Patent Application
20230073882
The present invention relates generally to automatic sample extraction system for numerous analytic processing systems and techniques.
Sample preparation and extraction for analytic processing systems involves manipulation and processing of multiple biologic samples in a substantially sterile environment. It is important to process the samples without contamination otherwise the results will be inaccurate, compromised and potentially lead to false positive in subsequent analytic processing and testing.
Biologic samples can be prepared for numerous analytic processing systems, such as a polymerase chain reaction “PCR” system. “PCR” is a technique used in molecular biology to amplify a single copy or a few copies of a piece of nucleic acid such as deoxyribonucleic acid “DNA” or ribonucleic acid “RNA”, across several orders of magnitude, generating thousands to millions of copies of a particular sequence.
“PCR” is typically considered to amplify a focused segment of nucleic acid, useful in the diagnosis and monitoring of genetic diseases, studying the function of targeted segments, forensic studies for identification of individuals, and other related uses.
Another example of an analytic processing system that may utilize samples prepared by the preferred system is enzyme-linked immunosorbent assay (ELISA), which detects antigen or antibody for immunology and toxicology. Purity of the biologic samples is important for the analytic processing systems to produce accurate results in the subsequent analytic processing systems. A problem with preparation of samples for analytic processing systems, such as PCR or ELISA enzyme-linked immunosorbent assay is that the preparation process risks contamination when the amplification vessels are open, and the samples are being prepared. In addition, during the movement of the samples and when the caps are removed, the possibility of spillage, droplet formation and/or aerosols can cause contamination risk. Cross contamination can also occur during introduction and removal of a pipette from the system due to the movement of the contaminated pipettes above open sample containers. Such contamination will quickly lead to false results or erroneous and incorrect test results. Care must be taken to prevent such contamination.
Physical separation between sample preparation, amplification and detection areas has been customarily used to limit contamination between samples and from the surrounding environment. Such measures are quite cumbersome, expensive and require rigorous training to prevent transfer of materials to lab coats, gloves, pipettes or laboratory equipment between such segregated areas.
The biologic material handling systems include a moving pipette assembly with several individual pipettes mounted to a movable frame that is movable in longitudinal and lateral directions relative to sample trays including sample tubes that are preferably loaded with biological materials, such as whole blood, serum, or other biological materials for nucleic acid amplification. The numerous stops and starts of the pipette assembly over the sample tubes, often after the pipettes are placed into contact with the samples in the sample tubes, results in extensive potential contamination of all of the samples on the sample tray when the robotic frame moves, starts, stops and vibrates over the sample tubes creating potential for cross-contamination and failure of the expensive and precise testing.
It is desirable to design a sample handling system that reduces or eliminates the risk of cross-contamination created when the contaminated pipettes move, stop and start under potential vibratory loads over the sample tray. The sample tubes also require the samples and other materials, such as buffers, in the sample tubes to enter and exit through a top opening, which further creates potential contamination issues.
Many methods for processing samples involve steps of shaking, heating, applying a magnetic field to the magnetic bead-target compounds complex, and liquid waste drainage. Conventionally, these steps are performed at independent and separate stations, for example using a shaker, a magnetic separation device, a heater and a waste container.
The abovementioned conventional procedures of shaking, heating, magnetic bead separation and liquid waste drainage require separate stations and consume excessive space on a workbench. The utilization of these separate stations also requires samples to be manually handled and transported from one station to another station, which is time consuming and generates the potential for cross contamination between samples. Accordingly, there is a need to address these problems.
The present invention relates generally to an automated system for isolating and extracting target compounds from biological specimens. In particular, the present invention is an automatic sample extraction system, which can be used to prepare samples for numerous analytic processing systems and techniques, such as PCR system.
The system comprises of units configured to process samples in succession so that it keeps a fixed processing turnaround time of each sample no matter when a sample would start the process. The present invention processes samples in a serial pattern in which a series of samples follow one another to be processed in a time sequence. The major units are controlled by a computer to achieve automatic nucleic acid extraction.
The system comprises of five different units: a storage unit, a sample preparation unit, a sample extraction unit, a waste unit, and a reaction tube unit. All units are configured to minimize the sample movement in the process and reduce the contamination risk.
The reaction tube unit is an especially designed reaction tube that has an upper section for sample extraction and a lower section to receive waste liquid from the upper section. The two section are separated by a valve.
The storage unit stores boxes of consumables that are easily accessible. The storage unit also stores the sample tubes and magnetic beads. The magnetic beads are kept in a cooler.
The sample preparation unit comprises of a rotary table that has a transferring unit comprising of a sample tube rack to receive a sample tube and a reaction tube rack to receive a reaction tube right next to each other. The rotary table can also hold boxes of consumables and reaction tubes for each quick access. The sample preparation unit also has a rack of samples to hold sample tubes. The rack of samples is located on one side of the rotary table. The rotary table rotates to position the sample rack next to the sample tube rack on the transferring unit and then the sample tube transferred. This minimizes the sample movement. The sample preparation unit also comprises of a cooler to hold magnetic beads.
The sample extraction unit, which is located close to the rotary table, comprises of a set of shakers to receive and shake the reaction tubes, and a set of magnetic racks with magnets to manipulate the magnetic beads inside the reaction tubes.
The disposal unit comprises of separate bins for disposal of the consumables, disposal of waste liquids and tubes.
The sample preparation unit is designed to have a minimum sample movement to reduce contamination risk. A sample has to be moved from a sample tube into a reaction tube, for extraction process. To minimize the sample movement, a sample tube rack and a reaction tube rack are placed next to each other on the rotary table. The sample robot moves a sample tube from the sample tube box into the sample tube rack and also moves a reaction tube from the reaction tube box in the reaction tube rack. Next, the sample robot prepares the sample in the reaction tube by adding different types of solutions, such as Lysis buffer.
Once the sample in the reaction tube is prepared, the rotary table rotates to bring the reaction tube rack with the reaction tube close to the sample extraction unit.
A reaction robot grabs and moves the reaction tube from the rotary table onto a shaker in the sample extraction unit. The extraction unit comprises of individual shakers and individual magnetic units. Each shaker with a reaction tube can be positioned at different distances from the magnetic units for changing the intensity of the magnets and the positioning of the magnetic beads inside the reaction tube.
First, the reaction tube is located at a position that the magnetic effect is small, and is shaken. Then a magnetic beads and binding buffer are added to the solution and the reaction tube is further shaken.
Next, the reaction tube is moved to a second position, such that the reaction tube is located between the vertical legs of the L shaped magnets. The magnets pull the magnetic beads that are holding onto the sample towards the wall of the tube. The waste valve is opened, and the waste liquid is discarded into the second compartment of the reaction tube. Valve is closed, a wash buffer is added, and the tube is shaken. The shaker is then moved back close to the magnets to hold the magnet onto the tube walls, while the valve is opened to discard the waste liquid into the second compartment. This process may be repeated several times (two or more washes) depending on the sample requirements to wash out impurities.
Once the sample is purified, an Elution buffer is added to the sample in the reaction tube and the tube is shaken to separate the sample from the magnetic beads. The reaction tube is then moved to a third position, where the magnetic beads attach completely towards the top portion of the tube, thereby allowing for easy removal of the sample by a pipette. The reaction robot grabs a pipette and removes the purified sample from the reaction tube and places it in a purified sample tube with a lid for storage.
Consolidation of each of these units on the frame reduces the footprint of the sample preparation system and reduces the need to transport associated components over relatively large distances, reducing the potential contamination.
Therefore, it is an object of the present invention to provide a biologic sample extraction system and method that reduces and eliminates the risk of contamination.
It is further another object of the present invention to process samples in a serial pattern in which a series of samples follow one another to be processed in a time sequence.
It is another object of the present invention to provide a fully automated sample extraction to automatically process a large number of biological samples per day in a minimum manual operation and a short operation time.
It is another object of the present, to provide a system to reduces cross contamination by reducing transferring time of the pipette and liquids.
Embodiments hereinafter will be described in conjunction with the appended drawings provided to illustrate and not to limit the scope of the claims, wherein like designations denote like elements, and in which:
Referring to
The system 100 comprises of a frame 10 having a horizontal platform 11, which divides the frame to a top section 12 and a bottom section 13. The frame 10 is preferably constructed of a relatively stiff, strong and sterilizable material that may be assembled to provide structural support to the various units of the system 100 and to be able to operate the system 100. The frame 10 may, for example, be constructed of a stainless steel that is biocompatible and sterilizable for use with the system 100. The system 100 comprises of a plurality of units positioned in the housing of the frame and supported by the frame 10 and movable in a manner to operate a fully automated sample extraction system.
The Storage Unit: The system comprises of a storage unit that compromises of a rotary storage 20 installed on the bottom section 13 close to the left side of the frame 10. The rotary storage 20 includes a number of movable trays, preferably eight trays 21, which are assembled in vertical position and each tray 21 comprises of a number of housings, preferable five housing to receive five boxes 22 of consumables. The operator of the machine can remove the trays 21 and load with boxes 22. The boxes 22 include samples and additional elements for the extraction process. The rotary storage 20 stores a large number of boxes, probably a total of forty boxes, of consumables for extraction process and is rotatable about a Z axis. The rotary storage area 20 is preferably configured to include multiple storage of consumables comprising reaction tube boxes, buffer boxes, elution tube boxes and various pipette tip boxes that are stored on the rotary storage 20 and transported by the box lift robot 30 for replacement. The rotary storage 20 can hold a large number of consumables for easy access. For example, 16 reaction tube boxes, 2 buffer boxes, 2 elution tube boxes, 12 (1 ml) pipette tip boxes, 4 (175 μL) pipette tip boxes and 4 (25 μL) pipette tip boxes.
As shown clearly in
The storage unit further has a cooler 90 to store consumables that need to be stored in cold temperatures, such as 4° C. environment. For example, magnetic beads solution is placed in cooler for storage and later transfer to the reaction tube 201. The cooler 90 can be any type of accessible cooler, preferably a Thermo-Electric Cooler. The function of the cooler 90 is to keep solutions between 4-8° C. so that they can be functional.
The box lift robot 30 carries boxes 22 from the rotary storage 20 to a rotary table 40 on the top section 12 of the frame. The box lift robot 30 is a vertical motion robot mounted on a railing on the bottom section 13 to allow for a two axis (X and Z) linear movement of the box lift 30. The box lift robot 30 extends through an opening 31 to the top section 12 and can move to a desired position where a consumable box 22 is to be grabbed and lifted from the rotary storage 20 to the rotary table 40 on the top section 12.
The sample preparation unit comprises of a rotary table 40. The rotary table 40 of the sample preparation unit comprises of a number of housings, preferably six, sized to receive the consumable boxes 22 for extraction process. The rotary table 40 is rotatably mounted on the horizontal platform 11 on top section 12 of the frame. It can rotate about an axis and stops in a predetermined position in front of the box lift 30 to receive the consumable boxes 22. Each of the housings of the rotary table 40 may comprise of various boxes of pipette tips, comprising: Long pipette tips 42, medium pipette tips 43 and short pipette tips 44. Other consumable boxes, such as Nucleic acid tubes 45, various buffers 46 and reaction tubes 201 are further positioned on the rotary table 40 for the extraction process. A transferring unit 41 is provided on the rotary table 40 that comprises of a sample tube rack 2, a reaction tube rack 3 and a waste hole 4. In this unit 41, samples can be transferred from a sample tube 1 to a reaction tube 201 which is located right next to it to reduce the cross-contamination risk.
To operate a fully automated sample extraction, the system 100 provides a sample robot 60 and a reaction robot 70 to transfer the consumables for extracting process. The robots 60 and 70 are Cartesian coordinate robots that can move along the Z axis. The robots 60 and 70 are equipped with electric gripper and electric pipette assembly. The robots 60 and 70 are equipped with an electric gripper and an electric pipette assembly to pick the consumables, place the consumables in various locations, transfer liquids based on sample extraction application of the system and dispose the waste materials. The grippers are used to transfer the tubes. The pipette assemblies are utilized to move samples during the sample extraction process, as would be understood by one having ordinary skill in the art. The functioning of the grippers and pipettes are controlled by a computer program controller during operation of the sample extraction system 100.
The sample extraction unit: Referring to
One embodiment of the present system 100 comprises of shakers 200 that are installed on four pieces of magnet racks 81 parallel to each other, wherein each magnet rack 81 receives six shakers 200. The magnet racks 81 are movable about an X and Y axis and are provided with a set of magnet gears 83 to control the movement of the shakers 200. The magnet gears 83 are installed on the rotating shafts 84, wherein each shaft 84 preferable has six magnet gears 83 installed thereon. The rotating shafts 84 preferably operate at 1200rpm.
Each shaker 200 is configured to operate independently and provide a shaking motor to integrate an orbital shaking, heating, magnetic bead separation and liquid waste drainage. Each magnet rack 81, has a number of housings, each housing configured to receive a shaker 200. Each housing has a pair of L shaped magnet 95 having a vertical leg and a horizontal leg. The shakers 200 can be located at different distances form the magnetic racks 81.
A Shaker Pusher robot pushes the shakers to different positions. As shown in FIGS.
7, 15A and 15B a two axis (X and Y) linear motion “Shaker Pusher” robot 82 is further provided in the sample extraction unit 80. The shaker pusher 82 is used to push shakers 200 to different positions. A push pad 85 pushes the shakers close or away of the rotating shaft 84. The shakers 200 will start shaking when approaching to a distance of about 1 mm to the rotating shaft 84. A sheet metal 87 is further installed on the bottom of the shakers to guide the shakers 200 close or away of the rotating shaft 84.
Reaction Tubes: Each reaction tube 201 comprises of two chambers. According to
The opening and closing of the valve 204 is by the force acting on the push buttons 205 through the reaction robot 70. After the whole extraction process is completed, the reaction robot 70 carries the reaction tube 201 with the waste liquid retained in the waste chamber 203 and disposes it into the waste bin. This action prevents the reaction sample from flowing into the waste chamber 203. The reaction tube 201 may be constructed from a biocompatible, sterilisable material.
The gripper of the reaction robot 70 having a rod gripper (not shown) movable in a vertical position to be inserted into the reaction area 202 to grip and transfer the reaction tube 201. The reaction robot 70 further has a sleeve (not shown) that slides over the rod gripper. The sleeve pushes on the push buttons 205 of the reaction tube 201 to open the valve 204.
Waste Unit: According to
Referring to
Each used pipette tip and tube are disposed after use into the first waste bin 51 through a waste hole 4. The waste hole 4 is next to the transferring unit 41 so the cross-contamination risk which can happen during the movement of the samples and when the caps are removed, the possibility of spillage, droplet formation and/or aerosols is significantly reduced. This design of the system not only reduces cross contamination but also reduces traveling time of the pipette and liquid transfer.
The system 100 further comprises a computer program to command and control the operation of the units of the system. A non-transitory computer readable memory comprising of one or more data structures that alone or together contain stored information pertaining to a plurality of operation of the system comprising the types of operations that the system may run. The controller of the system is coupled with a sample extraction application to store information pertaining to a plurality of sample extracting types. The system 100 further includes sample extraction control application. At least one control application comprises sample extraction instructions to cause the sample extraction units to move and cause the sample extraction system 100 to prepare an extract sample using one or more selected consumables corresponding to a selected sample.
The reaction robot 70 is movably mounted on a robot rail 71 that is secured to the vertical support of the frame 10 for movement in between the sample preparation unit and sample extraction unit 80 to continue the automated sample processing system. The reaction robot 70 has a gripper 73 mounted on a grip arm 72 extending downwardly that is movable to releasable grasp various pipette tips and move between the areas and place them in pre-programmed position. The reaction robot 70 selects a pipette tip for example a long pipette tip 42 as shown in
According to
The sample robot 60 picks a reaction tube 201 from the reaction tube box and places it on the reaction tube rack 3. The sample robot 60 further picks a sample tube 1 from the sample rack 50 and places it on the sample tube rack 2 next to the reaction tube 201. Then, the sample robot 60 picks a pipette tip to transfer some sample (Nucleic acid) from sample tube 1 into reaction tube 201. The rotary table 40 rotates to move the filled reaction tube 201 to the right side of the frame next to the extraction unit 80. So, cross contamination risk which can happen during the movement of the samples, the possibility of spillage, droplet formation and/or aerosols is significantly reduced.
After 10 minutes shaking, the shaker pusher 82 pushes the shaker 200 away from the rotating shaft to stop shaker 200. Then the Reaction robot 70 moves to the rotary table 40 to pick and add some magnetic beads 48 and binding buffer to the reaction tube 201. The buffer improves the attachment and separation efficiency of the magnetic beads 48 contained in the sample in combination of motion of the shakers 200. In this stage the sample (nucleic acid) binds to the magnetic beads 48. Then, shaker pusher 82 will push shaker 200 to shake for 5 mins on L shaped magnet rack 95. The most useful characteristic of the magnetic beads 48 and buffers are, that they can reversibly bind nucleic acid and, when in the presence of a strong magnet, can be safely immobilized throughout multiple wash and manipulation steps. On each stage the reaction robot 70 dispose the used pipette tip into the waste bin.
The process of extracting the sample is being achieved in plurality stages by pushing the reaction tube 201 on magnet rack, shaking the shaker 200 to separate the magnetic beads 48 and washing the impurities from the sample. The Shaker pusher 82 pushes the reaction tube 201 on the magnetic rack 81 to apply magnet and separate the magnetic beads 48 from sample. Magnetic beads will stick to the walls of the reaction area 202.
In this stage the valve 204 between the reaction area 202 and the waste tank 203 of the reaction tube 201 is being opened by force of the reaction robot on the push buttons 205 and the waste produced during the extraction process is discarded from the reaction area 202 to the waste tank 203 of the reaction tube 201. Then the reaction robot 70 adds some wash buffer (
According to
The Nucleic acid solution containing purified viral RNA/DNA is being transferred to an elution tube. The design of the reaction tube 201 allows the magnetic beads to clump together closer to the bottom of the tube so that the elution buffer can contact the beads effectively and completely. Then the reaction robot 70 carries the reaction tube 201 to the waste hole 4 and drains the waste out.
When magnetic beads 48 are presented into a reaction tube 201 in the shakers 200, The substances in the sample attach to the magnetic beads by collision of magnetic beads 48 with biological materials. Magnetic beads 48 are added to the reaction tube 201 to allow for example DNA molecules to bind to the beads 48. The reaction tube 201 is then placed on the shaker 200. The shaker 200 helps sample mixing to obtain a homogenous mixture of the magnetic beads 48 with the sample in order to enhance the yield of DNA bound to the magnetic beads 48. The magnetic beads 48 used in the process may be at least one of a stainless-steel bead, a zirconia bead, a ceramic bead, or a glass bead.
Systems and methods according to embodiments of the invention can be used to prepare different biological samples for various analytical procedures. Examples of such biological samples include, but are not limited to, blood, serum, plasma, urine, saliva, feces, organ tissues, etc., preferably a biological specimen from a patient. Depending on the heed, the processed sample can contain one or more isolated or enriched biological molecules that can be analyzed, detected or quantified in subsequent procedures. For example, a biological sample (such as a biological specimen from a subject) can be processed in a system of the invention to obtain a processed sample containing isolated or enriched nucleic acids, and the processed sample can be used for amplifying, detecting or quantifying one or more nucleic acids of interest, e.g., as the template in a PCR reaction, or in a hybridization processing using one or more chemiluminescent-labeled nucleic acids.
In a preferred embodiment, a method further comprises detecting or quantifying a nucleic acid in the processed sample using a PCR or a chemiluminescent assay. In another example, a biological sample (such as a biological specimen from a subject) can be processed in a system of the invention to obtain a processed sample containing peptides or proteins, and the processed sample can be used in an immunoassay, such as a radio immunoassay, ELIS A, immunofluorescence assay, or chemiluminescence immunoassay, for detecting or quantifying one or more peptides or proteins of interest.
In another embodiment, the method comprises detecting or quantifying a peptide or polypeptide in the processed sample using an ELISA, an immunofluorescence assay, or a chemiluminescence immunoassay (CLIA), more preferably, a CLIA. The CLIA is a more sensitive alternative to ELISA, which involves the generation of electromagnetic radiation as light by the release of energy from a chemical reaction and the measurement of light intensity, e.g., using a photomultiplier or photodiode and the associated electronics to convert and record signals, Known methods and reagents for detecting or quantifying biological molecules, such as the PCR, ELISA, immunofluorescence, assay or CLIA. procedures; can be used in the invention in view of the present disclosure.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/CA2020/050258 | 2/27/2020 | WO |
