Method of using a mechanical handler to transfer liquids from reagent reservoirs

Abstract

Described herein are methods of transferring liquid from a reagent reservoir using a mechanical liquid handler, the reagent reservoir having a sloped bottom along a width of the reagent reservoir, the sloped bottom defining a shallow end and a deep end of the reagent reservoir, wherein the shallow end is proximate to a first sidewall of the reagent reservoir, wherein the deep end is proximate to a second sidewall of the reagent reservoir opposite the first sidewall.

Description

[0001] CLAIM OF PRIORITY

[0002] This patent application claims priority to U.S. Provisional Application Serial No. 62 / 952,968, filed December 23, 2019, the entire contents of which are incorporated herein by reference. BACKGROUND

[0003] There are various shortcomings with existing bulk reagent reservoirs used in mechanical liquid handlers for processing and analyzing biological samples, such as preparing nucleic acid fragment libraries (e.g., fragment libraries derived from cellular DNA or RNA molecules) including next generation sequencing (NGS) libraries. One shortcoming arises when the amount of reagent in a reagent cartridge is not sufficient to provide an excess of each reagent used in automation. In standard reagent reservoirs, the dead volume (e.g., the amount in the reservoir that is sufficient to be uniform on the bottom of a well and pipetted) is too high, which results in a reduction in the actual number of samples that can be processed by the reagent cartridge. In other words, entropy and surface tension create an uneven liquid distribution at the bottom of a traditional / existing bulk reservoir as the volume is reduced. This uneven distribution can result in the local depletion of liquid as it is aspirated, resulting in uneven or complete missed aspiration of probes of a multi-channel pipettor. SUMMARY

[0004] The bulk reagent reservoirs described herein address the shortcomings of existing reagent reservoirs. Briefly, the bulk reagent reservoirs described herein include a slope from front to back at the bottom of the reservoir. This allows for at least eight pipette tips (e.g., a 16-tip pipette head with a pitch of 0.45 mm can still access the reservoir) with all tips above the slope of a multi-channel pipettor to access volumes greater than, for example, about 20 mL or as little as about 500 pL at the same time. The slope will also include a taper toward the single tip access point to concentrate the volume into a single tip’s simple location. After this volume is removed, a single tip from a single channel of a single channel pipettor or a multi-channel pipettor will be able to access the remaining volume to reduce the dead volume. The design of the bulk reservoir will allow for an increase in sample number by minimizing the dead volume. The sloped area will contain less than 0.5 mL of volume and can be left in the reservoir for non-volume critical reagents or a user-provided bulk of reagents, such as water and ethanol.

[0005] Accordingly, the present disclosure relates to a method of transferring liquid using a mechanical liquid handler, the method comprising: aspirating a first volume of liquid from a reagent reservoir using a multichannel pipettor of the mechanical liquid handler, the reagent reservoir having a sloped bottom along a width of the reagent reservoir, the sloped bottom defining a shallow end and a deep end of the reagent reservoir, wherein the shallow end is proximate to a first side wall of the reagent reservoir, wherein the deep end is proximate to a second side wall of the reagent reservoir opposite the first side wall; and

[0006] aspirating a second volume of liquid from the deep end of the reagent reservoir using a single channel of a single-channel pipettor or a single channel of a multichannel pipettor of the mechanical liquid handler, wherein aspirating the second volume from the deep end depletes the liquid in the shallow end of the reagent reservoir.

[0007] Further, the present disclosure relates to a method of transferring liquid using a mechanical liquid handler, the method comprising:

[0008] filling the reagent reservoir with liquid, thereby filling the sloped bottom of the reagent reservoir, wherein the sloped bottom forms the deep end and the shallow end;

[0009] removing a first portion of the liquid from the reagent reservoir using a multichannel pipettor having a first pipettor tip extending into a first location proximate to the shallow end and a second pipettor tip extending into a second location proximate to the deep end; and removing a second portion of the liquid from the reagent reservoir using the multichannel pipettor having a single pipettor tip extending into the second location proximate to the deep end or a single-channel pipettor having a pipettor tip extending into the deep end.

[0010] The present disclosure also relates to a method of transferring liquid using a mechanical liquid handler, the method comprising:

[0011] aspirating a first volume of liquid from a reagent reservoir using a first pipettor of the mechanical liquid handler, the first pipettor having a plurality of tips including a first tip and a second tip, the reagent reservoir having a sloped bottom along a width of the reservoir, the sloped bottom defining a shallow end and a deep end of the reagent reservoir, wherein during aspiration of the first volume of liquid, the first tip is positioned on the shallow end of the reagent reservoir and the other tip is positioned on the deep end of the reagent reservoir; and

[0012] aspirating a second volume of liquid from the reagent reservoir using a second pipettor of the mechanical liquid handler, the second pipettor having a number of tips less than the number of tips of the first pipettor, wherein during aspiration of the second volume, the tips of the second pipettor are positioned on the deep end of the reagent reservoir.

[0013] And the present disclosure relates to a method of transferring liquid from a bulk storage vessel using a mechanical liquid handler, the method comprising:

[0014] adding liquid to the bulk storage reservoir such that: a first volume of the bulk storage reservoir formed by the sloped bottom of the storage reservoir forming a deep end and a shallow end is filled; and a second volume of the bulk storage vessel located above the first volume formed by the first end wall and the second end wall of the bulk storage vessel above the deep end and the shallow end becomes at least partially filled; emptying the second volume using the multichannel pipettor; and

[0015] emptying the first volume using the single-channel pipettor or a single channel of the multichannel pipettor.

[0016] Embodiment 17 relates to the method of embodiment 16, wherein:

[0017] the multichannel pipettor extends between the first end wall and the second end wall above the first volume; and

[0018] the single-channel pipettor or the single channel of the multichannel pipettor extends across the deep end. BRIEF DESCRIPTION OF DRAWINGS

[0019] Figure 1 is a side view of an example of a reagent reservoir.

[0020] Figure 2 is a front view of an example of a reagent reservoir.

[0021] Figure 3 is a top view of an example of a reagent reservoir.

[0022] Figure 4 is a bottom view of a reagent reservoir.

[0023] Figure 5A is a cross-section of an example of a reagent reservoir at the “shallow” end of the reservoir.

[0024] Figure 5B is a cross-section of an example of a reagent reservoir at the “deep” end of the reservoir.

[0025] Figure 6 is a cross-section of an example of a reagent reservoir.

[0026] Figure 7 is a cross-section of an example of a reagent reservoir.

[0027] Figure 8 is a block diagram of an example of a mechanical liquid handler.

[0028] Figure 9 is a block diagram of an example of a mechanical liquid handler. Figure 8a perspective view of a mechanical liquid handler including a housing, a turntable, a reactor vessel, a thermal cycling module, and an imaging device.

[0029] Figure 10 is an example of a deck for loading into the housing of Figure 8 is a plan view of an example of a deck having space for various components including reagent reservoirs.

[0030] Figure 11 is a top view of a reagent reservoir. DETAILED DESCRIPTION

[0031] Reference will now be made in detail to certain embodiments of the disclosed subject matter, examples of which are illustrated in the accompanying drawings. While the disclosed subject matter will be described in conjunction with the enumerated claims, it will be understood that the subject matter exemplified is not intended to limit the claims to the disclosed subject matter.

[0032] Referring to Figure 1 , the reagent reservoir 100 has a longitudinal axis 101 along a width 104 of the reagent reservoir 100 and a sloped bottom 102. The sloped bottom 102 defines a shallow end 106 of the reagent reservoir 100 proximate a first side wall 110 of the reagent reservoir 100 and a deep end 108 proximate a second side wall 112 of the reagent reservoir 100 opposite the first side wall 110. Figure 1 The reagent reservoir 100 shown in

[0033] The reagent reservoir 100 also has a protrusion 120 for elevating a first end 122 relative to a second end 124. The protrusion 120 is for keeping the top of the reservoir level / in a horizontal position when resting on a work deck or flat surface 114. The protrusion 120 can take any suitable form such as a fin, tab, or notch so long as the protrusion 120 elevates the first end 122 relative to the second end 124. The protrusion 120 forms an angle (Q) 115 between the flat surface 114 and the first end 122. The angle Q can be any suitable angle such as an angle from about 3° to about 5°.

[0034] The reagent reservoir 100 optionally includes volume markings 125 as shown in Figure 1

[0035] Figure 2 An end view of the reagent reservoir 100 is shown as viewed from the first end 122.​Figure 2 The end view shown illustrates a 120 with multiple protrusions (in this case, two protrusions or fins). A and 120 B An example of a reagent reservoir 100, the plurality of protrusions 120 A and 120 B The first end 122 is raised relative to the second end 124. Furthermore, the end view of the reagent reservoir shows that the reservoir may have a first channel 126 and a second channel 128 spanning a width 104 of the reagent reservoir 100, and the reservoir is composed of a partition wall that also spans a width 104. Figure 3 The reference numeral 130 in the attached diagram separates the first channel 126 from the second channel 128. In short, the reagent reservoir may have multiple chambers, each with a sloping bottom.

[0036] exist Figure 3 The image shows a top view of a reagent reservoir 100 without a lid. Figure 3 A reagent reservoir 100 spanning a width of 104, a first channel 126, and a second channel 128 are shown. The channels are separated by a partition wall 130, also spanning a width of 104. Figure 3 The diagram also shows a lip 132 extending around the top portion of the reagent reservoir 100, and a cap that can be positioned on the lip 132 when present. A first channel 126 and a second channel 128 can be inclined at a constant slope from the first end 122 to the second end 124. Figure 1 It has channels 126 and 128 ( Figure 1 An example of a reagent reservoir 100 (not shown) has channels 126 and 128 having a constant slope from a first end 122 to a second end 128. Alternatively, the slopes of the first channel 126 and the second channel 128 can vary from the first end 122 to the second end 124. A specific slope can be selected based on the slope required for effective accumulation of aqueous liquids at a shallow end (e.g., the second end 124), without being so steep that suspended particles (e.g., magnetic beads described herein) would concentrate at the same end (e.g., the second end). This slope also affects the volume that all pipette tips can achieve compared to a single tip.

[0037] Furthermore, the first channel 126 can have a base plate 134 of any suitable shape. Similarly, the second channel 128 can have a base plate 136 of any suitable shape, wherein the base plate 136 has the same or different shape relative to the base plate 134. Figure 3 In the example presented, base plates 134 and 136 have approximately the same triangular shape from the first end 122 to the second end 124.

[0038] Figure 4 is a bottom view of the reagent reservoir 100. Figure 4 The reagent reservoir 100, the first channel 126, and the second channel 128 are shown spanning the width 104. The channels are separated by a dividing wall 130 that also spans the width 104. In Figure 4 the lip 132 is also shown, which extends around a top portion of the reagent reservoir 100, and the lid 114 is positioned on the lip 132. Figure 4 The first protrusion 120 A and the second protrusion 120 B (e.g., a tab or fin) are also shown. A The first protrusion 120 B and the second protrusion 120 A raise the first end 122 relative to the second end 124.

[0039] Figure 5A is a cross-section taken along an axis 140 B perpendicular to the longitudinal axis 101 in Figure 1 of the reagent reservoir 100 at the shallow end 106 along a direction perpendicular to Figure 4 the longitudinal axis 101 in A . Figure 5A The first protrusion 120 A and the second protrusion and 120 B (e.g., a tab or fin) are also shown. A The first protrusion 120 B and the second protrusion and 120 A raise the first end 122 relative to the second end 124 (not shown in Figure 5A ). Figure 5A The reagent reservoir 100 in Figure 5A also has a lip 132 that extends around a top portion 138 of the reagent reservoir 100. The first channel 126 has a floor 134 and the second channel 128 has a floor 136, the floors 134 and 136 having any suitable shape such as a shape with a cross-section that decreases along the width of the reagent reservoir from the first sidewall to the second sidewall, such as a V-shape, where the floor 136 has the same shape or a different shape relative to the floor 134. In Figure 5A the example presented in Figure 5A , the floors 134 and 136 have substantially the same flat shape along the width 104. But the floors 134 and 136 can also be independently rounded from the first end 122 to the second end 124.

[0040] Finally, Figure 5B is a cross-section taken along an axis 140 B perpendicular to the longitudinal axis 101 in Figure 1 of the reagent reservoir 100 at the shallow end 106 along a direction perpendicular to Figure 4 the longitudinal axis 101 in B .Figure 5B The reagent reservoir 100 in FIG. 1 also has a lip 132 extending around a top portion 138 of the reagent reservoir 100. The first channel 126 has a floor 134 and the second channel 128 has a floor 136, the floors 134 and 136 having any suitable shape, such as a V-shape, where the floor 136 has the same shape or a different shape relative to the floor 134. In Figure 5B In the example shown in FIG. 1, the floors 134 and 136 have substantially the same flat shape along the width 104. The floors 134 and 136 can also independently be rounded from the first end 122 to the second end 124.

[0041] The reagent reservoirs contemplated herein, such as the reagent reservoir 100, can be made of any suitable material, including but not limited to polymers such as polycarbonate, polyethylene, polypropylene, polyethylene terephthalate (PET), and the like. It should be understood that one portion of the reagent reservoirs contemplated herein can be made of a first material, while other portions can be made of a second material, so long as the first material can coexist with the second material.

[0042] The reagent reservoirs contemplated herein can be used in the context of a mechanical liquid handler 200 (see Figures 9 to 11 ). For purposes of explanation, the mechanical liquid handler 200 will be primarily described herein as a system for processing and analyzing biological samples, such as preparing a library of nucleic acid fragments (e.g., a library of fragments derived from DNA or RNA molecules) including but not limited to next generation sequencing (NGS) libraries.

[0043] The reagent reservoirs described herein can be used in a method of transferring liquid using a mechanical liquid handler, the method comprising: aspirating a first volume of liquid from a reagent reservoir 100 using a multichannel pipettor 204 of a mechanical liquid handler 200 (e.g., any pipettor capable of aspirating / dispensing liquid into more than one channel at a time, including Span-8 type multichannel pipettors with independent motion and aspiration / dispensing functions between different channels and other multichannel pipettors without independent motion and aspiration / dispensing functions. It does not matter whether the multichannel pipettor has independent probes or fixed probes, as long as the fixed system allows for loading a single tip for access to the sloped section and acts as a single channel pipettor or the independent system allows for enough vertical difference between the probes to accommodate the slope.) having a sloped bottom 102 along a width 104 of the reagent reservoir 100, the sloped bottom 102 defining a shallow end 106 and a deep end 108 of the reagent reservoir 100, wherein the shallow end 106 is proximate to a first side wall 110 of the reagent reservoir 100, wherein the deep end 108 is proximate to a second side wall 112 of the reagent reservoir 100 opposite the first side wall 110; and aspirating a second volume of liquid from the deep end 108 of the reagent reservoir 100 using a single channel pipettor 208 (see Figure 7 ; or a single channel of a multichannel pipettor) of the mechanical liquid handler, wherein aspirating the second volume from the deep end 108 of the reagent reservoir 100 depletes the liquid in the shallow end 106.

[0044] The multichannel pipettor can be any suitable pipettor, including, for example, four channel pipettors such as those available from manufacturers such as Genex Laboratory Products, Eppendorf, Raning, and Gilson. Further, the multichannel pipettor can be positioned in any suitable location in the deep end 108 of the reagent reservoir 100. For example, referring to Figure 6 , the multichannel pipettor can be positioned such that the multiple pipettor tips 210 of the multichannel pipettor are arranged longitudinally along the longitudinal axis 101, as shown. Thus, aspirating a first volume 202 of liquid from a reagent reservoir using a multichannel pipettor 204 of a mechanical liquid handler 200 can comprise aspirating the first volume along a width of the reagent reservoir 100 (e.g., along the longitudinal axis 101) from the first side wall 110 to the second side wall 112 using the multichannel pipettor.

[0045] The single channel pipettor (or single channel of a multichannel pipettor) can be any suitable pipettor and can be positioned in any suitable location in the shallow end 106. Referring to Figure 7 , the single channel pipettor or single channel of a multichannel pipettor can be positioned in the deepest portion 108 of the reagent reservoir 100A The deepest portion 108 A The second sidewall 112 is proximate the reagent reservoir 100.

[0046] The methods described herein can also include first depositing particles (e.g., beads, such as magnetic beads) in the reagent reservoir 100, then depositing reagent / liquid in the reagent reservoir 100, or by depositing bead reagent / liquid (already in the reagent reservoir); and suspending the beads in the liquid; wherein the beads settle (e.g., uniformly) along the sloped bottom, wherein the slope can be from about 3° to about 5°, such as Figure 1 described in the angle Θ. The beads can be, for example, magnetic particles. Magnetic particles suitable for use in the methods described herein include, but are not limited to, AMPure XP beads available from Beckman Coulter, Inc. of Brea, California. Suitable magnetic particles also include those described in U.S. Patent Nos. 5,705,628; 5,898,071; and 6,534,262; and PCT / US2019 / 042628, filed July 19, 2019, all of which are incorporated by reference as if fully set forth herein.

[0047] It is desirable to maintain a uniform suspension in the reservoir for the liquid or reagent containing particles when the beads are deposited in the reagent reservoir 100. Over time, the particles will settle to the bottom of the reservoir. The sloped portion of the reservoir causes the particles to settle uniformly across the width of the reservoir, rather than accumulating in the shallow end (or deep end, as the case can be). In this way, a multi-channel pipettor can be used to effectively re-suspend the particles to reform a uniform suspension just prior to use.

[0048] The magnetic particles of the present disclosure can include a magnetic or paramagnetic core surrounded by a coating. In examples, the magnetic or paramagnetic particles are coated with one or more layers of non-magnetic material. The use of coated magnetic particles that do not have exposed iron on their surface can eliminate the possibility of iron interfering with certain downstream operations on the sample. The coating can be, for example, a polymer layer or a silicon oxide layer.

[0049] Example polymer layers can include polyethylene, polystyrene, polymethyl methacrylate, polyvinyl alcohol, or any other suitable polymer. Example silicon oxide layers can include silica, borosilicate, soda lime, barium titanate, and other types of glass. The polymer layer or silicon oxide layer can be used to adjust the density of the magnetic particles. For example, the polymer layer or silicon oxide layer can adjust the density of the magnetic particles to be close to the density of a sample, e.g., an aqueous sample (e.g., approximately 1 g / cm 3 ).

[0050] The coating can also include ligands such as capture reagents or functional groups, including those mentioned herein, for selective or non-selective binding of target analytes. The functional groups can be used to adsorb biomolecules, such as nucleic acids, which can bind to the functional groups coating the magnetic particles non-sequence specifically and reversibly. The polynucleotides can be DNA, RNA, or polyamide nucleic acids (PNAs). In examples, the functional groups are carboxyl groups. Various coatings including functional groups suitable for these purposes are described in U.S. Patent No. 5,705,628, U.S. Patent No. 5,898,071, and U.S. Patent No. 6,534,262, the teachings of which are incorporated by reference in their entirety. Any of the coatings described herein can be functionalized with surface chemistry as described herein, for example with carbene, streptavidin, amine, hydrazide, silanol, azide. And those coatings can be further functionalized with biomolecules such as antibodies, enzymes, DNA or RNA fragments, catalysts, etc.

[0051] In some examples, the coating can include a capture reagent. The capture reagent can be used to capture an analyte in a sample. The surface of the magnetic particles can be coated with a capture reagent that is a suitable ligand or receptor (e.g., an antibody, a lectin, an oligonucleotide, other affinity groups, or any other capture reagent mentioned herein) that can selectively bind a target analyte or a group of analytes in a mixture. In some examples, the capture reagent can be an antibody.

[0052] Those skilled in the art will recognize that any number of capture reagents can be used for this purpose, such as aptamers, nanoparticles, binding proteins, etc. The capture reagent can be designed to capture a particular analyte or a particular group of analytes, such as a group of drugs or a group of endocrine hormones, etc.

[0053] Alternatively, the ligand can include an enzyme. In some embodiments, the enzyme can be attached to the coating so as to selectively interact with a substrate of the enzyme. Upon interaction with the substrate, the enzyme can act to modify, degrade, or digest the substrate. This can result in the production of a substance of interest by the action of the enzyme, or removal of the substrate from the sample. Depending on the embodiment, the enzyme can be trypsin.

[0054] As described herein, reagent reservoir 100 can be used in the context of a robotic liquid handler. Reagent reservoir 100 can have protrusions, such as tabs or fins 120A and 120B, which can align with slots on a liquid handler to position the reagent reservoir on a deck of a robotic liquid handler, as described in greater detail herein. Tabs or fins 120A and 120B can engage with a deck of robotic liquid handler 200 to raise shallow end 106 above deep end 108 and first and second side walls 110 and 112 to stand vertically on the deck.

[0055] Figure 8 is a high-level block diagram of a robotic liquid handler 200. Robotic liquid handler 200 can include a control computer 908 operatively coupled to a structure 940, a transport device 941, a processing device 901, and a thermal cycler system 907. Each of these devices can have an input / output interface to allow data transfer between the illustrated devices and external devices. Robotic liquid handler 200 can include a fluid handling system as described herein. Fluids can include various liquids such as reagents. An example of a processing system of the present disclosure can be implemented by the Biomek i7 Automated Workstation sold by Beckman Coulter, Inc. of Brea, California.

[0056] For purposes of explanation, robotic liquid handler 200 will primarily be described as a system for processing and analyzing biological samples, such as preparing a library of nucleic acid fragments (e.g., a library of fragments derived from DNA or RNA molecules) including, but not limited to, next generation sequencing (NGS) libraries.

[0057] Structure 940 can include a housing (e.g., Figure 9 housing 1002 of FIG. 1), legs or casters to support the housing, a power supply, a deck 905 loadable within the housing, and any other suitable features. Deck 905 can include a physical surface (e.g., Figure 9 platform 1012 of FIG. 1), such as a flat physical surface on which components can be placed and used to conduct experiments, analysis, and processing. In some cases, deck 905 can be a floor or table surface. Deck 905 can be subdivided into a plurality of discrete deck positions (e.g., Figure 11 positions LI through LI 6 of FIG. 1) for placing different components. These positions can be directly adjacent or can be spaced apart from one another. Each deck position can include dividers, inserts, and / or any other support structure to partition different deck positions and accommodate components. For example, Figure 8The diagram shows a first position 905A, a second position 905B, and a third position 905C on a platform 905, but additional positions may be included. One or more positions 905A through 905C may be fitted with a turntable (e.g., Figure 9 The turntable 1004) or one or more reagent reservoirs or liquid containers (e.g., Figure 9 The reactor vessel 103 may include space for holding one or more components. Structure 940 may additionally include a motor or other device for rotating the turntable relative to platform 905 to facilitate interaction with transport device 941, reagent reservoir, and thermal cycler system 907, among other things. Furthermore, the motor of structure 940 or an additional motor of structure 940 may be used to rotate individual vials loaded on platform 905, trays or reagent reservoirs loaded on platform 905, or the turntable located on platform 905.

[0058] The transport device 941, which may include a trolley system, bridging system, or carrier system capable of movement in the x and y directions and lifting capability in the z direction, and may represent multiple transport devices, is capable of preparing and / or transferring components between the platform 905 and the processing equipment 901, and between different locations on the platform 905. Examples of transport devices may include conveyors, cranes, sample tracks, pick-and-place grippers, independently movable laboratory transport elements (e.g., discs, hubs, or bases), robotic arms, and other tube or component transport mechanisms. In some embodiments, the transport device 941 includes a pipette tip configured to transfer liquids. Such a pipette tip can transfer liquids from removable pipette / pipette tips and may include grippers adapted to grasp or release other laboratory instruments, such as microplates or caps for reagent reservoir 100.

[0059] Processing device 901 may include any number of machines or instruments for performing any suitable process. For example, processing device 901 may include an analyzer, which may include any suitable instrument capable of analyzing samples such as biological samples. Examples of analyzers include spectrophotometers, luminometers, mass spectrometers, immunoassay analyzers, hematology analyzers, microbiology analyzers, and / or molecular biology analyzers. In some embodiments, processing device 901 may include a sample grading device. The sample grading device may include: a sample presentation unit for receiving sample tubes containing biological samples; a sample storage unit for temporarily storing sample tubes or sample preservation vessels; an apparatus or device for aliquoting samples, such as a separator; a device for holding at least one reagent set, including reagents required by the analyzer; and any other suitable features.

[0060] The thermal cycler system 907 can be positioned relative to the platform 905 and can be configured to receive liquid vessels. Reactor vessels (e.g., Figure 10 103) can be loaded into the thermal cycler system 907 manually or via transport device 941. See below for reference. Figure 10 In more detail, the thermal cycler system 907 can be configured to provide multiple different heating zones that can heat different parts of the liquid vessel to different temperatures. For example, the thermal cycler system 907 may include three stacked or vertical heating stages to provide a top heating zone, a middle heating zone, and a bottom heating zone to the liquid vessel. Thus, for example, depending on the amount and type of liquid contained in the liquid vessel, different amounts of heat can be applied, such as for thermal cycling and incubation processes.

[0061] The mechanical liquid processor 200 may be equipped with an imaging system, such as a camera, to read the labels of reagent vials loaded onto the platform 905. The imaging system ensures that all portions of any single reagent vial label loaded onto the mechanical liquid processor 200 are within the field of view of at least one camera. Therefore, for a reagent vial label wound around the circumference of a reagent vial, one or more imaging devices may have a complete 360-degree view of each vial, with or without a mirror or turntable. The imaging device may be any suitable means for capturing images of the platform 905 and any components on the platform 905 or the entire structure 940. The imaging device may include one of a plurality of imaging devices mounted to or near the structure 940. In another example, multiple imaging devices may be mounted to obtain multiple views of the reagent vials positioned on the platform 905. For example, the imaging device may be any suitable type of camera, such as a camera, video camera, 3D imaging camera, infrared camera, etc. Some embodiments may also include a 3D laser scanner, infrared depth sensing technology, or other tools for creating 3D surface maps of objects and / or spaces. In the example, the imaging device can utilize slit scanning technology to generate panoramic images. Images captured by the imaging system can be analyzed by a fluid processing system to identify visual cues such as numbers, text, or symbols.

[0062] The control computer 908 can control, initially configure, and check whether components have been properly prepared for processes running on the processing system 900. The control computer 908 can control and / or communicate messages to the processing devices 901, the transport 941, and / or the thermal cycler system 907. The control computer 908 can include a data processor 908A, a non-transitory computer-readable medium 908B coupled to the data processor 908A, and a data store 908C, one or more input devices 908D, and one or more output devices 908E. Although the control computer 908 is depicted as a single entity in Figure 8 it should be understood that the control computer 908 can exist in a distributed system or a cloud-based environment. Further, the embodiments allow some or all of the control computer 908, the processing devices 901, the transport 941, and / or the thermal cycler system 907 to be combined as components in a single device.

[0063] The output devices 908E can include any suitable devices that can output data. Examples of the output devices 908E can include a display screen, a video monitor, a speaker, an audio and video alarm, and a data transmission device. The input devices 908D can include any suitable devices that can input data into the control computer 908. Examples of the input devices can include a button, a keyboard, a mouse, a touch screen, a touch pad, a microphone, a video camera, and a sensor (e.g., a light sensor, a position sensor, a velocity sensor, a proximity sensor).

[0064] The data processor 908A can include any suitable data computation device or combination of such devices. Examples of the data processor can include one or more microprocessors working together to accomplish desired functions. The data processor 908A can include a CPU that includes at least one high-speed data processor sufficient to execute program components for executing user and / or system generated requests. The CPU can be a microprocessor such as AMD's Athlon, Duron, and / or Opteron; IBM and / or Motorola's PowerPC; IBM's and Sony's Cell Processor; Intel's Celeron, Itanium, Pentium, Xeon, and / or XScale; ARM-based processors; and / or similar processors.

[0065] The computer-readable medium 908B and the data store 908C can be any suitable device or devices capable of storing electronic data. Examples of memory can include one or more memory chips, disk drives, and the like. Such memory can operate using any suitable electrical, optical, and / or magnetic operating modes.

[0066] The computer-readable medium 908B can include code executable by the data processor 908A for performing any suitable method. For example, the computer-readable medium 908B can include code executable by the processor 908A for causing the processing system 900 to perform an automated reagent processing and heating method including mixing various reagents within a laboratory vessel to different levels, heating the laboratory vessel to different levels, adding additional reagents, and performing additional heating using the thermal cycler system 907.

[0067] The computer-readable medium 908B can include code executable by the data processor 908A for receiving and storing process steps for one or more protocols (e.g., a protocol for processing a biological sample or a protocol for a library construction process) and for controlling the thermal cycler system 907, the structure 940, the transport device 941, and / or the processing device 901 to perform the process steps for the one or more protocols, such as the process steps described with reference to the example section below. The computer-readable medium 908B can also include code executable by the data processor 908A for receiving results from the processing device 901 (e.g., receiving results from analyzing a biological sample) and for forwarding the results or using the results for further analysis (e.g., for diagnosing a patient). In addition, the computer-readable medium 908B can include code executable by the data processor 908A for obtaining an image of the deck 905, identifying information in the image of the deck 905, deciphering the information in the image using information stored in the data storage 908C or the computer-readable medium 908B by comparing the deciphered information to information included in the protocol 908F, and loading the thermal cycler system 907 accordingly.

[0068] The data storage component 908C can be internal or external to the control computer 908. The data storage component 908C can include one or more memories including one or more memory chips, disk drives, etc. The data storage component 908C can also include conventional, fault-tolerant, relational, scalable, secure databases such as those available from Oracle TM or Sybase TM Corporation. The data storage 908C can store the protocol 908F and the images 908G. The data storage component 908C can also include instructions for the data processor 908A including the protocol. The computer-readable medium 908B and the data storage component 908C can include any suitable storage devices such as non-volatile memory, magnetic storage, flash memory, volatile memory, programmable read-only memory, etc.

[0069] Protocols 908F in data storage component 908C can include information about one or more protocols. A protocol can include information about one or more processing steps to be completed, components used during processing, component position layout, loading of reagent reservoirs 100, and / or any other suitable information for completing a process. For example, a protocol can include one or more ordered steps for processing a biological sample or processing a DNA library. A protocol can also include steps to prepare a list of components before starting the process. Components can be mapped to specific locations in reagent reservoirs (e.g., reagent reservoirs 100), turntables (e.g., turntable 1004), or microplates mounted to environmental storage locations including indexed adapters or other reagents in a microplate, where the transport device 941 can obtain the components for delivering the components or vessels that the components are loaded into to the processing equipment 901 or thermal cycler system 907. This mapping can be encoded as instructions for operating the transport device 941, such as instructions that direct a pipette to aspirate a volume of liquid from a labware in a turntable and dispense the volume at a predetermined destination, and the mapping can also be represented by virtual images shown to a user so that the user can place components on the deck 905, reagent reservoirs, and turntables. The mechanical liquid handler 200 can be used for multiple processes (e.g., multiple different sample processes or preparation procedures). Thus, information about multiple protocols 908F can be stored and retrieved when needed. The components on the deck 905, reagent reservoirs, and turntables can be rearranged, changed, and / or supplemented as needed when changing from a first process to a second process, or when restarting a first process.

[0070] Images 908G in data storage component 908C can include real-world or simulated visual representations of the deck 905, reagent reservoirs, and turntables, and components disposed on or in the deck 905, reagent reservoirs, and turntables, and labels disposed on the components. In each image, the deck 905, reagent reservoirs, and turntables can be shown in a ready state for starting a certain process, with components for performing a protocol placed in positions that are accessible to the transport device 941. Each image in images 908G can be associated with a particular protocol from stored protocols 908F. There can be a single image for certain protocols, or there can be multiple images for certain protocols (e.g., multiple images from different angles, with different lighting levels, or containing acceptable labware substitutes in some positions). Images 908G can be stored as various types or formats of image files, including JPEG, TIFF, GIF, BMP, PNG, and / or RAW image files, and AVI, WMV, MOV, MP4, and / or FLV video files.

[0071] The platform 905 can be subdivided into multiple discrete platform positions for placing different components. These discrete positions can have any suitable size. Figure 10 An example of a platform 905 with multiple positions is shown. Figure 10 The platform 905 shows separate areas numbered L1 to L16 and a thermal circulator 1008, which can operate as a separate location for individual types of components or component packages. The platform 905 may have additional or fewer locations as needed. While these locations may be numbered or named, in the physical implementation of the system, these locations may be physically marked or labeled on the platform 905 or may not be physically marked or labeled on the platform 905.

[0072] Images, such as image 908G, can be used to verify that the correct components are loaded into the platform 905, reagent reservoirs, and caps, and if necessary, into the turntable and thermal cycler system 907 to complete the protocol 908F programmed by the operator into the processing system 900, and to verify that these components are in the correct positions for executing the programmed protocol—if required by the protocol. As described herein, the processing system 900 can then perform a mixing program on the liquid loaded into the reagent reservoir, such as reagent reservoir 100, and can controllably heat the reagent reservoir using the thermal cycler system 107 in various ways depending on the liquid loaded into the reagent reservoir, thereby eliminating the need for different types and sizes of reagent reservoirs and different capacities and configurations of thermal cycler systems included in the processing system 900.

[0073] Figure 9 This is a perspective view of a liquid handling system 1000, which may include... Figure 8 An example of a mechanical liquid processor 200. The liquid handling system 1000 may include a housing 1002, a turntable 1004, a reactor dish 103, an imaging device 1006, and a thermal circulator system 1008. Note that, for illustrative purposes, Figure 9 The components are not necessarily drawn to scale. The housing 1002 may include multiple walls or panels forming an enclosure in which the turntable 1004 can be positioned. This enclosure may have an opening onto which a door or other entry point for the user 1010 can be positioned to enclose the turntable 1004, imaging device 1006, and thermal cycler system 1008 within the enclosure. The housing 1002 may also include a platform 112 on which a table, such as table 905, can be positioned. Figure 8 ) or 905 (tabletop) Figure 10). The platen can include slots or pockets for receiving the carousel 1004 and one or more reagent reservoirs 100. In examples, the slots or pockets can be configured to hold the carousel 1004 and the reagent reservoirs 100 in predetermined or known positions relative to the imaging device 1006. The platform 1012 can hold the platen in predetermined or known positions relative to the imaging device 1006. The housing 1002 can also include a space for holding the controller 1014, such as a space for holding a controller of the control computer 908 Figure 8 ). The controller 1014 can be configured to communicate with the network 1016, such as via a wireless or wired communication link.

[0074] The imaging device 1006, which can include an imaging device described with reference to Figure 8 The imaging device 1006 can be positioned in a fixed location within the housing 1002. One or more imaging devices 1006 can be configured to point to a single location or multiple locations in the housing 1002. Meanwhile, the pipette of the transport device 941 or the processing apparatus 901 Figure 8 ) can be positioned within the housing 1002 proximate to a location of the carousel 1004. Further, the transport device 1041 can be configured to move the reagent reservoirs 100 into the thermal cycler system 1008. The carousel 1004 can turn or rotate to present different locations to the pipette and the imaging device 1006. In other examples, the imaging device 1006 can be mounted within the housing 1002 to move an observation area over different portions inside the housing 1002.

[0075] The controller 1014 can be configured to execute protocols for components loaded into the carousel 1004 and the reagent reservoirs 100, as well as components loaded onto the platen within the housing 1002. To cause the controller 1014 to perform one or more sequences of steps on a set of vials loaded into the carousel 1004 and the reagent reservoirs 100 according to a protocol, the controller 1014 should know the location of each vial within the carousel 1004 and the reagent reservoirs 100, such as the contents of each vial at each location within the carousel 1004 and the reagent reservoirs 100. As described herein, the controller 1014 can be configured to operate the imaging device 1006 to obtain images of the carousel 1004 and the reagent reservoirs 100, as well as components loaded into the carousel 1004 and the reagent reservoirs 100. In particular, the carousel 1004 can be loaded with vials of material, where each vial can have a label that provides identifying information about the contents of each vial, a set of vials to which each vial belongs, a manufacturer of the set of vials, one or more protocols that the liquid handling system 1000 performs using the set of vials, and the like. The controller 1014 can read the images of the vial labels to identify the information presented in the labels. The information read from the labels can be compared to information stored in a computer-readable medium, such as Figure 8information stored in the computer readable medium can include a protocol for the set of vials, including one or more sequences of steps for interacting with the set of vials, such as the order in which the transport device 941 can interact with each vial, such as for moving reagents to and between the carousel 1004 and the reagent reservoir 100.

[0076] The reaction vessels 103 can be moved into the thermal cycler system 1008 by the transport device 941, either manually or automatically. The controller 1014 can operate the thermal cycler system 1008 to perform or partially perform various protocols and protocol steps. The controller 1014 can operate the thermal cycler system 1008 and the transport device 941 to heat liquid vessels loaded into the thermal cycler system 1008. The thermal cycler system 1008 can include multiple heating zones, and the reaction vessels can have geometries that form multiple different shaped storage volumes, each of which can have different wall thicknesses for interacting with the heating zones. Thus, a single thermal cycler system 1008 and a single reaction vessel can be used to perform a large number of procedures using different combinations of heating zones and storage volumes, without the need for additional equipment or reaction vessels, such as those described in the example section below.

[0077] Figure 10 is a plan view of the deck 905 for loading onto the platform 1012 of the housing 1002 of Figure 10 The imaging device 1006 can be mounted within the housing 1002 relative to the platform 1012 such that the imaging device can produce a field of view that covers the entire platform 1012. However, in various examples, the field of view can be configured to cover only portions of the platform 1012, and multiple imaging devices can be used or a hinged imaging device can be used that can move the field of view across the platform 1012 to different positions to achieve full coverage. Likewise, the transport system, such as the transport device 941 of Figure 8 The transport device 941 of

[0078] Figure 10The deck 905 is shown including positions numbered LI through L16, as well as other components, such as the thermocycler system 908, which can operate as separate positions for separate types of components or component packs. Examples of the deck 905 can have additional or fewer positions as desired. While these positions can be numbered or named, in physical implementations of the liquid handling system 1000, these positions can or can not be physically marked or denoted on the deck 905. In examples of the liquid handling system 1000, some or all of the positions can be preoccupied by a predefined type of component according to a particular protocol. For example, positions LI through L10 can include storage positions for pipette tip racks 1018 and 1120 (e.g., pipette tips of various volumes), and position LI 1 can be loaded with the turntable 1004. Position L12 can include a cold reagent storage area for reaction vessels, caps, and plugs. Position L13 can include a warm reagent storage area for reaction vessels. Position L15 can include a storage area for reagent reservoirs 100. Position L14 can include a storage area for stacks of reaction vessels. Position L16 can include a waste storage area for the bin 1124. Some of the positions LI through L16 can include the same type of component. These components can include test tubes, micro- or microtiter plates, pipette tips, plate caps, reagent reservoirs 100, or any other suitable laboratory instrument components. These components can also include laboratory equipment items such as shakers, stirrers, mixers, temperature incubators, vacuum manifolds, magnetic plates, thermocyclers, centrifuges, etc. In examples, one or more positions can be physical portions of the structure 940 Figure 8 ), the housing 1002 Figure 9 ), or the deck 905 Figure 10 ), or can be separate components disposed on the platform 1012. The transport device 941 Figure 8 ) can access each of the positions LI through L16. For example, positions LI through L16 and the thermocycler 1124 can be physically separate from the structure 940 or the deck 905.

[0079] The imaging device 1006 can be configured to identify the presence of one or more components at each of the locations LI through LI 6, e.g., the presence of the carousel 1004 at location LI 1, and the presence of the reagent reservoir 100 at location LI 5. In addition, the imaging device 1006 can be configured to read information from one or more components located at each of the locations LI through LI 6. Components, e.g., liquid vials, can be loaded into the carousel 1004 in a desired manner, e.g., according to a protocol, and liquid from the carousel 1004 or another location can be loaded into one of the reactor vessels 103, and thus the thermal cycler system 1008, according to a protocol. Images of the carousel 1004 taken by the imaging device 1006 can be used to read information from labels of vials loaded into the carousel 1004. Thereafter, the thermal cycler system 1008 can perform heating methods, such as those discussed with reference to the example section below, to heat liquid loaded into the thermal cycler system 1008 according to a protocol.

[0080] Other methods contemplated herein include methods of transferring liquid using a mechanical liquid handler, the method comprising:

[0081] filling a reagent reservoir with liquid, thereby filling a sloped bottom of the reagent reservoir, wherein the sloped bottom is formed with a deep end and a shallow end; removing a first portion of the liquid from the reagent reservoir using a multichannel pipettor having a first pipettor tip extending into a first location proximate the shallow end and a second pipettor tip extending into a second location proximate the deep end; and removing a second portion of the liquid from the reagent reservoir using the multichannel pipettor having a single pipettor tip extending into the second location proximate the deep end or a single pipettor tip or a single channel of the multichannel pipettor extending into the deep end of the reagent reservoir. Removing the first portion of the liquid from the reagent reservoir using the multichannel pipettor causes the liquid to be evacuated from the shallow end of the reagent reservoir. Removing the first portion of the liquid from the reagent reservoir can further comprise repeating the aspirating of the liquid from the second volume with the second pipettor. Removing the second portion of the liquid from the reagent reservoir using the multichannel pipettor having the single pipettor tip extending into the second location proximate the deep end or the single pipettor tip or the single channel of the multichannel pipettor extending into the deep end of the reagent reservoir can remove all of the liquid in the first volume.

[0082] Other methods contemplated herein further include methods of transferring liquid using a mechanical liquid handler, the method comprising:

[0083] sucking a first volume of liquid from a reagent reservoir using a first pipettor of a mechanical liquid handler, the first pipettor having a plurality of tips including a first tip and a second tip, the reagent reservoir having a sloped bottom along a width of the reservoir, the sloped bottom defining a shallow end and a deep end of the reagent reservoir, wherein during the sucking of the first volume of liquid, the first tip is positioned on the shallow end of the reagent reservoir and the other tip is positioned on the deep end of the reagent reservoir; and

[0084] sucking a second volume of liquid from the reagent reservoir using a second pipettor of the mechanical liquid handler, the second pipettor having a number of tips that is less than the number of tips of the first pipettor, wherein during the sucking of the second volume, the tips of the second pipettor are positioned on the deep end of the reagent reservoir. The method can further include suspending the particles in the liquid such that the particles do not preferentially or substantially settle in the deep end.

[0085] Further methods contemplated herein include methods of transferring liquid from a bulk storage reservoir using a mechanical liquid handler, the method comprising:

[0086] adding liquid to the bulk storage reservoir such that:

[0087] a first volume of the bulk storage reservoir filled by a sloped bottom of the storage reservoir forming a deep end and a shallow end; and

[0088] a second volume of the bulk storage vessel above the first volume formed by a first end wall and a second end wall of the bulk storage vessel above the deep and shallow portions becomes at least partially filled;

[0089] emptying the second volume using a multichannel pipettor; and

[0090] emptying the first volume using a single channel pipettor or a single channel of a multichannel pipettor. The multichannel pipettor can extend between the first end wall and the second end wall above the first volume; and the single channel pipettor extends across the deep end.

[0091] In this document, unless the context clearly specifies otherwise, the terms “a,” “an,” or “the” are used to include one or more. Unless otherwise stated, the term “or” is used to mean a non-exclusive “or.” Furthermore, it should be understood that the wording or terminology used herein without further qualification is for descriptive purposes only and not for limiting purposes. Any use of section headings is intended to aid reading the document and should not be construed as restrictive. Additionally, information relating to section headings may appear within or outside that particular section. Moreover, all publications, patents, and patent documents referenced in this document are incorporated herein by reference in their entirety, as if individually. If there is any inconsistency between the usage of this document and those documents incorporated by reference, the usage in the incorporated references shall be considered supplementary to the usage in this document; in the case of any conflict, the usage in this document shall prevail.

[0092] In the methods described herein, unless the timing or order of operations is explicitly stated, these steps may be performed in any order without departing from the principles of the invention. Furthermore, unless the explicit language of the claims states that a particular step can be performed individually, certain steps may be performed simultaneously. For example, the claimed step X and the claimed step Y may be performed simultaneously in a single operation, and the resulting process will fall within the literal scope of the claimed process.

[0093] Those skilled in the art will understand that numerous modifications to the embodiments described herein are possible without departing from the spirit and scope of this disclosure. Therefore, this description is not intended and should not be construed as limiting to the examples given, but should be endowed with the full scope of protection provided by the appended claims and their equivalents. Furthermore, some features of this disclosure may be used without correspondingly using others. Thus, the foregoing description or illustrative embodiments are provided to illustrate the principles of this disclosure and not to limit it, and may include modifications and substitutions thereof.

[0094] Example

[0095] The invention can be better understood by referring to the following examples provided by way of illustration. The invention is not limited to the examples given herein.

[0096] The large volume reagent reservoirs described herein reduce dead volume / waste while allowing the systems described herein to process samples in a manner that improves speed and throughput. With 1 tip, the large volume reagent reservoirs can have a dead volume of 50 μΐ, and with 8 tips, can have a dead volume of approximately 500 μΐ. A 3% slope at the bottom portion of the reservoir relative to horizontal can cause the volume in the reservoir to decrease as the application runs, accumulating at the lowest point at the back of the reservoir. At the beginning of the method, the reservoir can be filled with the estimated volume of reagent needed to complete the application. As the reagent is aliquoted from the large volume reservoir and the volume decreases, the application can track the amount of liquid remaining in the reservoir. When it is automatically reached the point where the next pipetting action will cause the calculated remaining volume to be below 500 μΐ, the systems described herein can switch from using 8 tips to using 1 tip. This reduces the dead volume needed by the application to use the reservoir and allows the automation to efficiently process samples.

[0097] Example 1

[0098] If a user wishes to run 24 samples and plans to use 60 μΐ of Ampure XP beads per sample, the total volume needed for the run is 1440 μΐ assuming no dead volume. When we program the pipette to run in the following manner, the dead volume in the large volume reservoir is estimated to be 50 μΐ:

[0099] • Process 1 - 60 μΐ for each of the 8 tips, the total volume removed will be 480 μΐ. The remaining volume will be 610 μΐ (total volume of 1490 μΐ).

[0100] • Process 2 - 60 μΐ for each of the 8 tips, the total volume moved will be 480 μΐ. The remaining volume will be 690 μΐ.

[0101] • Process 3 - 60 μΐ is expected for each of the last 8 tips transferred. However, the total aspiration will reduce the tracked volume in the large volume reagent reservoir to a calculated volume below the 500 μΐ threshold. Therefore, starting with process 3, the systems described herein can be programmed to automatically switch to pipetting with 1 tip for the remaining 8 tips (process 3 through process 10).

[0102] By utilizing the reagent reservoirs described herein, the dead volume required for a large volume of reagent can be reduced by approximately 450 μΐ^. This is especially important for reagents that are not packaged in an application kit for use in an automated system. When automating an application, low volume excess is a problem. The reagent reservoirs described herein will enable the system to reduce the cost of running. Using standard costs, the reagents described above would cost the user $2.40 / ml. The reagent reservoirs described herein reduce the cost from $4.66 per run of 24 samples to $3.46.

[0103] Example 2

[0104] To wash the beads aliquoted from above, the user will utilize 50 μΐ^ of 80% ethanol. The total volume required is 50*24. Assuming no dead volume, the total volume run will be 1200. The dead volume in the large volume reservoir is estimated to be 50 μΐ^. When programmed as follows:

[0105] • Process 1 - for each of the 8 tips, 50 μΐ^, the total volume removed will be 400 μΐ^. The remaining volume will be 850 μΐ^ (total volume is 1250 μΐ^).

[0106] • Process 2 - for each of the last 8 tips transferred, 50 μΐ^ is expected. However, the total aspiration will reduce the tracked volume in the large volume reagent reservoir to a calculated volume below the 500 μΐ^ threshold. Therefore, starting with process 2, for the remaining 8 tips (process 2 through process 17), the system described herein can be programmed to automatically switch to pipetting with 1 tip at a time.

[0107] In this case, if optimization for speed is chosen, the system can be programmed for a larger dead input. This will depend on the expected speed for the dead volume and the cost of the reagent being pipetted. The large volume reagent reservoir design allows for a reduction in the volume required. In the case above, cost is not the issue. However, ethanol is flammable. Using a large volume reagent reservoir will reduce the volume of hazardous chemicals deployed in our pipetting system. This will also reduce the amount of hazardous waste generated by the automated platform.

[0108] Example 3:

[0109] This example uses Illumina TruSight Oncology 500 (Document Number 1000000067621 v02) with a 24 DNA ONLY workflow:

[0110] SPB (sample preparation beads) will be used in a large volume reagent reservoir, once every 2 days in a 2 day protocol for library creation and enrichment.

[0111] Day 1 Library Generation: The standard protocol calls for 112ul of beads to be added to each well to clean up the ligation reaction. The system described herein can use milli pipette tips to pipette mix the bead solution by aspirating and dispensing the bead mix until the beads are fully suspended in solution. The speed of the aspiration and dispensing pushes the beads away from the bottom of the bulk reservoir. When testing in the lab, if we maintain a 3% slope, the beads will not "slide" down the incline of the reservoir. Ampure XL beads do not come out of solution quickly. Each transfer set will require only 1 mix.

[0112] Total volume required for bulk reservoir: 112ul / sample plus 50ul dead volume. Total volume of reservoir: 2738ul

[0113] • Mix Ampure XL beads using 8 tips, 260ul / tip, mix 8 times to resuspend.

[0114] • Process 1 - Transfer 112ul using 8 tips to the first 8 samples (the remaining volume in the reservoir will be 892ul)

[0115] • Process 2 - Transfer 112ul using 8 tips to samples 9 through 16 (the remaining volume will be 945ul)

[0116] • Process 3 through 10 - Transfer 112ul using 1 tip at a time to each of the remaining 8 samples as the tracked volume in the reservoir will drop below the 500ul volume required to use 8 tips at a time.

[0117] Day 2 (Illumina Manual page 29): The standard protocol calls for 110ul of beads to be added to each well to clean up the amplified enriched library. The NGenius system will use milli pipette tips to pipette mix the bead solution by aspirating and dispensing the bead mix until the beads are fully suspended in solution. Ampure XL beads do not come out of solution quickly. Each transfer set will require only 1 mix.

[0118] Total volume required for bulk reservoir: 110ul / sample plus 50ul dead volume. Total volume of reservoir: 2690ul

[0119] • Mix Ampure XL beads using 8 tips, 260ul / tip, mix 8 times to resuspend.

[0120] • Process 1 - Transfer 110ul using 8 tips to the first 8 samples (the remaining volume in the reservoir will be 1810ul)

[0121] • Process 2 - use 8 tips to transfer 110 μL to samples 9 through 16 (the remaining volume will be 930 μL)

[0122] • Processes 3 through 10 - use 1 tip at a time to transfer 110 μL to each of the remaining 8 samples, as the tracked volume in the reservoir will drop below the 500 μL volume required to use 8 tips at a time.

[0123] The procedure described in this example can also be used for non-magnetic reagents in the Illumina kits (RSB - Resuspension Buffer, 80% EtOH - Ethanol, EEW - Enrichment Wash, LNA1 - Library Normalization Additive (contains formamide), and other magnetic bead solutions (LNB1 - Library Normalization Beads and SMB - Streptavidin Magnetic Beads).

[0124] The LNA1 reagent listed above produces a gas that is dangerous if inhaled. It is prudent to keep the volumes used in this system as low as possible.

[0125] Example 4

[0126] An experiment was performed to determine if beads (e.g., AmpureXP and Streptavidin beads) accumulate at the deeper end of the reagent reservoir when added to the reagent reservoir and allowed to settle. To do this, two separate reagent reservoirs were prepared: 1 mL of AmpureXP was added to one section, and 2 mL of AmpureXP was added to the second section. Prior to settling, a photograph was taken of the side of the tank. The reagent reservoir was covered by an adhesive seal and allowed to settle overnight. The next morning, the seal was removed. The photographs (not included here) showed that there did not appear to be any significant settling towards the deep end of the reagent reservoir when allowed to settle overnight.

[0127] Example 5

[0128] This experiment was designed to investigate the difficulty of resuspending beads (e.g., AmpureXP and Streptavidin beads) in the reagent reservoir. To do this, 10 mL of AmpureXP was added to one side of the reagent reservoir, and the beads were allowed to settle overnight. The next morning, a multichannel pipettor, specifically an i5Span-8 available from Beckman Coulter, Inc. of Brea, California, was used to resuspend the settled beads. After three to four mixings, the beads appeared to be completely resuspended.

[0129] Example 6

[0130] The AmpureXP suspension from Example 5 was completely removed from the reagent reservoir and 400 μL was returned to the reservoir. Using the modified pipetting template, eight 15 μL of Ampure XP from the 400 μL suspension were added to eight wells of the PCR plate, removing 120 μL from the 400 μL in the reagent reservoir. All eight samples were successfully pipetted.

[0131] Example 7

[0132] This experiment was performed to investigate the effect of the angle Θ (see Figure 1 ) on the ability to resuspend beads using multiple pipette tips (e.g., from an i5 Span-8 pipettor). To do this, 2 mL of AMPureXP was added to a series of six reagent reservoirs and the reservoirs were sealed to prevent evaporation. The beads were allowed to settle overnight. Three of the reservoirs had an angle Θ of 3° and three reservoirs had an angle Θ of 8°. As expected, as the slope increased, the triangle defined by the beads became as shown in Figure 11 Thus, the area in which the beads settled became smaller as Θ increased. The reduced area did not allow for more than one pipette tip to be used for resuspension of the beads. Thus, in some cases, a 3° to 4° slope can be better than a 7° to 8° slope.

[0133] Selected embodiments of the present disclosure include, but are not limited to, the following embodiments:

[0134] Embodiment 1 relates to a method of transferring liquid using a mechanical liquid handler, the method comprising: aspirating a first volume of liquid from a reagent reservoir using a multichannel pipettor of the mechanical liquid handler, the reagent reservoir having a sloped bottom along a width of the reagent reservoir, the sloped bottom defining a shallow end of the reagent reservoir and a deep end of the reagent reservoir, wherein the shallow end is proximate to a first sidewall of the reagent reservoir, wherein the deep end is proximate to a second sidewall of the reagent reservoir opposite the first sidewall; and

[0135] aspirating a second volume of liquid from the deep end of the reagent reservoir using a single channel pipettor or a single channel of a multichannel pipettor of the mechanical liquid handler, wherein aspirating the second volume from the deep end depletes the liquid in the shallow end of the reagent reservoir.

[0136] Embodiment 2 relates to the method of embodiment 1, wherein the single channel pipettor or the single channel of the multichannel pipettor is positioned at a deepest portion of the reagent reservoir, wherein the deepest portion is proximate to the second sidewall of the reagent reservoir.

[0137] Embodiment 3 relates to the method of embodiments 1-2, wherein the reagent reservoir has a cross-section that decreases along a width of the reagent reservoir from the first sidewall to the second sidewall.

[0138] Embodiment 4 relates to the method of embodiment 3, wherein aspirating the first volume of liquid from the reagent reservoir using the multichannel pipettor of the mechanical liquid handler includes aspirating the first volume using the multichannel pipettor along the width of the reagent reservoir from the first sidewall to the second sidewall.

[0139] Embodiment 5 relates to the method of embodiments 1-4, wherein the reagent reservoir has a plurality of chambers each having a sloped bottom.

[0140] Embodiment 6 relates to the method of embodiment 5, wherein the plurality of chambers are formed by a dividing wall extending along a width of the reservoir.

[0141] Embodiment 7 relates to the method of embodiments 1-6, further comprising: depositing a particle in the liquid; and allowing the particle to become suspended in the liquid; wherein the particle settles uniformly along the sloped bottom.

[0142] Embodiment 8 relates to the method of embodiments 1-7, further comprising: aligning a tab with a slot on a liquid handler to position the reagent reservoir on a deck of the mechanical liquid handler.

[0143] Embodiment 9 relates to the method of embodiments 1-8, further comprising: engaging a tab of the reagent reservoir with the deck of the mechanical liquid handler to raise the shallow end portion above the deep end portion and the first sidewall and the second sidewall to stand vertically on the deck.

[0144] Embodiment 10 relates to a method of transferring liquid using a mechanical liquid handler, the method comprising:

[0145] filling a reagent reservoir with liquid, thereby filling a sloped bottom of the reagent reservoir, wherein the sloped bottom is formed with a deep end portion and a shallow end portion;

[0146] removing a first portion of liquid from the reagent reservoir using a multichannel pipettor having a first pipettor tip extending into a first position proximate the shallow end and a second pipettor tip extending into a second position proximate the deep end; and removing a second portion of liquid from the reagent reservoir using a multichannel pipettor having a single pipettor tip extending into the second position proximate the deep end or a single channel pipettor having a pipettor tip extending into the deep end.

[0147] Embodiment 11 relates to the method of embodiment 10, wherein removing the first portion of liquid from the reagent reservoir using the multichannel pipettor causes liquid to be emptied from the shallow end of the reagent reservoir.

[0148] Embodiment 12 relates to the method of embodiment 10, wherein removing the first portion of liquid from the reagent reservoir can further comprise repeating aspirating liquid from a second volume by the second pipettor.

[0149] Embodiment 13 relates to the method of embodiment 10, wherein removing the second portion of liquid from the reagent reservoir using the multichannel pipettor having a single pipettor tip extending into the second position proximate the deep end or a single channel pipettor having a pipettor tip extending into the deep end is capable of removing all of the first volume of liquid.

[0150] Embodiment 14 relates to a method of transferring liquid using a mechanical liquid handler, the method comprising:

[0151] aspirating a first volume of liquid from a reagent reservoir using a first pipettor of the mechanical liquid handler, the first pipettor having a plurality of tips including a first tip and a second tip, the reagent reservoir having a sloped bottom along a width of the reservoir, the sloped bottom defining a shallow end and a deep end of the reagent reservoir, wherein during aspiration of the first volume of liquid, the first tip is positioned at the shallow end of the reagent reservoir and the other tip is positioned at the deep end of the reagent reservoir; and

[0152] aspirating a second volume of liquid from the reagent reservoir using a second pipettor of the mechanical liquid handler, the second pipettor having a number of tips less than the number of tips of the first pipettor, wherein during aspiration of the second volume, the tips of the second pipettor are positioned at the deep end of the reagent reservoir.

[0153] Embodiment 15 relates to the method of embodiment 14, further comprising suspending particles in the liquid such that the particles do not preferentially settle in the deep end.

[0154] Embodiment 16 relates to a method of transferring liquid from a bulk storage vessel using a mechanical liquid handler, the method comprising:

[0155] adding liquid to a bulk storage reservoir such that: a first volume of the bulk storage reservoir formed by a sloped bottom of the storage reservoir forming a deep end and a shallow end is filled; and

[0156] a second volume of the bulk storage vessel above the first volume formed by a first end wall and a second end wall of the bulk storage vessel above the deep end and the shallow end becomes at least partially filled;

[0157] emptying the second volume using a multi-channel pipettor; and

[0158] emptying the first volume using a single-channel pipettor or a single channel of a multi-channel pipettor.

[0159] Embodiment 17 relates to the method of embodiment 16, wherein:

[0160] the multi-channel pipettor extends between the first end wall and the second end wall above the first volume; and

[0161] the single-channel pipettor or the single channel of the multi-channel pipettor extends across the deep end.

Claims

1. A method for transferring liquid using a mechanical liquid processor, the method comprising: A first volume of liquid is aspirated from a reagent reservoir using the multichannel pipette of the mechanical liquid processor. The reagent reservoir has a sloping bottom along its width, defining a shallow end and a deep end, wherein the shallow end is adjacent to a first sidewall of the reagent reservoir, and the deep end is adjacent to a second sidewall of the reagent reservoir opposite the first sidewall. Then, using a single channel of the single-channel or multi-channel pipette of the mechanical liquid processor, a second volume of liquid is aspirated from the deep end of the reagent reservoir. Specifically, the second volume is drawn out from the deep end, causing the liquid in the shallow end of the reagent reservoir to be depleted; and Using the multichannel pipette of the mechanical liquid processor to aspirate the first volume of liquid from the reagent reservoir includes using the multichannel pipette to aspirate the first volume along the width of the reagent reservoir from the first sidewall to the second sidewall.

2. The method according to claim 1, wherein, The single channel of the single-channel pipette or the single channel of the multi-channel pipette is located at the deepest part of the reagent reservoir, wherein the deepest part is close to the second sidewall of the reagent reservoir.

3. The method according to claim 1, wherein, The reagent reservoir includes a base plate having a cross-sectional shape that decreases in width from the first sidewall to the second sidewall along the width of the reagent reservoir.

4. The method according to claim 1, wherein, The reagent reservoir has multiple chambers, each of which has a sloping bottom.

5. The method according to claim 4, wherein, The multiple chambers are formed by partition walls extending along the width of the reservoir.

6. The method according to claim 1, further comprising: The particles are deposited in the liquid; and The particles are allowed to become suspended in the liquid; The particles settle uniformly along the inclined bottom.

7. The method according to claim 1, wherein, The reagent reservoir has a protrusion, and the protrusion is in the form of a raised portion; the method further includes: Align the protrusion with the slot on the liquid processor to position the reagent reservoir on the platform of the mechanical liquid processor.

8. The method according to claim 1, wherein, The reagent reservoir has a protrusion, and the protrusion is in the form of a raised portion; the method further includes: The protrusion of the reagent reservoir is engaged with the platform of the mechanical liquid processor, such that the shallow end is raised above the deep end and the first and second sidewalls are vertically erected on the platform.

9. The method according to claim 1, further comprising: Fill the reagent reservoir with liquid; Aspirating the first volume also includes using a multichannel pipette having a first pipette tip extending to a first position near the shallow end and a second pipette tip extending to a second position near the deep end; as well as Aspirating the second volume also includes using a multichannel pipette having a single pipette tip extending into a second position near the deep end, or a single-channel pipette tip extending into the deep end.

10. The method according to claim 9, wherein, Using the multichannel pipette to aspirate the first volume of liquid from the reagent reservoir will cause the liquid to be emptied from the shallow end of the reagent reservoir.

11. The method according to claim 9, wherein, Drawing the first volume of liquid from the reagent reservoir can also include repeatedly drawing liquid from the second position using the second pipette.

12. The method according to claim 9, wherein, Using the multichannel pipette with a single pipette tip extending into a second position near the deep end or a single-channel pipette tip extending into the deep end, a second volume of liquid can be aspirated from the reagent reservoir, removing all liquid from the first position.

13. The method according to claim 1, further comprising: Aspirating the first volume of liquid from the reagent reservoir involves using a first pipette having multiple pipette tips, including a first tip and a second tip. During the aspiration of the first volume of liquid, the first pipette tip is positioned at the shallow end of the reagent reservoir and the second pipette tip is positioned at the deep end of the reagent reservoir; and Aspirating the second volume of liquid from the reagent reservoir includes using a second pipette with fewer tips than the first pipette, wherein during aspiration of the second volume, the tips of the second pipette are positioned at the deep end of the reagent reservoir.

14. The method according to claim 4, further comprising: Add liquid to the reservoir such that: The reservoir is filled with a first volume formed by the inclined bottom of the reservoir having the deep end and the shallow end; and The second volume of the reservoir, located above the first volume and formed by the first and second end walls of the reservoir, becomes at least partially filled; Empty the second volume using a multichannel pipette; as well as The first volume is emptied using a single channel of a single-channel pipette or a single channel of a multi-channel pipette.

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