic material covered with a polymeric material or a magnetic material incorporated into a polymer matrix. Such particles may sometimes be referred to as magnetic beads or paramagnetic beads.

[0041] In one example, the second chamber may not have an opening other than the interconnection with the first and third chambers. The second chamber can store air. When the first and third chambers are filled with liquid, since there is no vent in the second chamber, the air in the second chamber is compressed. The compressed air functions as a "cleaning" environment for the PMP that is transferred from the first chamber through the second chamber that stores the compressed air to the third chamber.

[0042] In one example, the third chamber has an opening in the bottom region of the chamber. This opening is configured to discharge from the third chamber. The third chamber has an opening in the bottom region of the chamber, and this opening is separate from the opening for discharging from the third chamber and is configured to fill the third chamber. In one example, the discharge hole may have a smaller diameter than the filling hole such that the discharge hole does not allow liquid to pass under atmospheric pressure and a higher pressure is required for the liquid to pass. In some cases, the opening at the bottom of the third chamber is fluidly connected to one or more collection containers. The collection containers can be two separate tubes suitable for PCR, for example, thin-walled polypropylene tubes. The opening at the bottom of the third chamber can be fluidly connected to two channels branching from the opening to fill two collection containers with substantially equal volumes of liquid discharged from the third chamber.

[0043] A cylindrical structure according to one embodiment is shown in FIG. 1A. In this example, the cylindrical structure 400 includes three cavities of an annular wall that form chambers 410a, 410b, and 410c having three open side surfaces of the annular wall, and two depressions that form an interconnecting portion 420 having an open side surface. As can be seen, the open side surfaces of chambers 410a, 410b, and 410c are on the outer surface of the annular wall, and chambers 410a, 410b, and 410c are arranged adjacent to each other. The two interconnecting portions 420 between chambers 410a, 410b, and 410c provide fluid communication between the chambers. In this example, the interconnecting portion 420 is a channel that is a depression in the annular wall, and the interconnecting portion 420 is disposed on the sides of the plurality of chambers 410a, 410b, and 410c. As illustrated in the drawing, the depressions that form the interconnecting portion 420 between chambers 410a, 410b, and 410c are at a substantially constant height above the lower end of the cylindrical structure 400. Also visible in the example is a drain hole 430 in one of the chambers. Each chamber further includes vents (450a, 450b, and 450c). The vents can be used to vent air from the chambers. Alternatively or in addition, the vents can also be used as inlets for filling the chambers with liquid. In one embodiment, the second chamber 410b is an air chamber and does not include a vent 450b. Further, the cylindrical structure 400 includes a well 440. As can be seen, the well 440 is disposed inside the cylindrical structure 400.

[0044] Cover As summarized above, the sample preparation cartridge includes interconnects for forming channels and one or more covers that cover the open side surfaces of the plurality of chambers. In certain embodiments, the cover is curved to conform to the outer surface of the cylindrical structure. Being curved means that the cover is not substantially flat when attached to the cylindrical structure. Covering the open side surfaces of the plurality of chambers means that the cover can be arranged to be present over the open side surfaces of the chambers formed in the annular wall. In one example, when the cover covers the chamber, the chamber cannot be accessed from the outside of the cylindrical structure. When the cover covers the chamber, the fluid disposed within the chamber is contained within the chamber. The use of a cover to form the walls of the chambers of the cylindrical device allows for walls that are significantly thinner than the annular wall of the cylindrical structure. The use of a cover to form the walls of the chambers of the cylindrical device allows for walls made from a material different from that of the cylindrical structure. In certain embodiments, a single cover can cover all of the plurality of chambers, or can cover all or a subset of the subset of the plurality of chambers and the interconnects between the chambers. The cover can be of any convenient size and shape, and the size and shape of the cover can be varied.

[0045] The cover can be made from any suitable material that can be attached to the outer surface of the curved and annular wall. For example, the cover can be made from plastic, metal, paper, glass, etc. When a metal material is used for the cover, the metal can be non-magnetic, i.e., it does not contain a large amount of iron. The paper cover can include a non-wetting coating, such as a wax coating. The cover can be substantially opaque or substantially transparent. The cover can be attached to the annular wall by any suitable means, such as by an adhesive, by locally heating the outer side of the annular wall or the cover or both, by fitting the cover into a groove made in the annular wall, or by screwing the cover onto the annular wall. The cover can be made sufficiently thin so that the magnetic force of the external magnet does not significantly decrease within the chamber. For example, the cover can be thin enough so that in response to the external magnet being arranged adjacent to the chamber, the paramagnetic particles (PMPs) present within the chamber aggregate, and in response to the relative movement between the cylindrical structure and the external magnet, the aggregated PMPs move through a channel connecting the adjacent chambers. The cover can have a thickness of less than 1 cm, less than 0.5 cm, less than 0.1 cm, for example, 1 mm to 5 mm. In certain embodiments, the cover can be a film, such as an adhesive film.

[0046] According to certain embodiments, the cover fluidly seals the opening side surfaces of the plurality of chambers. Fluidly sealing the opening side surfaces of the plurality of chambers means that when the cover is positioned on the cylindrical structure, the internal space of the chamber is not in fluid communication with the external space of the cylindrical structure through the opening side surface of the chamber.

[0047] According to certain embodiments, the inner surface of the cover facilitates the movement of the PMP on the cover. An analyte of interest can be attached to the PMP used for sample preparation, for example, a nucleic acid can be attached. The nucleic acid can be attached to the surface of the PMP by nucleic acid chemistry of silica or iron oxide. Facilitating the movement of the PMP means that the inner surface of the cover can be configured such that the PMP can move more reliably from a first position on the cover to a second position on the cover while remaining in contact with the inner surface of the cover. For example, the inner surface of the cover can be polished to reduce the friction between the PMP and the inner surface of the cover when the PMP moves along the cover. Moving from a first position on the cover to a second position on the cover means, in some cases, that the PMP moves along the inner surface of the cover, or in some cases, that the inner surface of the cover moves from the first position to the second position and the PMP is held in a fixed position, or in some cases, that both the PMP and the cover move.

[0048] A cylindrical structure according to an embodiment is shown in FIG. 1B. In this example, the cylindrical structure 500 is the same as that shown in FIG. 1A. FIG. 1B also shows a cover 510. The open side surface of the chamber (not shown) is on the outer surface of the annular wall. As can be seen, the cover 510 is curved to fit the outer surface of the cylindrical structure 500 and fluid-tightly seals the open side surfaces of the chamber and the interconnecting portion.

[0049] A cylindrical structure similar to the cylindrical structure shown in FIG. 1B according to an embodiment of the present disclosure is shown in FIG. 1C. In this figure, the cylindrical structure 500 and the cover 510 are shown disassembled for illustration purposes. In this example, the cylindrical structure 500 includes three cavities of an annular wall 530 that form a chamber 520 with a plurality of open side surfaces of the annular wall 530. As can be seen, the cover 510 is curved to fit the outer surface of the cylindrical structure 500 and fluid-tightly seals the open side surfaces of the chamber 520 and the interconnecting portion.

[0050] In FIGS. 1A - 1C, recesses 445 and 545 are also visible. These recesses can function as a housing for additional functions. For example, the recesses can implement a barcode or a QR code. The code may be printed directly on the cartridge or on a substrate that is attached to the cartridge. The code can be used to assign a unique identifier to the cartridge. The depth and position of the recesses can be matched to the position of the code reader to ensure proper focusing and alignment of the code reader.

[0051] FIG. 1C shows additional sealing films 550 and 560 that cooperate to provide upper and lower walls of channels 515a, 515b, and 515c that connect chambers 520a, 520b, and 520c to individual wells 540a, 540b, and 540c in an embodiment where the wells are included in cartridge 500. For example, channels 515a, 515b, and 515c are openings in the lower wall of the cartridge, and the openings extend from the bottom of the well to the vent / entrance of the chamber. The side walls of the openings are formed by the lower wall, and the upper and lower walls are provided by sealing films 550 and 560, respectively.

[0052] FIG. 1D shows an embodiment of a cartridge that includes a chamber 410a having a compartment 411 disposed in the bottom region. The compartment 411 includes an opening that fluidly connects the compartment to the interior of the chamber. The compartment stores paramagnetic particles (PMPs) (not shown). During use of the cartridge, in some examples, a buffer disposed in the first chamber 410a can fill the compartment, and the PMPs can flow into the chamber. In another example, a channel can be present below the compartment that is connected to a fluid pack of a buffer pack. The buffer pack (e.g., a lysis buffer) can flow into the channel and wash the PMPs from the compartment into chamber 410a.

[0053] In other embodiments, the cartridge may include a plurality of chambers having openings in the top region. The opening in the top region of the first chamber may be used to introduce a lysis buffer, a PMP, and a sample into the first chamber. The second chamber may store air as an immiscible phase and may not have an opening (other than the interconnections to the first and third chambers). The second chamber may store oil as an immiscible phase and may have an opening in the top region for introducing the oil into the second chamber. The third chamber may have an opening for introducing an elution buffer into the third chamber. This opening of the third chamber may also be used to remove the elution buffer or a portion thereof for analysis (e.g., PCR).

[0054] Buffer pack In certain embodiments, the sample preparation cartridge may include a buffer pack. The buffer pack may include one or more fluid packs. Each fluid pack may contain a fluid. The fluid pack may contain any convenient amount of any convenient fluid. In some embodiments, the fluid pack may include each of a lysis buffer pack, an immiscible phase pack, and an elution buffer pack. In some embodiments, the fluid pack may include a lysis buffer pack and an elution buffer pack. In certain embodiments, the immiscible phase may include oil. In certain embodiments, the immiscible phase may include air. In some cases, one or more of the fluid packs may further include a PMP. The fluid pack may contain any convenient amount of PMP measured, for example, based on the volume or mass of the PMP. For example, the PMP may be capable of mixing with the fluid when contained in the fluid pack. In some cases, the PMP may be contained in the fluid pack that contains the lysis buffer.

[0055] In certain embodiments, the buffer pack is configured to fit into a well of a cylindrical structure. For example, when the well is shaped as a substantially hollow cylinder, the buffer pack may be shaped as a cylinder that fits into the well of the cylindrical structure.

[0056] In some embodiments, the lysis buffer can be formulated to release nucleic acids from a wide variety of samples, such as tissue samples, cells, viruses, or body fluid samples. The lysis buffer can also be designed to lyse any type of pathogen, such as viral, bacterial, fungal, and protozoan pathogens. Such lysis buffers can contain chaotropic agents, particularly guanidine hydrochloride.

[0057] A buffer pack according to one embodiment of the present disclosure is shown in FIG. 4A. As can be seen, the buffer pack 700, in this example, consists of cylindrical structures 710, 720, and 730 such that the buffer pack can hold a fluid pack (not shown). In embodiments where the second chamber stores air as an immiscible phase, the buffer pack may not include a pack that contains oil.

[0058] A buffer pack similar to the buffer pack shown in FIG. 4A according to one embodiment of the present disclosure is shown in FIG. 4B. In this figure, the components inside the buffer pack are disassembled for illustration purposes.

[0059] The buffer pack can be inserted into the well 440 (see FIG. 1A) within the cylindrical structure 400. The buffer pack can be actuated to release the contained fluid and move it to the corresponding chambers 410a, 410, and 410c (see FIG. 1A). In some examples, the cylindrical structure 710 of the buffer pack 700 contains the lysis buffer and is fluidly connected to the first chamber 410a, the cylindrical structure 720 contains oil or a wash buffer and is fluidly connected to the second chamber 410b, and the cylindrical structure 730 contains the elution buffer and is fluidly connected to the third chamber 410c.

[0060] Sealing lid assembly As described above, the sample preparation cartridge disclosed herein includes a cylindrical structure including an upper end, a lower end, and an annular wall extending between the upper end and the lower end. In certain embodiments, a sealing lid assembly covers the upper end of the cylindrical structure. The sealing lid assembly may include a sealing plate and a protective cover. The sealing plate can be disposed at the upper end of the cylindrical structure. The protective cover can be disposed over the sealing plate. The protective cover surrounds the edge of the sealing plate and is sized to fit over and around the upper end of the cylindrical structure to hold the sealing plate in place.

[0061] The sealing plate is sized to fit over and close the upper end of the cylindrical structure. In certain embodiments, the sealing plate may have an opening aligned with an opening of a third (elution) chamber to remove an elution buffer for analysis of eluted nucleic acids. In other embodiments, the sealing plate may further include a plunger assembly. The plunger assembly may include a gasket seal mounted on a shaft, a spring, and a trigger that engages the spring and the shaft. The shaft can be any convenient length, such as a length shorter than the height of the corresponding chamber. The gasket seal can be shaped such that the size of the working end of the gasket seal is substantially the same as the corresponding chamber in which the plunger is integrated. In these embodiments, the spring can apply tension to the plunger in a retracted position. That is, when the plunger retracts, tension is applied to the spring. Retracting means that the gasket seal end of the plunger retracts. When in the retracted position, the plunger does not extrude fluid from the corresponding chamber. The amount of tension applied by the spring when the plunger retracts corresponds to the amount of tension applied by the spring to the plunger when the plunger no longer retracts and can vary as desired. The trigger that engages the spring and the shaft means that the trigger can control the release of the spring under tension holding the plunger in the retracted position.

[0062] In some embodiments, the trigger and the spring are mechanically interlocked such that the trigger actuates when the plunger is in the retracted position. Actuating means that when the trigger is depressed, the tension of the spring is released, causing the plunger to move from the retracted position to the plunger position.

[0063] In these embodiments, the gasket seal of the plunger can be arranged to engage with one of the chambers. Engaging with one of the chambers means that when the plunger assembly is in the plunger position, the gasket seal of the plunger substantially closes the bottom of the chamber, and when the plunger assembly is in the retracted position, the plunger assembly is arranged such that the gasket seal of the plunger does not close the bottom of the chamber. That is, the movement of the plunger from the retracted position to the plunger position is such that the plunger can plunge the chamber. Plunging the chamber means that when the plunger moves from the retracted position to the plunger position, the gasket seal of the plunger engages with the chamber and pressure is applied to any fluid within the chamber.

[0064] In these embodiments, the trigger can be arranged on the sealing cap assembly such that the trigger protrudes a certain distance beyond the outer wall of the cylindrical structure. Protruding a certain distance beyond the outer wall of the cylindrical structure means that the distance between the axis of the cylindrical structure and the farthest point on the trigger is greater than the distance between the axis of the cylindrical structure and the outer edge of the annular wall. The trigger can protrude any convenient distance beyond the outer edge of the annular wall. In these embodiments, the trigger can be oriented to be depressed laterally. Depressing the trigger means actuating the trigger to release the tension of the spring with which the trigger is mechanically interlocked. Being oriented to be depressed laterally means that the trigger is positioned such that it must be moved substantially laterally to depress the trigger.

[0065] The components of a sample preparation cartridge according to an embodiment of the present disclosure are shown in an exploded view in FIG. 2. In this figure, the cylindrical structure 210 and the protective cover 220 are shown exploded for explanation. Also, in this example, the sample preparation device includes a buffer pack 230 and a sealing lid assembly 240. Components of the sealing lid assembly 240, including a plunger 250, a spring 260, and a trigger 270, are also shown. Two PCR tubes 211 are provided for collecting the eluted nucleic acid. A PCR tube holding cap 213 is snap-fitted into the bottom region of the cartridge.

[0066] A sample preparation cartridge according to an embodiment of the present disclosure is shown in FIG. 3. In this example, the sample preparation device 300 includes a cylindrical structure 310, a cover 320, a protective cover 330, and a trigger 340. In this figure, it can be seen that the trigger 340 protrudes a certain distance beyond the outer surface of the annular wall 310 of the cylindrical structure.

[0067] A sealing lid assembly according to an embodiment of the present disclosure is shown in FIG. 8. In this example, the sealing lid assembly 800 includes a sealing plate 810, a plunger 815 having a gasket seal 820 mounted on a shaft 830, a spring 840, and a trigger 850. As can be seen, the shaft 830, the spring 840, and the trigger 850 are arranged such that the trigger 850 engages with the spring 840 and the shaft 830, and the spring 840 applies tension to the plunger 815 in the retracted position. In this example, it can also be seen that the trigger 850 protrudes a certain distance beyond the outer wall of a protective cover 140 (not shown), and the trigger 850 is oriented to move laterally.

[0068] Cap As summarized above, in certain embodiments, the sample preparation cartridge further includes a cap slidably disposed on top of the cylindrical structure. By slidably disposed, it means that the cap can be disposed on top of the cylindrical structure so that it can slide towards the cylindrical structure.

[0069] In some embodiments, the cap may comprise one or more arms arranged to mechanically engage the buffer pack. For example, the cap may be shaped substantially flat, and one or more arms are attached to one flat side of the cap. Such arms can be of any convenient dimension or shape. For example, the length of the arm can be long enough for the arm to reach into a well inside the cylindrical structure when the cap is placed on top of the cylindrical structure.

[0070] In some embodiments, the cap may include a plunger arranged such that when the cap slides into the cylindrical structure, the plunger enters the sample chamber and pushes the sample into the lysis chamber. The sample chamber may be adjacent to a first (lysis) chamber and connected to the lysis chamber via a channel. One of the arms of the cap enters the lysis buffer pack and can push the lysis buffer from the pack into the first (lysis) chamber. Another arm of the cap, if present, enters the immiscible phase pack and can push the oil into a second (immiscible phase) chamber, and a third arm of the cap enters the elution buffer pack and can push the elution buffer into a third (elution) chamber.

[0071] The cartridge can be loaded into a device equipped with a magnet, and the magnet is positioned relative to the cartridge so that it can be used to transfer the PMP from the lysis chamber, through the immiscible phase chamber, to the elution chamber. The device may include a motor that engages the cartridge and rotates the cartridge relative to the magnet, or the magnet may be configured to move along the annular surface of the cartridge.

[0072] Sample input component In certain embodiments, the sample preparation cartridge further includes a sample input component disposed on a protective cover. The sample input component can be used to insert a sample, such as a biological sample, into the sample preparation device. In particular, the sample can be loaded from the sample input component into the chamber of the sample preparation device.

[0073] Sample preparation system As summarized above, the sample preparation system includes a cylinder housing in which the sample preparation cartridge can be removably disposed. Removably disposed means that the cylindrical structure can be fitted into the cylinder housing such that the cylindrical structure can still be separated from the cylinder housing. For example, a user can place the cylindrical structure within the cylinder housing and remove the cylindrical structure from the cylinder housing after sample preparation. As summarized above, the cylinder housing includes a magnet. A magnet means any object having the ability to generate a magnetic field external to itself. For example, a magnet can generate a magnetic field that can attract paramagnetic particles. In some cases, the magnet can be an electromagnet. In certain embodiments, the magnet is disposed proximal to the outer surface of the annular wall. In some embodiments, the magnet is outside the cylindrical housing and is used to transfer magnetic particles between the chambers of the cylindrical housing.

[0074] In certain embodiments, the cylindrical structure rotates within the cylinder housing. Rotating means that the cylinder housing freely rotates the cylindrical structure about the axis of the cylindrical structure formed, for example, by connecting the center of the upper end and the center of the lower end of the cylindrical structure. In other embodiments, the cylindrical structure maintains a fixed position within the space and the cylinder housing rotates around the cylindrical structure.

[0075] In some embodiments, a reusable magnet is used to process a sample using a disposable consumable cylinder structure of a sample processing device. The use of the reusable magnet will reduce the waste associated with each consumable.

[0076] A cylinder housing according to an embodiment of the present disclosure is shown in FIG. 5A. In this example, the cylinder housing 600 includes a magnet 610. As can be seen, the magnet is disposed on the cylinder housing such that when the cylindrical structure is disposed within the cylinder housing 600, the magnet 610 is disposed proximal to the outer surface of the annular wall of the cylindrical structure. In some embodiments, the magnet 610 is external to the cylindrical housing and is used to transfer magnetic particles between chambers of the cylindrical housing.

[0077] A cylinder housing similar to the cylinder housing shown in FIG. 5A, according to an embodiment of the present disclosure, is shown in FIG. 5B. In this figure, the cylinder housing 600 and the magnet 610 are shown disassembled for illustration purposes.

[0078] A sample preparation system including a sample preparation cartridge 100 and a cylinder housing 130 according to an embodiment of the present disclosure is shown in FIG. 6. In this example, the sample preparation cartridge 100 includes a cylindrical structure 110, a cover 120, a protective cover 140, and a cap 150. Also shown in the drawing are an annular wall 155 of the cylindrical structure and three cavities of the annular wall that form chambers 160a, 160b, and 160c having three open side surfaces of the annular wall. As seen in the drawing, the open side surfaces of each of the chambers 160a, 160b, and 160c face outward of the cylindrical structure 110. Further, the open side surfaces of the chambers 160a, 160b, and 160c are surrounded by the cover 120. In FIG. 6, the cover 120 is depicted as transparent to aid visualization of the chambers 160a, 160b, and 160c, but the cover 120 need not be transparent. The cover 120 is curved to conform to the outer surface of the annular wall 155 and fluidly seals the open side surfaces of the chambers. Also seen in this figure is an interconnect 165 between the chambers 160a, 160b, and 160c. As seen in the figure, the interconnect 165 is a channel that is a depression in the annular wall between the chambers. This figure also shows a magnet 170 within the cylinder housing 130. As can be seen, the magnet 170 is disposed proximal to the outer surface of the annular wall 155 of the cylindrical structure 110.

[0079] A sample preparation device similar to the sample preparation device shown in FIG. 6 according to an embodiment of the present disclosure is shown in FIG. 7. In this figure, the cylinder housing 130, the sample preparation cartridge 110, and the cap 150 are disassembled for illustration purposes.

[0080] Figure 9 shows a diagram of a sample preparation cartridge that is rotatable to a position where a magnet is disposed proximal to a cover and enables magnetic capture of paramagnetic particles within a chamber. A sample preparation system 900 is shown that includes a sample preparation cartridge 905 and a magnet 910. The sample preparation cartridge includes a first chamber 915 that stores a lysis buffer and, optionally, paramagnetic particles to which nucleic acids can bind, and a sample containing cells, viruses, and / or nucleic acids, a second chamber 920 that stores an immiscible phase (e.g., oil or air), and a third chamber 925 that stores an elution buffer. The sample preparation cartridge 905 further includes a first recess 935 in an annular wall that interconnects the first chamber 915 and the second chamber 920, and a second recess 935 in the annular wall that interconnects the second chamber 920 and the third chamber 925. The magnet 910 is used to transfer magnetic particles between chambers of the sample preparation cartridge.

[0081] Figure 10 illustrates the transfer of PMPs from the first chamber to the third chamber of a sample preparation cartridge using a magnet. In the first stage of sample preparation, the sample is contacted with the lysis buffer and PMPs within the first chamber 1015. The PMPs are dispersed as indicated by the dark color of the solution within the first chamber 1015. The sample preparation cartridge can be rotated such that different regions of the cartridge are adjacent to the magnet. Alternatively, the magnet can be positioned adjacent to different regions of the cartridge by moving the magnet. By positioning the magnet 1010 adjacent to the first chamber, the PMPs aggregate and the aggregates of PMPs can be transferred through the second chamber to the third chamber by relative movement of the magnet and the cartridge. Panel B shows aggregates of paramagnetic particles 1025 within the third chamber 1020. In Panel C, the dark color of the solution within the third chamber 1020 indicates that the paramagnetic particles are mixed within the elution buffer within the third chamber 1020.

[0082] Automation of a method of using a sample preparation cartridge Some embodiments also provide a sample preparation cartridge that can be operated using a motor. The motor can be automated, thereby automating the method of using the sample preparation cartridge disclosed herein. The motor can also be controlled by a computer program that, when executed by a processor, causes the motor to implement a method of using the devices disclosed herein.

[0083] In some embodiments, the motor rotates a cylindrical structure in 1.8° angular increments.

[0084] In some embodiments, the motor rotates the cylindrical structure to return it to a predetermined position, such that, for example, a magnet is positioned proximal to the first chamber, the second chamber, or the third chamber.

[0085] The motor can be configured to provide only a small portion of a full 360° rotation. For example, the motor can be configured to provide only a 60° to 120° rotation, preferably an 80° to 110° rotation, more preferably a 90° to 100° rotation, and most preferably approximately a 90° rotation.

[0086] As shown in FIG. 11, the motor assembly can include a rotating component 1110 that includes a holder for the sample preparation cartridge disposed adjacent to a stationary component 1112 that holds a magnet.

[0087] In some embodiments, the motor can further facilitate mixing of the contents of the sample preparation cartridge. Such mixing can be accomplished by agitating the sample preparation cartridge via the motor. Appropriate mixing can be provided by controlling the starting position, amplitude, and / or agitation speed. Mixing can reduce sample preparation time and / or improve sample preparation by reducing non-specific binding and improving homogeneous mixing.

[0088] Exemplary embodiments Since the device has been outlined, various device configurations and representative specific embodiments of its components will now be described in more detail here.

[0089] FIG. 12 shows a sample processing apparatus 1200 configured to process a sample using a disposable sample preparation cartridge disclosed herein. A reusable magnet 1210 is attached to the sample processing apparatus. The reusable magnet is mounted on a support 1212 and is disposed in the apparatus such that the magnet is proximal to the cover of the sample preparation cartridge and can be used to transfer magnetic particles between different chambers of the disposable sample preparation cartridge by rotation of the sample preparation cartridge.

[0090] FIG. 13 shows a disposable sample preparation cartridge disposed within a sample processing apparatus such that the magnet is disposed adjacent to the sample preparation cartridge. In the embodiments shown in FIGS. 12 and 13, the magnet remains stationary during sample preparation and the cartridge rotates about a central axis. Rotation of the cartridge positions the chambers of the cartridge in the vicinity of the magnet.

[0091] Additional functions added to the sample preparation device In certain embodiments, the sample preparation device comprises additional functionality that can monitor certain aspects of the sample and / or the method of using the device.

[0092] For example, the sample preparation device can comprise a temperature sensor that can monitor and report, in particular, the temperature of reagents within different chambers of the sample preparation device. The sample preparation device can be equipped with means for controlling the temperature, such as a heater or cooler, that can provide a desired temperature within one or more chambers of the sample preparation device.

[0093] A sample preparation device can be equipped with a fluorometer for reading fluorescence within one or more chambers of a sample preparation cartridge. The fluorometer can preferably be configured to provide on-demand readings with specific parameters without the movement caused by a motor if a motor is present.

[0094] In a further embodiment, a sample preparation device can be equipped with a camera for capturing images during the sample preparation process. One or more cameras can be arranged or configured to capture images from one or more chambers of the device.

[0095] The devices disclosed herein are suitable for methods of detecting nucleic acids in a short time, such as less than 20 minutes, less than 15 minutes, less than 10 minutes, or less than 5 minutes. For example, nucleic acids isolated from a sample using a sample preparation device can be transferred to a collection chamber in fluid communication with a third chamber, such as one or more PCR tubes. See, for example, FIG. 2 showing a PCR tube 211 in fluid communication with a third chamber 410c (see FIG. 1A). An elution buffer can be used to elute nucleic acids from the PMP in the third chamber 410c. The elution buffer containing the nucleic acids can be discharged into the PCR tube 211 through the discharge hole 430. A plunger 250 (see FIG. 2) can be used to extrude the elution buffer from the discharge hole 430. The eluted nucleic acids can be further analyzed by an amplification reaction such as PCR.

[0096] In some cases, the cartridge and associated equipment are configured to be able to load a sample, and the remaining processing steps are automated. Thus, results can be obtained with a minimal number of steps for user intervention. In particular, the user, although not necessarily in this order, only needs to load the sample into the cartridge, load the cartridge into the equipment, and operate the analytical equipment to analyze the sample. The equipment is configured to process the sample to isolate nucleic acid from the sample, send the nucleic acid to an analysis component, such as a PCR component of the equipment, perform an analysis such as PCR, and present the results, for example, display on a screen, provide a printout, store in a computer system, or transmit the results to a remote computer system. Thus, the cartridge disclosed herein can be used with a suitable sample analysis equipment such as Abbott's ID NOW (trademark) equipment, and the only steps for user intervention are to load the sample into the cartridge and load the cartridge into the analysis equipment (not necessarily in this order). A suitable computer program for controlling existing sample analysis equipment can be modified to operate to process samples from the cartridge disclosed herein. Compared with such automated cartridges and sample analysis equipment, in conventional sample processing devices and equipment, the user needs to manually perform a binding-washing-elution process using a solid support (e.g., silica membrane or silica beads).

[0097] Figure 14 shows a typical sample processing workflow using a sample preparation cartridge and a sample preparation system equipped with a magnet disclosed herein. The first chamber of the cartridge is filled with a sample, a lysis buffer, and a PMP. The PMP is initially a solution. After sample lysis, the released nucleic acid binds to the PMP (see steps 1-2 in Figure 14). The PMP is washed by exposing the PMP to a magnetic force to form aggregates and transferring the aggregated PMP to a third chamber storing an elution buffer via a second chamber of the cartridge (see step 3 in Figure 14). For elution of the nucleic acid, the magnetic force is removed and the PMP is mixed with the elution buffer to release the nucleic acid from the PMP (see step 4 in Figure 14).

[0098] Examples of automated cartridges and sample analysis instruments are provided in Figures 15 and 16. The cartridge is configured to function in conjunction with current analysis instruments such as the Abbott ID NOW™ instrument. A sample preparation cartridge used in such an automated analysis instrument is referred to herein as an "integrated sample processing device" or ISPD. As illustrated in Figures 15 and 16, a sample 1012 can be prepared by loading the sample into a sample preparation cartridge 1005 loaded into a sample analysis instrument, placing a cartridge cap, closing the instrument, and starting the instrument. The only steps involving the user are loading the cartridge into the sample analysis instrument, loading the sample into the cartridge (not necessarily in this order), placing the cartridge cap, closing the lid of the analysis instrument, and operating the instrument to analyze the sample. Figure 16 shows a point-of-care procedure for using a sample preparation system that includes placing a blood sample 1012 into a first chamber of a sample preparation cartridge 1005, placing a cap 150 over the cartridge, and closing the lid of the instrument 1200.

[0099] FIG. 17 shows various components of an example of a sample preparation cartridge 110 (integrated sample processing device (ISPD)) and two types of cylinder housings 600 that can be used to isolate nucleic acids using paramagnetic particles.

[0100] The magnet portion of the sample preparation system can be provided as part of the instrument or as an accessory, such as the cylinder housing 600 shown in FIG. 17. The cylinder housing 600 can be configured to fit into a sample analysis instrument such as Abbott ID NOW™. One such example is provided in FIG. 17. The cylinder housing can include means for attaching the housing to the instrument. Such means can include an adhesive. In one example, the means comprises snap-in features. Such features include one or more grooves that receive mating protrusions disposed on the instrument, or vice versa. FIGS. 18A and 18B show an embodiment of a cylinder housing with two supports having protrusions that extend upward from a flat region of the cylinder housing and snap into recesses in the instrument at the top region. In other cases, the flat region at the bottom of the cylinder housing may have an adhesive layer covered with a release tape. Such embodiments are shown in FIGS. 18C and 18D. Thus, the ISPD devices illustrated in FIGS. 18A-18D provide robustness and reliability. The ISPD, in combination with the appropriate analysis instrument, is suitable for automated sample analysis because user involvement is minimal.

[0101] Method As summarized above, a method is provided by the present disclosure. In one aspect, the method is a method of preparing a nucleic acid sample. Such a method includes mixing a sample, including cells, virus, bacteria, fungi, etc., with a lysis buffer in a lysis chamber of a sample preparation cartridge, the sample preparation cartridge including a cylindrical structure having an annular wall, a plurality of cavities of the annular wall configured to form a chamber having an open side surface of the annular wall, and one or more interconnects providing fluid communication between the chambers, and one or more covers covering the open side surface of the chamber. The lysis buffer or the chamber may have PMPs. Alternatively, the method further includes mixing paramagnetic particles (PMPs) with the mixture of the sample and the lysis buffer, stirring the mixture, and binding nucleic acids in or released from cells, virus, bacteria in the sample to the paramagnetic particles. The method further includes rotating the cylindrical structure to a first position to dispose a magnet proximal to the cover and magnetically capture the paramagnetic particles into the lysis chamber, rotating the cylindrical structure to a second position to transfer the paramagnetic particles from the lysis chamber to an immiscible phase chamber storing an immiscible phase (e.g., oil or air), and rotating the cylindrical structure to a third position to transfer the nucleic acids from the immiscible phase chamber to an elution chamber of a device storing an elution buffer.

[0102] In one aspect, the sample is a sample such as whole blood, serum, plasma, sputum, nasal fluid, saliva, mucus, semen, vaginal fluid, tissue, organ of a mammal (e.g., human, rodent (e.g., mouse), or any other mammalian of interest). In other aspects, the sample is a collection of cells from a non-mammalian source such as bacteria, yeast, insects (e.g., Drosophila), amphibians (e.g., frog (e.g., Xenopus)), virus, plants, or any other non-mammalian nucleic acid sample source.

[0103] In some embodiments, rotating the sample preparation cartridge from the first position to the second position includes rotating the sample preparation cartridge such that the entire span of the lysis chamber rotates across the magnet. That is, the sample preparation cartridge can rotate such that the entire lateral span of the lysis chamber is exposed to the magnet.

[0104] Similarly, in some embodiments, rotating the sample preparation cartridge from the second position to the third position includes rotating the sample preparation cartridge such that the entire span of the immiscible phase chamber rotates across the magnet. That is, the sample preparation cartridge can rotate such that the entire lateral span of the immiscible phase chamber is exposed to the magnet.

[0105] The methods of the present disclosure can further include the step of filling the lysis chamber with lysis buffer and paramagnetic particles from a fluid pack contained within a buffer pack, and filling the elution chamber with elution buffer from a fluid pack contained within the buffer pack. In embodiments that use an immiscible phase that is not air, the step can further include filling the immiscible phase chamber with the immiscible phase from a fluid pack contained within the buffer pack.

[0106] In some embodiments, the fluid is transferred from a fluid pack contained within the buffer pack to the chamber by applying pressure to the fluid within the fluid pack to force the fluid through channels within the cylindrical structure of the sample preparation device. For example, the fluid can include lysis buffer, which can optionally include paramagnetic particles, an immiscible phase, and elution buffer. Optionally, the immiscible phase includes oil.

[0107] In certain embodiments, when fluid is transferred from the fluid pack, pressure is applied to the fluid within the fluid pack by applying a mechanical force to a cap having an arm of the sample preparation device to engage the fluid pack. The cap means any convenient mechanical structure having an arm for engaging the fluid pack. For example, the cap comprises a substantially flat base with an arm protruding from one side, and when a force is applied to the flat side of the cap, such force is transmitted along the arm protruding from the base and engaging the fluid pack, thereby applying pressure to the fluid within the fluid pack and forcing it to pass through a channel within a cylindrical structure.

[0108] The method of the present disclosure may include a further step of transferring the eluted nucleic acid from the elution chamber of the sample preparation device by pushing the contents of the elution chamber out of the discharge hole of the chamber. The extrusion in the elution chamber can take any convenient form. For example, the sample preparation device includes a plunger assembly including a plunger configured to engage the elution chamber, and the plunger can be automatically triggered to extrude in the elution chamber when the cylindrical structure is rotated to a specific position.

[0109] In certain embodiments, when the eluted nucleic acid is extruded from the elution chamber, the sample preparation device further comprises a plunger, a spring, and a trigger interlocked with each other, and thus the extrusion in the elution chamber includes applying pressure to the trigger to release the tension of the spring, thereby driving the plunger into the elution chamber. In certain embodiments, the cylindrical structure rotates to a fourth position that allows a mechanical arm to apply pressure to the trigger. In such a case, the trigger can protrude beyond the outer diameter of the cylindrical structure. The mechanical arm means any convenient device used when pushing down the trigger. For example, such a mechanical arm can be mounted at a fixed position and arranged to engage the trigger only when the cylindrical device rotates to a position where the mechanical arm abuts the trigger.

[0110] In one embodiment, a sample containing cells is introduced into a lysis buffer by applying pressure to a sample input component of a sample preparation device such that the sample containing cells is introduced into the lysis buffer. The sample input component refers to any convenient structure for surrounding the cells such that when a force is applied to the housing, pressure is applied to the sample, thereby forcing the sample into the lysis chamber of the sample preparation device.

[0111] Accordingly, the foregoing merely illustrates the principles of the invention. It will be understood that those skilled in the art can devise various configurations that embody the principles of the invention and are within the spirit and scope of the invention, although not explicitly described or illustrated herein. Further, all of the examples and conditional language recited herein are principally intended to aid the reader in understanding the principles and concepts of the invention provided by the inventors for the advancement of the art and are to be construed as not being limited to such specifically recited examples and conditions. Moreover, all statements in this specification listing the principles, aspects, and embodiments of the invention, as well as specific examples thereof, are intended to encompass both structural and functional equivalents thereof. Additionally, such equivalents are intended to include both currently known equivalents and equivalents developed in the future, i.e., any elements developed that perform the same function regardless of structure. Accordingly, the scope of the invention is not intended to be limited to the exemplary embodiments illustrated and described herein. Rather, the scope and spirit of the invention are embodied by the appended claims.

Claims

1. A sample preparation cartridge, comprising: an upper end, a lower end, an annular wall extending between the upper end and the lower end, a plurality of chambers present in the annular wall, and one or more channels providing fluid communication between the plurality of chambers, wherein the chambers extend between an outer surface of the annular wall and an interior of a cylindrical structure, the annular wall comprising cavities forming open side surfaces of the respective chambers, the channels being formed by depressions in the annular wall and having open side surfaces, a cylindrical structure, and one or more covers attached over the outer surface of the annular wall to fluid-tightly cover the open side surfaces of the chambers and the open side surfaces of the channels. A sample preparation cartridge comprising the above.

2. The sample preparation cartridge according to claim 1, wherein the plurality of chambers includes at least three chambers.

3. The sample preparation cartridge according to claim 1 or claim 2, wherein the depression extends between sides of two adjacent chambers.

4. The sample preparation cartridge according to any one of claims 1 to 3, wherein the depression is disposed at a substantially constant height above a lower end of the cylindrical structure and on a side of one or more chambers.

5. The sample preparation cartridge according to any one of claims 1 to 4, wherein the chambers are shaped such that a lateral portion of the chamber proximal to the channel tapers towards the channel.

6. The sample preparation cartridge according to any one of claims 1 to 5, wherein one or more of the chambers include an opening configured to vent the chamber, fill the chamber with fluid, and / or discharge fluid from the chamber.

7. The sample preparation cartridge according to any one of claims 1 to 6, wherein the plurality of chambers includes a first chamber, a second chamber, and a third chamber, and the second chamber is disposed between the first chamber and the third chamber.

8. The sample preparation cartridge according to claim 7, wherein the first chamber has an opening at a top of the chamber, and the opening is configured as an inlet.

9. The sample preparation cartridge according to claim 8, wherein the inlet is configured as an inlet for introducing a lysis buffer, a sample, and / or a mixture thereof.

10. The first chamber comprises a compartment disposed at or below the bottom region of the first chamber, the compartment comprising an opening that fluidly connects the compartment to the interior of the first chamber, the compartment storing paramagnetic particles (PMPs) disposed therein, the PMPs being lyophilized, the sample preparation cartridge according to any one of claims 7 to 9.

11. The first chamber has an opening at the bottom of the chamber, the opening being configured as an inlet for a lysis buffer, the first chamber having an opening configured as a sample inlet at the top of the first chamber, the sample preparation cartridge according to claim 10.

12. The compartment comprises an inlet that fluidly connects the compartment to a channel and an outlet that fluidly connects the compartment to the interior of the first chamber, the sample preparation cartridge according to claim 10 or claim 11.

13. The second chamber has no opening other than the interconnection with the first and third chambers, the sample preparation cartridge according to any one of claims 7 to 12.

14. The third chamber has an opening in the bottom region of the chamber, the opening being configured to discharge from the third chamber, the sample preparation cartridge according to claim 13.

15. The opening at the bottom of the third chamber is fluidly connected to one or more collection containers, the sample preparation cartridge according to claim 14.

16. The third chamber has an opening in the bottom region of the chamber, the opening being separate from the opening for discharging from the third chamber and being configured to fill the third chamber, the sample preparation cartridge according to claim 14 or claim 15.

17. The first chamber is fluidly connected to a well storing a lysis buffer, the sample preparation cartridge according to any one of claims 7 to 16.

18. The second chamber stores an immiscible phase, the sample preparation cartridge according to any one of claims 7 to 17.

19. The immiscible phase comprises oil or air, the sample preparation cartridge according to claim 18.

20. The sample preparation cartridge according to any one of claims 1 to 19, comprising one or more wells inside the cylindrical structure.

21. The sample preparation cartridge according to claim 20, further comprising a channel inside the cylindrical structure that provides fluid communication between the well and one or more of the plurality of chambers.

22. The sample preparation cartridge according to claim 21, wherein each well is interconnected with a separate chamber via the one or more channels.

23. The sample preparation cartridge according to any one of claims 1 to 22, further comprising a buffer pack.

24. A sealing lid assembly including a sealing plate disposed at the upper end of the cylindrical structure, and a protective cover disposed on the sealing plate, The sample preparation cartridge according to any one of claims 1 to 23, wherein the protective cover surrounds the sealing plate.

25. The sample preparation cartridge according to claim 24, further comprising a cap configured to be disposed on the cover.

26. The sample preparation cartridge according to claim 25, wherein the cap includes one or more arms disposed to mechanically engage with a buffer pack disposed in one or more wells of the cylindrical structure.

27. The sealing plate includes a plunger with a gasket seal mounted on a shaft, a spring, and a trigger that engages with the spring and the shaft, The sample preparation cartridge according to claim 26, further comprising a plunger assembly.

28. The sample preparation cartridge according to claim 27, wherein the spring applies tension to the plunger in the retracted position.

29. The sample preparation cartridge according to claim 28, wherein the trigger and the spring are mechanically interlocked such that the trigger operates when the plunger is in the retracted position.

30. The sample preparation cartridge according to claim 29, wherein the gasket seal of the plunger is disposed to engage with one of the chambers.

31. The sample preparation cartridge according to claim 30, wherein the trigger protrudes from the cylindrical structure.

32. The sample preparation cartridge according to claim 31, wherein the trigger is oriented to be pushed down laterally.

33. A sample preparation system, comprising the sample preparation cartridge according to any one of claims 1 to 32, a cylinder housing having an opening sized to surround the annular wall of the cartridge, and the cartridge is removably disposed within the opening of the cylinder housing, and the cylinder housing includes a magnet disposed within the housing such that when the cartridge is disposed within the housing, the magnet is adjacent to the annular wall and substantially adjacent to the channel providing fluid communication between the plurality of chambers. A sample preparation system.

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