Patent Description:
Versions of systems including sample cartridges and fluidic systems for sample extraction and analysis are described in, for example, <CIT>; <CIT>; <CIT>; <CIT>; <CIT> and <CIT>; <CIT>; <CIT>;<CIT>;<CIT>;<CIT>;<CIT> and <CIT>; and International Patent Applications <CIT> and <CIT>.

<CIT> refers to a valve for use in micro fluidic structures.

<CIT> refers to a mechanically-actuated microfluidic pinch valve.

<CIT> refers to a process for producing a micro fluidic apparatus and related laminating devices.

International publication <CIT> refers to a heat weldable film for labeling plastic polymeric reaction tubes.

<CIT> refers to a microvalve and method of forming a microvalve.

<CIT> refers to microfluidic systems and methods for combining discreet fluid volumes.

<CIT> refers to integrated microfluidic control employing programmable tactile actuators.

<CIT> discloses an automated neutral marker for capillary electrophoresis.

<CIT> discloses sample preparation, processing and analysis systems.

<CIT> refers to an integrated temperature control/alignment system for use with a high performance capillary electrophoretic apparatus comprising a complementary pair of capillary column mounting plates formed from an electrically insulative, high thermal conductivity material for mounting a capillary column.

<CIT> refers to an electrophoretic method and an electrophoretic instrument therefor.

<CIT> refers to a capillary electrophoresis device.

<CIT> refers to a capillary electrophoresis apparatus.

<CIT> refers to a capillary cassette and method for manufacturing same.

<CIT> refers to optimized sample injection structures in microfluidic separations.

<CIT> refers to a system comprising an electrophoresis assembly.

<CIT> refers to a capillary electrophoresis device in which capillaries are thermally regulated on a thermally responsive electrical path attached to an electrically insulating circuit board.

<CIT> refers to an electrophoresis method and apparatus capable of maintaining high reliability upon a repeated use of the same gel.

<CIT> refers to an electrode plate of a sample plate set on the body of an electrophoretic apparatus, while a plug is inserted into a migration high voltage line connection hole and connected to a high-tension distribution cable.

<CIT> refers to a capillary electrophoresis apparatus a capillary array unit having a capillary array including capillaries having a capillary head and a detection unit, a frame for supporting the capillary array, and a load header for holding cathode ends of the capillaries.

<CIT> refers to an integrated and automated sample-to-answer system that, starting from a sample comprising biological material, generates a genetic profile in less than two hours.

<CIT> refers to methods and devices for separating and detecting nucleic acid fragments labeled with a plurality of spectrally resolvable dyes using a single light source or multiple light sources.

<CIT> shows an electrophoresis cartridge comprising an electrophoresis assembly with an electrophoresis capillary and an integrated reagent container coupled with an external pump for transferring the reagent to the electrophoresis capillary.

The present disclosure provides systems that may be used in various applications, such as sample preparation, processing and/or analysis. Also provided herein are integrated electrophoresis cartridges that can releasably engage with such systems.

In one aspect of the present invention, an electrophoresis cartridge adapted to releasably engage with a cartridge interface of a system is provided according to claim <NUM>. In some embodiments, the electromagnetic communication is wireless communication (e.g., radio frequency identification, WiFi communication or Bluetooth communication) between the system and the electrophoresis cartridge, which may be used, for example, to identify the cartridge or transmit information and/or instructions from the system to the cartridge, or vice versa.

In some embodiments, the electrophoresis cartridge further comprises an electrophoresis separation medium container for holding an electrophoresis separation medium, wherein the electrophoresis separation medium container is in fluidic communication with the anode.

In some embodiments, the electrophoresis separation medium container is contained in a cartridge that is removably insertable into the electrophoresis cartridge.

In some embodiments, the electrophoresis cartridge is engageable with the cartridge interface to place at least one sample inlet port of the electrophoresis cartridge in fluid communication with a sample outlet port of the system.

In some embodiments, the electrophoresis cartridge further comprises a fluid handling device configured to move the electrophoresis separation medium into the at least one electrophoresis capillary. In some embodiments, the fluid handling device comprises a pump.

In some embodiment, the electrophoresis cartridge further comprises a source of capillary regeneration fluid in communication with the anode sub-assembly. In some embodiments, the regeneration fluid is an inorganic fluid. In some embodiments, the regeneration fluid is an organic fluid. In some embodiments, the regeneration fluid is an alkaline fluid. In some embodiments, the regeneration fluid comprises alkali hydroxide.

In some embodiments, the electrophoresis cartridge further comprises a source of electrophoresis medium in communication with the cathode sub-assembly. In some embodiments, the electrophoresis cartridge further comprises a detection window that exposes at least a portion of the at least one electrophoresis capillary, wherein the electrophoresis cartridge is engageable with the cartridge interface to place an optical source of the system in optical communication with the detection window.

In some embodiments, the electrophoresis cartridge further comprises an electrical interface communicating with the anode and the cathode, wherein the engagement of the electrophoresis cartridge places the electrical interface in electrical communication with a power source for applying a voltage gradient between the anode and the cathode.

In some embodiments, the electrophoresis cartridge further comprises a first waste container in fluidic communication with the cathode sub-assembly. In some embodiments, the electrophoresis cartridge further comprises a second waste container in fluidic communication with the anode sub-assembly. In some embodiments, the electrophoresis cartridge further comprises a lysis buffer container in fluidic communication with a first reagent port in the cathode sub-assembly that engages ports in the system. In some embodiments, the electrophoresis cartridge further comprises a water container in fluidic communication with a second reagent port in the cathode sub-assembly that engages ports in the system.

In some embodiments, the engagement of the electrophoresis cartridge with the cartridge interface automatically establishes a plurality of the communications. In some embodiments, the engagement of the electrophoresis cartridge with the cartridge interface automatically establishes (i). In some embodiments, the engagement of the electrophoresis cartridge with the cartridge interface automatically establishes (ii). In some embodiments, the engagement of the electrophoresis cartridge with the cartridge interface automatically establishes (iii). In some embodiments, the engagement of the electrophoresis cartridge with the cartridge interface automatically establishes (iv). In some embodiments, the engagement of the electrophoresis cartridge with the cartridge interface automatically establishes (v). In some embodiments, the engagement of the electrophoresis cartridge with the cartridge interface automatically establishes (vi). In some embodiments, the engagement of the electrophoresis cartridge with the cartridge interface automatically establishes any two, three, four, five or all of (i)-(vi).

In another aspect of the present invention, a method is provided according to claim <NUM>.

In some embodiments, the method further comprises providing a voltage gradient between a first end of the at least one electrophoresis capillary having the anode and a second end of the at least one electrophoresis capillary having the cathode.

In some embodiments, the system further comprises a voltage control assembly, an optics module, at least one thermal control assembly, at least one sample outlet, and at least one fluid control assembly.

In some embodiments, the automatically establishing comprises automatically establishing at least one of (i) an electrical communication between the voltage control assembly and the anode and the cathode, (ii) a sensing communication between the optics module and the at least the portion of the at least one electrophoresis capillary, (iii) a thermal communication between the at least one thermal control assembly and the at least one electrophoresis capillary, and (iv) a fluidic communication between the at least one fluid control assembly and the at least one electrophoresis capillary.

In some embodiments, the method further comprises, with the aid of the at least one fluid control assembly, directing flow of a sample from the at least one sample outlet through the at least one electrophoresis capillary. In some embodiments, the optics module comprises a light source and an optical detection assembly. In some embodiments, the light source is laser.

In some embodiments, the method further comprises detecting with the optical detection assembly a signal from the at least the portion of the at least one electrophoresis capillary upon the flow of the sample through the at least one electrophoresis capillary. In some embodiments, the method further comprises providing an electrophoresis separation medium container for holding an electrophoresis separation medium and communicating through a fluid line with the anode. In some embodiments, the electrophoresis separation medium container is contained in a cartridge that is removably insertable into the electrophoresis cartridge.

In some embodiments, the method further comprises providing a control module that tests a robustness of the at least one communication established in (c). In some embodiments, the method further comprises removing the electrophoresis cartridge from the electrophoresis cartridge interface.

In some embodiments, the automatically establishing comprises automatically establishing at least two of (i)-(vi). In some embodiments, the automatically establishing comprises automatically establishing at least three of (i)-(vi). In some embodiments, the automatically establishing comprises automatically establishing at least four of (i)-(vi). In some embodiments, the automatically establishing comprises automatically establishing at least five of (i)-(vi). In some embodiments, the automatically establishing comprises automatically establishing all of (i)-(vi). In some embodiments, the automatically establishing is in response to user instructions provided to a control module of the system.

In some embodiments, the method further comprises, with the aid of the at least one fluid control assembly, directing flow of at least one reagent through a fluid line from the electrophoresis cartridge to the system. In some embodiments, the at least one reagent comprises a lysis buffer. In some embodiments, the at least one reagent comprises water.

In some embodiments, the method further comprises performing sample separation in the system followed by sample analysis.

In another aspect of the present invention, a system is provided according to claim <NUM>.

In some embodiments, the system further comprise a fluid handling system that moves the analyte from the sample outlet port to the at least one electrophoresis capillary when the electrophoresis cartridge is engaged with the electrophoresis cartridge interface. In some embodiments, the system further comprises a control module that is programmed to test a robustness of the at least one of the automatic communications.

In some embodiments, the automatically establishing is in response to user instructions provided to a control module of the system.

In some embodiments, the electrophoresis cartridge interface is engageable with the electrophoresis cartridge to automatically establish at least two of (i)-(vi). In some embodiments, the electrophoresis cartridge interface is engageable with the electrophoresis cartridge to automatically establish at least three of (i)-(vi). In some embodiments, the electrophoresis cartridge interface is engageable with the electrophoresis cartridge to automatically establish at least four of (i)-(vi). In some embodiments, the electrophoresis cartridge interface is engageable with the electrophoresis cartridge to automatically establish at least five of (i)-(vi). In some embodiments, the electrophoresis cartridge interface is engageable with the electrophoresis cartridge to automatically establish all of (i)-(vi).

In some embodiments, the electrophoresis cartridge interface is engageable with the electrophoresis cartridge to automatically establish a fluidic communication between at least one sample outlet of the system and the at least one electrophoresis capillary.

In some embodiments, the system further comprises a signaling mechanism that signals a user to replace the electrophoresis cartridge. In some embodiments, the system further comprises an electronic display with a user interface, wherein the user interface provides the signaling mechanism.

Additional aspects and advantages of the present disclosure will become readily apparent to those skilled in this art from the following detailed description, wherein only illustrative embodiments of the present disclosure are shown and described. As will be realized, the present disclosure is capable of other and different embodiments, and its several details are capable of modifications in various obvious respects, all without departing from the disclosure. Accordingly, the drawings and description are to be regarded as illustrative in nature, and not as restrictive.

A better understanding of the features and advantages of the present invention will be obtained by reference to the following detailed description that sets forth illustrative embodiments, in which the principles of the invention are utilized, and the accompanying drawings (also "figure" and "FIG. " herein), of which:.

While various embodiments of the invention have been shown and described herein, it will be obvious to those skilled in the art that such embodiments are provided by way of example only. Numerous variations, changes, and substitutions may occur to those skilled in the art without departing from the invention. It should be understood that various alternatives to the embodiments of the invention described herein may be employed.

As used herein, the singular form "a", "an", and "the" include plural references unless the context clearly dictates otherwise.

Whenever the term "at least" or "greater than" precedes the first numerical value in a series of two or more numerical values, the term "at least" or "greater than" applies to each one of the numerical values in that series of numerical values.

Whenever the term "no more than" or "less than" precedes the first numerical value in a series of two or more numerical values, the term "no more than" or "less than" applies to each one of the numerical values in that series of numerical values.

The term "sample", as used herein, refers to a sample containing biological material. A sample may be, e.g., a fluid sample (e.g., a blood sample) or a tissue sample (e.g., a cheek swab). A sample may be a portion of a larger sample. A sample can be a biological sample having a nucleic acid, such as deoxyribonucleic acid (DNA) or ribonucleic acid (RNA), or a protein. A sample can be a forensic sample or an environmental sample. A sample can be preprocessed before it is introduced to the system; the preprocessing can include extraction from a material that would not fit into the system, quantification of the amount of cells, DNA or other biopolymers or molecules, concentration of a sample, separation of cell types such as sperm from epithelial cells, concentration of DNA using an Aurora system (Boreal Genomics) or bead processing or other concentration methods or other manipulations of the sample. A sample can be carried in a carrier, such as a swab, a wipe, a sponge, a scraper, a piece punched out a material, a material on which a target analyte is splattered, a food sample, a liquid in which an analyte is dissolved, such as water, soda. A sample can be a direct biological sample such as a liquid such as blood, semen, saliva; or a solid such a solid tissue sample, flesh or bone.

The system provided in the present disclosure can also be applied to process and analyze a sample that has been previously preprocessed, for example, by extraction of DNA from large object such as a bed sheet or chair and other processing which may include quantification of DNA concentration, cell concentration, or other manipulations before input of the pre-processed sample into the sample cartridge of the system.

Recognized herein is the need for highly integrated and automated systems and methods for sample preparation, processing and analysis. Systems provided herein may be capable of preparing, processing and analyzing a single sample or a plurality of samples. Several operations can be performed by the system provided herein, for example, (a) receiving one or more samples; (b) isolating and extracting target material from the received sample; (c) purifying and amplifying the whole target material or selective portion of the target material to produce an analyte ready to be examined; and (d) separating, detecting and analyzing the prepared analyte. These operations can be conducted and performed in a system that comprises several integrated sub-systems, for example, at least about <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, or <NUM> sub-systems. In some cases, a system may comprise a user interface, a sample cartridge interface, and an electrophoresis interface. The sample cartridge interface and the electrophoresis interface are configured to releasably engage with a sample cartridge for sample processing, and an electrophoresis cartridge for sample analysis respectively. Systems provided herein can be fully automated, enabling a user to receive, process and analyze a sample without substantial labor and input. Sample preparation, processing and analysis can be accomplished in provided systems without the necessity of manually removing and transferring the sample, reagents and analytes among different parts in the system. Since the incorporated sub-units (e.g., sample cartridge and electrophoresis cartridge) are highly integrated and bear small sizes, systems provided herein can be dimensioned to minimize footprint, enabling the portability and usefulness in a wide context of applications. For example, the systems may be used in on-the-go situations, such as remote locations, or they may be used in situations in which transportation is not readily available or user mobility is desired, such as battlefields scenarios and crime scenes.

<FIG> shows a system for sample processing and analysis. System <NUM> can include several functional elements. System <NUM> can include a sample preparation sub-system, a sample analysis sub-system and a control sub-system.

A sample preparation sub-system of the system <NUM> can include a sample cartridge interface <NUM> configured to engage a sample cartridge <NUM>, sources of reagents for performing a biochemical protocol, a fluidics assembly configured to move reagents within the sample preparation sub-system. A fluidics assembly can include a pump, such as a syringe pump. The pump is fluidically connectable through valves to the outlets for reagents such as water and lysis buffer and to a source of air. The pump can be configured to deliver lysis buffer and water through fluidic lines <NUM> and <NUM>, respectively, to inlet port <NUM> in the sample cartridge. Air or liquid pressure applied by the pump to inlet port <NUM> can pump analyte out outlet port <NUM> and through line <NUM> into the analyte inlet in the electrophoresis cartridge.

An example sample cartridge is shown in <FIG>. Cartridge body <NUM> includes the following valve bodies: <NUM> Cycler Out (A0), <NUM> Lysis (A1), <NUM> Waste Shut Off (A3), <NUM> Waste In (A4), <NUM> Cycler In (B0), <NUM> Lysis Transfer (B1), <NUM> Product Bottom (B2), <NUM> Product Top (B3) and <NUM> Vent (B4).

The valve bodies can include various types of valves, such as valves actuated with the aid of rams described in <CIT>, and <CIT>. As an alternative, the valve bodies can include Micro-Robotic on-Chip Valve and Pump valves (MOVe), as described, for example, in <CIT> and <CIT>.

As shown in <FIG>, cartridge body <NUM> includes lysis chamber <NUM>. Cartridge <NUM> can include reagent chambers filled with, e.g., nucleic acid size standards (molecules of known sizes), PCR master mix and PCR primers, respectively, and sealed with, e.g., balls acting as closures for ball valves. When opened, the reagent chambers come into fluidic communication with fluidic channels in sample cartridge <NUM>, for example, through ports <NUM> (internal lane standard), <NUM> and <NUM> (PCR Master Mix and PCR Primer Mix). Pistons can actuate the ball valves, pushing fluids through the ports and into the channels to which they are connected. Sample cartridge <NUM> also can include inlet port <NUM> and output port <NUM>. Upon engagement with the cartridge interface, inlet port <NUM> and outlet port <NUM> each engage a fluid line. The fluid line connected to inlet port <NUM> can be attached to a pressure source, e.g., a syringe, to exert positive or negative pressure to fluidic channels via the inlet port, transporting liquids, such as lysis buffer, water or air, into or out of the cartridge. The fluid line connected to output port <NUM> can conduct analyte from the cartridge to a sub-system for analyte analysis.

In some examples, cartridge body <NUM> includes lysis chamber <NUM> and, optionally, closable cap <NUM> to close lysis chamber <NUM>. Cartridge <NUM> includes pump <NUM>. Pump <NUM> (e.g., an air pump) is configured as a chamber defined by walls of the cartridge body. Pump <NUM> is fluidically connected to at least one fluidic channel in the cartridge body. Walls of the pump comprise, at least in part, the malleable material of the cartridge body. Accordingly, the walls can be deformed, for example by mechanical force, increasing pressure in the chamber to pump liquid or air in fluidic channels in fluidic communication with the pump. Pump <NUM> can be actuated with a plunger or piston that depresses walls of pump <NUM> and forces, for example, air from the pump body through the fluidic channel to which it is connected. Pump <NUM> can be used to clear fluid from a fluidic channel. For example, in this embodiment, reagent introduced from port <NUM> into reaction chamber <NUM> may leave dead volume in channel <NUM>. Pump <NUM> can be used to pump this dead volume of reagent into reaction chamber <NUM>.

A sample analysis sub-system can include an electrophoresis assembly including an anode, a cathode and an electrophoresis capillary in electric and fluidic communication with the anode and cathode, and a sample inlet communicating between a sample outlet in the sample cartridge and an inlet to the capillary. These can be contained, e.g., within an electrophoresis cartridge <NUM>. The sample analysis sub-system can further include an optical assembly including a source of coherent light, such as laser <NUM>, an optical train, including, e.g., lenses <NUM>, and a detector, configured to be aligned with the electrophoresis capillary and to detect an optical signal, e.g., fluorescence, therein. In an example, the electrophoresis cartridge also includes a source of electrophoresis separation medium and, in some cases sources of liquid reagents, such as water and lysis buffer, delivered through outlets in the electrophoresis cartridge to the system. Separation channels for electrophoresis can take two main forms. One form is a "capillary", which refers to a long and typically cylindrical structure. Another is "microchannel", which refers to a microfluidic channel in a microfluidic device, such as a microfluidic chip or plate.

A control sub-system can include a computer <NUM> programmed to operate the system. The control sub-system can include user interface <NUM> that receives instructions from a user which are transmitted to the computer and displays information from the computer to the user. The user interface <NUM> may be as described in <CIT>.

In some cases, the control sub-system includes a communication system configured to send information to a remote server and to receive information from a remote server.

<FIG> present the system of <FIG> in further detail. As described above, a sample cartridge interface <NUM> and an electrophoresis interface <NUM> are comprised in the system, for engaging the sample cartridge and the electrophoresis cartridge. Both the sample cartridge and the electrophoresis cartridge provided herein can be releasably or removably engaged with the system. The system of <FIG> can be used in forensic analysis to decode the genetic information of a single sample. In some cases, the system may be used to determine the genetic profile of a sample in less than about <NUM> hours, <NUM> hours, <NUM> hours, <NUM> hours, <NUM> hours, <NUM> hours, <NUM> hours, <NUM> hour, <NUM> minutes, <NUM> minutes, <NUM> minutes, <NUM> minutes <NUM> minute or less. Such time may depend upon, for example, the number of steps included in sample processing operations.

A schematic of the system of <FIG> is illustrated in <FIG>. A chassis <NUM> is included for structural support, which may be formed of a metallic material, such as aluminum or steel, a polymeric material, or a combination thereof. In some cases, the chassis may be structured to minimize the weight of the system. A user interface which comprises system electronic controls <NUM>, embedded computer <NUM>, and a user interface screen capable of identifying and reading fingerprint <NUM> and sample patch barcode <NUM>, is included in the system. The user interface receives and processes requests or instructions from and delivers information to a user. It can include software programmed to execute routines for performing the operations mentioned, above, and transmit and receive information, such as computer files, from remote locations, e.g., over the internet. The user interface can also enable the user to monitor the progress of the operation and make changes to the operation of system if measurements are not within selected parameters. A sample cartridge interface <NUM> is provided for receiving a sample cartridge for sample processing. The sample cartridge described herein can be configured to receive one or more samples and to perform at least one of sample isolation, extraction, purification, amplification or dilution, when the sample cartridge is engaged with the sample cartridge interface of the system. Sample amplification can include polymerase chain reaction (PCR). One or more reagents that are needed for performing one or more steps of sample processing may be pre-loaded or comprised in the sample cartridge, for example, washing buffer, lysis buffer, diluent, or amplification reagents. Also comprised in the system is a fully integrated electrophoresis cartridge <NUM> which is releasably engageable with the system via an electrophoresis cartridge interface. The electrophoresis system comprises all essential parts for performing an electrophoretic analysis, such as an electrophoresis capillary, electrodes (e.g., anode and cathode), electrophoresis separation medium, or electrophoresis buffer. In some cases, it may comprise reagent that can be used to perform STR analysis. It may further comprise one or more reagent container for holding reagents that are used for sample processing, e.g., a lysis buffer container. The lysis buffer may be placed in fluidic communication with the sample cartridge and used for isolating the target material out of the sample during sample processing, after both the sample cartridge and the electrophoresis cartridge are engaged with the system. Once the engagement of the electrophoresis cartridge is completed, at least one automatic communication between the electrophoresis cartridge and the system may be established, for example, an electrical communication <NUM> between the electrophoresis cartridge and the system electronic controls <NUM>, an optical communication <NUM> between a portion of the electrophoresis capillary in the electrophoresis cartridge and an optics module <NUM> of the system, a fluidic communication <NUM> between a sample inlet port of the electrophoresis cartridge and a sample outlet port of the sample cartridge, a mechanical and thermal <NUM> communication between the electrophoresis cartridge and a motorized drives and cooling module <NUM> of the system.

In an example, the integrated electrophoresis cartridge <NUM> has all or substantially all of the components necessary for electrophoresis in a compact unit that is readily insertable into and removable from the electrophoresis cartridge interface. This may permit a user to readily engage the cartridge <NUM> with the system without having to open the system. In some examples, all or substantially all of the components necessary for electrophoresis (e.g., anode, cathode and at least one electrophoresis capillary are included on a single board or support or multiple boards or supports that are securably integrated with one another.

Various chemistries are commercially available to perform STR analysis and, in particular, CODIS-compatible STR analysis. These include, for example, Globalfiler® and Globalfiler® Express (<NUM>-dye, <NUM>-locus STR kit, from Life Technologies/Thermo Fisher Scientific (Grand Island, NY) (worldwide web site: lifetechnologies. com/us/en/home/industrial/human-identification/globalfiler-str-kit. html), and PowerPlex® Fusion (e.g., PowerPlex® Fusion 6C) from Promega Corporation (Madison, WI) (worldwide web site: promega. com/Products/Genetic-Identity/STR-Analysis-for-Forensic-and-Patemity-Testing/PowerPlex-Fusion-STR-Kits?utm_medium=print&utm_source=ishi_poster&utm_campaign=powerplex&utm_content =October).

The system provided herein may further comprise a power source <NUM> for supplying the power for the system, AC mains <NUM> for applying a voltage gradient across the anode and the cathode, one or more fans <NUM> for dissipate the heat for one or more parts of the system, and one or more USB ports <NUM> for collecting and transferring data either within the system or outside the system.

Also provided herein the present disclosure is the electrophoresis cartridge may comprise one or more of sub-containers or sub-cartridges that are removably insertable in the electrophoresis cartridge, such as, sub-containers for holding electrophoresis separation medium, reagents for sample processing, or reagents for sample analysis. <FIG> shows an example of an electrophoresis cartridge comprising an electrophoresis separation medium sub-container. As shown in <FIG>, an electrophoresis cartridge is manufactured to have a space <NUM> configured to specifically receive and accommodate a secondary or sub-container. A sub-container <NUM> used for holding the electrophoresis separation medium can be stored outside the electrophoresis cartridge <NUM> before the engagement of the electrophoresis cartridge with the system. The sub-container which holds the electrophoresis separation medium may be installed into the electrophoresis cartridge <NUM> a short time before the engagement of the electrophoresis cartridge with the system, for example, less than <NUM> hour, <NUM> minutes, <NUM> minutes, <NUM> minutes, <NUM> minutes, <NUM> minutes, <NUM> minutes, <NUM> minutes before engaging the electrophoresis cartridge with the system. Once the electrophoresis cartridge is installed into the system <NUM>, the sub-container may be placed in thermal communication with a thermal control module of the system, which may adjust the temperature of the sub-container to a desired value and maintain it for a period of time.

The present disclosure also provides an integrated electrophoresis cartridge for sample analysis which has a small footprint and configured to removably engage with a system for sample preparation, processing and analysis. The electrophoresis cartridge includes a capillary electrophoresis assembly which comprises an anode sub-assembly, a cathode assembly and at least one electrophoresis capillary having a first and a second end, across which a voltage gradient may be applied. The anode sub-assembly comprises a single anode or a number of anodes. The cathode sub-assembly comprises one cathode or a number of cathodes. The first and second end of the electrophoresis capillary is in communication with the anode and cathode sub-assemblies respectively.

As described herein, the term "footprint" generally refers to the horizontal surface area or the area of a surface covered when the electrophoresis cartridge is placed on that surface. In some cases, the electrophoresis cartridge can have a footprint of less than or equal to about <NUM><NUM>, <NUM><NUM>, <NUM><NUM>, <NUM><NUM>, <NUM><NUM>, <NUM><NUM>, <NUM><NUM>, <NUM><NUM>, <NUM><NUM>, <NUM><NUM>, <NUM><NUM>, <NUM><NUM>, <NUM><NUM>, <NUM><NUM>, <NUM><NUM>, <NUM><NUM>, <NUM><NUM>, <NUM><NUM>, <NUM><NUM>, <NUM><NUM>, <NUM><NUM>, <NUM><NUM>, <NUM><NUM>, <NUM><NUM>, <NUM><NUM>, <NUM><NUM>, <NUM><NUM>, <NUM><NUM>, <NUM><NUM>, <NUM><NUM>, <NUM><NUM>, <NUM><NUM>, <NUM><NUM>, <NUM><NUM>, <NUM><NUM>, <NUM><NUM>, <NUM><NUM>, <NUM><NUM>, <NUM><NUM>, <NUM><NUM>, <NUM><NUM>, <NUM><NUM>, <NUM><NUM> or <NUM><NUM>. In some cases, the electrophoresis cartridge may have a footprint between any of the two values described herein. In an example, the electrophoresis cartridge has a footprint between about <NUM><NUM> and <NUM><NUM>.

In some cases, the electrophoresis cartridge may further comprise an electrophoresis separation medium container for holding an electrophoresis separation medium and communication with at least one anode in anode sub-assembly through a fluid line. In some cases, a fluid handling device may be included in the electrophorese cartridge, with the aid of which, the electrophoresis separation medium may be moved into the at least one electrophoresis capillary. Any type of devices that is capable of moving the fluid may be used, such as valves, pumps, electrostatic fluid accelerators, and various other forms of process equipment.

The electrophoresis cartridge may also comprise a sample inlet port, which is able to receive a sample from a sample outlet port of the system and in fluid communication with at least one cathode in cathode sub-assembly and an opening of electrophoresis capillary.

<FIG> show clear shell views of an example of an electrophoresis cartridge of the present disclosure. In general, the electrophoresis cartridge may comprise a cartridge casing <NUM>, a sub-container (or sub-cartridge) casing <NUM>, an optical interface <NUM> for providing a light source and detecting signals from analytes, one or more hydrodynamic devices (e.g., fluid coupling) <NUM>, an anode sub-assembly <NUM>, a cathode sub-assembly <NUM>, an electrophoresis capillary <NUM>, an electrical interface <NUM>, one or more mechanical interfaces (e.g., <NUM>, <NUM>, <NUM> and <NUM>) for applying pressure or forces on parts of the electrophoresis cartridge, a thermal interface <NUM> for control the temperature of the sub-container <NUM>, and an electrical interface <NUM> for providing a voltage between at least one anode in the anode sub-assembly and at least one cathode in the cathode sub-assembly.

An example of the cathode sub-assembly that can be included in an electrophoresis cartridge of the present disclosure is shown in <FIG>. Three cathode nodes <NUM> are included in the cathode sub-assembly and places in electrical communication with an electrophoresis capillary port <NUM>. In some cases, the cathode nodes can be disposed in close proximity to the electrophoresis capillary port, for example, at least one cathode node is positioned opposite the electrophoresis capillary port, as shown in <FIG>. The cathode nodes may be also placed in fluidic communication with a sample inlet port <NUM>, a first reagent port <NUM>, a second reagent port <NUM> and a waste port <NUM>, through a passage of the cathode sub-assembly. The sample inlet port <NUM> may further communicate with at least one sample outlet port of the sample cartridge interface and receive the prepared sample from it. The received sample may flow though a sample line into the passage of the cathode sub-assembly and with the application of the voltage gradient, be pushed into the electrophoresis capillary. One or more reagents (e.g., electrophoresis buffer, water etc.) that may aid in performing the electrophoretic analysis may be provided and communicating with the electrodes and the electrophoresis port. A waste container is provided and in fluid communication with all other fluid ports (e.g., the sample inlet port, the electrophoresis capillary port, and the first and the second reagents ports), through the waste port and the passage of the cathode sub-assembly. Any excessive fluid or liquid leak from any one of the ports and the cathode sub-assembly may flow into the waste container and be collected.

<FIG> shows an example of the anode sub-assembly comprised in an electrophoresis cartridge of the present disclosure. The anode sub-assembly comprises an anode node <NUM> which is in electrical communication with an electrophoresis capillary port <NUM>. The anode sub-assembly may further comprise an electrophoresis separation medium port <NUM>, one or more reagent ports (<NUM> and <NUM>), and a waste port <NUM>. All these ports are in fluid communication with the anode node <NUM> and the electrophoresis capillary port <NUM>, through a passage of the anode sub-assembly. Further comprised in the anode sub-assembly are two mechanical interfaces that are in mechanical communication with the rest parts of the anode sub-assembly and aid in delivering and transferring fluid flow of the electrophoresis separation medium and the reagents among different parts of the anode sub-assembly.

In some examples, the mechanical interface may comprise a high pressure piston <NUM> that may move vertically and apply a high pressure onto the passage of the anode sub-assembly. The mechanical interface may comprise an anode main piston <NUM> which moves horizontally and is capable of relieving the pressure from the high pressure piston. The electrophoresis separation medium port <NUM> may receive an electrophoresis separation medium from the electrophoresis medium sub-container. The received electrophoresis separation medium may then be moved through a fluid line into the passage of the anode sub-assembly and placed in communication with the electrophoresis capillary port <NUM>. The high pressure piston <NUM> then moves down to apply a high pressure onto the passage and pushes the electrophoresis separation medium into at least one electrophoresis capillary via the electrophoresis capillary port <NUM>. One or more reagents (e.g., water, electrophoresis buffer) may be received via the reagent ports <NUM> and <NUM> and pumped into the electrophoresis capillary for the following sample analysis. In some cases, one of the reagent ports may be used to receive a regeneration fluid and in communication with the passage and one or more other parts of the anode sub-assembly. As described elsewhere herein, the regeneration fluid may be used to flush and rinse the electrophoresis capillary to renew or restore its function or performance, after one or more times of use. Time period and frequency for applying the regeneration fluid may vary, depending upon a number of factors. Non-limiting examples of factors may include temperature, property of regeneration fluid (e.g., viscosity), type of regeneration fluid, quantity of regeneration fluid, pressure or force used to drive the regeneration fluid, size of opening of the electrophoresis capillary, total surface area of the electrophoresis capillary to be regenerated, substances or material adsorpted on inner wall or surface of the electrophoresis capillary that needs to be removed, or combinations thereof. Any type of fluid that is capable of cleansing the inner wall or surface of the electrophoresis capillary may be used in the present disclosure. A regeneration fluid can be an organic fluid, an aqueous fluid, a non-aqueous inorganic fluid, or mixtures thereof. In some cases, a regeneration fluid may comprise one or more types of alkali hydroxide, such as LiOH, NaOH, KOH, RbOH, or CsOH. In some cases, a regeneration fluid may comprise one or more salts, such as sodium tetraborate and trisodium phosphate. In some cases, more than one type of regeneration fluid may be used in certain application. For example, following the rinse of a first regeneration fluid, a second and a third regeneration fluid may be used to further cleanse the electrophoresis capillary. In some cases, a regeneration fluid may have a high pH value, such as <NUM>. In some cases, a regeneration fluid may have a low pH value, such as <NUM>. In some cases, pH value of a regeneration fluid may vary depending on different applications.

Similar to the cathode sub-assembly, a waste container is provided to receive and collect any excess fluid or possible leak from the anode sub-assembly via the waste port <NUM> included in the anode sub-assembly.

The electrophoresis cartridge can be configured to releasably engage with a cartridge interface of a sample-profiling system. As further provided, engagement of the electrophoresis cartridge may automatically establish at least one communication between the electrophoresis cartridge and the system. Non-limiting examples of communications may include fluidic communication, electrical communication, optical communication, mechanical communication, electromagnetic communication, thermal communication, electrochemical communication, radiofrequency communication, magnetic communication and combinations thereof. Electromagnetic communication can include, for example, optical communication and/or wireless communication (e.g., radio-frequency identification (RFID), WiFi, Bluetooth). The automatic communication may be established between at least one part of the electrophoresis cartridge and at least one component of the system. For example, in some cases, an optical communication may be made between a portion of at least one electrophoresis capillary and an optics module of the system. In some examples, an electrical communication may be made between a voltage control assembly of the system and the anode and the cathode of the electrophoresis cartridge. In some cases, a fluidic communication may be established between at least one sample inlet of the electrophoresis cartridge and at least one sample outlet of the system. In some cases, one or more mechanical communication may be established between one or more mechanical interfaces of the system and the anode sub-assembly and the cathode sub-assembly of the electrophoresis cartridge.

The optics module may comprise at least one light source and one optical detector. The light source can comprise a lamp, such as an incandescent, halogen, fluorescent, gas-discharge, arc, laser, UV, or LED lamp. The light source can comprise a laser. The light source can produce a specific wavelength or range of wavelengths, including but not limited to visible light, infrared light, UV light, and combinations thereof. The light source can comprise multiple light sources, of the same or of different types, which can be used separately or in combination. In some cases, an electrical communication may be made between the electrodes (i.e., anode and cathode) and a voltage control assembly of the system. In some cases, a thermal communication may be made between at least one electrophoresis capillary and a thermal control assembly of the system. In some cases, a fluidic communication may be made between at least one electrophoresis capillary and a fluid control assembly of the system. In some cases, engagement of the electrophoresis cartridge and establishment of at least one automatic communication may occur concurrently. In some cases, engagement of the electrophoresis cartridge and establishment of at least one automatic communication may occur sequentially. For example, at least one communication may be automatically established after the electrophoresis cartridge is engaged with the system. In cases where more than one automatic communication is made, they may be made simultaneously or sequentially, or in some cases these automatic communications may be grouped and different groups of communication may occur simultaneously or sequentially. In some cases, the automatic communication is made in response to user instructions provided to a control module of the system. In some cases, the automatic communication may be triggered by some manual operation, for example, pressing a button by the user. In some cases, automatic communication is established by mechanical engagement of the cartridge with the system. For example, such engagement can place fluid conduits in into communication by sliding or snapping them into place during engagement. Automatic electrical communication can be achieved when engagement physically connects electrical terminals on both the cartridge and the interface. Automatic optical communication can occur when placement of the cartridge in the interface places a detection element, such as a capillary, in the path of an optical train of an optical assembly in the instrument. Alternatively, the system can be configured to establish communication once the system senses that the cartridge is engaged. For example, once the cartridge is engaged, the system can automatically move fluid conduits into engagement with fluid ports n the cartridge. Alternatively, one the cartridge is engaged, the system can be configured to automatically establish radio communication with the cartridge.

Once at least one automatic communication is established, it may be desirable to check or test the robustness of the communication. For example, in some cases, it may be required to check whether the automatic communication is made properly. In cases where more than one automatic communication is made, it may be useful to check the number of proper and accurate communications that have been made. Built-in circuits may be used to transform the checking results into an output signal which may subsequently be displayed on a user interface screen of the system. In some cases, each of the automatic communications may have an individual built-in circuit. In some cases, a signal built-in circuit may be used for all communications. In some cases, a number of communications may share one built-in circuit. A variety of signals may be outputted and used herein as an indicator of the checking results, e.g., audio, visual, tactile, or combinations thereof. In some cases, the outputted signal may include lights that may light up to indicate the number of accurate communications. In detail, a number of lights corresponding to each of automatic communications may be used and the number of lights that are lit off out of the total number of lights may indicate the number of communications that are inaccurately established. For example, if a total of five automatic communications are to be checked and after checking, three lights out of five are lit, then it may indicate only two automatic communications are properly established. In some instances, a numerical value may be displayed that is indicative of number of properly established communications. For example, a number may indicate that two out of five communications are made correctly. In some cases, a color may be displayed that is indicative of the proper communication. For example, a green color may indicate that the communication is accurately established. A yellow light may indicate that the communication is acceptable for further operations but not optimal, and a red light may indicate that the communication is incorrectly made and needs to be repeated. In some cases, a visual indicator such as a bar may be utilized. The quality of the communication may be indicated based on how full the bar is. In some cases, audio signals may be outputted indicating the accuracy of the communication. For example, when communication is improperly made and a fix is required, a beeping or words of warning may be produced. In some cases, the system may vibrate or provide any other type of tactile warning if the communication is not made properly.

With reference to <FIG>, a schematic of an electrophoresis cartridge <NUM> is shown. As described elsewhere herein, the electrophoresis cartridge <NUM> may comprise an electrophoresis assembly which includes an anode sub-assembly <NUM>, a cathode sub-assembly <NUM>, and at least one electrophoresis capillary <NUM> to be used in sample separation and analysis for at least one sample. In some cases, at least one capillary is one capillary or one to <NUM> capillaries. In some cases, a plurality of electrophoresis capillaries may be used for performing electrophoresis analysis on a number of samples. For example, in some cases, the plurality is less than or equal to about <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM> electrophoresis capillaries may be used. In some cases, greater than or equal to about <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM> or <NUM> electrophoresis capillaries may be used. In some cases, the number of electrophoresis capillaries may fall into a range of any of the two values described herein, for example, <NUM>.

The cathode sub-assembly can include at least about <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, or <NUM> cathode nodes. The anode sub-assembly can include at least about <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, or <NUM> anode nodes. In the illustrated example of <FIG>, three cathode nodes <NUM> are included in the cathode sub-assembly and in fluidic and electrical communication with a first end of the electrophoresis capillary. At least one anode node <NUM> is comprised in the anode sub-assembly and in fluidic and electrical communication with a second end of the electrophoresis capillary. Although presented in the present disclosure are an anode sub-assembly and a cathode sub-assembly comprising one anode node and three cathode nodes, it shall be appreciated that any number of anodes and cathodes may be used, dependent upon, different applications. For example, in some cases, equal to or less than about <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, or <NUM> anodes or cathodes may be utilized. In some cases, greater than or equal to about <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM> or <NUM> anodes or cathodes may be utilized. In some cases, the number of anodes or cathodes used in a certain application may be between any of the two values described herein, for example, <NUM>.

The electrophoresis cartridge may also comprise more than one container for holding electrophoresis separation medium and more than one reagent for sample processing and analysis. As shown in <FIG>, an electrophoresis separation medium container <NUM>, a first reagent container <NUM>, a second reagent container <NUM>, a third reagent container <NUM>, and a fourth reagent container <NUM> are included in the electrophoresis cartridge <NUM>. As provided in the present disclosure, one or more containers may be configured to be removably insertable into the electrophoresis cartridge. After each run of sample analysis is completed, one or more containers may be replaced or reused, depending upon, the applications. In some cases, it may be desirable to store or transport one or more containers at a pre-determined temperature, for example, if a thermal-sensitive electrophoresis separation medium or electrophoresis reagent is used and the trivial change of temperature may impair its performance and thereafter result in the failure of the whole analysis. In some cases, the container may be stored or transported at room temperature. In some cases, the container may be stored or transported at a high temperature. In some cases, the container may be stored or transported at a low temperature. In some cases, the container may be stored or transported at a temperature less than or equal to about <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, -<NUM>, -<NUM>, -<NUM>, -<NUM>, -<NUM>, -<NUM>, -<NUM>, -<NUM>, -<NUM>, -<NUM>, or -<NUM>. In some cases, the container may be stored or transported at a temperature greater than or equal to - <NUM>, -<NUM>, -<NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, or <NUM>. In some cases, the container may be stored or transported at a temperature between any of the two values described herein, for example, <NUM>. Once the containers are installed in the electrophoresis cartridge, they may be kept at the same or a different temperature. Installation of the containers may be realized manually or automatically.

Any type of electrophoresis separation media that may move and separate the sample with the separation channel in an electrophoretic analysis may be used herein the present disclosure. An electrophoresis separation medium can be solid, semi-solid, liquid (e.g., gel), such as organic material, natural macromolecules, synthetic or semi-synthetic polymers (e.g., linear homopolymer or block copolymer, cross-linked homopolymer or block copolymer), or combinations thereof. Non-limiting examples of electrophoresis separation media may include agarose, sucrose, cellulose acetate, starch-gel, polyacrylamide (e.g., the LPA line (including LPA-<NUM>) of separation gels (Beckman Coulter), the POP™ line (including POP-<NUM>™, POP-<NUM>™ and POP-<NUM>™) of separation polymers (Life Technologies), and a modified LPA with a self-coating polymer (e.g., LPA V2E (IntegenX Inc. )), hydroxyethylcellulose, and other biopolymers. To separate single-stranded nucleic acid fragments, denaturing gel electrophoresis can be performed using a separation polymer or gel that comprises a chemical denaturant (e.g., urea, formamide or N-methyl-pyrrolidone) or at a temperature (e.g., at least about <NUM>° C, <NUM>° C, <NUM>° C or <NUM>° C or higher) that denatures double-stranded nucleic acid fragments.

Once the electrophoresis separation medium container <NUM> is properly engaged with the electrophoresis cartridge, with the aid of a first mechanical interface <NUM> for controlling one or more fluid handling devices (e.g., a pump), the electrophoresis separation medium may be driven and moved into the anode sub-assembly <NUM>. The electrophoresis separation medium may be further pushed into at least one of the electrophoresis capillary with the application of a second and a third mechanical interface <NUM> and <NUM> by exerting a force (or pressure) on a high pressure piston <NUM> and an anode main piston (not shown).

Any suitable reagent may be used in the present disclosure. Reagents may be solid, semi-solid or liquid. In cases where liquid reagents are used, they may comprise organic fluid, inorganic fluid, or a mixture thereof. For example, reagents may comprise water, electrophoresis buffer, sample processing buffer (e.g., a lysis buffer), loading buffer, regeneration fluid, or combinations thereof. For example, reagents can be provided (e.g., stored) in an aqueous solution, or can be provided (e.g., stored) in a solid or dry (e.g., lyophilized) form and then placed into solution by addition of a liquid (e.g., an aqueous solution) as appropriate. Alternatively, reagents can be provided (e.g., stored) in a substantially water-free non-ionic organic solvent (e.g., an alcohol solvent) or in a substantially water-free ionic organic solvent (e.g., a deep eutectic solvent) and can be rehydrated by addition of an aqueous solution as appropriate, as described in <CIT>, which is entirely incorporated herein by reference. As used in the present disclosure, the term "regeneration fluid" generally refers to a fluid that is able to renew or restore the function or performance of one or more parts of the electrophoresis cartridge, for example, the electrophoresis capillary. In some cases, the regeneration fluid may comprise an aqueous solution. In some cases, the regeneration fluid may comprise an alkaline fluid. In some cases, the regeneration fluid may comprise one or more alkali hydroxides.

To collect any liquid or fluid that mat leak from, for example, an electrophoresis capillary, the anode sub-assembly, or the cathode sub-assembly, two waste containers <NUM> and <NUM> may be included in the electrophoresis cartridge and communicate with the anode-subassembly and the cathode sub-assembly, respectively. The collection capacity (e.g., volume) of the waster container may vary, dependent upon, the applications. In some cases, a high collection capacity may be desirable, for example, if a large amount of samples are to be analyzed and a large quantity of reagents is expected to be consumed. In some cases, a low collection capacity may be sufficient. In some cases, the collection capacity may be less than or equal to about <NUM> milliliter (mL), <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, or <NUM>. In some cases, the collection capacity of the waste container may be greater than or equal to about <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, or <NUM>. In some cases, the collection capacity of the waste container may be between any of the two values described herein, for example, <NUM>. Any number of water containers (e.g., at least <NUM>, <NUM>, <NUM>, <NUM>, or <NUM>) may be included in the electrophoresis cartridge, as provided in the present disclosure. For example, besides the waste containers that are in communication with the anode sub-assembly and cathode sub-assembly, each of the reagent containers and the electrophoresis separation medium container may be provided with its water container.

In some aspects of the present disclosure, the electrophoresis cartridge may further comprise a plurality of fluid handling devices which place various parts or components of the electrophoresis cartridge in fluidic communication. As described above and elsewhere herein, any type of devices that is capable of moving or transferring the fluid may be used, such as valves, pumps, electrostatic fluid accelerators, and various other forms of process equipment. As shown in <FIG>, pumps <NUM> and <NUM> are used to drive the reagents stored in the first and the second reagent containers <NUM> and <NUM> to the anode sub-assembly <NUM>, through their respective fluid conduits. Similarly, pumps <NUM> and <NUM> are utilized to transfer the reagents kept in the second and the third reagent containers <NUM> and <NUM> to the cathode sub-assembly <NUM>, through two separate fluid conduits.

In some cases, it may be desirable that at least one of the reagent containers communicate with more than one part of the electrophoresis cartridge or the system. For example, as illustrated in <FIG>, the second and the third reagent containers <NUM> and <NUM> are placed in communication with parts outside of the electrophoresis cartridge, besides their communication with the cathode sub-assembly <NUM> of the electrophoresis cartridge as described above. In detail, both of the reagent containers are in fluidic communication with the sample cartridge interface <NUM> and a fluid handling device <NUM> through a fluid line. A four-port valve <NUM> and a three-port valve <NUM> are utilized to direct, control and regulate different types of fluid flow in the fluid line. Alternatively or additionally, it may be advantageous to have one or more reagent containers installed inside the electrophoresis cartridge while communicate only with parts or components which are outside of the electrophoresis cartridge. For example, in the present example as shown in <FIG>, a fourth reagent container <NUM> is engaged with the electrophoresis cartridge and placed in fluidic communication with the sample cartridge interface <NUM> through a fluid line. In some cases, one or more hydrodynamic devices (e.g., fluid couplings <NUM>, <NUM> and <NUM>) may be included in the electrophoresis cartridge which may aid in delivering and transferring the reagents, analytes or samples through the fluid line.

The electrophoresis cartridge may also comprise a sample delivery assembly comprising at least one sample inlet port and at least one sample line, with each sample line placing a sample inlet port in communication with the first end of the electrophoresis capillary through a passage in the cathode sub-assembly. The sample inlet port may be further configured to communicate with a sample outlet port comprised in a sample cartridge interface <NUM>, via a hydrodynamic device <NUM>, for example, a fluid coupling or a hydraulic coupling. With the sample delivery assembly, the processed sample from a sample cartridge that is engaged with the sample cartridge interface may be directed to a separation channel (e.g., an electrophoresis capillary), via the sample line. Any suitable method for moving the prepared sample into the separation channel may be used in the context of the present disclosure. For example, field-amplified stacking (FAS) may be performed by positioning in an electrophoresis sample line a diluted mixture comprising the sample of lower salt concentration or lower ionic strength between areas comprising an electrophoresis buffer of higher salt concentration or higher ionic strength. In another example, a bolus of a material (e.g., air) can be positioned downstream of the sample in the sample line, wherein the material has an electrical conductivity that differs from the electrical conductivity of the electrophoresis buffer or the sample. When the sample is positioned across the separation channel, the sample can be electrokinetically injected into the separation channel at an appropriate voltage (e.g., about <NUM> kV to about <NUM> kV, or about <NUM> kV) over an appropriate amount of time (e.g., about <NUM> sec to about <NUM> sec, or about <NUM> sec). In some other examples, a pump may be used to drive the sample into the separation channel. In one embodiment, the capillary can be inserted into the sample line so that sample flows across the opening to the capillary. In another embodiment, the sample line can be co-axial with the electrophoresis capillary.

Once the prepared sample is moved into the separation channel, the sample may then be subjected to sample separation and analysis within the separation channel, with the aid of an electric field, as can be generated upon the application of a voltage gradient across the anode <NUM> and the cathode <NUM>. Upon the effect of the electric field, analytes in the electrophoresis capillary move through the matrix (i.e., electrophoresis separation medium) at different rates, determined by one or more factors, such as mass, charge, or a combination thereof.

A portion of the electrophoresis capillary can be used as an optical window <NUM> which is capable of receiving a light from a light source and emitting signals that can be captured and detected by one or more detectors included in a detection assembly. In some cases, an optics module may be provided, which may comprise both the light source and the detection assembly. The light source is positioned to deliver a beam to at least one electrophoresis capillary via the optical window. One or more optical detectors (e.g., charge-coupled device (CCD), complementary metal-oxide-semiconductor (CMOS), photodetector, photo diode, or photomultiplier detector) may be optically coupled to receive signals emitted from at least one electrophoresis capillary through the optical window. As discussed elsewhere in the present disclosure, the optical communication between the optical window in the electrophoresis cartridge and both the light source and the optics module may be automatically established at the same time as the occurrence of the engagement of the electrophoresis cartridge. In one embodiment, the capillary can be movably supported by a compliant member, which can be spring-biased toward the optics assembly. The optics module in the system physically engages the compliant member causing rough lateral alignment of the capillary with the optics. Features on the engagement assembly of the optics module, when engaging the compliant member, can provide fine alignment through movement of the capillary across the compliant member.

The capillary can be thermally regulated, e.g., heated, to maintain an appropriate running temperature. The capillary can be heated by, for example, flowing temperature-controlled air over the capillary, by placing the capillary in thermal contact with a thermoelectric heater (e.g., a Peltier), or by placing the capillary in thermal contact with a resistive heater. An example of an assembly using a resistive heater to heat a capillary is described in <CIT>. In another embodiment, a capillary heater assembly can comprise a flexible heater circuit comprising a resistive heater (e.g., a wire trace) in a polymeric substrate. Such flexible heater circuits are commercially available from Mod-Tronic (Thermofoil®), Kapton (polyimide heater) and McMaster-Carr (ultrathin heat sheet). One embodiment of a capillary thermal regulating assembly includes the following elements: A capillary is sandwiched between hook and loop layers of a fabric hook-and-loop fastener (e.g., a Velcro® strip). A resistive heater, such as a nicrome wire, is placed in thermal contact with the capillary through one of the fabric layers, e.g., placed in physical contact an external surface of the layer. This assembly can be supported by a thermal spreader, such as graphite, e.g., flexible graphite. In another embodiment, the capillary is sandwiched between two strips of a thermal conductive gel, such as Thermacool TC3008 (Saint Gobain, Courbevoie, France). This sandwich is, in turn, sandwiched between heat spreaders, such as a graphite film (e.g., KERATHERM® Graphite Film, Kerafol, Eschenbach, Germany). This sandwich, in turn, is sandwiched between strip heaters (e.g., Kapton).

After each cycle of sample processing and analysis is completed, it is not necessary to replace and discard the electrophoresis cartridge. Provided herein the present disclosure are electrophoresis cartridges that can be reusable for at least <NUM> times, <NUM> times, <NUM> times, <NUM> times, <NUM> times, <NUM> times, <NUM> times, <NUM> times, <NUM> times, <NUM> times, <NUM> times, <NUM> times, <NUM> times, <NUM> times, <NUM> times, <NUM> time, <NUM> time, <NUM> times, <NUM> times, <NUM> times, <NUM> times, <NUM> times, <NUM> times, <NUM> times, <NUM> times, <NUM> times, <NUM> times, <NUM> times, or <NUM> times. As discussed elsewhere herein, a regeneration fluid is included in the electrophoresis cartridge and used to flush and rinse the electrophoresis capillary after each time of use.

Also provided in the present disclosure are methods for preparing, processing and analyzing a genetic material comprising sample with systems described herein. In general, the method may comprise: (a) providing a system comprising an electrophoresis cartridge interface that releasably engages with an electrophoresis cartridge comprising (<NUM>) an anode sub-assembly comprising an anode, (<NUM>) a cathode sub-assembly comprising a cathode, and (<NUM>) at least one electrophoresis capillary that is in fluid communication with the anode and the cathode; (b) receiving the electrophoresis cartridge at the electrophoresis cartridge interface; (c) automatically establishing at least one of (i) an optical communication between an optical detection assembly of the electrophoresis system and a portion of the at least one electrophoresis capillary, (ii) an electrical communication between the system and the anode and the cathode, (iii) a fluidic communication between the system and the at least one electrophoresis capillary, (iv) a thermal between the system and the electrophoresis cartridge or the at least one electrophoresis capillary, and (v) a magnetic communication between the system and the electrophoresis cartridge; (d) providing a voltage gradient between a first end of the at least one electrophoresis capillary communicating with the anode and a second end of the at least one electrophoresis capillary communicating with the cathode.

In some cases, the system may further comprise a voltage control assembly (e.g., a power source) which is capable of applying a voltage gradient across the anode and the cathode, at least one thermal control assembly, at least one sample outlet, an optics module, and at least one fluid control assembly. The optics module may comprise a light source and a detection assembly comprising one or more optical detectors. The fluid control assembly may comprise a fluid container for holding one or more of reagents or fluid that are necessary for sample preparation, processing and analysis, and at least one fluid handling device that is capable of moving the fluid within the electrophoresis cartridge or the system.

In some cases, the automatically established communication comprises at least one of (i) an electrical communication between the voltage control assembly and the anode and the cathode, (ii) a sensing communication between the optics module and at least a portion of the electrophoresis capillary, (iii) a thermal communication between at least one thermal control assembly and the electrophoresis capillary, (iv) a first fluidic communication between at least one sample outlet and the electrophoresis capillary, and (v) a second fluid communication between at least one fluid control assembly and the electrophoresis capillary.

As discussed elsewhere herein, engagement of the electrophoresis cartridge and establishment of at least one automatic communication may occur concurrently or sequentially. For example, at least one communication may be automatically established after the electrophoresis cartridge is engaged with the system. In cases where more than one automatic communication is made, they may be made simultaneously or sequentially. In some cases, these automatic communications may be grouped and different groups of communication may occur simultaneously or sequentially. In some cases, the automatic communication is made in response to user instructions provided to a control module of the system. In some cases, the automatic communication may be triggered by some manual operation, for example, pressing a button by the user.

The sample cartridges of this disclosure can be used in an integrated system for preparing a sample, for example, DNA isolation and amplification. For example, in one example (<FIG>), a sample contained on for example a swab or a card punch, can be introduced into sample chamber <NUM>. The cartridge can be engaged with sample cartridge interface <NUM>. Cell lysis buffer contained in an off-chip reservoir can be feed through port <NUM> into the fluidic channel in the cartridge and into the sample chamber <NUM> by closing valves <NUM>, <NUM>, <NUM>, and <NUM>. Port <NUM> can be connected to a syringe or to another source of positive or negative pressure. After lysis, lysate can be moved through a fluidic channel on the cartridge, for example, with a plunger that applied vacuum through port <NUM> to draw the fluid into reaction chamber <NUM> by opening valves <NUM>, <NUM>, <NUM>, and <NUM>; and closing valves <NUM>, <NUM>, <NUM>, <NUM>, and <NUM>. In one embodiment, the DNA reaction chamber can include material that captures a pre-determined amount of analyte. Excess fluid can be moved into waste chamber <NUM> while the reaction chamber is filled. Reagents for performing PCR or other reactions can be introduced into the reaction chamber through ports <NUM> and <NUM>. In one embodiment, as detailed in U. Patent Application Publication No. <CIT> and International Patent Application Publication No. <CIT>, an actuator pushes on ball valves (not shown), to push the master mix in port <NUM> and the primers in port <NUM> into reaction chamber <NUM>. A thermal control mechanism in the system can apply heat to perform thermal cycling in reaction chamber <NUM> of the cartridge with valves <NUM> and <NUM> closed. Following thermal cycling, valves <NUM>, <NUM>, <NUM> and <NUM> are opened and valves <NUM>, <NUM>, <NUM>, <NUM>, <NUM> are closed, and internal lane standard is dispensed from port <NUM> into reaction chamber <NUM> and pushed into mix chamber <NUM>. Following mixing, valves <NUM>, <NUM>, <NUM>, <NUM> are closed; valves <NUM> and <NUM> are opened and the amplified STR mixture with internal lane standard is pushed to through port <NUM> to a capillary electrophoresis analysis module for separation, detection, and analysis.

In some cases, cartridges of this disclosure can be used to perform DNA amplification and subsequent preparation for cycle sequencing. The target for sequencing can be, for example, a diagnostic target, such as a gene for genotyping, a polynucleotide bearing a somatic mutation, e.g., from a tumor, or a polynucleotide from an infectious microorganism such as a bacterium or a virus.

An exemplary cartridge <NUM> for such an embodiment is shown in <FIG>. Cartridge <NUM> has input <NUM>. A sample <NUM> can be introduced into sample chamber <NUM>. The cartridge can be engaged with an interface of instrument <NUM> configured to supply reagents and motive forces. Cell lysis buffer contained in an off-chip reservoir <NUM> can be fed through port <NUM> into a fluidic channel in the cartridge and into the sample chamber <NUM> by opening valve <NUM>. Port <NUM> can be connected to a syringe <NUM> or to another source of positive or negative pressure.

After lysis, lysate can be moved through a fluidic channel on the cartridge into isolation chamber <NUM> by opening valve <NUM>; if required vacuum can be applied by syringe <NUM> by opening valve <NUM>. Magnetically responsive particles, e.g., beads <NUM>, can be introduced into the isolation chamber before or after introduction of the lysate by opening valve <NUM>. In another embodiment, the beads can be preloaded into isolation chamber <NUM>. Polynucleotides can be captured on the particles and immobilized by application of a magnetic force to the isolation chamber <NUM> by magnetic actuator <NUM>. The particles can be washed with, e.g., ethanol <NUM>, and the wash moved to a waste chamber on cartridge (not shown) or off-cartridge <NUM>.

Then the polynucleotides can be moved into a reaction chamber <NUM> for PCR by opening valve <NUM>. Reagents for amplifying a specific nucleotide sequence can be introduced into the reaction chamber from sealed compartments through ports <NUM> and <NUM> or these sealed compartments can contain the reagents in an integrated vial with seals by for example Teflon balls. These include primers, nucleotides, and hot start DNA polymerase. Primers are typically kept separate in a "primer mix" from the other ingredients, mixed as "master mix". A thermal control mechanism in the system, e.g., thermal cycler <NUM>, can apply heat to perform thermal cycling in reaction chamber <NUM> of the cartridge. Following thermal cycling, remaining primers and nucleotide triphosphates can be degraded by adding, for example, exonuclease I and shrimp alkaline phosphatase from a sealed compartment through port <NUM>. Following reaction, the exonuclease I and shrimp alkaline phosphatase can be degraded by heating to <NUM> by thermal cycler <NUM>.

Reagents for performing cycle sequencing can then be introduced into the reaction chamber, for example, from sealed compartments on the cartridge through ports <NUM> and <NUM>. These include a sequencing primer, nucleotides, hot start DNA polymerase, and labeled dideoxynucleotides (e.g.BigDye® terminators form Life Technologies ®) for dye terminator sequencing. Primers are typically kept separate in a "primer mix" from the other ingredients, mixed as "master mix". Thermal cycling produces dideoxynucleotide-terminated polynucleotides with base specific fluorescent label.

This mixture can then be moved back into isolation chamber <NUM>. Magnetically responsive particles can be introduced into isolation chamber <NUM> for polynucleotide capture and clean up.

Cleaned up polynucleotides can then be pushed, e.g., with air <NUM> through output port <NUM> to a capillary electrophoresis analysis module for separation, detection, and analysis.

In some cases, some or all reagents are stored in compartments on the cartridge for movement into the fluidic circuit as needed.

Another example of a sample cartridge configured to perform this method is depicted in <FIG> and <FIG>. Cartridge <NUM> includes inlet <NUM>, pressure port <NUM>, lysis chamber <NUM>, filter chamber <NUM>, isolation chamber <NUM>, reaction chamber <NUM>, magnetically attractable beads <NUM> in the reaction chamber, ports <NUM> and <NUM> for PCR reagents, ports <NUM> and <NUM> for cycle sequencing reagents, exit port <NUM>, and valves <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM> and <NUM>. The cartridge aspect in <FIG> shows ports <NUM> and <NUM>, as well as open compartments for ports <NUM>, <NUM>, <NUM>, <NUM> and <NUM>.

In some cases, a sample cartridge of this disclosure has a fluidic circuit with a plurality of branches, each branch adapted to perform a separate biochemical reaction. For example, each of two branches can be used to perform one of forward and reverse strand cycle sequencing on a sample. The forward strand can be prepared for sequencing in a first branch and the reverse strand can be prepared for sequencing in a second branch. Alternatively, different branches can be used to amplify different target nucleotide sequences from the same sample.

An exemplary cartridge <NUM> for such an embodiment is shown in <FIG>. Cartridge <NUM> has input <NUM>. A sample <NUM> can be introduced into sample chamber <NUM>. The cartridge can be engaged with an interface of instrument <NUM> configured to supply reagents and motive forces. Cell lysis buffer contained in an off-chip reservoir <NUM> can be fed through port <NUM> into a fluidic channel in the cartridge and into the sample chamber <NUM> by opening valve <NUM>. The lysis solution can be compatible with particles used to capture polynucleotides. Port <NUM> can be connected to a syringe or to another source of positive or negative pressure.

After lysis, lysate can be moved through a fluidic channel on the cartridge into isolation chamber <NUM> by opening valve <NUM>. Magnetically responsive particles, e.g., beads <NUM>, can be introduced into the isolation chamber before or after introduction of the lysate by opening valve <NUM>. Polynucleotides can be captured on the particles and immobilized by application of a magnetic force to the isolation chamber <NUM> by magnetic actuator <NUM>. The particles can be washed with, e.g., ethanol <NUM>, and the wash moved to a waste chamber or off-cartridge <NUM>.

Then, aliquots of the polynucleotides can be moved into reaction chambers 2240a-c for PCR by opening valves 2222a-c. This can be done, for example, by opening and closing these valves sequentially, and moving material into each open chamber. Reagents for amplifying a specific nucleotide sequence can be introduced into the reaction chamber from sealed compartments or may be present in lyophilized form. A thermal control mechanism in the system, e.g., thermal cycler <NUM>, can apply heat to perform thermal cycling in reaction chamber <NUM> of the cartridge.

Following thermal cycling, the products can be moved into chambers 2250a-c by opening valves 2242a-c. Here, primers and nucleotide triphosphates are degraded by, for example, exonuclease I and shrimp alkaline phosphatase present in lyophilized form or added from a sealed compartment. Following reaction, the exonuclease I and shrimp alkaline phosphatase can be degraded by heating to <NUM> by thermal cycler <NUM>.

The samples are then moved into reaction chambers 2250a-c by opening valves 2251a-c for preparation for cycle sequencing. Again, reagents for performing cycle sequencing can be introduced into the reaction chamber, for example, from sealed compartments on the cartridge or may be present in lyophilized form. Thermal cycling produces dideoxynucleotide-terminated polynucleotides with base specific labels.

The product of the thermal cycling reactions is then moved into clean-up chambers 2254a-c by opening valves 2253a-c. Magnetically responsive particles can be introduced into clean-up chambers 2254a-c for polynucleotide capture and clean up.

Cleaned up polynucleotides can then be pushed, e.g., with air <NUM> through output ports 2223a-c by opening valves 2255a-c to a capillary electrophoresis analysis module for separation, detection, and analysis.

In some cases, sample cartridges of this disclosure include a DNA quantification function. Such a function can be useful to meter an amount of DNA for amplification determined appropriate for down-stream applications such as STR amplification.

Then, a predetermined amount of the particles with captured DNA can be moved into a reaction chamber <NUM> by opening valve <NUM>. Magnetic actuator <NUM> immobilizes the beads in reaction chamber <NUM>. Human-specific qPCR reagents, such as Quantifiler from Thermo Fisher Scientific™ or Plexor HY System from Promega™, are introduced into the reaction chamber from sealed compartments through ports <NUM> and <NUM>. A thermal control mechanism in the system, e.g., thermal cycler <NUM>, can apply heat to perform thermal cycling in reaction chamber <NUM> of the cartridge for qPCR. A detection device <NUM>, e.g., using illumination, determines the course of the reaction. This information is used to determine how much DNA is captured per unit bead volume. The amount of beads necessary to carry the predetermined quantity of DNA needed is calculated.

Material in reaction chamber <NUM> can then be pushed, e.g., with air, <NUM> through output port <NUM>.

Next, a volume of beads from isolation chamber <NUM> determined to carry the desired amount of DNA is moved into reaction chamber <NUM>. Reagents for performing PCR can then be introduced into the reaction chamber, for example, from sealed compartments on the cartridge through ports <NUM> and <NUM>, and the reaction thermal cycled.

Internal ladder standard <NUM> can then be pushed, e.g., with air <NUM> through output port <NUM> to a capillary electrophoresis analysis module for separation, detection, and analysis.

The cartridges of this disclosure can be used in an integrated system for analyzing a sample, for example, DNA isolation and amplification with real time or end point detection. For real time measurement, the samples can be interrogated by an optical detection system while amplifying in reaction chamber <NUM>. The readout can be the change in fluorescence or by melting point. The probes can be human specific for human identification, forensics, or molecular diagnostic applications, or specific for pathogens for molecular diagnostic applications, or for bioagents for biodefense applications or nonspecific intercalators for determining the amount of DNA present. Amplification methods include, for example, thermal or isothermal amplification reactions, for example, PCR, rolling circle amplification, whole genome amplification, nucleic acid sequence-based amplification, and single strand displacement amplification, single primer isothermal linear amplification (SPIA), loop-mediated isothermal amplification, ligation-mediated rolling circle amplification and the like.

The sample cartridges of this disclosure can be used in an integrated system for analyzing a sample. The assay can detect a polypeptide (e.g., immunoassay) or a nucleic acid (e.g., PCR or reverse transcriptase followed by amplification). To detect an immunoassay, after lysis of the sample and movement of the lysed sample to reaction chamber <NUM>, ports <NUM> and <NUM> can be used to add primary and secondary antibodies to the sample. The detection can be in sample chamber <NUM> or the sample can be moved through port <NUM> to a detector.

The assay can be multiplex or single analyte. They can involve any assay to measure the presence, amount, activity, or other characteristics of the sample. These include assays that involve detection by fluorescence, luminescence, chemiluminescence, absorbance, reflectance, transmittance, birefringence, refractive index, colorimetric, and combinations thereof. In this instant disclosure, the enzyme master mix and the substrate might be individually added to the reaction and the progress or endpoint of the assay monitored optically.

In some cases, sample cartridges of this disclosure can be used to prepare samples for additional analytical devices. Analytical methods can include sequencing, chromatography, (e.g., gas or size exclusion) electrometry, ellipsometry, refractrometry, interferometry (e.g., back scattering interferometry), spectrometry (e.g., mass spectrometry, NMR spectrometry, Raman spectroscopy, Surface-enhanced Raman Spectroscopy), surface plasmon resonance. Sequencing methods can include high-throughput sequencing, pyrosequencing, sequencing-by-synthesis, single-molecule sequencing, nanopore sequencing, semiconductor sequencing, sequencing-by-ligation, sequencing-by-hybridization, RNA-Seq (Illumina), Digital Gene Expression (Helicos), Next generation sequencing, Single Molecule Sequencing by Synthesis (SMSS)(Helicos), massively-parallel sequencing, Clonal Single Molecule Array (Solexa), shotgun sequencing, Maxim-Gilbert sequencing, Sanger sequencing, primer walking, sequencing using PacBio, SOLiD, Ion Torrent, or Nanopore platforms.

For STR applications, after thermal cycling, other reagents such as molecular weight markers (size standards) can be combined with the PCR product. Products of the PCR can be moved off chip for analysis through an output line connected to port <NUM> (sample out).

In cases where the reaction is a short tandem repeat (STR) reaction, in some jurisdictions for casework samples, the amount of human DNA may need to be quantified. The typical forensic process is to quantify an extracted sample using real time polymerase chain reaction (PCR) in a separate instrument before the sample is STR amplified. In this instant disclosure, a human specific probe is added to the STR mixture which has fluorescence outside the range used by the STR kit. The reaction chamber <NUM> is interrogated by a suitable wavelength of light for the human specific probe while the STR is being PCR amplified. The human specific probe can be a quencher such as a Black Hole Quencher® or a TaqMan® probe or other chemistries well know to one skilled in the art. As the PCR cycles increase, the fluorescence from the human specific probe is monitored to quantify the amount of human DNA in the reaction. In a preferred embodiment, the number of amplification cycles can be adjusted based upon the amount of human DNA measured; this can be on a cartridge-by-cartridge monitoring if independent thermal cyclers are in use. One advantage is that the human specific probe will allow the concurrent STR amplification to achieve an optimal amplification and produce an amount of STR product that is optimal for the kit. A second advantage is the real time monitoring concurrent with the STR amplification allows integration of a sample-to-answer system without having an additional separate quantification process. A third advantage is for low copy number samples where there is barely enough sample to produce a good STR profile the integration of the quantification with the STR amplification prevents the aliquot typically used for quantification from causing the remaining sample to not have enough DNA for a good STR amplification.

The present disclosure provides computer control systems that are programmed to implement methods of the disclosure. <FIG> shows a computer system <NUM> that is programmed or otherwise configured to facilitate sample preparation, processing and/or analysis. The computer system <NUM> can regulate various aspects of sample preparation, processing and/or analysis of the present disclosure, such as, for example, engaging an electrophoresis cartridge with an electrophoresis interface of a system for sample preparation, processing and/or analysis (see, e.g., <FIG>). The computer system <NUM> can be integrated with such system.

The computer system <NUM> includes a central processing unit (CPU, also "processor" and "computer processor" herein) <NUM>, which can be a single core or multi core processor, or a plurality of processors for parallel processing. The computer system <NUM> also includes memory or memory location <NUM> (e.g., random-access memory, read-only memory, flash memory), electronic storage unit <NUM> (e.g., hard disk), communication interface <NUM> (e.g., network adapter) for communicating with one or more other systems, and peripheral devices <NUM>, such as cache, other memory, data storage and/or electronic display adapters. The memory <NUM>, storage unit <NUM>, interface <NUM> and peripheral devices <NUM> are in communication with the CPU <NUM> through a communication bus (solid lines), such as a motherboard. The storage unit <NUM> can be a data storage unit (or data repository) for storing data. The computer system <NUM> can be operatively coupled to a computer network ("network") <NUM> with the aid of the communication interface <NUM>. The network <NUM> can be the Internet, an internet and/or extranet, or an intranet and/or extranet that is in communication with the Internet. The network <NUM> in some cases is a telecommunication and/or data network. The network <NUM> can include one or more computer servers, which can enable distributed computing, such as cloud computing. The network <NUM>, in some cases with the aid of the computer system <NUM>, can implement a peer-to-peer network, which may enable devices coupled to the computer system <NUM> to behave as a client or a server.

The CPU <NUM> can execute a sequence of machine-readable instructions, which can be embodied in a program or software. The instructions may be stored in a memory location, such as the memory <NUM>. The instructions can be directed to the CPU <NUM>, which can subsequently program or otherwise configure the CPU <NUM> to implement methods of the present disclosure. Examples of operations performed by the CPU <NUM> can include fetch, decode, execute, and writeback.

The CPU <NUM> can be part of a circuit, such as an integrated circuit. One or more other components of the system <NUM> can be included in the circuit. In some cases, the circuit is an application specific integrated circuit (ASIC).

The storage unit <NUM> can store files, such as drivers, libraries and saved programs. The storage unit <NUM> can store user data, e.g., user preferences and user programs. The computer system <NUM> in some cases can include one or more additional data storage units that are external to the computer system <NUM>, such as located on a remote server that is in communication with the computer system <NUM> through an intranet or the Internet.

The computer system <NUM> can communicate with one or more remote computer systems through the network <NUM>. For instance, the computer system <NUM> can communicate with a remote computer system of a user (e.g., operator). Examples of remote computer systems include personal computers (e.g., portable PC), slate or tablet PC's (e.g., Apple® iPad, Samsung® Galaxy Tab), telephones, Smart phones (e.g., Apple® iPhone, Android-enabled device, Blackberry®), or personal digital assistants. The user can access the computer system <NUM> via the network <NUM>.

Methods as described herein can be implemented by way of machine (e.g., computer processor) executable code stored on an electronic storage location of the computer system <NUM>, such as, for example, on the memory <NUM> or electronic storage unit <NUM>. The machine executable or machine readable code can be provided in the form of software. During use, the code can be executed by the processor <NUM>. In some cases, the code can be retrieved from the storage unit <NUM> and stored on the memory <NUM> for ready access by the processor <NUM>. In some situations, the electronic storage unit <NUM> can be precluded, and machine-executable instructions are stored on memory <NUM>.

The code can be pre-compiled and configured for use with a machine have a processer adapted to execute the code, or can be compiled during runtime. The code can be supplied in a programming language that can be selected to enable the code to execute in a pre-compiled or as-compiled fashion.

Aspects of the systems and methods provided herein, such as the computer system <NUM>, can be embodied in programming. Various aspects of the technology may be thought of as "products" or "articles of manufacture" typically in the form of machine (or processor) executable code and/or associated data that is carried on or embodied in a type of machine readable medium. Machine-executable code can be stored on an electronic storage unit, such memory (e.g., read-only memory, random-access memory, flash memory) or a hard disk. "Storage" type media can include any or all of the tangible memory of the computers, processors or the like, or associated modules thereof, such as various semiconductor memories, tape drives, disk drives and the like, which may provide non-transitory storage at any time for the software programming. All or portions of the software may at times be communicated through the Internet or various other telecommunication networks. Such communications, for example, may enable loading of the software from one computer or processor into another, for example, from a management server or host computer into the computer platform of an application server. Thus, another type of media that may bear the software elements includes optical, electrical and electromagnetic waves, such as used across physical interfaces between local devices, through wired and optical landline networks and over various air-links. The physical elements that carry such waves, such as wired or wireless links, optical links or the like, also may be considered as media bearing the software. As used herein, unless restricted to non-transitory, tangible "storage" media, terms such as computer or machine "readable medium" refer to any medium that participates in providing instructions to a processor for execution.

Hence, a machine readable medium, such as computer-executable code, may take many forms, including but not limited to, a tangible storage medium, a carrier wave medium or physical transmission medium. Non-volatile storage media include, for example, optical or magnetic disks, such as any of the storage devices in any computer(s) or the like, such as may be used to implement the databases, etc. shown in the drawings. Volatile storage media include dynamic memory, such as main memory of such a computer platform. Tangible transmission media include coaxial cables; copper wire and fiber optics, including the wires that comprise a bus within a computer system. Carrier-wave transmission media may take the form of electric or electromagnetic signals, or acoustic or light waves such as those generated during radio frequency (RF) and infrared (IR) data communications. Common forms of computer-readable media therefore include for example: a floppy disk, a flexible disk, hard disk, magnetic tape, any other magnetic medium, a CD-ROM, DVD or DVD-ROM, any other optical medium, punch cards paper tape, any other physical storage medium with patterns of holes, a RAM, a ROM, a PROM and EPROM, a FLASH-EPROM, any other memory chip or cartridge, a carrier wave transporting data or instructions, cables or links transporting such a carrier wave, or any other medium from which a computer may read programming code and/or data. Many of these forms of computer readable media may be involved in carrying one or more sequences of one or more instructions to a processor for execution.

The computer system <NUM> can include or be in communication with an electronic display <NUM> that comprises a user interface (UI) <NUM>, for example, for enabling the user to instruct the computer system <NUM> to begin sample preparation, processing and/or analysis. Examples of UI's include, without limitation, a graphical user interface (GUI) and web-based user interface. The user interface <NUM> may be as described in <CIT>, which is entirely incorporated herein by reference.

Methods and systems of the present disclosure can be implemented by way of one or more algorithms. An algorithm can be implemented by way of software upon execution by the central processing unit <NUM>. The algorithm can, for example, implement the general operation of a system for sample preparation, processing and/or analysis. In some examples, the algorithm can regulate the sequential opening and closing of valves or the operation of an electrophoresis cartridge.

The sample cartridge is a polypropylene molding with an integrated syringe barrel and sample chamber with a polyethylene heat seal over the area of the fluidics. There is an absorbent material in the waste chamber and a small dot of capture material in the reaction chamber. The barrel is loaded with a quantity of lysis solution (<NUM>-1000µL) isolated between two rubber plungers. There are three reagent vessels on the chip that seal with top and bottom Teflon balls; two for the two parts of the Global Filer mastermix/primer which are loaded with <NUM>-10µL of solution and one containing a water/ILS solution that is used as a diluent before transfer to the cathode.

Another protocol, performed on cartridge <NUM>, includes the following steps. Valve configurations are shown in <FIG>.

Another protocol, performed on cartridge of <FIG>, includes the following steps. All valves begin in open configuration.

This example shows a method to perform cycle sequencing on a nucleic acid. (Refer to <FIG>.

Perform PCR amplification (make enough of target region to sequence; if multiple regions are being sequenced, the sample had to be split or parallel samples for each loci).

ExoI/SAP (destroys PCR primers and nucleotide triphosphates).

Cleanup cycle sequencing products using paramagnetic beads.

Send products to capillary electrophoresis.

This example shows a method to perform amplification of markers, e.g., diagnostic markers, followed by cycle sequencing of the amplification product. (Refer to <FIG>.

Destroy PCR primers and nucleotide triphosphases.

This example shows a method to quantify amount of human DNA before STR amplification for human identification or diagnostic fragment sizing (Refer to <FIG>.

Cleanup STR amp products using a bead-based cleanup (optional based on quantification).

Move amp product to capillary electrophoresis system.

The electrophoresis cartridge is a polypropylene molding comprising an anode sub-assembly, a cathode sub-assembly, an electrophoresis capillary and a gel sub-cartridge containing cross-linked polyacrylamide. The electrophoresis capillary has a first and a second end, each of which is in electrical communication with the anode sub-assembly and the cathode sub-assembly respectively. A portion of the electrophoresis capillary is used as an optical window for receiving a light from a light source and providing signals of the analytes for detection and further analysis. The cathode sub-assembly comprise there cathodes and a cathode main piston, and in fluid communication with the first end of the electrophoresis capillary, a water container, a buffer container and a first waste container. The anode sub-assembly comprises an anode main piston and a high pressure piston, and is in fluid communication with the second end of the electrophoresis capillary, the gel sub-cartridge, the water container, a regeneration fluid container and a second waste container. The electrophoresis cartridge further comprises a lysis buffer container, a sample inlet port in fluidic communication with a sample cartridge interface having a sample outlet port.

The electrophoresis system is highly integrated and configured to removably engage with a system for sample preparation, processing and analysis. In general, the system comprises there fully-integrated and automated components, i.e., a user interface, a sample cartridge interface and an electrophoresis cartridge interface. The sample cartridge interface and the electrophoresis cartridge interface are configured to releasably engage a sample cartridge for sample processing and an electrophoresis cartridge for sample analysis. The user interface further comprises a control module, a user interface screen and an embedded computer system. The user interface is configured to read and identify the fingerprint of a user and barcodes of sample packaging. A user inputs one or more instructions or requests via the user interface screen and the embedded computer processes the requests and transforms the requests into signals which then initiate the operation of the system.

A user removes an electrophoresis cartridge from packaging and load into the instrument. Instrument senses the cartridge and engages. Multiple communications between the electrophoresis cartridge and the system including: (i) a fluidic communication between an inlet port of the electrophoresis cartridge and an outlet port of a sample cartridge comprised in the system, (ii) an electrical communication between electrodes (i.e., anode and cathode) of the electrophoresis cartridge and a power source of the system, (iii) an optical communication between an optical window of the electrophoresis cartridge and an optics module of the system, (iv) a first thermal communication between the electrophoresis capillary and a first thermo control assembly of the system, (v) a second thermal communication between a gel sub-cartridge of the electrophoresis cartridge and a second thermal control assembly of the system, (vi) a first mechanical communication between an anode sub-assembly of the electrophoresis cartridge and a first mechanical interface of the system, (vii) a second mechanical communication between a cathode sub-assembly of the electrophoresis cartridge and a second mechanical interface of the system, and (viii) a magnetic communication between the electrophoresis cartridge and the system, are established concurrently with the engagement of the electrophoresis cartridge.

Electrophoresis gel stored in the gel sub-cartridge is pumped and injected into the electrophoresis capillary by a high pressure piston comprised in the anode sub-assembly. Once the gel injection is completed, a washing buffer is pumped into a passage of the cathode sub-assembly for removing excessive gel remained in the cathode sub-assembly. Subsequently, a prepared analyte is directed into the electrophoresis capillary from the sample line in the cathode sub-assembly. A voltage gradient is then applied across two ends of the electrophoresis capillary to perform electrophoretic analysis and separate different components of the analyte which emit distinguishable optical signals upon the illumination of a laser. The signals are detected by a CCD camera comprised in the optics module and subjected to further analysis. Conclusion is drawn based on the results.

Claim 1:
An electrophoresis cartridge (<NUM>, <NUM>, <NUM>) adapted to releasably engage with an electrophoresis cartridge interface of a system, wherein the electrophoresis cartridge (<NUM>, <NUM>, <NUM>) comprises:
(a) an electrophoresis assembly including:
(<NUM>) an anode sub-assembly (<NUM>, <NUM>) comprising an anode,
(<NUM>) a cathode sub-assembly (<NUM>, <NUM>) comprising a cathode (<NUM>); and
(<NUM>) at least one electrophoresis capillary (<NUM>, <NUM>) having a first end in fluidic communication with the cathode sub-assembly (<NUM>, <NUM>) and a second end in fluidic communication with the anode sub-assembly (<NUM>, <NUM>), wherein said cathode (<NUM>) and said anode (<NUM>) are configured to provide a voltage gradient across said first end and said second end of said at least one electrophoresis capillary (<NUM>, <NUM>),
(b) a plurality of containers (<NUM>, <NUM>, <NUM>, <NUM>) comprising reagent;
(c) at least one pump (<NUM>, <NUM>, <NUM>, <NUM>) configured to transfer reagent from one or more container (<NUM>, <NUM>, <NUM>, <NUM>) to the cathode sub-assembly (<NUM>, <NUM>) through at least one respective fluid conduit, and at least one pump configured to transfer reagent from one or more container (<NUM>, <NUM>, <NUM>, <NUM>) to the anode sub-assembly (<NUM>, <NUM>) through at least one respective fluid conduit; and
(d) a sample inlet port and at least one sample line, wherein the sample line places the sample inlet port in fluidic communication with the first end of the electrophoresis capillary (<NUM>, <NUM>) through a passage in the cathode sub-assembly (<NUM>, <NUM>) and the sample inlet port (<NUM>) is configured to fluidically communicate with the sample cartridge interface (<NUM>, <NUM>) of the system so as to direct a sample to the at least one electrophoresis capillary.