Method for analyzing a plurality of samples

A diagnostic system performs a first nucleic acid amplification reaction and a second, different nucleic acid amplification reaction. The diagnostic system includes a compartment configured to store at least a first bulk reagent container comprising a first bulk reagent for performing a sample preparation process, and a second bulk reagent container comprising a second bulk reagent for performing the first reaction. The system including a compartment configured to store at least one unit-dose pack comprising a plurality of unit-dose reagents for performing the second reaction. The diagnostic system is configured to perform the sample preparation process using the first bulk reagent on each of a plurality of samples provided to the diagnostic system. The system is configured to perform the first reaction using the second bulk reagent on a first sample subset, and perform the second reaction using the plurality of first unit-dose reagents on a second sample subset.

BACKGROUND

The present disclosure relates to diagnostic systems and methods for performing a plurality of different molecular assays on a plurality of samples and, particularly, molecular assays that comprise target nucleic acid amplification reactions.

None of the references described or referred to herein are admitted to be prior art to the claimed invention.

Molecular assays are nucleic acid-based tests that are used in clinical diagnosis, screening, monitoring, industrial and environmental testing, health science research, and other applications to detect the presence or amount of an analyte of interest in a sample, such as a microbe or virus, or to detect genetic abnormalities or mutations in an organism. Molecular assays enabling quantification may permit practitioners to better calculate the extent of infection or disease and to determine the state of a disease over time. Quantitative molecular assays are also useful for monitoring the effectiveness of a therapy. A variety of known molecular assays can be employed to detect various diagnostic indicators.

Molecular assays generally include multiple steps leading to the detection or quantification of a target nucleic acid in a sample. Targeted nucleic acids often include a region that is specific to an identifiable “group” of organisms or viruses, where the group is defined by at least one shared sequence of nucleic acid that is common to all members of the group and is specific to the group in the particular sample being assayed. Examples of nucleic acid-based detection methods are disclosed by Kohne in U.S. Pat. No. 4,851,330 and Hogan et al. in U.S. Pat. No. 5,541,308.

Most molecular assays include a detection step in which the sample is exposed to a detection probe or amplification primer that is designed or selected to exhibit specificity under the particular conditions of use for a nucleic acid sequence belonging to an organism or virus of interest. The detection probe or amplification primer can be labeled for detection with a reporter moiety, such as a chemiluminescent or fluorescent agent, or an intercalating dye can be used to indiscriminately detect the presence of double-stranded nucleic acids in a sample. See, e.g., Livak et al. in U.S. Pat. No. 5,538,848, Hogan et al. in U.S. Pat. No. 5,541,308, Tyagi et al. in U.S. Pat. No. 5,925,517, Higuchi in U.S. Pat. No. 5,994,056, Wittwer et al. in U.S. Pat. No. 6,174,670, Whitcombe et al. in U.S. Pat. No. 6,326,145, and Wittwer et al. in U.S. Pat. No. 6,569,627. To render a nucleic acid available for hybridization to the detection probe or amplification primer, cells may be lysed or permeabilized by a variety of known techniques, including by chemical (e.g., detergent), mechanical (e.g., sonication), and/or thermal procedures. See, e.g., Clark et al. in U.S. Pat. No. 5,786,208.

Before or after exposing a target nucleic acid to a detection probe or amplification primer, the target nucleic acid can be immobilized on a solid support (e.g., particles or beads comprising a magnetically-responsive material) that directly or indirectly binds the target nucleic acid. A solid-phase extraction method for directly binding nucleic acids onto silica beads in the presence of a chaotropic substance is described by Boom et al. in U.S. Pat. No. 5,234,864. An example of indirect immobilization is described Weisburg et al. in U.S. Pat. No. 6,534,273, which discloses the use of a capture probe that binds to the target nucleic acid under a first set of sample conditions and to an oligonucleotide covalently attached to the solid support under a second set of sample conditions. If the solid support comprises a magnetically-responsive particle or bead, magnets can be used to attract the solid support to the side of a receptacle containing the solid support. Once the immobilized target nucleic acid is isolated within the receptacle, the isolated target nucleic acid can be separated from a least a portion of the fluid contents of the sample by, for example, contacting and aspirating the fluid contents of the receptacle with a robotic pipettor or other substance transfer device. See, e.g., Ammann et al. in U.S. Pat. No. 6,605,213. One or more wash steps with a buffered solution or water may be performed to further purify the isolated nucleic acid.

To increase the sensitivity of an assay, a target nucleic acid can be amplified by a nucleic acid amplification reaction, many of which are well known in the art. Known methods of amplification include Polymerase Chain Reaction (“PCR”) (see, e.g., Mullis et al. in U.S. Pat. Nos. 4,683,195, 4,683,202 and 4,800,159; and Mullis et al.,Methods in Enzymology155:335-350 (1987)); Strand Displacement Amplification (“SDA”) (see, e.g., Walker,PCR Methods and Applications,3:25-30 (1993); Walker et al.,Nucleic Acids Res.,20:1691-1996 (1992); and Walker et al.,Proc. Natl. Acad. Sci.,89:392-396 (1991)); Ligase Chain Reaction (“LCR”) (see, e.g., Birkenmeyer in U.S. Pat. No. 5,427,930 and Carrino et al., in U.S. Pat. No. 5,686,272); and transcription-based methods of amplification (Boothroyd et al. in U.S. Pat. No. 5,437,990; Kacian et al., in U.S. Pat. Nos. 5,399,491 and 5,480,784; Davey et al. in U.S. Pat. No. 5,409,818; Malek et al. in U.S. Pat. No. 5,130,238; and Gingeras et al. in International Publication Nos. WO 88/01302 and WO 88/10315). A review of many amplification reactions, including PCR and Transcription-Mediated Amplification (“TMA”), is provided in Lee et al., Nucleic Acid Amplification Technologies, BioTechniques Books (1997).

PCR is the oldest and most common form of amplification. Like other amplification methods, PCR amplifies one or more copies of a region of nucleic acid by several orders of magnitude, generating thousands to millions of copies of a particular nucleic acid sequence. PCR has broad applications in clinical and biological research labs. The uses of this procedure are too enumerable, and well known at this time, to recite in this patent application.

PCR employs thermal cycling, which consists of repeated cycles of heating and cooling of a reaction mixture. The reaction is generally initiated with primers (short DNA fragments containing sequences complementary to the target nucleic acid region), along with enzymes and additional reaction materials. Once under way, the replicated nucleic acid can be used as an additional template in the amplification reaction, thereby leading to the exponential amplification of a target nucleic acid sequence.

Because a probe hybridizes to the targeted sequence, the strength of a signal associated with the probe is proportional to the amount of target nucleic acid sequence that is present in a sample. Accordingly, by periodically measuring, during the amplification process, a signal indicative of the presence of amplicon, the growth of amplicon over time can be detected. Based on the data collected during this “real-time” monitoring of the amplification process, the amount of the target nucleic acid that was originally in the sample can be ascertained. In one context, collecting data in “real-time” means collecting data while a reaction or other process is in progress, as opposed to collecting data at the conclusion of the reaction or process. Systems and methods for real-time detection and for processing real-time data to ascertain nucleic acid levels are disclosed by, for example. Lair et al. in U.S. Pat. No. 7,932,081.

To detect different nucleic acids in a single assay, distinct probes may be designed or selected to separately hybridize to the different nucleic acids, where the probes may include reporter moieties that can be differentiated from each other. See, e.g., Livak et al. in U.S. Pat. No. 5,538,848, Tyagi et al. in U.S. Pat. No. 5,925,517, Morrison in U.S. Pat. No. 5,928,862, Mayrand in U.S. Pat. No. 5,691,146, and Becker et al. in U.S. Pat. No. 5,928,862. For example, different probes designed or selected to hybridize to different targets can have fluorophores that fluoresce at a predetermined wavelength when exposed to excitation light of a prescribed excitation wavelength. Assays for detecting different target nucleic acids can be performed in parallel by alternately exposing the sample material to different excitation wavelengths and detecting the level of fluorescence at the wavelength of interest corresponding to the probe for each target nucleic acid during the real-time monitoring process. Parallel processing can be performed using different signal detecting devices configured to periodically measure signal emissions during the amplification process, and with different signal detecting devices being configured to generate excitation signals of different wavelengths and to measure emission signals of different wavelengths.

SUMMARY

Aspects of the present disclosure are of bodied in systems, apparatuses, and processes that, inter alia, enhance the functionality of certain diagnostic first modules by supporting processing capabilities that are not available in the base first module or existing modules within the base first module. In one embodiment, the systems, apparatuses, and processes extend the functionality of a nucleic acid diagnostic first module by supporting PCR assay processing and analysis capabilities in addition to isothermal amplification processing and analysis capabilities. A second module is operatively coupled to the base first module to extend the overall system capabilities of the diagnostic system. Providing this extension module imparts sample-to-answer capabilities for a single automated instrument that, when incorporated, will be capable of automatically performing both thermal cycling and isothermal amplification assays, and which may incorporate end-point and real-time formats using chemiluminescent and/or fluorescent labels.

In some embodiments, a diagnostic system can be configured to perform a first nucleic acid amplification reaction and a second nucleic acid amplification reaction different than the first nucleic acid amplification reaction. The diagnostic system comprises at least one bulk reagent container compartment configured to store at least a first bulk reagent container comprising a first bulk reagent for performing a sample preparation process, and a second bulk reagent container comprising a second bulk reagent for performing the first nucleic acid amplification reaction. The at least one bulk reagent container compartment is further configured to store a unit-dose reagent compartment configured to store at least one unit-dose reagent pack comprising a plurality of unit-dose reagents for performing the second nucleic acid amplification reaction. The diagnostic system is configured to perform the sample preparation process using the first bulk reagent on a first subset of the plurality of samples provided to the diagnostic system. The diagnostic system is also configured to perform the first nucleic acid amplification reaction using a second bulk reagent on the first subset of the plurality of samples. And the diagnostic system is configured to perform the second nucleic acid amplification reaction using the plurality of unit-dose reagents on a second subset of the plurality of samples.

In some embodiments, an automated method for analyzing a plurality of samples comprises performing a first assay on a first sample subset of the plurality of samples. The first assay comprises a first reaction that uses a first unit-dose reagent. The method also comprises performing a second assay on a second sample subset of the plurality of samples. The second assay comprises a second reaction that uses at least one of (a) a second unit-dose reagent different than the first unit-dose reagent and (b) a first bulk reagent. Performing the first assay and performing the second assay occur within a same diagnostic system that stores the first unit-dose reagent and at least one of the second unit-dose reagent and the first bulk reagent.

In one exemplary embodiment, the base first module comprises a dual format molecular diagnostic instrument designed to run specific target-amplified assays, utilizing chemiluminescence and fluorescence detection technologies for both qualitative and real-time quantitative assays. With the addition of the second module, additional automated assays, such as PCR assays, can be run (intermixed) with assays performed by the base first module and achieve similar throughput that is achieved by the base first module.

In one exemplary embodiment, the second module comprises a thermal cycler with real-time fluorescence detection capabilities, a reagent pack storage bay that allows for loading and cooled storage of new reagent packs containing reagents (e.g., PCR reagents), additional disposable pipette tip trays, PCR- and assay-specific reagents, and one or more pipettor systems to perform the assay steps needed for the PCR or other reaction and/or receptacle transport. The second module may rely on the base first module for sample input, sample preparation, target capture, and other processing steps, such as the addition of elution for subsequent PCR assays, and thus the second module further leverages those capabilities of the base first module and supports additional processing and detection capabilities without requiring that the sample input and preparation functionality be built into the second module.

Aspects of the disclosure are embodied in a second module for enhancing the capabilities of a first module configured to process substances within each of a plurality of receptacles and including a first substance transfer device configured to dispense substances into each receptacle and a receptacle transfer device configured to move receptacles within the first module. The second module is configured to be coupled to or decoupled from the first module and comprises a container transport configured to transport at least one container from a location within the second module to a location within the first module that is accessible to the first substance transfer device to transfer substance from the container to a receptacle within the first module, a receptacle distribution module configured to receive a receptacle from the receptacle transfer device of the first module, transfer the receptacle into the second module, and move the receptacle between different locations within the first module, and a second substance transfer device configured to dispense substances into or remove substances from the receptacle within the second module.

According to some aspects of the disclosure, the receptacle distribution module comprises a receptacle distributor configured to move a receptacle onto the receptacle distributor at a first location on the second module, carry the receptacle from the first location to a second location on the second module that is different from the first location, and move the receptacle off the receptacle distributor at the second location on the second module. A receptacle handoff device can be configured to receive a receptacle from the receptacle transfer device of the first module and to reposition the receptacle to present the receptacle to the receptacle distributor to be moved by the receptacle distributor from the receptacle handoff device onto the receptacle distributor.

According to some aspects of the disclosure, the receptacle distributor is configured to rotate about an axis of rotation to move a receptacle carried thereby in an arced path between locations within the second module. Other configurations for moving a receptacle between locations within the second module are contemplated. Therefore, the disclosure is not limited to receptacle distributors that rotate about an axis of rotation.

According to some aspects of the disclosure, the second module further comprises receptacle storage stations for holding one or more receptacles transferred from the first module to the second module, wherein the receptacle storage stations are arranged in a configuration corresponding to the arced path of the receptacle distributor.

According to some aspects of the disclosure, the receptacle distributor is configured to move vertically a receptacle carried thereby between different vertically-disposed locations within the second module.

According to some aspects of the disclosure, the receptacle handoff device is configured to rotate between a first position for receiving a receptacle from the receptacle transfer device of the first module and a second position for presenting the receptacle to the receptacle distributor.

According to some aspects of the disclosure, the second module further comprises a container compartment, configured to hold one or more fluid containers. In certain embodiments, the container compartment can be a container drawer configured to be moved between an opened position and a closed position and to, when moved to the closed position, place at least one fluid container into an operative position with respect to the container transport so that the container can be transported by the container transport from the container compartment into the first module. In an alternate embodiment, the container compartment can comprise a door with a sliding tray that is configured to be moved between an opened position and a closed position and to, when moved to the closed position, place at least one fluid container into an operative position with respect to the container transport so that the container can be transported by the container transport from the container compartment into the first module.

According to some aspects of the disclosure, the second module further comprises a container carriage configured to carry one or ore containers and to be movable with the container compartment and further configured to be engaged by the container transport when the container compartment is in the closed position such that the container transport is operable to move the container carriage and the one or more containers carried thereby from the container compartment into the first module.

According to some aspects of the disclosure, the second module further comprises a carriage transport and a carriage lock. The carriage transport is moveable with the container receptacle and configured to carry the container carriage between a first position when the container receptacle is in the opened position and a second position when the container receptacle is in the closed position. The carriage lock is configured to lock the container carriage to the carriage transport when the carriage transport is in the first position and to release the container from the carriage transport when the carriage transport is in the second position to permit the container carriage to be removed from the carriage transport by the container transport.

According to some aspects of the disclosure, the container transport comprises a track extending from the container compartment into the first module, a carriage hook configured to engage the container carriage when the container compartment is in the closed position, and a motorized carriage hook drive system configured to move carriage hook along the carriage track.

According to some aspects of the disclosure, the motorized carriage hook drive system comprises a motor and a belt driven by the motor and coupled to the carriage hook.

According to some aspects of the disclosure, the processing apparatus further comprises one or more position sensors disposed at one or more locations along the track to detect a position of the carriage on the track.

According to some aspects of the disclosure, the second module further comprises a reagent pack changer comprising a pack input device and a pack storage compartment. The pack input device is configured to enable an opera or to place a reagent pack containing at least one reagent into the second module or remove a reagent pack from the second module. The pack storage compartment is configured to hold a plurality of reagent packs until a reagent pack is needed for processing within the second module. The receptacle distribution module is further configured to move a reagent pack between the pack input device and the pack storage compartment.

According to some aspects of the disclosure, the second module further comprises one or more reagent pack loading stations, each configured to hold a reagent pack in a manner that permits the second substance transfer device to transfer a substance to or from the reagent pack. Therefore, in some embodiments, the reagent pack loading station is configured to change the orientation of the reagent pack from an initial loaded position to a position aligned with the second substance transfer device.

According to some aspects of the disclosure, the second module further comprises a charged field generator operatively associated with at least one of the pack input device, the pack storage compartment, and the reagent pack loading stations and configured to generate electrostatic forces to position and hold a reagent present in a reagent pack held in the pack input device or pack storage compartment. In related aspects the charged field generator is situated below at least one of the pack input device, the pack storage compartment, and the reagent pack loading stations such that electromagnetic forces are applied to, or adjacent to, the bottom of one or more wells of a reagent pack, when present.

According to some aspects of the disclosure, wherein the pack input device comprises a reagent pack carousel that is rotatable about an axis of rotation, wherein the pack carousel includes a plurality of reagent pack stations, each configured to hold a reagent pack, disposed around the axis of rotation.

According to some aspects of the disclosure, the pack carousel is disposed in a compartment, such as a drawer, that is movable between an open position providing access to the pack carousel and a closed position closing off access to the pack carousel. The pack carousel can also be accessed through an access panel revealing a slidable tray on which is mounted the pack carousel.

According to some aspects of the disclosure, the second module further comprises a code reader operatively disposed with respect to the pack input device and configured to read a machine readable code on each reagent pack carried in the pack input device. In some embodiments, the code reader reads the machine readable code on a respective reagent pack in close proximity to the code reader.

According to some aspects of the disclosure, the second module further comprises a pack storage carousel disposed within the pack storage compartment. The pack storage carousel is rotatable about an axis of rotation and includes a plurality of reagent pack stations, each configured to hold a reagent pack, disposed around the axis of rotation.

According to some aspects of the disclosure, the reagent pack stations of the pack storage carousel are disposed on more than one level of the second module.

According to some aspects of the disclosure, the second module further includes a cooling system for maintaining the storage compartment at a lower than ambient temperature.

According to some aspects of the disclosure, the second substance transfer device comprises a robotic pipettor having a pipettor probe, and the second module further comprises one or more disposable tip compartments configured to hold a plurality of disposable tips configured to be placed on the pipettor probe of the robotic pipettor.

According to some aspects of the disclosure, the second module further comprises a cap/vial tray configured to hold a plurality of processing vials and/or associated caps. Each cap is configured to be coupled to an associated vial to close the associated vial. The vials are accessible by the robotic pipettor to dispense processing material into the vials, and the associated caps are accessible by the robotic pipettor to move each cap into an associated vial to form a cap/vial assembly. The robotic pipettor is configured to move the cap/vial assembly from the cap/vial tray to another location on the second module.

According to some aspects of the disclosure, the second module further comprises a centrifuge, wherein the robotic pipettor is configured to move a cap/vial assembly from the cap/vial tray to the centrifuge.

According to some aspects of the disclosure, the second module further comprises a thermal cycler configured to hold a plurality of cap/vial assemblies and to subject the contents of the plurality of cap/vial assemblies to cyclically varying temperatures and a robotic vial transfer pipettor configured to move a con/vial assembly from the centrifuge to the thermal cycler.

According to some aspects of the disclosure, the second module further comprises one or more magnetic receptacle holding slots configured to hold a receptacle transferred from the first module to the second module. Each magnetic receptacle holding slot comprises a magnet and is configured to draw magnetic particles contained within the receptacle to a wall of the receptacle and out of solution within the fluid contents of the receptacle.

According to some aspects of the disclosure, the first module and the second module are configured to conduct nucleic acid amplification reactions.

According to some aspects of the disclosure, the nucleic acid amplification reactions conducted in the first module and the second module are different types of amplification reactions.

According to some aspects of the disclosure, the nucleic acid amplification reaction conducted in the first module comprises a qualitatively monitored reaction and the nucleic acid amplification reaction conducted in the second module comprises a quantitatively monitored reaction.

According to some aspects of the disclosure, the nucleic acid amplification reaction conducted in the second module comprises a reaction monitored in real-time.

According to some aspects of the disclosure, wherein the nucleic acid amplification reaction conducted in the first module is an isothermal reaction, and the nucleic acid amplification reaction conducted in the second module comprises the use of a polymerase chain reaction.

Aspects of the disclosure are further embodied in an automated system capable of performing multiple molecular assays on a single sample. The system comprises a sample input portal configured to accept samples contained in one or more receptacles, a sample preparation module configured to prepare a sample provided to the sample input portal for a nucleic acid amplification reaction, a first module configured to conduct an isothermal nucleic acid amplification assay with the sample, a second module configured to conduct a nucleic acid amplification assay involving temperature cycling with the sample, and a transport mechanism configured to effect automated transport of one or more receptacles containing the sample between the sample input portal, the sample preparation module, the first module, and the second module.

According to some aspects of the disclosure, the automated system further comprises a substance transfer device configured to access the sample when present in the sample second module, the first module, or the second module.

According to some aspects of the disclosure, the system further comprises a reagent storage compartment configured to hold a plurality of reagent containers, wherein the reagent storage compartment is held at a temperature below ambient temperature.

According to some aspects of the disclosure, the system further comprises a reagent container transport mechanism configured to transport one or more reagent containers between the reagent storage compartment and a separate location within the second module.

According to some aspects of the disclosure, the reagent container transport mechanism is configured to transport the reagent containers within the second module and to transport the receptacles within the second module.

Some aspects of the disclosure are embodied in a method for improved thermal cycling of low volume nucleic acid amplification reaction mixtures. The method comprises combining a fluid sample together with one or more amplification reaction reagents in a reaction receptacle using an automated pipettor, transporting the reaction receptacle to a centrifuge using the automated pipettor, centrifuging the fluid contents of the reaction receptacle, automatically removing the reaction receptacle from the centrifuge after centrifugation and placing the reaction receptacle in a thermal cycler, and subjecting the fluid contents of the reaction receptacle to one or more temperature cycles within the thermal cycler.

According to some aspects of the disclosure, the reaction receptacle is removed from the centrifuge and transported to the thermal cycler using the vial transfer arm.

According to some aspects of the disclosure, the reaction receptacle is placed in the centrifuge at a first location, and the reaction receptacle is removed from the centrifuge at a second, different location.

According to some aspects of the disclosure, the method further comprises a second automated pipettor, and the second automated pipettor automatically removes the reaction receptacle from the centrifuge after centrifugation and places the reaction receptacle in the thermal cycler.

According to some aspects of the disclosure, the receptacle is sealed by a cap before transporting the sealed receptacle to the centrifuge.

According to some aspects of the disclosure, the automated pipettor transports the cap to the receptacle and seals the receptacle by coupling the cap to the receptacle.

Some aspects of the disclosure are embodied in an improved method of preparing multiple different nucleic acid reaction mixtures within the workflow of an automated molecular instrument. The method comprises providing two or more reaction receptacles, providing two or more unit dose reagent containers, each unit dose reagent container corresponding to a respective reaction receptacle, and each unit dose reagent container containing a nucleic acid amplification reagent that is specific for one or more target nucleic acids, providing a receptacle containing a first bulk reagent, and combining at least a portion of the sample with at least a portion of the unit dose reagent and at least a portion of the bulk reagent in each of the two or more reaction receptacles. After combination, each reaction receptacle contains a different sample, a different unit dose reagent, and the same first bulk reagent.

According to further aspects of the disclosure, the method further comprises a receptacle containing a second bulk reagent, wherein the second bulk reagent is dispensed into each of the two or more unit dose reagent containers before combining at least a portion of the sample with at least a portion of the unit dose reagent and at least a portion of the bulk reagent in each of the two or more reaction receptacles.

According to some aspects of the disclosure, the second bulk reagent comprises a reconstitution reagent.

According to some aspects of the disclosure, the method further comprises transporting each of the two or more reaction receptacles to a heater, such as a heated incubator or a heating plate, to conduct a nucleic acid amplification assay.

Other features and characteristics of the present disclosure, as well as the methods of operation, functions of related elements of structure and the combination of parts, and economies of manufacture, will become more apparent upon consideration of the following description and the appended claims with reference to the accompanying drawings, all of which form a part of this specification, wherein like reference numerals designate corresponding parts in the various figures.

The features and advantages of the present disclosure will become more apparent from the detailed description set forth below when taken in conjunction with the drawings, in which like reference characters identify corresponding elements throughout. In the drawings, like reference numbers generally indicate identical, functionally similar, and/or structurally similar elements.

DETAILED DESCRIPTION

Unless defined otherwise, all terms of art, notations and other scientific terms or terminology used herein have the same meaning as is commonly understood by one of ordinary skill in the art to which this disclosure belongs. Many of the techniques and procedures described or referenced herein are well understood and commonly employed using conventional methodology by those skilled in the art. As appropriate, procedures involving the use of commercially available kits and reagents are generally carried out in accordance with manufacturer defined protocols and/or parameters unless otherwise noted. All patents, applications, published applications and other publications referred to herein are incorporated by reference in their entirety. If a definition set forth in this section is contrary to or otherwise inconsistent with a definition set forth in the patents, applications, published applications, and other publications that are herein incorporated by reference, the definition set forth in this section prevails over the definition that is incorporated herein by reference.

References in the specification to “one embodiment,” “an embodiment,” a “further embodiment,” “an example embodiment,” “some aspects,” “a further aspect,” “aspects,” etc., indicate that the embodiment described may include a particular feature, structure, or characteristic, but every embodiment may not necessarily include the particular feature, structure, or characteristic. Moreover, such phrases are not necessarily referring to the same embodiment. Further, when a particular feature, structure, or characteristic is described in connection with an embodiment, such feature, structure, or characteristic is also a description in connection with other embodiments whether or not explicitly described.

As used herein, “sample” refers to any substance suspected of containing a virus or organism of interest or, alternatively, nucleic acid derived from the virus or organism of interest, or any substance suspected to have a nucleic acid of interest, such as a nucleic acid suspected of having genetic abnormalities or mutations. The substance may be, for example, an unprocessed clinical specimen, such as a blood or genitourinary tract specimen, a buffered medium containing the specimen, a medium containing the specimen and lytic agents for releasing nucleic acid belonging to the virus or organism, or a medium containing nucleic acid derived from the virus or organism which has been isolated and/or purified in a reaction receptacle or on a reaction material or device. For this reason, the term “sample” will be understood to mean a specimen in its raw form or to any stage of processing to release, isolate and purify nucleic acid derived from the virus or organism. Thus, references to a “sample” may refer to a substance suspected of containing nucleic acid derived from a virus or organism at different stages of processing and is not limited to the initial form of the substance.

This description may use relative spatial and/or orientation terms in describing the position and/or orientation of a component, apparatus, location, feature, or a portion thereof. Unless specifically stated, or otherwise dictated by the context of the description, such terms, including, without limitation, top, bottom, above, below, under, on top of, upper, lower, left of right of, inside, outside, inner, outer, proximal, distal, in front of, behind, next to, adjacent, between, horizontal, vertical, diagonal, longitudinal, transverse, etc., are used for convenience in referring to such component, apparatus, location, feature, or a portion thereof in the drawings and are not intended to be limiting.

The section headings used in the present application are merely intended to orient the reader to various aspects of the disclosed system. The section headings are not intended to limit the disclosed and claimed inventions. Similarly, the section headings are not intended to suggest that materials, features, aspects, methods, or procedures described in one section do not apply in another section. Therefore, descriptions of materials, features, aspects, methods or procedures described in one section are intended to apply to other sections.

Nucleic Acid Diagnostic Assays

Aspects of the present disclosure involve diagnostic systems and methods that can be used in conjunction with nucleic acid diagnostic assays, including “real-time” amplification assays and “end-point” amplification assays.

Real-time amplification assays can be used to determine the presence and amount of a target nucleic acid in a sample which, by way of example, is derived from a pathogenic organism (e.g., bacterium, fungus, or protozoan) or virus. Thus, real-time amplification assays are often referred to as quantitative assays. By determining the quantity of a target nucleic acid in a sample, a practitioner can approximate the amount or load of the organism or virus in the sample. In one application, a real-time amplification assay may be used to screen blood or blood products intended for transfusion for blood borne pathogens, such as hepatitis C virus (HCV) and human immunodeficiency virus (HIV). In another application, a real-time assay may be used to monitor the efficacy of a therapeutic regimen in a patient infected with a pathogenic organism or virus, or that is afflicted with a disease characterized by aberrant or mutant gene expression. Real-time amplification assays may also be used for diagnostic purposes, as well as in gene expression determinations. Exemplary systems and methods for performing real-time amplification assays are disclosed by Macioszek et al. in U.S. Pat. No. 7,897,337.

In addition to implementation of embodiments of the disclosure in conjunction with real-time amplification assays, embodiments of the disclosure may also be implemented in conjunction with end-point amplification assays. In end-point amplification assays, the presence of amplification products containing the target sequence or its complement is determined at the conclusion of an amplification procedure. Thus, end-point amplification assays are often referred to as qualitative assays in that such assays do not indicate the amount of a target analyte present, but provide a qualitative indication regarding the presence or absence of the target analyte. Exemplary systems and methods for end-point detection are disclosed by Ammann et al. in U.S. Pat. No. 6,335,166. The determination may occur in a detection station that is integral with or at an external location relative to the incubator(s) in which the amplification reactions occur. In contrast, in “real-time” amplification assays, the amount of amplification products containing the target sequence or its complement is determined during an amplification procedure. In a real-time amplification assay, the concentration of a target nucleic acid can be determined using data acquired by making periodic measurements of signals that are a function of the amount of amplification product in the sample containing the target sequence or its complement, and calculating the rate at which the target sequence is being amplified from the acquired data. An example of such a real-time amplification assay is described by Light II et al. in U.S. Pat. No. 8,615,368.

In an exemplary real-time amplification assay, the interacting labels include a fluorescent moiety, or other emission moiety, and a quencher moiety, such as, for example, 4-(4-dimethylaminophenylazo)benzoic acid (DABCYL). The fluorescent moiety emits light energy (i.e., fluoresces) at a specific emission wavelength when excited by light energy at an appropriate excitation wavelength. When the fluorescent moiety and the quencher moiety are held in close proximity, light energy emitted by the fluorescent moiety is absorbed by the quencher moiety. But when a probe hybridizes to a nucleic acid present in the sample, the fluorescent and quencher moieties are separated from each other and light energy emitted by the fluorescent moiety can be detected. Fluorescent moieties having different and distinguishable excitation and emission wavelengths are often combined with different probes. The different probes can be added to a sample, and the presence and amount of target nucleic acids associated with each probe can be determined by alternately exposing the sample to light energy at different excitation wavelengths and measuring the light emission from the sample at the different wavelengths corresponding to the different fluorescent moieties. In another embodiment, different fluorescent moieties having the same excitation wavelength, but different and distinguishable emission wavelengths are combined with different probes. The presence and amount of target nucleic acids associated with each probe can be determined by exposing the sample to a specific wavelength light energy and the light emission from the sample at the different wavelengths corresponding to the different fluorescent moieties is measured.

A variety of different labeled probes and probing mechanisms are known in the art, including those where the probe does not hybridize to the target sequence. See, e.g., Brow et al. in U.S. Pat. No. 5,846,717 and Chun et al. in U.S. Patent Application Publication No. 2013/0109588. Some embodiments of the present disclosure operate regardless of the particular labeling scheme utilized, provided the moiety to be detected can be excited by a particular wavelength of light and emits a distinguishable emission spectra.

Where a nucleic acid amplification reaction is used to increase the amount of target sequence and/or its complement present in a sample before detection, it is desirable to include a “control” to ensure that amplification has taken place. See, for example, the amplification controls described by Wang in U.S. Pat. No. 5,476,774. Such a control can be a known nucleic acid sequence that is unrelated to the sequence(s) of interest. A probe (i.e., a control probe) having specificity for the control sequence and having a unique fluorescent dye (i.e., the control dye) and quencher combination is added to the sample, along with one or more amplification reagents needed to amplify the control sequence, as well as the target sequence(s). After exposing the sample to appropriate amplification conditions, the sample is alternately exposed to light energy at different excitation wavelengths (including the excitation wavelength for the control dye) and emission light is detected. Detection of emission light of a wavelength corresponding to the control dye confirms that the amplification was successful (i.e., the control sequence was indeed amplified), and thus, any failure to detect emission light corresponding to the probe(s) of the target sequence(s) is not likely due to a failed amplification. Conversely, failure to detect emission light from the control dye may be indicative of a failed amplification, thus calling into question the results from that assay. Alternatively, failure to detect emission light may be due to failure or deteriorated mechanical and/or electrical performance of an instrument for detecting the emission light.

In some embodiments, the assays performed in accordance with the description herein capture, amplify, and detect nucleic acids from target organisms in patient samples employing technologies, such as target capture, reverse transcription, and real-time polymerase chain reaction. The combination of reverse transcription and PCR is abbreviated “RT-PCR.” The following is a generalized assay processing description of the different technologies that may be implemented in accordance with aspects of the disclosure.

The target capture process isolates nucleic acid of the target (e.g., virus, bacterium, fungus, protozoan, mammalian cells, etc.) and purifies nucleic acid for amplification. The target organism, which can be in a variety of biological matrices from urine to blood, can be lysed by target capture reagents (“TCR”), whereby the nucleic acid is released. In one approach, capture oligonucleotide probes hybridize to a target nucleic acid. The capture probe/target nucleic acid complexes attach to magnetic particles in the TCR through nucleic acid hybridization. Exemplary disclosures for performing these methods are provided by U.S. Pat. Nos. 6,140,678, 5,234,809, 5,693,785, and 5,973,138, and EP Patent No. 0 389 063. The magnetic particles are pulled to the side of a container and isolated by a magnet, and potential inhibitory substances are washed away (multiple wash cycles may be performed) to thereby provide a target nucleic acid. Hogan et al. provide an exemplary disclosure of this protocol in U.S. Pat. No. 7,172,863. See also International Publication No. WO 2003/097808 by Fort et al. If the target capture process is specific for the target nucleic acid, then it is the target nucleic acid that will primarily remain after the purification step. As a result, target capture enables the enrichment of a variety of sample types and significantly reduces the inhibition rate and can increase assay sensitivity. Exemplary methods of target nucleic acid capture are disclosed by, for example, Boom et al. in U.S. Pat. No. 5,234,864, Hawkins in U.S. Pat. No. 5,705,628, Collins et al. in U.S. Pat. No. 5,750,338, and Weisburg et al. U.S. Pat. No. 6,534,273.

After completing the target capture process, the magnetic particles on which the target nucleic acid is immobilized are re-suspended, for example, with 20-60 μL of a wash solution comprising a low salt buffer or water. This will de-hybridize the target nucleic acid from the magnetic particles and, in the presence of a strong magnet, allow 5-50 μL of purified nucleic acid to be recovered as input into the amplification process.

Reverse transcription and PCR can be optimized to run in a single receptacle using common reagents as a one-step process. This method provides a sensitive means to detect low-abundance RNAs, and, although the method is not necessarily quantitative, specific controls can be included in the experiment if quantitative results are desired. (A reverse-transcription step is not required if the target nucleic acid is DNA.) In an exemplary implementation, before performing the real-time PCR reaction, RNAs are incubated with a retroviral enzyme (reverse transcriptase) under oil at 42° C. for approximately 30 minutes. This process creates a single-stranded DNA copy of the RNA target sequence. If the goal is to copy all RNAs present in the source material into DNA, non-specific primers or prime sets are used. In the case of mRNA, which has a polyadenylated (poly A) tail, an oligo dT primer can be used. Alternatively, a collection of randomized hexanucleotide primers can be used to ensure an primer will be present that is complementary to each of the messages. If only one RNA target is sought, a sequence-specific primer complementary to the 3′ end of the desired amplification product is used. RNase H is used to degrade the RNA molecule contained in the hybrid RNA-DNA duplex, so that the DNA strand is available to direct second-strand synthesis. Single-stranded DNA thus generated can serve as the template for PCR using sequence-specific primers to amplify the region of interest.

The polymerase is inactive at low temperatures and can be heat activated at 95° C. for several minutes (for example, approximately 10 minutes) before beginning PCR. Both reactions occur inside a thermal cycler (i.e., a module configured to expose the contents of the receptacle to temperatures that are cycled between two or more different temperatures), but real-time PCR requires accurate/rapid thermal cycling between denaturation (˜95° C.), annealing (˜55° C.), and synthesis (˜72° C.) temperatures. Fluorescence monitoring occurs at one or many color wavelengths—relating to one or many probes adapted to detect one or many target analytes—during each cycle or at another predetermined interval. PCR components may include, for example, the forward and reverse primers and a fluorogenic probe containing a reporter fluorescent dye on the 5′ end and a quencher dye on the 3′ end. (See, e.g., Holland et al., Proc. Natl. Acad. Sci. USA, 88(16):7276-7280 (1991).) During PCR, nucleic acid primers hybridize to opposite strands of the target nucleic acid and are oriented with their 3′ ends facing each other so that synthesis by a nucleic acid polymerization enzyme, such as a DNA polymerase, extends across the segment of the nucleic acid between them. While the probe is intact, the proximity of the quencher dye to the reporter dye greatly reduces the fluorescence emitted by the reporter dye. During amplification if the target nucleic acid is present, the fluorogenic probe anneals downstream from one of the primer sites and is cleaved by the 5′ nuclease activity of the polymerization enzyme during primer extension. The cleavage of the probe separates the reporter dye from the quencher dye, thus rendering detectable the reporter dye signal and removing the probe from the target strand, allowing primer extension to continue to the end of the template strand.

One round of PCR synthesis will result in new strands of indeterminate length which, like the parental strands, can hybridize to the primers upon denaturation and annealing. These products accumulate arithmetically with each subsequence cycle of denaturation, annealing to primers, and synthesis. The second cycle of denaturation, annealing and synthesis produces two single-stranded products that together compose a discrete double-stranded product which is exactly the length between the primer ends. Each strand of this discrete product is complementary to one of the two primers and can therefore participate as a template in subsequent cycles. The amount of this product doubles with every subsequent cycle of synthesis, denaturation and annealing. This accumulates exponentially so that 30 cycles should result in a 228-fold (270 million-fold) amplification of the discrete product.

Multiple Receptacle Devices

FIG. 2illustrates one embodiment of MRD160that comprises a plurality of individual receptacles, or tubes,162, preferably five. The receptacles162are formed to have open top ends and closed bottom ends (preferably in the form of cylindrical tubes), and are connected to one another by a connecting rib structure164which defines a downwardly facing shoulder extending longitudinally along either side of the MRD160.

Alternatively, the receptacle may be any container suitable for holding a fluid or liquid, including, for example, a cuvette, beaker, well of a microtiter plate, test tube, and in some embodiments, a pipette tip. Unless explicitly stated or the context dictates otherwise, descriptions of an MRD or receptacle of an MRD are exemplary and should not be construed as limiting of the scope of the disclosure, as aspects of the disclosure are applicable to any suitable “receptacle.”

The MRD160in certain embodiments is formed from injection molded polypropylene, such as those sold by Montell Polyolefins, of Wilmington, Del., product number PD701NW or Huntsman, product number P5M6K-048. In an alternative embodiment, the receptacles162of the MRD are releasably fixed with respect to each other by means such as, for example, a sample tube rack or other holding structure.

An arcuate shield structure169can be provided at one end of the MRD160. An MRD manipulating structure166extends from the shield structure169. In certain embodiments, the manipulating structure166is configured to be engaged by an extendible and retractable hook of a receptacle distributor or a transport mechanism for moving the MRD160between different components of a first module of a diagnostic system. An exemplary transport mechanism that is compatible with the MRD160is disclosed by Ammann et at. in U.S. Pat. No. 6,335,166. The transport mechanism, in certain embodiments, engages the manipulating structure166from the underside of the manipulating structure as shown with arrow60. In certain embodiments, the MRD manipulating structure166comprises a laterally extending plate168extending from shield structure169with a vertically extending piece167on the opposite end of the plate168. A gusset wall165can extend downwardly from lateral plate168between shield structure169and vertical piece167.

As shown inFIG. 3, the shield structure169and vertical piece167have mutually facing convex surfaces. This, however, is just one way that the shield structure169and vertical piece167can be configured. The MRD160may be engaged by a receptacle distributor, a transport mechanism, and other components, by moving an engaging member, such as an extendible and retractable hook, laterally (in the direction “A”) into the space between the shield structure169and the vertical piece167. The convex surfaces of the shield structure169and vertical piece167provide for wider points of entry for an engaging member undergoing a lateral relative motion into the space between the shield structure169and the vertical piece167. Of course, as the engaging member is robotically controlled, it is understood that the convex surfaces are merely a design choice of the present embodiment and that other shaped surfaces are contemplated.

A label-receiving structure174having a flat label-receiving surface175can be provided on an end of the MRD160opposite the shield structure169and MRD manipulating structure166. Human and/or machine-readable labels, such as scannable bar codes, can be placed on the surface175to provide identifying and instructional information on the MRD160.

Further details regarding a representative MRD160are disclosed by Horner et al. in U.S. Pat. No. 6,086,827.

Diagnostic System

FIG. 1illustrates a diagnostic system10according to an embodiment. Diagnostic system10can be configured to perform a plurality of different molecular assays on a plurality of samples. In some embodiments, diagnostic system10can be configured to perform different target nucleic acid amplification reactions. For example, diagnostic system10can be configured to perform a first target nucleic acid amplification reaction on a first subset of a plurality of samples, and perform a second, different target nucleic acid amplification reaction on a second subset of the plurality of samples.

In some embodiments, diagnostic system10comprises a first module100configured to perform at least one of the steps of a first target nucleic acid amplification reaction, and a second module400configured to perform at least one of the steps of a second target nucleic acid amplification.

In some embodiments, diagnostic system10is an integral, self-contained structure—first module100cannot be selectively coupled to and decoupled from second module400.

In some embodiments, diagnostic system10is configured such that first module100can be selectively and operatively coupled to second module400, and first module100can be selectively decoupled from second module400. In some embodiments, first module100can be selectively coupled to second module400using, for example, mechanical fasteners (for example, bolts or screws), clamps, any combination thereof, or any other suitable attachment device. In some embodiments, suitable power and/or data lines are provided between the second module400and the first module100. For example, in embodiments in which first module100can be selectively coupled to second module400, second module400can extend the overall system capabilities of a diagnostic system including only first module100that was previously purchased by a customer.

The configurations and functions of first module100and second module400according to various embodiments are described below.

First Module

A first module100in which embodiments of the present disclosure may be implemented is shown schematically in plan view and designated by reference number100inFIG. 4. The first module100includes various devices configured to receive one or more reaction receptacles (described in more detail below), within each of which is performed one or more steps of a multi-step nucleic acid test (NAT) designed to detect a virus or organism (e.g., bacterium, fungus, or protozoan). First module100can include receptacle-receiving components configured to receive and hold one or more reaction receptacles and, in some instances, to perform processes on the contents of the receptacles. Exemplary processes include, but are not limited to, adding substances such as sample fluid, reagents (e.g., target capture reagents, amplification reagents, buffers, oils, labels, probes, or any other reagent) and/or removing substances from a reaction receptacle; agitating a receptacle to mix the contents thereof; maintaining and/or altering the temperature of the contents of a reaction receptacle; heating or chilling the contents of a reaction receptacle; altering the concentration of one or more components of the contents of a reaction receptacle; separating or isolating constituent components of the contents of a reaction receptacle; detecting an electromagnetic signal emission (e.g., light) from the contents of a reaction receptacle; deactivating or halting an on-going reaction; or any combination of two or more of such processes.

In some embodiments, the first module100may include a receptacle input device102that includes structure for receiving and holding one or more empty reaction receptacles before the receptacles are used for performing one or more process steps of a NAT. The receptacle put device102may comprise a compartment, for example, a drawer or cabinet, that may be opened and loaded with a plurality of receptacles and may include a receptacle feeding device for moving receptacles, for example, one or more at a time, into a receptacle pick-up position. In some embodiments, the receptacle pick-up position comprises a registered or known position of the receptacle to facilitate removal of the receptacle by a receptacle distributor.

In some embodiments, the first module100may further include one or more bulk reagent container compartments configured to store one or more bulk containers that hold bulk reagents or hold waste material. In some embodiments, the bulk reagents include fluids such as water, buffer solution, target capture reagents, nucleic acid amplification reagents. In some embodiments, the bulk reagent container compartments may be configured to maintain the contents of such containers at prescribed storage temperatures and/or to agitate such containers to maintain the contents of the containers in solution or suspension.

In some embodiments, first module100comprises a first bulk reagent container compartment configured to store at least one bulk container that holds a nucleic acid amplification reagent, for example, a reagent for performing TMA, and a separate second bulk reagent container compartment configured to store at least one bulk container that holds a sample preparation reagent, for example, a target capture reagent. In some embodiments, first module100comprises a bulk reagent container compartment that stores both a bulk container that holds a nucleic acid amplification reagent and a bulk container that holds a sample preparation reagent, for example, a target capture reagent. In some embodiments, a bulk reagent container compartment that is configured to store at least one bulk container can be a compartment that houses a mixer, for example, an orbital mixer, that is configured to carry a container holding a sample preparation reagent, for example, a target capture reagent. In some embodiments, the one or more bulk container compartments can comprise a holding structure for carrying and agitating containers (e.g., containers of TCR with magnetically-responsive solid supports). Buse et al. in U.S. Provisional Application No. 61/783,670, “Apparatus for Indexing and Agitating Fluid Containers,” filed Mar. 14, 2013, which enjoys common ownership herewith, discloses an exemplary holding structure. In some embodiments, one or more bulk container compartments comprise a slidable tray that defines at least one recess configured to closely receive respective bulk containers.

In some embodiments, one or more of the bulk reagent container compartments of first module100can be configured to store at least two containers containing sample preparation reagents, for example, target capture reagents. In some embodiments, each target capture reagent is specific for a particular assay type (i.e., target nucleic acid), the type of nucleic acid (e.g., RNA or DNA), and/or the sample type (e.g., stool, urine, blood, etc.). For example, the target capture reagents can comprise probes having a region specific for the target nucleic acid. See, e.g. Weisburg et al. in U.S. Pat. No. 6,534,273.

The first module100may further include a sample loading device configured to receive and hold containers, such as test tubes, containing samples. The first module100may also include one or more substance transfer devices for transferring fluids, for example, sample fluids, reagents, bulk fluids, waste fluids, etc., to and from reaction receptacles and/or other containers. In some embodiments, the substance transfer devices may comprise one or more robotic pipettors configured for controlled, automated movement and access to the reaction receptacles, bulk containers holding reagents, and containers holding samples. In some embodiments, the substance transfer devices may also include fluid dispensers, for example, nozzles, disposed within other devices and connected by suitable fluid conduits to containers, for example, bulk containers holding the reagents, and to pumps or other devices for causing fluid movement from the containers to the dispensers.

In some embodiments, the first module100may further include a plurality of load stations, such as load stations104,106,108depicted inFIG. 4, which are configured to receive racks and other forms of holders for carrying sample receptacles and various reagent containers that can be accessed by a substance transfer device. Examples of a load station and receptacle holder that can be used with embodiments are illustrated and described by Clark et al. in U.S. Pat. No. 8,309,036. In an embodiment where the first module100comprises a platform for performing a NAT, reaction reagents may comprise target capture reagents, lysis reagents, nucleic acid amplification reagents (e.g., the polymerases and nucleoside triphosphates needed for amplification), and/or nucleic acid detection reagents, such as detectable probes or intercalating dyes.

In some embodiments, the first module100may further comprise temperature ramping stations110configured to hold one or more reaction receptacles in an environment that is maintained at higher than ambient temperatures so as to raise the temperature of the contents of the receptacles. Exemplary temperature ramping stations are disclosed by Ammann al in U.S. Pat. No. 8,197,992.

In some embodiments, the first module100may further include one or more heater modules. The illustrated first module100includes three heated incubators112,114,116each of which is configured to receive a plurality of reaction receptacles and maintain the receptacles in an elevated temperature environment. Exemplary incubators are disclosed by Macioszek et al. in U.S. Pat. No. 7,964,413 and Heinz et al. in U.S. Patent Application Publication No. 2012/0221252. A heater module may alternatively be a heating plate. In certain embodiments, it is possible to have a heater module configured with one or more heated incubators and one or more heating plates.

Also, in an embodiment in which the first module100comprises a platform for performing a NAT, the first module may include sample-processing components, such as magnetic separation wash stations118,120, adapted to separate or isolate a target nucleic acid immobilized on a magnetically-responsive solid support from the remaining contents of the receptacle. Exemplary magnetic separation wash stations are disclosed by Hagen et at. in U.S. Patent Application Publication No. 2010/0288395 and Ammann et al. in U.S. Pat. No. 6,605,213.

Although not exemplified in the plan drawings of first module100, the first module100may comprise one or more substance transfer devices, for example, robotic pipettors, in some embodiments.FIG. 21, which is a perspective view of the robotic pipettor of the second module400, exemplifies at least one way to configure a substance transfer device for the first module100.

In some embodiments, the first module100may further include chilling modules122adapted to receive one or more reaction receptacles and hold the receptacles in a lower than ambient temperature environment so as to reduce the temperature of the contents of the receptacles.

And in some embodiments, the first module100may include a detector124configured to receive a reaction receptacle and detect a signal (e.g., an optical signal emitted by the contents of the reaction receptacle. In one implementation, detector124may comprise a luminometer for detecting luminescent signals emitted by the contents of a receptacle and/or a fluorometer for detecting fluorescent emissions. The first module100may also include one or more signal detecting devices, such as fluorometers, coupled to one or more of the incubators112,114,116and which are configured and controlled to detect, preferably at specified, periodic intervals, signals emitted by the contents of the receptacles contained in the incubator while a process, such as nucleic acid amplification, is occurring within the reaction receptacles. An exemplary luminometer and an exemplary fluorometer are disclosed by Macioszek et al, in U.S. Pat. No. 7,964,413 and another exemplary fluorometer is disclosed by Heinz et in U.S. Patent Application Publication No. 2012/0221252.

The first module100further includes a receptacle transfer device, which, in the illustrated embodiment, comprises a receptacle distributor150. The components of first module100, for example, incubators112,114,116, load stations104,106,108, temperature ramping stations110, wash stations118,120, and chilling modules122, can also include a receptacle transfer portal through which receptacles can be inserted into or removed from the respective components. Each component may or may not include an openable door covering its receptacle portal. The receptacle distributor150is configured to move receptacles between the various components and retrieve receptacles from the components and deposit receptacles into the components. In one exemplary embodiment, the receptacle distributor150includes a receptacle distribution head152configured to move in an X direction along a transport track assembly154, rotate in a theta. (Θ) direction, and move receptacles in an R direction into and out of the receptacle distribution head152and one of the components of first module100. An exemplary receptacle distributor is disclosed by Hagen et al. in U.S. Patent Application Publication No. 2012/0128451.

Second Module

Aspects of the disclosure are embodied in a second module400a diagnostic system. In some embodiments, the second module400is integral with the first module100, and in other embodiments, the second module400may be selectively and operatively coupled to the first module100as described above. In some embodiments, the first module100to which the second module400can be operatively coupled include, for example, molecular instruments, such as the Panther® instrument system available from Hologic, Inc.

In one exemplary embodiment, the second module400is configured to perform nucleic acid amplification reactions, for example, PCR, and, in certain embodiments, to measure fluorescence in real-time (i.e., as the amplification reaction is occurring). A controller directs the components of the first module100and components of the second module400to perform the assay steps. In one exemplary embodiment, the first module100houses a computer and all fluids, reagents, consumables, and mechanical modules needed to perform the specified amplification-based assays, such as assays based on transcription-based amplification methods, for example, TMA or nucleic acid sequence-based amplification (NASBA). (TMA methods are described by Kacian et al. in U.S. Pat. Nos. 5,399,491 and 5,480,784; and NASBA methods are described by Davey et al. in U.S. Pat. No. 5,409,818 and Malek at. in U.S. Pat. No. 5,130,238.) As explained above, the controller may comprise a computer and preferably can accommodate LIS (“laboratory information system”) connectivity and as well as remote user access. In some embodiments, second module400houses component modules that enable second amplification assays, melting analyses, and optionally additional functionalities. Other components may include a printer and an optional uninterruptible power supply.

Embodiments of the general configuration of the second module400are shown inFIGS. 1, 5, 6, and 14.FIG. 1is a perspective view of diagnostic system10comprising a second module400and the first module100.FIG. 5is a top plan view of the second module400separated from the first module100.FIG. 6is a top plan view of an amplification processing deck430, for example, a deck containing components for performing PCR, of the second module400.FIG. 14is a top plan view of a receptacle processing deck600of the second module400. Referring toFIGS. 1, 5, 6, and 14, the component of the second module400can include, for example, a substance transfer device (for example, a robotic pipettor402), a thermal cycler/signal detector432, tip compartments580(e.g., two or more) configured to contain trays of disposable tips for the pipettor(s), processing cap/vial compartments440(e.g., two or more) configured to contain trays of disposable processing vials and associated caps, a bulk reagent container compartment500, a bulk reagent container transport550, a receptacle distribution system comprising a receptacle handoff device602and a receptacle distributor312, which, in the exemplary embodiment shown, comprises a rotary distributor, MRD storage units608,610,612configured to store MRDs160, magnetic elution slots620(e.g., two or more), a waste bin access door652, a waste bin652, a centrifuge588, a reagent pack changer700, reagent pack loading stations (e.g., two or more)640, and a compartment590configured to store accessories, including, for example, consumables, output cards, and/or post-processing cap/vial assemblies.

As shown inFIG. 1, the components may be positioned on different levels, or decks, arranged vertically through the module400. In some embodiments, the substance transfer and handling device402can be a robotic pipettor402as shown inFIG. 1. The robotic pipettor402is disposed near the top of the second module400, above all other components, in some embodiments. The depicted configurations represent only a single embodiment. The vertical order of the decks and components may vary according to the intended use of diagnostic system10. In the depicted embodiment, below the robotic pipettor402, the amplification processing deck430includes the bulk reagent container compartment500and bulk reagent container transport520, the centrifuge588, the top of the thermal cycler/signal detector432, the tip compartments580, and the processing cap/vial compartments440. Below the amplification processing deck430, the receptacle processing deck600includes the receptacle handoff device602, the rotary distributor312, the MRD storage units608,610,612, the magnetic elution slots620, the reagent pack changer700, and the reagent pack loading stations640. As can be seen inFIG. 6, the magnetic elution slots620and the reagent pack loading stations640on the receptacle processing deck600are accessible by the robotic pipettor402through a gap between modules of the amplification processing deck430.

The receptacle distribution system comprising the receptacle handoff device602and the rotary distributor312, is configured to receive a receptacle or group of receptacles (e.g., MRD160) from the receptacle transfer device (e.g., the receptacle distributor150) of the first module100and transfer the receptacle to the second module400and configured to move the receptacle into different positions in the second module400. The rotary distributor312and the receptacle handoff device602are shown schematically inFIG. 14. Further details regarding these components are described below.

In some embodiments, the second module100is operatively positioned adjacent to the first module100, with the bulk reagent container transport550extending into the first module100so that elution containers502,504can be transported by the bulk reagent container transport550from the bulk reagent container compartment500to a position in the first module100at which a substance transfer device, for example, a robotic pipettor, in the first module100can access the containers502,504.

In some embodiments, the second module400is generally self-supporting relative to first module100such that the second-module/first-module assembly is not over-constrained. Thus, in some embodiments, the second module400does not include any feet that contact the ground beneath the second module and support some or all of the weight of the module. In some embodiments, if the second module400includes its own rigid feet (e.g., two, three, or four feet), the feet of the first module100and the feet of the second module400could create an over-constrained geometry. In this case, one would carefully level all feet of the second module400and the first module100relative to each other to ensure that the assembly is level and that excessive stresses are not applied to attachment points between the second module400and the first module100. To avoid such a potentially over-constrained geometry, the second module400, in some embodiments, is cantilevered off the first module100if the first module feet can support the additional weight of the second module. In some embodiments, some of the weight of the second module400may be supported by a single foot on a far edge of the second module400away from the first module100.

In some embodiments, second module400and first module100are mounted to an integral frame.

In some embodiments, the interface between the second module400and the first module100is blocked and sealed where possible to prevent airflow between the two modules. Existing air inlets on the side of the first module100facing the second module400may be ducted through the second module400to a fresh air source. The side wall of the second module400facing the first module100can be covered by panels to block airflow into the first module100. Such panels can include openings where necessary for receptacle or container transfer between the second module400and first module100, cable routing, etc.

Components of exemplary embodiments of the second module400are described below.

Reagent Packs

In some embodiments, amplification reagents and other reagents may be provided in the second module400in lyophilized form in a reagent pack comprising a cartridge that includes wells within which the lyophilized reagent may be reconstituted. Examples of cartridges that can be used in this embodiment are disclosed by Knight et al. in U.S. Provisional Application No. 61/782,320, “Systems, Methods, and Apparatus for Performing Automated Reagent-Based Assays,” filed Mar. 14, 2014, which enjoys common ownership herewith (these cartridges are both identified by reference number500inFIGS. 10A and 10B). The reagent pack is further configured to be stored within the second module400and, in some embodiments, to be moved within the second module400by the distributor312, and inserted and removed from the reagent pack changer700.

Details of a reagent pack760, according to one embodiment, are shown inFIGS. 19 and 20. The reagent pack760may include a plurality of mixing wells762, each of which contains a lyophilized unit-dose, assay-specific reagent768, which may be in pellet form. (As used herein, “unit-dose” or “unitized” means an amount or concentration of a reagent sufficient to perform one or more steps of a single assay for a single sample.) In some embodiments, the unit-dose reagent768comprises a component for performing a nucleic acid amplification reaction. For example, the nucleic acid amplification reaction component can be a polymerase, nucleoside triphosphates, or any other suitable component. In the illustrated embodiment, the reagent pack760includes ten mixing wells762. But in some embodiments, the reagent pack760may include more or fewer than ten mixing wells. Each mixing well762of a single reagent pack760may hold the same reagent, or the wells762may hold different reagents, or some wells762may hold the same reagent and some may hold different reagents. Exemplary assay specific reagents768held in the reagent pack760include unitized reagents for performing a single amplification reaction, for example, PCR and/or a detection reaction utilizing a sample. Such reagents may be specific for one target nucleic acid or a plurality of different target nucleic acids. For example, the plurality of different target nucleic acids may be part of a respiratory panel, and the unitized reagents are sufficient to conduct a PCR reaction targeting Flu A, Flu B, RSV, parainfluenza 1, 2, and 3, Human Metapneumovirus, Adenoviris, H1, H3, 2009 H1N1, and/or Tamiflu resistance. In an embodiment, each reagent pellet768is held at the bottom of the associated mixing well762with an electrostatic charge imparted to the pellet768and/or the mixing well762. In other embodiments, each reagent pellet768is held at the bottom of the associated mixing well762with one or more physical feature present in the mixing well762, for example, those disclosed by Knight et al. in U.S. Provisional Application No. 61/782,320.

In some embodiments, the mixing wells762are covered by a pierceable foil766adhered to the top of the reagent pack760. Foil766can be pierced by a pipette tip584to enable reconstitution agents or other substances to be dispensed into the mixing well762and to enable reconstituted reagent to be aspirated from the mixing well762.

In some embodiments, the reagent pack760further includes a manipulating structure764, for example, a manipulating hook, that is similar to the manipulating structure166of the MRD160and is configured to be engageable by a manipulating structure, for example, a hook, of the rotary distributor312. The reagent pack760may include a rear recess770that is configured to align the reagent pack within a reagent pack carrier, as will be described below.

Tip Compartments

As shown inFIGS. 1, 5, and 6, tip compartments580are configured to hold trays582of disposable pipette tips in a manner that enables the tips held in the drawers580to be accessed by the robotic pipettor402. In the illustrated embodiment, the second module400includes two tip compartments580, each configured to hold up to three trays582of disposable pipette tips. The compartments580may be configured to accept commercially-available trays of disposable pipette tips. Exemplary, commercially available pipette tips and trays are available from TECAN (TECAN Inc., Research Triangle Park, N.C.). Such tips are available in a variety of volumetric capacities, and each tip may be conductive to facilitate capacitive liquid level sensing and tip-present detection, as is well known in the art. Exemplary trays hold ninety-six pipette tips.

The tip compartments580are configured to be accessible to an operator for reloading of trays582. In one contemplated embodiment, the tip compartment580comprises a drawer configured to be pulled out of the second module400to enable an operator to place the trays582of tips into the drawers580and to remove empty trays from the drawers580. A door or cover panel that is either part of each drawer580or the housing of diagnostic system10is opened to access each tip compartment580behind it. The door or cover panels may provide an esthetically pleasing appearance to the front of the second module400. Manual or automated locks, controlled by the system controller, may be provided to prevent the compartment580from being opened when the second module400is operating. In some embodiments, visible and/or audible warning signals may be provided to indicate that a compartment580is not closed properly. In an alternative embodiment, compartment580comprises an access door and a slidable tray, wherein the tray is configured to slide out from second module to thereby provide loading access to an operator.

Substance Transfer and Handling System

The substance transfer and handling system402, for example, a robotic pipettor, shown inFIGS. 1, 21, and 22is a dual arm system comprising a front arm408and a back arm416. However, other robotic pipettor and handling configurations are contemplated, and the presently depicted embodiment is only exemplary. Substance transfer and handling system402can be configured to dispense and/or aspirate substances into and/or from a container, receptacle, well, etc., in second module400. In an exemplary embodiment, the front arm408includes a substance transfer pipettor410configured to aspirate fluid and dispense fluid and includes a pump, for example, an integrated syringe pump, and the back arm416includes a vial transfer arm418and does not perform substance transfer. The robotic pipettor system402comprises a Cartesian gantry assembly with two transverse tracks404,406, a back arm longitudinal rack420, and a front arm longitudinal track412. The designations “longitudinal” and “transverse” are merely for distinguishing the two sets of tracks, which may be orthogonal to one another, but otherwise the designations are arbitrary.

The substance transfer pipettor410may be driven back and forth along the front arm longitudinal track412by a belt, drive screw, or other motion transmission device coupled to a motor, and the vial transfer arm418may be driven back and forth along the back arm longitudinal track420by a belt, drive screw, or other motion transmission device coupled to a motor. The front arm longitudinal track412may be driven back and forth along the transverse tracks404,406by a belt, drive screw, or other motion transmission device coupled to a motor, and the back arm longitudinal track420may be driven back and forth along the transverse tracks404,406by a belt, drive screw, or other motion transmission device coupled to a motor. The substance transfer pipettor410and the vial transfer arm418include probes that are driven along the Z, or vertical, axis, for example, by a motor coupled to the probes, e.g., by a gear, a rack and pinion, a lead screw, or other suitable device. The motors may be under the control of a system controller. The motors may be stepper motors and may include rotary encoders for controlling and monitoring the position of the track or pipettor to which it is coupled. Each of the tracks has home sensors (or limit switches) for indicating when the substance transfer pipettor410or the vial transfer arm418is in one or more designated positions, such as a designated “home” position. Similarly, each device may have a vertical home sensor for indicating when the probe is in one or more designated vertical positions, such as a designated vertical “home” position. Such sensors for indicating a home position may include optical sensors (e.g., slotted optical sensors), proximity sensors, magnetic sensors, capacitive sensors, etc.

In one exemplary embodiment, the substance transfer pipettor410is configured to accept TECAN 1 mL disposable pipette tips by inserting the probe thereof into a disposable pipette tip, and an interference fit between the probe and the pipette tip frictionally secures the pipette tip to the end of the probe. The front arm408and the substance transfer pipettor410are configured to access at least parts of both the amplification processing deck430and the receptacle processing deck600on the second module400. The substance transfer pipettor410may include integrated tip sensing for confirming the presence or absence of a disposable pipette tip, capacitive level sensing for detecting contact by the pipette tip with the surface of the fluid contents of a reaction receptacle or other container and determining the level of the fluid contents based on the detected vertical position of the pipettor, and pressure sensing for sensing pressure fluctuations within the substance transfer system during fluid dispensing or aspiration. The substance transfer pipettor410is capable of transferring fluids, caps, or cap/processing vial assemblies such as those described below.

The vial transfer arm418is a “pick and place” device configured pick up a cap/vial assembly by inserting the probe thereof into a cap that is coupled to a vial, as will be described below.

Pipettor Pump

In an exemplary embodiment, the pump for the substance transfer pipettor410comprises a ceramic piston driven by a servomotor and a lead screw. The servomotor is controlled by the system controller, and the device can include rotary encoder feedback to the system controller and home sensors for monitoring the position of the piston. The syringe may have a volume of between 0.5 and 3 mL (preferably 1.05 mL) and, in certain embodiments, is a ceramic. The pump can preferably dispense very small volumes (5 μL) of fluid with +/−5% coefficient of variation (CV) measured across 30 discrete dispenses. To achieve this performance, in certain embodiments, the pump includes a solenoid valve to release pressure at the end of the stroke to ensure consistent fluid shear.

Processing Cap/Vial Assembly

In general, the processing vial provides a receptacle for containing reaction fluids for performing PCR or other process. The cap is configured to be placed into or onto the vial in an automated manner so as to close off the vial. In some embodiments, the cap is configured to receive the end of the vial transfer arm418with a friction fit, so that the transfer arm418can thereafter pick up the cap and place it into or onto the vial. The cap and vial are configured to lock together so that, once the cap is placed into or onto the vial, the cap and the vial are interlocked to form a cap/vial assembly. The robotic pipettor, with the probe of the transfer arm418inserted into the cap, can then pick up the cap/vial assembly and transfer it from one location within the second module400to another location. Exemplary caps and processing vials are disclosed by, for example, Knight et al. in U.S. Provisional Application No. 61/782,320.

Details of an exemplary embodiment of the processing vial464, the processing vial cap476, and the vial transfer arm probe422are shown inFIGS. 23-26.

In the embodiment shown inFIGS. 23-25, the processing vial464may have a conical shape and an open top end465surrounded by a locking collar466. Lateral through holes468are formed through the locking collar466at diametrically opposed locations. A latch hook472is located above each through hole468.

The processing vial cap476has an open top end478and a closed lower end480. An annular collar482extends about the cap476at a position between the top end478and lower end480. Collar482of the vial476sits atop the thermal cycler when the vial476is placed therein, ensuring a close fit of the vial within the wells of the thermal cycler. An exemplary thermal cycler for use with processing vial476is disclosed by Buse et al. in U.S. Patent Application Publication No. 2014/0038192. A lower portion of the cap476beneath the collar482defines a plug that fits into the open top end465of the processing vial464. This plug is sized so as to fit into the processing vial464with an interference, friction fit. A latch collar484extends about the cap476at a position below the collar482. Seal rings486,488extend about the cap476at positions below the latch collar484.

FIGS. 24 and 25show, in cross-section, a processing vial cap464, initially held in a cap well490of a cap/vial tray460, and a processing vial464held in a vial well474of the cap/vial tray460. After fluids are dispensed into the processing464with the disposable pipette tip584(connected to a robotic pipettor), the processing vial464is capped by a processing vial cap476by inserting the closed lower end480of the cap476into the open top end465of the vial464, until a bottom surface of the collar482of the cap476abuts a top surface of the locking collar466of the vial464. The latch collar484of the cap476snaps in beneath the latch hooks472of the vial464to secure the cap476to the vial464. The cap476and the vial464are thereafter locked together and the cap/vial assembly may be picked up and moved by the pipettor. The cap/vial assembly can be removed from the pipettor probe422by an eject device engaging a rim479surrounding open end478to pull the cap/vial assembly off the probe422. The seal rings486,488of the cap476preferably have outer diameters that are slightly larger than the inner diameter of the upper portion of the vial464, thereby forming a tight seal between the cap476and the vial464as the cap and vial are made of materials, such as suitable plastics, that are at least partially resilient.

An alternative processing cap/vial assembly is shown inFIG. 26, which is an exploded perspective view of a processing vial670and a processing vial cap660. Processing vial cap660includes closed lower end662, a tapered opening668, and a latch collar664having latch fingers666. The vial670includes a lock collar672surrounding the open top end of the vial670and a collar674. Collar674the vial670sits atop the thermal cycler when the vial670is placed therein, ensuring a close fit of the vial within the wells of the thermal cycler. After fluid is dispensed into the vial670, the vial is capped by first inserting the pipettor probe422into the tapered opening668of the processing vial cap660to frictionally secure the cap660to the pipettor probe422and then picking up the cap660with the pipettor and inserting the closed lower end662of the cap660into the open top end of the vial670until the latch fingers666lockingly snap onto the lock collar672of the vial670. The cap660and the vial670are thereafter locked together and the cap/vial assembly may be picked up and moved by the pipettor. The cap/vial assembly can be removed from the probe422by an eject device engaging a rim669surrounding opening668to pull the cap/vial assembly off the probe422.

The second module400may include “vial present” sensors. The vial present senor is used as a process control measure to verify that a vial is attached to the cap. The substance transfer pipettor410(front arm408) and the vial transfer arm418(back arm416) will detect when a cap is attached to the arm. One way substance transfer pipettor410or the vial transfer arm418will detect when a cap is present is by a strip sleeve on the probe422. When the cap is picked by the probe, the upper rim of the cap pushes on and raises the sleeve (e.g., a few millimeters), and this movement may be detected by a sensor. However, pipettors often cannot detect if a vial is attached to the cap. In one exemplary embodiment, the vial present sensor is an optical sensor (or multiple sensors) that either arm408,416can move past/through as it transports a capped vial into or out of the centrifuge588. The vial present sensor will trigger on the vial (if present) as the arm moves past the sensor.

Bulk Reagent Container Compartment and Bulk Reagent Container Transport

In one exemplary embodiment, the bulk reagent container compartment500is configured to hold a plurality of bulk reagent containers. Each bulk reagent container can hold a reagent for use in multiple reaction receptacles. In some embodiments, the bulk reagent containers are bottles or any other container suitable for containing reagents in bulk. In some embodiments, the bulk reagents within the bulk reagent containers can include a sample preparation reagent (e.g., target capture reagent (TCR), a wash solution, an elution reagent, or any other sample preparation reagent), a reconstitution reagent, or any other required bulk reagent. In some embodiments, the bulk reagent containers hold a quantity of the bulk reagent sufficient to perform between about 50 to 2000 assays. In some embodiments, the bulk reagent containers hold a quantity of the bulk reagent sufficient to perform between about 250 to 1000 assays. In some embodiments, the bulk reagent containers hold a quantity of the bulk reagent sufficient to perform less than about 250 assays, or more than about 1000 assays. In some embodiments, the bulk reagents are for performing isothermal nucleic acid amplification reactions, for example, a transcription-based amplification reaction such as TMA.

In some embodiments, the bulk reagent container compartment500can be configured to hold two elution buffer containers, two oil containers, and four reconstitution fluid containers. The bulk reagent container compartment500may be opened by an operator to load containers. For example, bulk reagent container compartment500may be a drawer that is slid out from the main body of diagnostic system10. In some embodiments, once closed, the bulk reagent container transport550moves the elution buffer containers into the first module100to a location in which a substance transfer mechanism, for example, a robotic pipettor, can access the containers. In some embodiments, the bulk oil containers and the bulk reconstitution fluid containers remain in the bulk reagent container compartment500, where they are accessible to the substance transfer pipettor410.

Containers carried on the bulk reagent container compartment500may be identified by machine-readable code, such as RFID. An indicator panel507having visible (e.g., red and green LEDs) and/or audible indicators provides feedback to the operator regarding container status.

The bulk reagent container compartment500and bulk reagent container transport550are shown inFIGS. 5-10. In some embodiments, the bulk reagent container compartment500is located on the amplification processing deck430adjacent the tip compartments580and may be accessed from the front of the second module400. The bulk reagent container compartment500may be pulled out to enable an operator to place two containers502,504containing an elution buffer as well as a number of bulk containers, or other types of fluid containers, containing other reagents, such as, for example, oil or reconstitution buffer, into the drawer500. The number of containers accommodated by the drawer500is dictated by considerations of intended throughput and desired time period between required re-stocking of supplies.

A door or cover panel, which is either part of the bulk reagent container compartment500or the housing of diagnostic system10is opened to access the bulk reagent container compartment500behind it. The door or cover panel can provide an esthetically pleasing appearance to the front of the second module400. Automated locks, controlled by the system controller, may be provided to prevent the bulk reagent container compartment500from being pulled open en the second module400is operating. In some embodiments, visible and/or audible warning signals may be provided to indicate that the bulk reagent container compartment500is not closed properly.

When the bulk reagent container compartment500is closed, the containers502,504are moved to the far end of the drawer500, where they are positioned in operative engagement with the bulk reagent container transport550extending laterally from an end of the drawer500into the first module100. Upon closing the bulk reagent container compartment500, the bulk reagent container transport550is activated to move the containers502,504into the first module100to a position at which the robotic pipettor of the first module100can access the containers502,504. The bulk reagent container transport550may be activated manually by an operator (e.g., pressing a button or switch) or automatically by the system controller upon receipt of an input signal indicating that the bulk reagent container compartment500has been fully closed, thereby placing the containers502,504into operative position with respect to the bulk reagent container transport550.

Details of the bulk reagent container compartment500are shown inFIGS. 9-13. In some embodiments, the bulk reagent container compartment500includes a container tray506configured to hold the plurality of reagent containers, and a container carriage512disposed at the end of the container tray506and configured to carry elution reagent containers502,504. In some embodiments, the container tray506and the container carriage512are moveable along a track508between a withdrawn position as shown inFIG. 9(see alsoFIG. 7) and a closed position as shown inFIG. 10(see alsoFIG. 8).

The container carriage512is carried on a carriage transport522configured to be movable with the container tray506along the track508. As shown inFIGS. 11 and 12, the carriage transport522includes horizontal carriage rails524and526that engage rail slots514,516, respectively, formed in the container carriage512to retain the container carriage512within the carriage transport522.

The bulk reagent container compartment500is configured to permit an operator to place reagent containers502,504within the container carriage512when the drawer is in the open position, as shown inFIGS. 7 and 9. Upon closing the drawer, to the position shown inFIGS. 8 and 10, the reagent container carriage512can be released from the carriage transport522and engaged by the bulk reagent container transport550to pull the carriage512to a lateral position with respect to the track508of the container tray506, as shown inFIG. 10. In this manner, it is possible to transfer bulk reagents from the second module400to the first module100.

More particularly, the carriage transport522moves along the track508as the container tray506is moved into the open or closed positions. As shown inFIG. 11, the carriage transport522includes a pivoting carriage lock532configured to pivot about pivot pin534and including a locking leg536that extends upwardly through an opening528formed in the bottom of the carriage transport522and into a lock recess520formed in the bottom of the container carriage512. A trigger leg538extends below the carriage transport522. As the container tray506is moved into the closed position (to the left inFIG. 11) the trigger leg538of the pivoting carriage lock532engages a lock trigger510projecting upwardly from the track508, thereby causing the carriage lock532to pivot counterclockwise, as shown inFIG. 12, to withdraw the end of the locking leg536from the lock recess520of the container carriage512. With the trigger leg538withdrawn from the lock recess520, the container carriage512and the containers502,504carried therein, are able to slide laterally out of the carriage transport522and onto the bulk reagent container transport550.

The bulk reagent container transport550includes a powered carriage transport mechanism for moving the container carriage512and containers502,504. In one exemplary embodiment, as shown inFIGS. 9, 10, and 13, the carriage transport comprises motor552and a continuous belt554disposed over the output shaft of the motor and an idler wheel556located on an opposite end of the container transport550from the motor552. Motor552may comprise a stepper motor and may include a rotary encoder for monitoring and controlling, via control signals and feedback data, the position of the motor.

The carriage transport mechanism further includes a sled558with a carriage hook564extending therefrom. The belt554is attached to a portion of the sled558so that movement of the belt by the motor552causes a corresponding translation of the sled558in one direction or the other along the transport550.

As shown inFIGS. 12 and 13, as the container tray506is moved to a closed position in which the trigger leg538of the pivoting carriage lock532engages the lock trigger510to withdraw the locking leg536from the lock recess520, the carriage hook564passes into a carriage hook slot530formed in the carriage transport522and engages a hook catch518formed in the container carriage512. The sled558and carriage hook564may then be translated laterally along the container transport550by the belt554to pull the container carriage512off of the carriage transport522and onto the bulk reagent container transport550. As shown inFIG. 11, the bulk reagent container transport includes carriage rails566,568that will engage the rail slots514,516, respectively, of the container carriage512as the container carriage512is pulled onto the bulk reagent container transport550.

As shown inFIG. 13, a home flag560projects from the sled558and engages a slotted optical sensor562to indicate that the sled558and the carriage hook564are in the fully-extended position shown inFIG. 13. A second slotted optical sensor570is provided closer to the motor552(seeFIG. 9). The second optical sensor570is engaged by the home flag560when the sled558and hook564are in the fully retracted position, as shown inFIG. 9. Signals from the sensors562,570are communicated to a system controller to monitor the position of the sled558. Alternatively, the bulk reagent container transport550may include limit switches (e.g., contact switches) to stop operation movement of the sled558at the fully extended and/or fully retracted positions, for example, by generating stop signals communicated to a controller which then sends stop commands or terminates power to the motor552. Still other types of sensors may be used for indicating extended and retracted stop positions, including proximity sensors, magnetic sensors, capacitive sensors, etc.

Cycler deck430comprises a cycler432, such as, for example, a thermal cycler. The cycler432is used in nucleic acid amplification reactions and the selection of cycler type depends on the nature of the amplification reaction intended to be run on the second module400. For purposes of the present disclosure, exemplification will be made using a thermal cycler. However, it is understood that the cycler type incorporated into the second module400depends on the amplification reaction tended to be run on the second module400.

An exemplary embodiment of a thermal cycler432is disclosed by Buse et al. in U.S. Patent Application Publication No. 2014/0038192. An exemplary embodiment of a signal detector432is disclosed by Hagen et al. in U.S. application Ser. No. 14/200,460, “indexing Signal Detection Module,” filed Mar. 7, 2014, which enjoys common ownership herewith.

In certain embodiments, the thermal cycler can have different thermal zones. Such thermal cyclers allow the system to run separate assays under different conditions. For example, in a two zone thermal cycler, a first assay can be run under a first set of time and temperature conditions and a second assay can be run under a second set of time and temperature conditions. It is contemplated that the multi-zone thermal cycler can have two, three, four, five, or even six or more separate thermal zones. Generally, to the extent that a multi-zone thermal cycler is implemented in the system, the number of zones for the multi-zone thermal cycler is evenly divisible into 96 (i.e., 2, 1, 6, 8, etc.)

As shown inFIGS. 1, 5, and 6, a centrifuge588can be located on the amplification processing deck430of the second module400. In one exemplary embodiment, the centrifuge588will centrifuge one or more (up to five in one embodiment) capped processing vials464,670at a time. In an exemplary embodiment, each vial is centrifuged before PCR to ensure that sample material is concentrated primarily in the bottom of the processing vial464,670and to remove any air bubbles from the contents of the vial464,670, which can affect heat transfer and optical transmission quality. The substance transfer pipettor410of the front arm408places the capped vial464,670into the centrifuge588at an access port indicated at reference number589. After centrifuging is complete, the vial transfer arm418of the back arm416removes the capped vial464,670from the centrifuge588at an access port indicated at reference number587and places it in the thermal cycler432. In an embodiment, the centrifuge configuration (e.g., by providing separate ports587,589) allows the substance transfer pipettor410(front arm408) and the vial transfer arm418(back arm416) to load/unload capped vials464,670simultaneously without colliding with each other. As such, in one embodiment, the centrifuge not only performs its function of providing centrifugation of loaded vials, but also functions as a vial transport mechanism by transporting capped vials464,670from a position589accessible to the substance transfer pipettor410to a position587where the capped vials464,670are accessible to the vial transfer arm418. In certain embodiments the substance transfer pipettor410is unable to access position587and the vial transfer arm418is unable to access position589.

In addition, the centrifuge588may be configured to track the position(s) of the loaded vial(s) within the centrifuge and determine when a vial is positioned at either access port587,589. For example, a turntable or other rotating structure on which the loaded vial(s) is (are) centrifuged may be driven by a stepper motor that may include a rotary encoder for precise movement of the turntable and tracking motor counts and/or the turntable or rotating structure may include a rotational position indicator, such as a home flag sensor, configured to indicate one or more rotational positions or reference points.

In one exemplary embodiment, the maximum revolution speed of the centrifuge is 3000 revolutions per minute, but other revolution speeds are contemplated based on, inter alia, the composition of the solution being centrifuged and the time period required to provide adequate centrifugation.

Receptacle Distribution System and Rotary Distributor

In one embodiment, the receptacle distributor, which is configured to move a receptacle onto the receptacle distributor at a first location on the second module, carry the receptacle from the first location to a second location on the second module that is different from the first location, and move the receptacle off the receptacle distributor at the second location on the second module, comprises a rotary distributor. In an exemplary embodiment, the rotary distributor of the receptacle distribution system does not constitute a robotic pipettor, such as substance transfer and handling device402described above, or other substance transfer device comprising a vial transfer arm that is supported on a structure for automatically moving the pipettor in different Cartesian directions (i.e., a x-y-z directions), but is also a 3-axis robot designed to transport MRDs160and reagent packs760between different components of the second module400. In one exemplary embodiment, rotary distributor312works by a hook and rail system in which an extendible and retractable hook pulls or pushes MRDs160or reagent packs760into or from a distributor head of the rotary distributor312. Within the distributor head, the MRD160or reagent pack760is supported and guided by rail and wall features within the head. The rotary position of the distributor head is controlled and monitored by a rotary encoder on the motor for position feedback and has a home sensor. The distributor hook may be belt driven with home and end of travel sensors (e.g., slotted optical sensors, limit switches, etc.) The rotary distributor312is also configured for powered, vertical (or z-axis) motion of the distributor head for vertical translation of an MRD160or reagent pack760. In one exemplary embodiment, the rotary distributor312is configured to allow for at least 100 mm of z-axis travel. The distributor head may include an MRD/reagent pack presence sensor in the head. In one exemplary embodiment, the rotary distributor is configured to transfer an MRD160between any two modules of the second module400within four seconds. In certain embodiments, each axis can make a full travel move in approximately one second.

Details of an exemplary receptacle distribution system are shown inFIGS. 27 and 28. In the illustrated embodiment, a receptacle distribution system200includes a frame202comprising legs203,204and205extending between a bottom panel208and a top panel206. The receptacle handoff station602is mounted on a handoff station bracket606attached to the bottom panel208of frame202and will be discussed further below. Magnetic elution slots620and reagent pack loading stations640are supported on a bracket642attached to legs204and205of frame202and will be discussed further below. A rotary distributor312is supported on a first upright wall218and a second upright wall220within the frame202.

Details of an exemplary rotary distributor312are shown inFIGS. 29-31. The exemplified rotary distributor312includes a distributor head314defining a partial enclosure for holding an MRD160or reagent pack760and a receptacle hook318configured to engage the manipulating structure166of an MRD160or the manipulating hook764of the reagent pack760.

A hook actuator system316linearly translates the receptacle hook318with respect to the distributor head311between an extended position, as exemplified inFIG. 30, and a retracted position, as exemplified inFIG. 29. The exemplified hook actuator system316includes a hook carriage320to which the receptacle hook318is attached. A drive belt344is attached to the hook carriage320by a screw and bracket indicated at322. Drive belt344is carried on a drive wheel334and idler wheels336,338,340,342. Although exemplified using a drive belt-based system, it is understood that other mechanisms, such as screw-drive systems and linear piston actuators, are equally suited for the hook actuator system

Referring toFIG. 31, which is a prospective of an opposite side of the distributor head314, a drive belt motor370having a rotary encoder372is attached to the distributor head314. Drive belt motor370is coupled to the drive wheel334that drives the drive belt344of the hook actuator system316.

The hook actuator system316can include a belt tensioner346for maintaining proper tension in the belt344. Belt tensioner346includes a pivoting idler wheel bracket348to which idler wheel336is attached and which is pivotally attached to the distributor head314by a pivot screw352. A slot350is formed in an end of the pivoting idler wheel bracket348, and a position lock screw354extends through the slot350into the distributor head314. A spring356bears against a portion of the pivoting idler wheel bracket348. Tension in the belt344can be adjusted by loosening the position lock screw354, thereby allowing the spring356to pivot the pivoting idler wheel bracket348and thus urge the idler wheel336upwardly to create the proper tension in the drive belt344. When proper tension is achieved in the drive belt344, the position lock screw354can thereafter be retightened.

The hook carriage320includes a rail channel324that translates along a hook carriage guide rail330attached to an upper, internal portion of the distributor head314. The receptacle hook318is attached to a mount326disposed between the rail channel324and the hook318.

A hook home sensor, e.g., a slotted optical sensor or limit switch, may be provided to indicate when the hook318is in the retracted, or “home,” position when a sensor flag extending from the mount326extends into the slotted optical sensor. Other types of sensors may be used for indicating a home position, such as proximity sensors, magnetic sensors, capacitive sensors, etc. The receptacle hook318and hook carriage320are operatively coupled for electronic communication with the remainder of the rotary distributor312by means of a flexible cable366attached at one end to the hook carriage320and at a printed circuit board or other connector located on the distributor head314. Strain reliefs368and369may be provided for securing the flexible cable366to the distributor head314and the hook carriage320, respectively.

FIG. 32illustrates a manner in which a reagent pack760may be transported within the module400by means of the rotary distributor312. As shown inFIG. 32, the rotary distributor312may be configured to receive and hold a reagent pack760that is pulled into the distributor312by the manipulating hook of the rotary distributor312with the bottom edge765of the pack760supported on a rail373formed on the inner walls of the distributor312.

Similarly,FIG. 33illustrates a manner in which an MRD160may be transported within the module400by the rotary distributor312. As shown inFIG. 33, the rotary distributor312may be configured to receive and hold an MRD160that is pulled into the distributor312by the manipulating hook of the rotary distributor312with the connecting rib structure164of the MRD160supported on a rail373formed on the inner walls of the distributor312.

The receptacle distribution system200includes a distributor moving device configured to move the distributor head314in a circular path or in a vertical, linear path. More specifically, in one exemplary embodiment, the distributor moving device includes a rotary drive system212configured to move the distributor head314in a circular path and an elevation system230configured to move the distributor head314in a vertical direction.

Details of an exemplary rotary drive system212are shown inFIGS. 27, 28, 34, and35. Although in certain embodiments, it is contemplated that the rotary drive system212is configured to freely rotate in 360°, it is understood that in at least certain embodiments the rotary drive system212is configured to rotate 180° between the two respective loading positions.

The first upright wall218and the second upright wall220, on which the distributor head314is supported, are mounted onto a turntable214that is mounted for rotation about its central axis on the bottom panel208of the frame202. A motor222, attached to the bottom panel208and having a rotary drive224, such as a rotary drive gear, extending above the bottom panel208, engages peripheral teeth of the turntable214so that powered rotation of the motor222effects rotation of the turntable214, as well as the first and second upright walls218,220and the distributor head314supported thereon. Although exemplified as having teeth configured to engage each other, it is understood that the rotary drive224and the turntable214can engage each other without having teethed parts. In such an embodiment, both the rotary drive and the turntable can be wheels with rubberized outer surfaces to facilitate traction. Rotary motor222is preferably a stepper motor for providing precise control of the rotation of the turntable214and preferably includes a rotary encoder223for providing rotational position feedback to a control system controlling the rotary motor222. Other means for rotationally coupling the distributor head314to the motor222are encompassed within this disclosure and include, for example, belt(s) and pulley(s), gear trains comprising one or more gears, drive shafts and worm gears, etc.

As shown inFIG. 35, a positional sensor226, which may comprise a slotted optical sensor including an optical transmitter-receiver pair, provides a rotational position feedback signal of the turntable214. Optical sensor226may be configured to detect a passing of one or more positional flags on the turntable214for indicating one or more specific rotational positions. Sensor226includes prongs, or portions, located above and below the turntable214and thus the positional flag(s) may comprise one or more openings (e.g.,227) formed through the turntable. Passage of an opening between the portions of sensor226located above and below the turntable214complete the optical signal transmission between the transmitter and receiver portions of the sensor226and thus generate a signal corresponding to the passage of the opening. Other types of sensors may be used for indicating particular rotational positions, including proximity sensors, magnetic sensors, capacitive sensors, etc.

A second optical sensor228may be provided below the turntable214. Sensor228may comprise a slotted optical sensor including an optical transmitter-receiver pair for detecting the passage of one or more sensor flags (not shown) extending beneath the turntable214for indicating a rotational position. Other types of sensors may be used for indicating a home position, including proximity sensors, magnetic sensors, capacitive sensors, etc.

Details of a distributor elevation system230are shown primarily inFIG. 35. The depicted elevation system230includes a threaded rod232extending upwardly from the turntable214through a motor234and internal thread drive236mounted to the distributor head314(see alsoFIG. 31). Rotation of the internal thread drive236by the motor234causes the motor and the distributor head314to which it is attached to translate up or down the threaded rod232. A guide rail238extends vertically up one edge of the second upright wall220, and the motor234is coupled to the guide rail238by a rail coupling240. Alternatives to the threaded rod and the internal thread drive for moving the distributor head314vertically are encompassed in this disclosure and include, for example, a rack and pinion or a belt drive system.

Referring to the embodiment ofFIGS. 27, 28, and 34, a sensor246extends below the distributor head314. As the distributor head314is lowered by the elevation system230, separate prongs of the sensor246extend into openings216formed in the turntable214. Sensor246may be a slotted optical sensor with the prongs thereof forming a transmitted-receiver pair. An optical signal between the spaced prongs is broken when the prongs enter the openings216, thereby sending a signal to a control system that the distributor head314is at its lowermost position. Other types of sensors may be used for indicating a down position for the distributor head314, including, for example, proximity sensors, magnetic sensors, capacitive sensors, etc.

Data and power are communicated between the rotary distributor312and the module400by means of a coiled cable244that can accommodate rotation of the rotary distributor312with respect to the frame202by, for example, 180° in either direction.

To transfer an MRD160, the distributor head314is rotated a few degrees by the rotary drive system212of the rotary distributor312, the hook318is extended by the hook actuator system316, and the head314is rotated in an opposite direction to engage the manipulating structure166of the MRD160. The distributor hook318is then retracted, and the MRD160is coupled to the distributor head314. Similarly, to transfer a reagent pack760, the distributor head314is rotated a few degrees by the rotary drive system212, the hook is extended by the hook actuator system316, and the head314is then rotated in the opposite direction to engage the manipulating hook764of the reagent pack760. The distributor hook318is then retracted, and the reagent pack760is pulled into the distributor head314.

Receptacle Handoff Device

The receptacle handoff device602is configured to transfer a receptacle, such as the MRD160, between the receptacle distributor150of the first module100and the rotary distributor312of the second module400. Both the receptacle distributor150of the first module100and the rotary distributor312of the second module400manipulate the MRD160using a hook or other similar device to engage the manipulating structure166of the MRD160. Therefore, after the MRD160is disengaged by the receptacle distributor150of the first module100, the MRD160is positioned and oriented in such a manner as to present the manipulating structure166to the rotary distributor312of the second module400. The handoff device602performs this function.

Details of the handoff device602are shown inFIGS. 27, 28, 39, 40. The receptacle handoff device602comprises a receptacle yoke604configured to receive and hold an MRD160placed into the yoke604by the receptacle distributor150of the first module100. The yoke604is mounted on a handoff device bracket606, attached to and extending from the bottom panel208of the frame202, so as to be rotatable about a vertical axis of rotation. In one exemplary embodiment, the yoke604is coupled to a handoff device motor680attached to the bracket606. Motor680may be a stepper motor for precise motion control and may include a rotary encoder682for providing rotational position feedback of the receptacle yoke604to a controller. A sensor684, which may be a slotted optical sensor comprising an optical transmitter-receiver pair, is mounted to the bracket606and detects a home flag686extending from the yoke604for providing rotational position feedback. Other types of sensors may be used for providing position or orientation feedback, including proximity sensors, magnetic sensors, capacitive sensors, etc. After the MRD160is placed in the yoke604by the receptacle distributor150of the first module100and the receptacle distributor150disengages the MRD160, the housing604is rotated to present the manipulating structure166of the MRD160to the rotary distributor312of the second module400.

Alternatively, the handoff device602may be passively actuated by the rotary distributor312. For example, the handoff device rotation may be tied to the rotation of the rotary distributor312(e.g., via a cable, belt, gear, or other means) such that when the rotary distributor312rotates to the handoff position, the handoff device602would spin around to face the rotary distributor312. When the rotary distributor312rotates away from the handoff device602, the handoff device602would rotate back toward the receptacle distributor150of the first module100.

MRD Storage Station

As shown inFIG. 14, the MRD storage stations608,610,612are located on the receptacle processing deck600of the second module400and serve as temporary locations for MRDs in the second module400. Storage stations608,610,612include a number of slots614, each configured to receive an MRD160. The storage stations608,610,612are arranged in an arc, thereby accommodating the rotational path of motion of the rotary distributor312. Providing additional storage for MRDs within second module400provides the advantage of enhancing workflow by permitting flexibility in the timing that any particular MRD, or contents thereof, is/are utilized within second module400. This permits MRDs that may arrive in second module400later to be processed out of order, for example, to address urgent needs in a laboratory.

Although exemplified as having three MRD storage stations608,610,612, it is understood that embodiments can be constructed having two or more such storage stations. Similarly, although exemplified as being configured in an arc arrangement, it is understood that the distributor312in certain embodiments does not rotate about an arc and that the arc arrangement is convenient for the rotary distributor312embodiment. To the extent that an alternate configuration of the distributor312is implemented, the MRD storage stations similarly would match the alternate arrangement to maximize workflow of the system.

Magnetic Elution Slots/Reagent Pack Loading Stations

The magnetic elution slots620(two in the illustrated embodiment) and the reagent pack loading stations640are supported on a bracket642attached to frame202. The purpose of each magnetic elution slot620is to hold an MRD160and apply magnetic force to the contents of the MRD to pull the magnetic beads to the side walls of each receptacle162while the substance transfer pipettor410aspirates the eluate fluid from the receptacles162.

Details of the magnetic elution slots620and the reagent pack loading stations640are shown inFIGS. 36-38. Each magnetic elution slot620comprises a block622within which is formed a slotted opening624. An MRD160placed within the slotted opening624is supported within the opening624by the connecting rib structure164of the MRD160resting on the top of bracket642. The manipulating structure166extends out of the opening624, and a cutout632in each side wall of the block622enables the hook318of the rotary distributor312to move laterally into or laterally out of the MRD manipulating structure166of an MRD160located within the slotted opening624. The top of the MRD is uncovered, thus enabling pipettor access to the receptacles162of the MRD160held within the elution slot620. Magnets628are attached to or embedded within one or both walls defining the slotted opening624. Individual magnets628may be provided for each receptacle162of the MRD160, as shown inFIGS. 37 and 38, or a single magnet may be provided for a receptacle that comprises one or more individual receptacles.

The reagent pack loading stations640are defined by spaced-apart, hold-down features644extending above the bracket642and a backstop646defining a back end of each reagent pack loading station640. A reagent pack760is inserted between the hold-down features644, under a lateral flange, and is pushed into the loading station640until the back end of the reagent pack760contacts the backstop646.

Reagent Pack Trash Chute

A reagent pack trash chute428is supported on the bracket642. In an exemplary embodiment, reagent pack trash chute428includes an entrance structure, defined by side walls434,436and a top panel438, through which a reagent pack760is inserted into the trash chute428. Sidewalls434,436are attached to the top of the bracket642and are bent or flared outwardly at their forward edges to provide a funneling entrance to the trash chute428. Resilient tabs442extend down from the top panel438.

To discard a reagent pack760, the rotary distributor312inserts the pack760into the trash chute428between the side walls434,436. When the reagent pack760is inserted into the trash chute428, there is a clearance between the top panel438and the top of the reagent pack760. The resilient tabs442bear against the top of the reagent pack760and hold the reagent pack760down within the trash chute428. The angle the resilient tabs442permits the reagent pack760to be pushed into the of the trash chute428, but resists movement of the reagent pack760out of the trash chute.

When a subsequent reagent pack760is inserted into the reagent pack trash chute, it is pushed against the reagent pack760previously inserted into the trash chute428, thereby pushing the previously-inserted pack further into the trash chute428. A cut-out648is formed in the bracket642, so the previously-inserted pack760eventually falls from the trash chute428and, guided by a guide ramp444extending down from the bracket642, into a trash bin located below the trash chute428.

Reagent Pack Changer

Details of an exemplary reagent pack changer700are shown inFIGS. 15-17. The purpose of the reagent pack changer700is to provide fully independent reagent pack loading and test execution whereby an operator may place reagent packs in a reagent pack input device and/or remove reagent packs760from the reagent pack input device while previously loaded reagent packs760are stored within a storage compartment, which may be temperature controlled, and are available for access by the instrument independently of the status of the reagent pack input device. The reagent pack changer is configured to move reagent packs760between the reagent pack input device and the storage compartment,

As shown inFIGS. 15-17, in one exemplary embodiment, the reagent pack input device comprises a reagent pack carousel compartment702which may be pulled open from the second module400and which contains a rotatable reagent pack carousel704. The pack carousel704includes a number of reagent pack stations706, each of which is adapted to receive and carry a reagent pack760and which are defined by radially inner dividers708and radially outer dividers710. As can be seen inFIGS. 15-17, the reagent pack stations706of the reagent pack carousel704are arranged about the outer perimeter of the reagent pack carousel704, but the elongated reagent pack stations706, and reagent packs760carried thereby, are not oriented in a radial direction with respect to the center of the reagent pack carousel704. Each reagent pack station706is oriented at an angle (e.g. 5-20°) with respect of a true radial orientation. This configuration of reagent packs optimizes the placement of reagent packs760on the carousel704, thereby enabling the reagent pack carousel704to carry the maximum number of reagent packs760and providing access of identifiable indicia present on each reagent pack760to the barcode reader774.

A gap712between each inner divider708-outer divider710pair enables an operator to insert his or her fingers into the gap712to thereby grasp the sides of the reagent pack760for placing the reagent pack760into the reagent pack station706or for removing the reagent pack760from the reagent pack station706. Each reagent pack station706of the reagent pack carousel704also includes an alignment block714at a radially inner end of the reagent pack station706. The alignment block within the rear recess770of the reagent pack760helps to maintain the proper alignment and position of the reagent pack760within the reagent pack station706.

In some embodiments, the reagent pack carousel compartment702includes a carousel frame716, preferably disposed on a track that enables the frame716to be slid into or out of the module400as a drawer. The frame716includes a drawer front720. The reagent pack carousel704is rotatably disposed within the frame716, which may include a circular recess722shaped so as to conform to the reagent carousel704.

The reagent pack carousel704is motorized to effect powered rotation of the carousel. In one exemplary embodiment, the reagent pack carousel compartment702may include a motor (not shown) that is coupled, for example by a belt and pulley arrangement (not shown), to the reagent pack carousel704for powered rotation of the reagent pack carousel704. The motor may be mounted to the reagent pack carousel frame716and move in and out with the reagent pack carousel compartment702, connected to the module400by a flex cable. The reagent pack carousel compartment702may include one or more position sensors for detecting when the carousel is in an open or closed position and communicating a corresponding signal to the system controller. Such sensor(s) may include optical sensors, proximity sensors, magnetic sensors, capacitive sensors, etc.

The reagent pack carousel compartment702may also include a software-controlled lock.

The reagent pack carousel compartment702can also include one or more sensors for tracking the positions of the reagent pack station706. For example, the reagent pack carousel704may include a home flag, such as a tab and an optical sensor that detects the position of the tab at a specified rotational position of the reagent pack carousel704. Other types of sensors may be used for indicating a home position, including proximity sensors, magnetic sensors, capacitive sensors, etc. Furthermore, the motor driving the reagent pack carousel704may be a stepper motor including a rotary encoder for generating signals corresponding to a rotational position of the reagent pack carousel704.

The second module400may include a machine pack reader configured to read a machine code provided on each reagent pack760providing information regarding the reagent pack760, such as the identity of the assay reagents carried within the reagent pack760, manufacturer, lot number, expiration date, etc. The machine code may also include a unique identifier specifically identifying that particular reagent pack760. The machine code reader device may comprise a barcode reader774configured to read a barcode label772disposed on the reagent pack760. Barcode label772may be a two dimensional or one dimensional barcode. A scanning slot718formed in the carousel frame716provides an opening through which the barcode reader774may read a label772on the reagent pack760. Similarly, the orientation of the reagent pack760carried in the pack station706of the pack carousel704, may be set at an angle with respect to a true radial orientation, and the shape of the outer dividers710, being generally trapezoidal in shape, creates a clearance opening through which the barcode reader774can read the barcode label772disposed on the reagent pack760. Together with the rotary encoder, the barcode reader772provides an indication where each reagent pack760is positioned within each reagent pack station706of the reagent pack carousel704. Although a barcode scanner is exemplified, the use of other technologies such as RFID and QR codes are contemplated.

Each reagent pack station706may include a station empty barcode disposed on a side of each outer divider710that will be read by the barcode reader774if a reagent pack760is not positioned within the reagent pack station706.

In another exemplary embodiment, the reagent pack input device comprises an alternative reagent pack carousel730shown inFIG. 18. Reagent pack carousel730is not carried on drawer be pulled out of the module400, but instead, includes radially oriented reagent pack stations732arranged about the perimeter of the reagent pack carousel730and is accessible through a slot in front of the second module400which may be covered by a door that is openable by the operator. Powered rotation of the reagent pack carousel730may be provided by a carousel drive system that may include a motor734having an output drive wheel736that is coupled to a drive pulley739of the carousel730by means of a drive belt738. Motor734may comprise a stepper motor having a rotary encoder, and a home flag may be provided on the carousel730to detect and monitor the rotational position of the reagent pack carousel730and thus each reagent pack station732.

FIG. 18also shows an exemplary embodiment of a reagent pack storage compartment represented by reference number740. The storage compartment740is disposed beneath the reagent pack carousel730. In the embodiments described above, the reagent pack carousel compartment702would be disposed within the module400above the storage compartment740and would be movable with respect thereto.

In some embodiments, storage compartment740includes a housing742that defines a temperature controlled chamber therein. The desired storage temperature may be as low as 4° C., but could be any temperature at or below ambient temperature, for example, 15° C. In some embodiments, the chamber of the storage compartment740further has a humidity control module configured to control the humidity level of the air circulating within the temperature controlled chamber. As part of this process, the humidity control module is optionally equipped to collect condensed water, and route it outside the cooled storage area for disposal.

Housing742may be insulated and may be cooled by Peltier devices that can be mounted directly onto the housing742or by Peltier devices coupled to a heat cools a fluid, such as water or a refrigerant, which is circulated around the housing742. In one embodiment the storage compartment740is cooled by two separate Peltier devices mounted directly onto the housing742, each at different temperatures or temperature ranges. In this embodiment the first Peltier device is held at a temperature close to the freezing temperature of water. The second Peltier device is provided at a location within the storage compartment740distant or adjacent to that of the first Pettier device and is provided at a temperature higher than that of the first Peltier device, e.g., 15° C. The second Peltier device is in operable communication with a temperature sensor within the storage compartment740, positioned near the top of the storage compartment740. The second Peltier device would operate based on the measured temperature to maintain a predetermined temperature in the storage compartment740. In this embodiment a fan may be provided within the storage compartment740to cause air circulation within the storage compartment740through the fan, and past the first and second Peltier devices. When air passes the first Peltier device, which is held at a very low temperature, the air will cool, thus decreasing its capacity to hold moisture which moisture will condensate on the Peltier device or another designated element. Therefore, this dual Peltier device embodiment provides both a temperature and humidity controlled environment, which is beneficial for increasing the shelf-life of lyophilized reagents which are vulnerable to rapid degradation in the presence of increased temperatures and atmospheric moisture.

Other ways to cool and/or dehumidify the storage compartment740are contemplated and the disclosure is not limited to the exemplified embodiments.

The housing742should be provided with a liquid collection and/or drainage system for handling condensing liquid inside the housing742. Such a system may, for example, include piping for directing the collected condensate away from the housing742and to a drain or an evaporator.

A storage carousel744is rotatably mounted within the housing742, for example, on shaft745. Storage carousel744includes a plurality of pack stations746disposed around the perimeter thereof and positioned on one or more levels of the carousel744. In the illustrated embodiment, storage carousel744includes pack stations746on two levels, one above the other.

A carousel drive can power rotation of the storage carousel744within the storage compartment740. The carousel drive may include a motor748, which may be a stepper motor, having an output drive wheel750coupled by means of a drive belt752to a drive pulley749of the pack carousel744. Motor748may be located outside the housing742—to keep heat generated by the motor748from heating the storage compartment740—and the drive belt752may extend through an opening in the housing742. Alternatively, a drive pulley coupled to the carousel744may be located outside the housing740. The motor748may include a rotary encoder, and the reagent pack carousel744may include a home flag for monitoring the rotational position of each of the reagent pack stations746of the pack carousel744.

Operation of the reagent pack changer700will now be described.

After the reagent packs760are placed in the reagent pack carousel704or reagent pack carousel730of the pack input device, the barcode of each reagent pack760is read by a barcode reader774and the identity and other information provided by the barcode is associated with a particular reagent pack station706,732of the reagent pack carousel704. Alternatively, the reagent packs760may be scanned externally of the module400, for example, by a hand operated barcode scanner, before the reagent pack760being placed into the pack input device.

After reagent packs760have been placed into the reagent pack input device, such as reagent pack carousel704or reagent pack carousel730, pack carousel compartment702is shut or a door in front of the carousel access opening is closed. Next, the rotary distributor312removes one or more reagent packs760from the reagent pack carousel704,730and moves the reagent pack760into a pack station746of the storage carousel744of the storage compartment740. As shown inFIG. 16, the carousel frame716of the reagent pack carousel compartment702includes a reagent pack access slot724through which the rotary distributor312can access the manipulating hook764of a reagent pack760disposed within the reagent pack station706. To enable the rotary distributor312to transfer reagent pack760between the reagent pack input carousel704or730, to the one or more levels of the storage carousel744of the storage compartment740, the rotary distributor312provides powered and controlled vertical, i.e., z-axis, motion. It is preferable that access to the reagent pack access slot724by the rotary distributor312is controlled by a door when the reagent carousel704or730is temperature controlled.

Once a reagent pack760is present in the storage compartment740, it is available to be utilized in an amplification assay, for example, a PCR assay. When a sample is present requiring a particular assay, the carousel of the storage compartment740rotates to a position where a reagent pack760containing the specific unit dose reagents for that particular assay are accessible by the rotary distributor312. Generally, such access will be through a door to maintain a tightly controlled temperature environment in the storage compartment740. The distributor312will access the reagent pack760through the door and move it to a reagent pack loading station640for reconstitution of one or more lyophilized reagents contained on the reagent pack760. When the reagent pack760is empty, or when the reagents of one or more wells on the reagent pack760have been reconstituted and removed, the distributor312will again move the reagent pack760. If there are reagents remaining in the reagent pack760, the distributor312will transfer the reagent pack760back to the storage compartment740. If the reagent pack760contains no more reagents, or is otherwise designated as inappropriate for continued use (e.g., contaminated or expired reagents), the distributor312will transfer the reagent pack760to either a waste chute426or back to the reagent pack input carousel704or730for removal.

A further alternative for scanning each reagent pack760is for the distributor312to present each reagent pack760to a barcode scanner as each reagent pack is removed from the reagent pack input carousel and before placing the reagent pack760into the storage carousel744.

Reagent identity control is maintained after the bar code (or other machine code) is read on the reagent pack760by monitoring the position of each reagent pack station706,732of carousel704,730and each reagent pack station746on the storage carousel744and associating the reagent pack760identity—from the bar code—with the reagent pack station position.

The reagent pack carousels704,730rotate independently of the storage carousel744of the storage compartment740to allow an operator to load and unload reagent packs760from the reagent pack carousel704,730while the module400(i.e., rotary distributor312) independently accesses reagent packs760stored in the storage carousel744for assay processing.

The reagent pack changer700preferably stores at least 28 to 30 or more reagent packs760.

The second module400may further include an electrostatic generator to impart an electrostatic charge for positioning and holding the lyophilized reagent768present in the reagent pack760at the bottom of each of the mixing wells762of the reagent pack760. Though the reagent768may be held at the bottom of the associated mixing well768with a previously-imparted electrostatic charge, as noted above, the inclusion of a mechanism, such as a electrostatic generator, to actively pull the lyophilized reagent768down to the bottom of the mixing well762at the time that the reagent is reconstituted will ensure its positioning in the correct spot in the mixing well during reconstitution. In an embodiment, the electrostatic generator is positioned below the reagent pack loading station640,730. Alternatively, or in addition, an electrostatic generator could be provided in the reagent pack carousel704,730present in the reagent pack loading drawer and/or the storage carousel744present in the storage compartment740. In such an embodiment, the electrostatic generator may be located under or operatively coupled to the reagent pack station706,732or the reagent pack station746below the reagent pack760, as providing an electrostatic generator within the storage compartment710will have an enhanced electrostatic effect due to the lower temperature and low humidity.

Details of compartment590for storing accessories or to accommodate possible expansion of the second module400are shown inFIGS. 5, 6, 14, and 15. In one exemplary embodiment, compartment590can house a standard 96 well plate. The plate is located such that both pipettor arms408,416can access the 96 well plate location. The expansion space has access to the front (via a drawer mechanism) so that the operator can load and unload the plate. The expansion space can also be accessed from the side of the instrument. A drive system comprising, for example, a motor-driven belt, may be provided for translating a well plate or other container or component into or out of the second module400. Compartment590can be utilized as an area for collecting cap/vial assemblies that have undergone a PCR and/or melting assay to provide for the ability to perform additional assays (e.g., ELISAs) on the sample contained in the cap/vial assembly. (A procedure for performing a thermal melt analysis is disclosed by Wittwer et al. in U.S. Pat. No. 8,343,754.) In certain embodiments an arrangement of cap/vial assemblies the format of a 96 well plate has advantages if further processing of the samples is desired since the 96 well plate size is compatible with a variety of known sample processing and molecular assay instruments.

Instrument Theory of Operation

The first module100is used for the sample preparation portion of the amplification assay (i.e., minimally the steps for isolating and purifying a target nucleic acid that may be present in a sample). Samples and TCR, which may include a magnetically-responsive solid supports, are loaded onto the first module100. Elution buffer containers502,504are loaded on the second module400. The second module400then automatically moves these containers into a space within the first module100that can be accessed by a substance transfer device, for example, a reagent pipettor (not shown inFIG. 1), of the first module100. Through information provided to the first module100by, for example, an operator via a user interface or through automated, machine-readable information, such as a bar code, provided on the sample container (not shown inFIG. 1), the first module recognizes that a particular amplification assay will be initiated. To process samples, the receptacle distributor150of the first module100pulls a new MRD160from an input queue102and places it into a sample dispense position within the first module100. TCR and sample are transferred from a reagent container and sample tube, respectively, to each receptacle162the MRD160by a pipettor within the first module100. The contents of the MRD160are then incubated for a prescribed period at a prescribed temperature before the MRD160is transferred to a magnetic separation wash station118,120for a magnetic wash procedure.

After the target capture process, the MRD160is moved by the receptacle distributor150to an amplification reagent dispense position in the first module100. The substance transfer device of the first module100then adds elution fluid to each receptacle162of the MRD160to separate target (sample) material from the magnetic particles, and the first module100mixes the contents of each receptacle162before sending the MRD160to the second module400. The second module400places the MRD160into one of a series of slots configured to hold MRD160. When signaled by the system controller, the second module400moves the MRD160to a magnetic elution slot620to separate the eluted nucleic acid material from the magnetic particles. The substance transfer device402, for example, a robotic pipettor, then initiates the amplification process. The pipettor402first dispenses oil to all processing vials464,670queued for use in testing. The pipettor402then aspirates eluate/sample from the MRD160, and then aspirates a reconstitution reagent solution from a reconstitution reagent cartridge or reservoir, dispensing them into a lyophilized-reagent well of reagent pack760. The reconstitution reagent and a lyophilized amplification reagent in the reagent well of reagent pack760may be drawn into and released from the pipette tip one or more times to ensure adequate and rapid reconstitution. The reconstituted amplification reagent is pipetted to the processing vial464,670and is then capped. The reconstituted amplification reagent, sample, and oil may be drawn into and released from the pipette tip one or more times to ensure adequate mixing. The capped vial464,670is transferred to the centrifuge and then to the thermal cycler432, such as thermal cycler432for PCR amplification and fluorometric detection.

Results may be displayed on an instrument monitor or user interface and either printed or communicated to the LIS.

In an embodiment, the first module100is configured to perform one or more isothermal nucleic acid amplification reactions on nucleic acid material contained within an MRD160. In one embodiment, such an isothermal process may be performed on the contents of the MRD160before transporting the MRD160to the second module400to perform PCR on a portion of the MRD content material, as discussed above. Alternatively, after the MRD160is processed in the second module400and an amount of eluate/sample is transferred from the MRD to one or more vials464,670for performing PCR or other process(es) that the second module400is configured to perform. The MRD160may be transported back to the first module100to perform an isothermal nucleic acid amplification reaction on the remaining contents of the MRD160.

Exemplary Processes

Details of operation and a process embodying aspects of the present disclosure are shown in the flow charts ofFIGS. 41-43. The following processes are exemplary. Other processes may be performed and/or the processes shown herein and described below may be modified, e.g., by omitting and/or reordering certain steps.

A sample eluate preparation process that can be performed using the first module100and the second module400described above is represented by flow chart800inFIG. 41. In step S802of method800, a reaction receptacle is moved to a location at which reaction materials can be added to the receptacle. See, e.g., Clark et al. in U.S. Pat. No. 8,309,036. For example, the receptacle distributor150of the first module100moves an MRD160from the input device102to one of the load stations104,106or108. See, e.g., Hagen et al. in U.S. Patent Application Publication No. 2012/0128451.

In step S804a substance transfer device of the first module100transfers reaction materials to the receptacle. See, e.g., Buse et al. in U.S. Provisional Application No. 61/783,670. For example, a robotic pipettor of the first module100transfers a target capture reagent (“TCR”) (e.g., 500 μL), sample fluid (e.g., 360 μL), and target enhancer reagent (“TER”) (e.g., 140 μL) into each receptacle162of the MRD160.

In step S806, the reaction materials added to the receptacle in step S804are mixed. For example, the TCR, sample fluid, and TER added to the receptacles162of the MRD160are mixed by, for example, oscillating the MRD160at a high frequency (e.g., 60 seconds at 16 Hz).

In step S808, the receptacle is moved into an environment that will promote the desired reaction. For example, the receptacle distributor150removes the MRD160from the load station104and transfers the MRD160to one of the incubators112,114,116(referred to as the AT Binding Incubator “ATB Incubator” inFIG. 41) to incubate the contents of the MRD160at a prescribed temperature for a prescribed period of time (e.g., 1800 seconds at 63° C.). Before moving the MRD160to an incubator, the MRD160may first be placed in one of the temperature ramping stations110(e.g., 300 seconds at 65° C.) to elevate the temperature of the MRD160and its contents to a temperature that is closer to that of the incubator into which the MRD160will be transferred so as to minimize temperature fluctuations within the incubator.

The desired reaction may require two or more incubations at different temperatures. Thus, in accordance with one implementation of the disclosure, in step S810, the receptacle distributor150removes the MRD160from one of the incubators and transfers the MRD160to another incubator (referred to as the “High Temp Incubator” inFIG. 41) that is at a different (e.g., higher or lower) temperature than the first incubator to continue to incubate the contents of the MRD160at a prescribed temperature for a prescribed period of time (e.g., 600 seconds at 43.7° C.).

In step S812, the receptacle distributor150removes the MRD160from the second temperature incubator and returns the MRD160to another incubator at a different temperature, which may be the same incubator (e.g., the “ATB Incubator”) the MRD160was placed into in step S808.

At the conclusion of the incubation step(s), it may be desirable to cool the temperature of the contents of the receptacle, for example to terminate any reaction occurring within the receptacle. Thus, in one example, in step S814, the receptacle distributor150may remove the MRD160from the incubator and transfer the MRD160to a chiller module122(referred to as a “Chiller Ramp” inFIG. 41), maintained at a predetermined temperature.

Next, assuming the reaction performed within the receptacle includes immobilizing a target nucleic acid on a magnetic-responsive solid support, a magnetic separation procedure is performed on the contents of the receptacle. Thus, in step S816, the receptacle distributor150removes the MRD160from a chiller module122after a predetermined period of time (e.g., 830 seconds), and transfers the MRD160to a magnetic parking station comprising magnets for attracting magnetically-responsive solid support within each receptacle162to the walls of the receptacles162to pull the solid support out of suspension. See, e.g., Davis et al. in U.S. Pat. No. 8,276,762. In step S818, after a prescribed period of time within the magnetic parking station (e.g., 300 seconds), the receptacle distributor150removes the MRD160from the magnetic parking station and transfers the MRD160to a magnetic separation wash station118or120. See, e.g., Hagen et al. in U.S. Patent Application Publication No. 2010/0288395. In step S820, a magnetic wash procedure is performed on the contents of the MRD160placed into the magnetic wash station118or120. One exemplary embodiment of the magnetic separation procedure involves a number magnetic dwells during which the contents of the receptacle are exposed to a magnetic force for a predetermined period of time, and after each magnetic dwell, while the contents are still exposed to the magnetic force, the fluid contents are aspirated from the receptacle, leaving the magnetic particles behind in the receptacle. In one exemplary embodiment, three magnetic dwells of 120 seconds each are performed. At the conclusion of each magnetic dwell, the magnetic force is removed from the contents of the receptacle. After each magnetic dwell, except the last magnetic dwell, an amount of wash fluid (e.g., 1000 μL of wash buffer) is added to the receptacle to re-suspend the magnetic particles before beginning the next magnetic dwell.

After the magnetic wash process is complete (e.g., after the last magnetic dwell followed by an aspiration of the non-magnetic fluid contents of the receptacle), in step S822, the receptacle distributor150retrieves the MRD160from the magnetic separation wash station118or120and moves the MRD160to one of the load stations104,106or108. In the load station, an amount of elution buffer (e.g., 50-110 μL) is transferred by, for example, a substance transfer device such as a robotic pipettor, from one of the elution containers502,504transferred into the first module100by the bulk reagent container transport550of the bulk reagent container compartment500of the second module400.

In some embodiments, it may be desirable to heat or incubate the contents of the MRD160to improve the efficiency of the nucleic acid elution.

In step S824, following the addition of the elution buffer, the contents of the MRD160are mixed by agitating the MRD160.

In step S826, the MRD160is transferred from the first module100to a magnetic elution slot620in the second module400. First, the receptacle distributor150of the first module100retrieves the MRD160from the load station104,106or108and transfers the MRD160to an end of the transport track assembly154closest to the second module400. The distribution head152of the receptacle distributor150places the MRD into the receptacle handoff device602of the second module400. The receptacle handoff device602then rotates the MRD160and presents it to the rotary distributor312. The rotary distributor312, extends its hook318and engages the manipulation structure166of the MRD160by rotating a few degrees to place the hook318into the manipulation structure166and then withdraws the hook318to pull the MRD160into the distributor head314of the rotary distributor312. The rotary distributor312then rotates to align the MRD160carried therein with one of the magnetic elution slots620of the second module400(or optionally MRD storage608). The rotary distributor312then extends its hook318to push the MRD160into the magnetic elution slot620and rotates a few degrees to remove the hook318from the manipulation structure166.

The process next proceeds to process830shown inFIG. 42.

Referring toFIG. 42, a reaction mixture preparation process is represented by flow chart830. One or more of the steps of process830may proceed in parallel with one or more of the steps of process800shown inFIG. 41.

At step S832the substance transfer pipettor410of the second module400picks up a disposable tip584from a disposable tip tray582carried in one of the tip compartments580.

In step S834, the substance transfer pipettor410transfers an amount of oil (e.g., 15 μL) from an oil container carried in the bulk reagent container compartment500to one or more processing vials464held in the cap/vial trays460of the processing cap/vial compartment440.

In step S836, the substance transfer pipettor410moves to a trash chute426to strip the disposable pipette tip584therefrom and discard the tip into the trash chute426. Substance transfer pipettor410then returns to the disposable tip tray582and picks up another disposable pipette tip584.

In step S838, substance transfer pipettor410transfers an amount of reconstitution reagent (e.g., 20 μL) from a reconstitution reagent container held in the bulk reagent container compartment500to a mixing well762of a PCR reagent pack760that was previously transferred by the rotary distributor312from the storage compartment740to a reagent pack loading station640. In one embodiment, before the reconstitution reagent is dispensed into the mixing well762, the pipettor110performs a level sense at the foil766before piercing the foil766with the pipette tip584. The level-sense performed on the foil of the reagent pack760to “calibrate” the height of the reagent pack760relative to the pipettor. Generally, the pipettor410is configured to extend the pipette tip to the bottom of the mixing well for more accurate reagent aspiration.

In step S840, the fluid within the mixing well762is mixed to dissolve the lyophilized reagent768. In one example, the substance transfer pipettor410mixes the fluid within the mixing well762by alternately aspirating the fluid into the pipette tip584and dispensing the fluid back in the well762one or more times to dissolve the lyophilized reagent768.

In step S842, the substance transfer pipettor410transfers an amount, (e.g., 20 μL) of the reconstituted reagent from the mixing well762of the PCR reagent pack760(referred to as “Mastermix” inFIG. 42), into a vial464. A PCR master mix provides the key ingredients necessary for performing PCR in a premixed and optimized format. Included in the master mix are Taq DNA polymerase, deoxynucleoside triphosphates (dNTPs), and magnesium chloride (MgCl2). Not typically included are the forward and reverse primers.

In step S844, the substance transfer pipettor410moves to the trash chute426and strips the pipettor tip584into the trash chute. The substance transfer pipettor410then moves to the disposable tip tray582and picks up anew disposable pipette tip584.

Block “B” inFIG. 42represents the integration of process800shown inFIG. 41with process830shown inFIG. 42. An MRD160containing a sample mixture (which, in this exemplary embodiment, was purified in a magnetic separation procedure) and an elution buffer is held in a magnetic elution slot620, having been placed there in step S826of process800. In one embodiment, the MRD160is held in the magnetic elution slot620for dwell period of at least 120 seconds.

In step S846of process830, the substance transfer pipettor410transfers an amount of eluate (e.g., 5 μL) from the MRD160held in the elution slot620to the processing vial464to which oil and reagent were added in steps S834and S842, respectively.

In step S848, the substance transfer pipettor410moves back to the trash chute426and strips the disposable pipette tip584into the trash chute.

The process now proceeds to process850shown inFIG. 43.

Referring toFIG. 43, a process for performing an automated biological process, such as a PCR reaction, is represented by flow chart850. Block “C” inFIG. 43represents the integration of process830shown inFIG. 43with process850shown inFIG. 43.

In step S852, the substance transfer pipettor410picks up a processing vial cap476from the cap well440of the cap/vial tray460by inserting the pipettor probe422(without a disposable pipette tip thereon) into the cap476(seeFIG. 26, which shows an alternative cap600and vial670combination). The substance transfer pipettor410then picks up the cap476, which is held onto the pipettor probe422by friction, and inserts the cap476into the processing vial464held in the processing vial well474until the cap476locks with the vial464to form a cap/vial assembly (seeFIG. 25).

In step S854, the substance transfer pipettor410transfers the cap/vial assembly held to the pipettor probe422by friction to the centrifuge588, where a stripping device removes the cap/vial assembly from the pipettor probe422, to deposit the cap/vial assembly into the centrifuge588.

In Step856, following a specified period of time in the centrifuge, the vial transfer pipettor418inserts its pipettor probe422into the cap476of the cap/vial assembly held in the centrifuge588and removes the cap/vial assembly from the centrifuge588and transfers the cap/vial assembly to an incubator module, such as the thermal cycler432. A stripping device removes the cap/vial assembly from the pipettor probe422of the vial transfer pipettor418.

In step S858, an incubation process is performed. The incubation process may include PCR thermal cycling comprising multiple cycles of temperatures varying between 95° C. for denaturation, 55° C. for annealing, and 72° C. for synthesis. During the thermal cycler process an emission signal from the contents of the processing vial may be monitored. For example, fluorescence monitoring at one or more colored wavelengths during each PCR cycle may be measured using a signal detecting device, such as a fluorometer, operatively integrated with the thermal cycler432. Periodic fluorescence intensity measurements at each wavelength may be made at regular intervals to generating fluorescence time series data for later processing and analysis.

In step S860, following the PCR process of step S858, the vial transfer pipettor418retrieves the cap/vial assembly from the thermal cycler432and transfers the cap/vial assembly to a trash chute424where the cap/vial assembly is stripped from the pipettor probe422into the trash chute424, or the cap/vial assembly is transported to an output reagent pack760in the storage/expansion module.

In some embodiments, diagnostic system10can be used to perform two or more assays that include nucleic acid amplification reactions that require different reagents, including one or more unit-dose reagents.FIG. 44illustrates a method of using diagnostic system10, which includes first module100and second module400, according to one such embodiment.

At step862, a plurality of samples is loaded in diagnostic system10. A first sample subset of the plurality of samples has been designated for at least one assay, and a second sample subset of the plurality of samples has been designated for at least one different assay. In some embodiments, barcodes on the sample receptacles indicate the appropriate assay, and in other embodiments, the assay is entered manually into the system by an operator using a user-interface of diagnostic system10.

In some embodiments, a first assay comprising a first nucleic amplification reaction has been designated for the first sample subset. For example, the first nucleic amplification reaction can be PCR, and the target nucleic acid can be a nucleic acid associated with a particular virus or organism, for example. In some embodiments, the first nucleic amplification reaction uses a unit-dose reagent stored and operatively accessible within the diagnostic system10. For example, the first nucleic amplification reaction can be PCR or any other desired thermal cycling reaction that can be performed by second module400of diagnostic system10.

In some embodiments, a second assay comprising a second nucleic amplification reaction will be designated for the second sample subset. The second nucleic amplification reaction may be the same or a different nucleic acid amplification reaction than the first nucleic acid amplification reaction of the first assay, but the reagent used in the second nucleic amplification reaction may target a different nucleic acid than the target of the first reagent used in the first assay in some embodiments. In some embodiments, the second nucleic amplification reaction can be PCR or any other desired thermal cycling reaction that is performed, for example, by second module400of diagnostic system10. In some embodiments, the second nucleic amplification reaction is TMA or any other isothermal reaction that is performed, for example, by first module100of diagnostic system10. The reagent used for the second assay can be a unit-dose reagent different than the unit-dose reagent used for the first assay, a bulk reagent, or both. For example, if the second nucleic amplification reaction is PCR, the second reagent used in the second assay can be a unit-dose reagent, and if the second nucleic amplification reaction is TMA, the second reagent used in the second assay can be a bulk reagent. In some embodiments, the second unit-dose reagent, the first bulk reagent, or both are stored and operatively accessible within diagnostic system10.

Each of the first and second assays has a temporal workflow schedule associated with the respective assay. In some embodiments, at step864, the diagnostic system10coordinates the schedule for performing the first assay with the schedule for performing the second assay such that use of resources of the diagnostic system is maximized. For example, the first assay schedule may require use of one of the substance transfer devices, and the second assay schedule may also require use of the same substance transfer device. Diagnostic system10can be configured to shift one or both of schedules such that once the first assay is finished with the substance transfer device, the substance transfer device can be used for the second assay. Such coordination increases throughput and minimizes processing time.

At step866, diagnostic system10performs the first assay on the first sample subset. At step868, diagnostic system10begins to perform the second assay on the second sample subset. Accordingly, diagnostic system10, which stores and provides operative access to the first unit-dose reagent used in the first assay and at least one of the second unit-dose reagent or the first bulk reagent used in the second assay, performs both steps866and868according to an embodiment. In some embodiments, step868starts while step866is being performed the diagnostic system can simultaneously perform the first assay and the second assay. In some embodiments, during steps866and868when the respective assays require a unit-dose reagent, for example, for a PCR assay, diagnostic system10verifies whether a reagent pack760containing the required reagent is positioned at one of the loading stations640. If not, the distributor system replaces a reagent pack706located at the loading station640with a reagent pack760containing the unit-dose reagent needed for the requested assay. In some embodiments, step868starts after step866is completed. And in some embodiments, although step868can start after step866, step868can be completed before step866is completed.

In some embodiments, diagnostic system10can alternate between step866and868. For example, diagnostic system10can perform the first assay on a first sample of the first sample subset, and then perform the second assay on a first sample of the second sample subset. Diagnostic system10can then switch back to step866and perform the first assay on a second sample of the first sample subset.

In some embodiments, the first assay and the second assay each comprise preparing the respective sample subsets using a second bulk reagent different than the first bulk reagent that may be used in the second nucleic acid amplification reaction. For example, each sample of the first and second sample subsets can be prepared according to process800described above referencingFIG. 41.

In some embodiments, the first sample subset and the second sample subset comprise different samples. In some embodiments, the first sample subset and the second sample subset comprise the same samples. In such embodiments, multiple assays, for example, the first and second assays explained above, are performed on the same samples.

In some embodiments, steps866and868are performed without additional equipment preparation (for example, wiping down the equipment of diagnostic system10), reagent preparation (replacing reagent battles stored in diagnostic system10), and consumable preparation (replacing empty tip trays).

Hardware and Software

Aspects of the disclosure are implemented via control and computing hardware components, user-created software, data input components, and data output components. Hardware components include computing and control modules (e.g., system controller(s)), such as microprocessors and computers, configured to effect computational and/or control steps by receiving one or more input values, executing one or more algorithms stored on non-transitory machine-readable media (e.g., software) that provide instruction for manipulating or otherwise acting on the input values, and output one or more output values. Such outputs may be displayed or otherwise indicated to an operator for providing information to the operator, for example information as to the status of the instrument or a process being performed thereby, or such outputs may comprise inputs to other processes and/or control algorithms. Data input components comprise elements by which data is input for use by the control and computing hardware components. Such data inputs may comprise positions sensors, motor encoders, as well as manual input elements, such as graphic user interfaces, keyboards, touch screens, microphones, switches, manually-operated scanners, voice-activated input, etc. Data output components may comprise hard drives or other storage media, graphic user interfaces, monitors, printers, indicator lights, or audible signal elements (e.g., buzzer, horn, bell, etc.).

Software comprises instructions stored on non-transitory computer-readable media which, when executed by the control and computing hardware, cause the control and computing hardware to perform one or more automated or semi-automated processes.

While the present disclosure has been described and shown in considerable detail with reference to certain illustrative embodiments, including various combinations and sub-combinations of features, those skilled in the art will readily appreciate other embodiments and variations and modifications thereof as encompassed within the scope of the present disclosure. Moreover, the descriptions of such embodiments, combinations, and sub-combinations is not intended to convey that the disclosure requires features or combinations of features other than those expressly recited in the claims. Accordingly, the present disclosure is deemed to include all modifications and variations encompassed within the spirit and scope of the following appended claims.