Classifications

• • B—PERFORMING OPERATIONS; TRANSPORTING
  • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
  • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
  • B01L3/00—Containers or dishes for laboratory use, e.g. laboratory glassware; Droppers
  • B01L3/50—Containers for the purpose of retaining a material to be analysed, e.g. test tubes
  • B01L3/508—Containers for the purpose of retaining a material to be analysed, e.g. test tubes rigid containers not provided for above
  • B01L3/5085—Containers for the purpose of retaining a material to be analysed, e.g. test tubes rigid containers not provided for above for multiple samples, e.g. microtitration plates
  • B01L3/50851—Containers for the purpose of retaining a material to be analysed, e.g. test tubes rigid containers not provided for above for multiple samples, e.g. microtitration plates specially adapted for heating or cooling samples
• • B—PERFORMING OPERATIONS; TRANSPORTING
  • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
  • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
  • B01L3/00—Containers or dishes for laboratory use, e.g. laboratory glassware; Droppers
  • B01L3/50—Containers for the purpose of retaining a material to be analysed, e.g. test tubes
  • B01L3/508—Containers for the purpose of retaining a material to be analysed, e.g. test tubes rigid containers not provided for above
  • B01L3/5085—Containers for the purpose of retaining a material to be analysed, e.g. test tubes rigid containers not provided for above for multiple samples, e.g. microtitration plates
  • B01L3/50855—Containers for the purpose of retaining a material to be analysed, e.g. test tubes rigid containers not provided for above for multiple samples, e.g. microtitration plates using modular assemblies of strips or of individual wells
• • B—PERFORMING OPERATIONS; TRANSPORTING
  • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
  • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
  • B01L9/00—Supporting devices; Holding devices
  • B01L9/06—Test-tube stands; Test-tube holders
• • B—PERFORMING OPERATIONS; TRANSPORTING
  • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
  • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
  • B01L2200/00—Solutions for specific problems relating to chemical or physical laboratory apparatus
  • B01L2200/02—Adapting objects or devices to another
  • B01L2200/025—Align devices or objects to ensure defined positions relative to each other
• • B—PERFORMING OPERATIONS; TRANSPORTING
  • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
  • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
  • B01L2200/00—Solutions for specific problems relating to chemical or physical laboratory apparatus
  • B01L2200/02—Adapting objects or devices to another
  • B01L2200/028—Modular arrangements
• • B—PERFORMING OPERATIONS; TRANSPORTING
  • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
  • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
  • B01L2200/00—Solutions for specific problems relating to chemical or physical laboratory apparatus
  • B01L2200/12—Specific details about manufacturing devices
• • B—PERFORMING OPERATIONS; TRANSPORTING
  • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
  • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
  • B01L2200/00—Solutions for specific problems relating to chemical or physical laboratory apparatus
  • B01L2200/18—Transport of container or devices
• • B—PERFORMING OPERATIONS; TRANSPORTING
  • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
  • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
  • B01L2300/00—Additional constructional details
  • B01L2300/02—Identification, exchange or storage of information
  • B01L2300/021—Identification, e.g. bar codes
• • B—PERFORMING OPERATIONS; TRANSPORTING
  • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
  • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
  • B01L2300/00—Additional constructional details
  • B01L2300/08—Geometry, shape and general structure
  • B01L2300/0809—Geometry, shape and general structure rectangular shaped
  • B01L2300/0829—Multi-well plates; Microtitration plates
• • B—PERFORMING OPERATIONS; TRANSPORTING
  • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
  • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
  • B01L2300/00—Additional constructional details
  • B01L2300/08—Geometry, shape and general structure
  • B01L2300/0848—Specific forms of parts of containers
  • B01L2300/0851—Bottom walls
• • B—PERFORMING OPERATIONS; TRANSPORTING
  • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
  • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
  • B01L2300/00—Additional constructional details
  • B01L2300/08—Geometry, shape and general structure
  • B01L2300/0848—Specific forms of parts of containers
  • B01L2300/0858—Side walls
• • B—PERFORMING OPERATIONS; TRANSPORTING
  • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
  • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
  • B01L3/00—Containers or dishes for laboratory use, e.g. laboratory glassware; Droppers
  • B01L3/52—Containers specially adapted for storing or dispensing a reagent
  • B01L3/527—Containers specially adapted for storing or dispensing a reagent for a plurality of reagents
• • B—PERFORMING OPERATIONS; TRANSPORTING
  • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
  • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
  • B01L3/00—Containers or dishes for laboratory use, e.g. laboratory glassware; Droppers
  • B01L3/54—Labware with identification means
  • B01L3/545—Labware with identification means for laboratory containers
  • B01L3/5453—Labware with identification means for laboratory containers for test tubes
• • B—PERFORMING OPERATIONS; TRANSPORTING
  • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
  • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
  • B01L7/00—Heating or cooling apparatus; Heat insulating devices
  • B01L7/52—Heating or cooling apparatus; Heat insulating devices with provision for submitting samples to a predetermined sequence of different temperatures, e.g. for treating nucleic acid samples

Definitions

• the technology described herein generally relates to process tubes used in amplification processes and the carrier trays in which the process tubes are securely stored for transport and processing, as well as methods of making and using the same.
• a biological sample such as those obtained from a patient, can be used in nucleic acid amplification assays, in order to amplify a target nucleic acid ⁇ e.g., DNA, RNA, or the like) of interest.
• PCR Polymerase chain reaction
• nucleic acid amplification assays involve multiple steps, which can include nucleic acid extraction and preparation, nucleic acid amplification, and target nucleic acid detection.
• nucleic acid-based diagnostic assays the biological, environmental, or other samples to be analyzed, once obtained, are mixed with reagents for processing.
• processing can include combining extracted nucleic acids from the biological sample with amplification and detection reagents, such as probes and fluorophores. Processing samples for amplification is currently a time-consuming and labor intensive step.
• Processing samples for amplification often occurs in dedicated process tubes, used to hold the extracted DNA samples prior to and during the amplification process.
• the process tubes are placed directly in a thermal cycler for amplification.
• process tubes are first placed in a tube rack for pre- amplification processing (such as filling up the tubes with the amplification reagents, drying the reagents, and marking the tubes by hot stamping them).
• the process tubes are often removed from the tube rack by a lab technician and placed individually and separately in contact with a heater unit of the thermal cycler. Placing the process tubes individually in the thermal cycler is inefficient, time consuming, and can be difficult to automate. Further, such processes are susceptible to human error.
• racks containing the process tubes can be placed directly in the thermal cycler.
• this approach too has drawbacks because the process tubes may shift in the rack during handling and transport and consequently will likely not line up correctly with the heaters of the thermal cycler. Additional intervention by a lab technician is required align the tubes and fit them into the heaters of the thermal cycler. Furthermore, if the process tubes are not securely connected to the rack, the process may become dislodged during marking of the process tubes, being pulled up and out of the rack by the stamping apparatus.
• Process tubes are often conical in shape, having an outside diameter larger at the top of the process tube than at the bottom of the process tube. Some process tubes are cylindrical in shape, having a constant diameter from top to bottom.
• the ports of the rack in which the process tubes are placed must be of a greater diameter than the largest outside diameter of the process tubes (at the top of the process tube).
• the ports in the rack are often appreciably larger than the outside diameter of the process tubes, allowing the tubes to move around in the rack and potentially fall out. Without a secure fit in the rack, the process tube may tilt to one side or another.
• the tilting process tubes may bump into each other and break and/or cause loss of sample and/or reagents stored therein. Furthermore, it can be very difficult to line up the differently tilted process tubes into the rigid heaters of the thermal cycler.
• Certain embodiments disclosed herein contemplate a process tube having a securement region that includes an annular ledge, a protrusion, and a neck between the ledge and the protrusion.
• the process tube also includes a body extending below the protrusion and a top ring extending vertically up from the annular ledge which defines an opening to the tube.
• an outside surface of the neck can be parallel to a longitudinal axis through the process tube.
• the protrusion can include an apex, an upper slope from the apex to the neck, and a lower slope from the apex to the body.
• the angle of the upper slope on the protrusion can be steeper than the angle of the lower slope on the protrusion.
• the annular ledge of the process tube can have an upper surface, a lower surface, and an outside surface.
• the protrusion can have a larger outside diameter than the outside diameter of the neck.
• the annular ledge can have a larger outside diameter than the outside diameter of the protrusion.
• the process tube can further include a base below the body which defines a bottom of the process tube.
• Certain embodiments disclosed herein include a process tube strip having a plurality of process tubes.
• the plurality of process tubes is connected by a tab adjoining the annular ledges of the plurality of tubes.
• Certain embodiments contemplate a process tube having an annular ledge extending laterally from the tube, the annular ledge comprising an upper surface, a lower surface, and an outer surface.
• the process tube can include a top ring extending vertically up from the upper surface of the annular ledge which defines an opening to the process tube.
• the process tube can further include an annular protrusion extending laterally from the process tube, at a location on the tube below the annular ledge.
• the protrusion can have an apex, an upper slope, and a lower slope.
• the process tube can include a neck between the annular ledge and the protrusion, a body below the protrusion, and a base which defines a bottom of the tube.
• Embodiments of the process tube disclosed can be configured to securely fit in a carrier tray.
• the carrier tray can have a shelf and a base, such that the shelf has a plurality of ports through a top of the shelf, and the ports having an interior wall.
• the protrusion of the process tube disclosed can have a larger outside diameter than the diameter of the port in the carrier tray.
• the neck of the process tube can have a smaller outside diameter than the diameter of the port in the carrier tray.
• the process tube can be securely fit into a port of the carrier tray.
• the lower surface of the annular ledge of the process tube can rest on an exterior of the shelf top and the upper slope of the protrusion can rest on a bottom edge of the interior wall of the port.
• a gap can exist between the neck of the process tube and the interior wall of the port and the gap can allow the process tube to tilt or adjust within the port of the carrier tray.
• FIG. 1 For embodiments of the disclosure contemplate a system having a carrier tray with a plurality of ports therethrough and a process tube having a securement region.
• the securement region of the process tube can include an annular ledge, a neck, and a protrusion.
• the securement region of the process tube can fit securely in a port of the carrier tray.
• the annular ledge and protrusion of the process tube can have outside diameters that are larger than the diameter of the port of the carrier tray and the neck of the process tube can have an outside diameter that is smaller than the diameter of the port.
• FIG. 1A shows an isometric view of an exemplary process tube strip as described herein.
• Fig. IB is a side plan view of the process tube strip of Fig. 1A.
• Fig. 1C is a top view of the process tube strip of Fig. 1A.
• Fig. ID shows an isometric view of another exemplary process tube strip as described herein.
• Fig. IE shows an isometric view of another exemplary process tube strip as described herein.
• Fig. 2A is an isometric view of an exemplary, single process tube as described herein.
• Fig. 2B is a cross-sectional view of the process tube of Fig. 2A taken along line 2B in Fig. 1C.
• Fig. 3A shows an exemplary carrier tray, as described herein.
• Fig. 3B shows a plurality of exemplary process tube strips in the carrier tray of Fig. 3 A.
• Fig. 4 is a cross-sectional view of 12 process tubes positioned in the carrier tray prior to securing the process tubes in the carrier tray.
• Fig. 5 is a cross-sectional view of two exemplary process tubes positioned in the carrier tray prior to securing the process tubes in the carrier tray.
• Fig. 6A is a cross-sectional view, taken along line 6A in Fig. 3B, of the 12 process tubes of Fig. 4 after securing the process tubes in the carrier tray.
• Fig. 6B is a cross-sectional view, taken along line 6B in Fig. 3B, of a process tube strip positioned in the carrier tray after securing the process tubes in the carrier tray.
• Fig. 7 is a cross-sectional view of the process tubes of Fig. 5 positioned in the carrier tray after securing the process tubes in the carrier tray.
• Fig. 8 is an isometric view of an exemplary heater assembly of a thermal cycler.
• Fig. 9 is a cross-sectional view of exemplary process tubes positioned in heater wells of a heater assembly, as described herein.
• the process tubes and carrier tray described herein can be used together to provide a safe and efficient system of preparing, storing, and transporting the process tubes prior to use in a thermal cycler and also for positioning the process tubes accurately and securely in the thermal cycler during amplification.
• Fig. 1A shows an isometric view of an exemplary process tube strip 100 according to the embodiments described herein.
• Fig. IB is a side plan view of the process tube strip of Fig. 1A.
• Fig. 1C is a top view of the process tube strip of Figure 1A.
• the process tube strip 100 is a collection of process tubes 102, connected together by a connector tab 104.
• the exemplary process tube strip 100 can also include a top end tab 106, as shown in Figures 1A-1C, indicating the top of the process tube strip 100 and a bottom end tab 108 indicating the bottom of the process tube strip 100.
• the process tube strip 100 shown in Figures 1A-1C includes eight process tubes 102 connected together in the process tube strip 100.
• the process tube strip 100 can include, for example any other number of process tubes, e.g., 40, 30, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 7, 6, 5, 4, 3, or 2 process tubes 102 connected in the process tube strip 100.
• An embodiment of the process tube strip 100 can include an insignia or indication on the upper surface of the top and bottom end tabs 106, 108.
• the top end tab 106 can be marked with an "A" indicating the top of the process tube strip 100 and the bottom end tab 108 can be marked with the letter of the alphabet corresponding to the number of process tubes 102 in the process tube strip 100 (for example, an "H” would be marked on the bottom end tab 108 of the process tube strip 100 for a process tube strip 100 having eight process tubes 102 connected together in the process tube strip 100).
• an "H” would be marked on the bottom end tab 108 of the process tube strip 100 for a process tube strip 100 having eight process tubes 102 connected together in the process tube strip 100.
• top and bottom end tabs 106, 108 can be used to indicate the top and bottom of a process tube 102 and the number of process tubes 102 in a process tube strip 100.
• the end tabs 106, 108 can be marked with a color marking, a barcode, or some other designation to identify, for example, the contents of the process tubes 102, the assay type being performed in the process tube strip 100, and the date and location of manufacture of the process tube strip 100.
• Fig. ID is another embodiment of the process tube strip 100 that includes a ledge extension 110 on each of the process tubes 102.
• Fig. IE is an additional embodiment of the process tube strip 100 that includes a tube tag 112 positioned on the ledge extension 110 of each process tube 102.
• Process tubes 102 can be receptacles for, or house, solids or liquids.
• process tubes 102 can hold reagents and/or samples, e.g., nucleic acid samples to be used in amplification assays.
• the process tubes 102 can be circular in cross-section, but other cross sections are possible and consistent herewith.
• the process tubes 102 can be manufactured via a unitary construction, although in certain instances the process tubes may be constructed from two or more parts fused or otherwise joined together as applicable.
• the process tubes 102 have an opening that is configured to accept/receive a pipette tip for deposit and/or retrieval of fluids within the process tube 102.
• the process tubes 102 can be constructed from polypropylene or other thermoplastic polymers known to those skilled in the art. Alternatively, process tubes 102 can be constructed from other appropriate materials, such as polycarbonate or the like. In some embodiments, the polypropylene is advantageously supplemented with a pigment, such as titanium dioxide, zinc oxide, zirconium oxide, or calcium carbonate, or the like. Preferably, the process tubes 102 are manufactured using materials such that they do not fluoresce and thus do not interfere with detection of the amplified nucleic acid in the process tubes 102.
• FIGs. 2A and 2B show, respectively, an isometric and a cross-sectional view of an exemplary single process tube 102.
• Connector tabs 104 are shown in Fig. 2A, connecting the process tube 102 to other process tubes 102 on either side of the process tube 102.
• the shown connector tab 104 includes a connector recess 232 on the underside of the connector tab.
• the connector recess 232 provides a separation point to easily break apart different process tubes 102 connected as part of a process strip 100.
• the process tubes 102 can be broken apart by the end user in order to mix and match different process tubes 102 having different dried reagents, and rearranging the process tubes in the carrier tray 300 to match the necessary operation of the amplification assay in the thermal cycler.
• a connector tab 104 can also be positioned between the process tube 102 at the end of a process tube strip 100 and the top or bottom end tab 106, 108. Such a connector tab 104 allows the end process tube 102 to be removed easily and also mixed and matched with process tubes 102 from other process tube strips 100 or to be used individually in a thermal cycler. [0044] As shown in Figs.
• the process tube 102 can have a top ring 202, the top ring 202 defining an opening 226 at the top of the process tube 102.
• the top ring 202 extends around the circumference of the opening 226.
• an annular ledge 204 extends laterally out from the side of the process tube 102 below the top ring 202. In this manner, the top ring 202 extends upwards from an upper surface 206 of the annular ledge 204.
• the annular ledge 204 is also defined by an outer surface 208 and a lower surface 210.
• a neck 228 of the process tube 102 which extends vertically from the annular ledge 204, parallel to the longitudinal axis 230 of the process tube 102.
• the exterior of the process tube 102 at the neck 228 can be parallel to a longitudinal axis 230 running vertically through the process tube 102.
• the exterior neck 228 can be at an angle to the longitudinal axis 230 to aid in removal of the process tube 102 from an injection mold during the manufacturing process.
• a protrusion 212 extending laterally from the side of the process tube 102.
• the protrusion 212 is defined by an upper slope 214 when extends from the neck 228 to an apex 215 of the protrusion 212.
• the apex 215 of the protrusion 212 has the largest outside diameter of the protrusion 212 and then the protrusion 212 includes a lower slope 216 which extends from the apex 215 down the exterior of the process tube 102.
• the upper slope 214 of the protrusion 212 slopes away from the longitudinal axis 230 and the lower slope 216 slopes back towards the longitudinal axis 230.
• the angle of the upper slope 214 on the protrusion is steeper than the angle of the lower slope 216 on the protrusion 212.
• the lower slope 216 of the protrusion 212 meets a longer body portion 218 of the process tube 102.
• the body 218 extends to a base 220 of the process tube 102.
• the base 220 includes an annular bottom ring 224 on the bottom of the process tube 102, defined by a divot 222 in the bottom of the process tube 102.
• the top ring 202, the annular ledge 204, the neck 228, the protrusion 212, and the body 218 are coaxial with the longitudinal axis 230.
• the annular ledge 204, neck 228, and protrusion 212 together define a securement region 200 of the process tube 102.
• the securement region 200 provides a way to easily and securely attach the process tube 102 ( or plurality of process tubes 102 in the form of a process strip 100) to a carrier tray for transport and later processing in the heater of an thermal cycler.
• the process tubes 102 can be manufactured as a strip 100 of tubes 102 connected together by a connector tab 104. Multiple process tube strips 100 can then be inserted securely in a carrier tray 300.
• Fig. 3A shows an exemplary carrier tray 300. As seen in Fig.
• the carrier tray 300 can house a plurality of ports 306 in a shelf 302 of the carrier tray 300.
• the plurality of ports 306 can be configured to receive the individual process tubes 102, and the number of ports 306 in a column of the carrier tray 300 can be advantageously designed to fit the length of the process tube strips 100.
• the number of ports 306 in the y-direction can be designed to correspond to the number of process tubes 102 in a process tube strip 100.
• the carrier tray 300 can have eight ports 306 in the y-direction such that a process tube strip 100 consisting of eight process tubes 102 can be inserted and secured in the ports 306 of the carrier tray 300 in the y-direction.
• the ports 306 in the carrier tray 300 are elliptical in shape, having a larger cross-sectional diameter in the y-direction. In this manner, the larger diameter cross-sections of the elliptical ports 306 are lined up in the same direction as the process tube strips 100 when inserted in the carrier tray 300.
• Fig. 3B shows a plurality of process tube strips 100 securely fit in an exemplary carrier tray 300.
• assay reagents e.g., amplification and detection reagents
• liquid reagents can be pipetted into the individual process tubes 102 and then the carrier tray 300 can optionally be placed in a drier to dry the liquid reagents in the bottom of the process tubes as a solid mass formed to the shape of the internal base 220 of the process tube 102.
• liquid reagents are not dried down in the process tubes 102.
• each process tube 102 in a carrier tray 300 can be deposited with identical reagents.
• some or each of the process tubes 102 in process tube strip 100 can be filled with differing reagents or samples.
• the process tubes 102 can be marked with an indicator to identify the contents (for example, the specific reagents) of the process tubes 102.
• marking of the process tubes 102 can be accomplished by hot stamping the top ring 202 of the process tubes 102 with a specific color indicating the contents (e.g., reagents) of the process tubes 102.
• the top ring 202 also provides a surface to which an adhesive seal can be applied to seal the opening 226 of the process tube 102.
• Fig. ID shows a process tube strip 100 wherein each process tube 100 includes a ledge extension 1 10 extending from one side of the annular ledge 204 of the process tube 100.
• the ledge extension 1 10 provides additional surface area on the annular ledge 204 for marking of the individual process tubes 102.
• the ledge extension 1 10 can be pre-marked with an alphanumeric identifier (e.g., A, B, C, etc, or 1 , 2, 3, etc.) to identify an individual process tube 102 within a process tube strip 100.
• an alphanumeric identifier e.g., A, B, C, etc, or 1 , 2, 3, etc.
• the ledge extension 1 10 of the process tubes 102 can be hot stamped, or otherwise marked, to identify the contents (e.g., reagents) of the process tubes 102 following the deposit of the reagents in the process tubes 102.
• a 2-D bar code (ink or laser) can be printed directly on the ledge extension 1 10.
• the individual process tubes 102 of the process tube strip 100 can include a tube tag 1 12 affixed to the top of the ledge extension 1 10.
• the tag 1 12 can be used in addition to, or in conjunction with, marking (e.g., hot stamping) the top ring 202 of the process tubes 102 to identify the contents, such as reagents, in a particular process tube 102.
• the tag 1 12 can be a 2-dimensional matrix bar code (for example, a QR code or Aztec code) encoded with data identifying the contents of the associated process tube 102.
• a camera e.g., a CCD camera
• a camera can be used to scan and verify the contents of the process tube 102 and ensure the correct amplification assays are being performed with the associated reagents.
• the camera can efficiently and quickly verify the contents of each process tube 102 by reading the tag 1 12, thus avoiding the possibility of user error in pairing incorrect reagents with a specific amplification assay required for a given polynucleotide sample.
• each tube strip 100 can include eight process tubes 102 and then 12 tube strips can be securely fit into a 96-port carrier tray 300. Identical reagents can then be added to each of the 96 process tubes in the carrier tray 300. If all process tubes 102 are provided with identical reagents, all process tubes 102 in the entire carrier tray 300 can be hot stamped with the same color. A number of carrier trays 300 can be stacked and sent together to the end user.
• each or some of the process tubes 102 in tube strip 100 can include different reagents. In such instances, process tubes 102 that contain identical reagents can be marked with the same color. Different colors can be used to identify process tubes 102 containing different reagents.
• the end user may need different stamped process tubes 102 to run different amplification assays with the different reagents provided.
• the end user may need to use different reagents in an amplification assay, so a carrier tray 300 having process tubes 102 of all the same reagents could not be used.
• the end user can remove one or more process tube strips 100 from a single-color carrier tray 300 and exchange them with differently colored process tube strips 100 in a different carrier tray 300 to achieve the desired number and type of reagents for a given amplification assay.
• the manufacturer could provide the end user with a carrier tray 300 having different colored process tube strips 100.
• the end user can further refine the collection of different reagents in an amplification assay by breaking apart an individual process tube strip 100 at the connector recess 232 between process tubes 102.
• an eight-tube process tube strip 100 can be broken into smaller collections of process tubes 102 having 1, 2, 3, 4, 5, 6, or 7 process tubes 102. Breaking apart the process tube strips 100 allows the end user to include process tubes 102 of different reagents in the same column of the carrier tray 300.
• FIG. 3B provides an illustration of the process tubes 102 when the process tubes are already securely fit into the carrier tray 300.
• Fig. 4 is a cross- sectional view of 12 process tubes 102 positioned in the carrier tray 300 prior to securing the process tubes 102 in the carrier tray 300. This view is analogous to the cross-sectional view 6A shown in Fig. 3, but shows the process tubes 102 resting in the ports 306 of the carrier tray 300 prior to securing the process tubes 102 in the carrier tray 300.
• the carrier tray 300 has a base 304 and a shelf 302, the base 304 being wider and longer than the shelf 302 and, thus, having a larger planar surface area than shelf 302.
• the shelf 302 of the carrier tray 300 includes a shelf side 308 and a shelf top 310.
• the shelf top 310 is the horizontal, planar portion of the shelf 302 and covers the top of the carrier tray 300.
• the shelf top 310 includes an exterior surface 312 and an interior surface 314.
• the base 304 of the carrier tray 300 is wider and longer than the shelf 302, the base 304 includes a bridge 320 running horizontally connecting the shelf side 308 and a base side 305.
• the bridge 320 includes an interior side 322.
• the shelf side 308 of the shelf 302 on the carrier tray 300 extends down from the shelf top 310 and joins the base 304 of the carrier tray 300 at the bridge 320.
• the process tubes 102 of a process tube strip 100 can be positioned in the ports 306 in the shelf 302 of the carrier tray 300.
• FIG. 5 is a close-up, cross-sectional view of two exemplary process tubes 102 positioned in an exemplary carrier tray 300, prior to securing the process tubes 102 in the carrier tray 300.
• the process tube 102 Prior to securing a process tube 102 in the carrier tray 300, the process tube 102 is able to rest in the port 306 of the carrier tray 300.
• the outside diameter of the body 218 of the process tube 102 is smaller than the diameter of the port 306, thus, the body 218 of the process tube 102 can be inserted through the port 306.
• the protrusion 212 on the process tube 102 has a larger diameter than at least one diameter of the port 306.
• the smaller diameter of the port 306 (for example the width diameter in the x-direction of Figs. 3 A and 3B) is smaller than the diameter of the protrusion 212.
• the larger diameter of the port 306 (for example the length diameter in the y- direction of Figs. 3A and 3B) can be larger than the diameter of the protrusion 212.
• the body 218 of the process tube 102 when the body 218 of the process tube 102 is inserted into the port 306, the body 218 enters the underside area of the carrier tray 300, but a top portion of the process tube 102, including the securement region 200 (comprising the protrusion 212, the neck 228, and the annular ledge 204) and the top ring 202, is prevented from entering the port 306.
• the protrusion 212 comes to rest on a top edge 318 of the port 306. More specifically, the lower slope 216 of the protrusion 212 comes to rest on the port top edge 318.
• the apex 212 of the protrusion 212 is circular, having a constant outside diameter.
• the port 306 can have a length diameter larger than the width diameter.
• the diameter of the port 306 width (in the x direction) can be less than the diameter of the apex 215 of the protrusion 212.
• the process tube 102 comes to rest, at the protrusion 212, on the top edge 318 of the port 306.
• the length diameter (in the y direction) of the port 306 can be greater than the diameter of the apex 215 of the protrusion 212.
• a small gap on two ends (in the y-direction) of the port 306 is provided that facilitates easier securement of the process tube 102 in the port 306 and also facilitates easier removal of the process tube 102 from the port 306, if needed.
• the port 306 can be round, having a constant diameter.
• a force can be applied to the top of the process tube 102 to press the process tube 102 further into the port 306 to secure the process tube 102 in the port 306 of the carrier tray 300.
• the force to secure the process tube 102 into the port 306 can be applied to the top ring 202 of the process tube 102 or the force can be applied to the upper surface 206 of the annular ledge 204.
• Securing the process tube 102 in the port 306 initially involves applying sufficient force to the top of the process tube 102 to force the lower slope 216 of the protrusion 212 into the port 306.
• the lower slope 216 is angled towards the longitudinal axis 230 of the process tube 102.
• the lower slope 216 of the protrusion 212 slides down along the port top edge 318 until the apex 215 of the protrusion 212 reaches the port top edge 318.
• the port top edge 318 can be rounded or sloped to facilitate the travel of the protrusion 212 through the port 306.
• the portions of the lower slope 216 of the protrusion 212 that have passed into the port 306 do not contact the port interior wall 316 because the lower slope 216 is angled towards the longitudinal axis 230.
• the lower slope 216 of the protrusion 212 gradually widens (the outside diameter increases) as the lower slope 216 extends upwards towards the apex 215 of the protrusion 212. The wider the diameter of the lower slope 216, the greater resistance to pushing the process tube 102 into the port 306. Thus, a resistive force is generated which counters the force applied to push the process tube 102 into the port 306.
• the resistive force against the process tube 102 increases (and the force necessary to push the process tube 102 increases), the farther down the process tube 212 travels into the port 306.
• the resistive force against the process tube 102 continues to increase until the apex 215 of the protrusion 212 reaches the port top edge 318.
• the larger diameter of the port 306 in the y direction may more easily allow the process tube 102 to be pushed into the port 306 and secured in the carrier tray 300, thus reducing the force required to secure the process tube.
• An elliptical port 306 can provide extra space (e.g., a gap) between the protrusion 212 of the process tube 102 and the port interior 316 on two ends that allows the process tube 102 to flex and elongate in the y direction and compress in the x direction.
• the apex 215 of the protrusion 212 comes into contact with the port interior wall 316.
• the apex 215 is the widest portion (largest outside diameter) of the protrusion 212.
• the apex 215 is forced to slide down the port interior wall 316 until it completely passes through the port 306 at the bottom edge 319 of the port 306. Once the apex 215 breaches the bottom edge 319, the strain on the process tube 102 is released and the process tube 102 "snaps" securely into place in the port 306 and becomes secured in the carrier tray 300.
• the force necessary to secure each process tube 102 of the process tube strips 100 in a carrier tray 300 can range from approximately 0.7 lbs. force to approximately 1.7 lbs. force. In one embodiment, the force necessary to insert and secure process tube 102 in a port 306 can be approximately 1 lb. force.
• the force necessary to secure a process tube 102 in a port 306 can be approximately 1.18 lbs. force.
• the carrier tray 300 can be advantageously designed for efficient stacking and transport of the carrier trays 300.
• the carrier tray 300 can be constructed from polycarbonate resin thermoplastic. Referring to Figs. 3, 4, and 5, the carrier tray 300 can include a bridge 320 at the top of the base 220. The bridge 320 provides a platform on which the bottom surface 326 of another empty carrier tray 300 can positioned.
• the bridge interior 322 of a top carrier tray 300 comes to rest on the shelf top 310 of a bottom carrier tray 300 and the bottom surface 326 of the top carrier tray 300 comes to rest on the bridge 320 of the bottom carrier tray 300.
• the carrier trays 300 When the carrier trays 300 are populated with the process tube strips 100, they can be efficiently stacked in a similar manner.
• the body 218 of the process tubes 102 in a top carrier tray 300 can be placed in the opening 226 of the process tubes 102 in a bottom carrier tray 300.
• the process tubes 102 in the top carrier tray 300 can further receive the body 218 of the process tubes 102 in another carrier tray 300 to be stacked on top of it.
• Fig. 6A is a cross-sectional view, taken along line 6A in Fig. 3B, of the 12 process tubes 102 shown in Fig. 4.
• Fig. 6A shows the process tubes 102 now secured in the carrier tray 300.
• the direction of cross-section 6A in Fig. 3B provides a view of 12 process tubes 102, each from a different process tube strip 100.
• Fig. 6B is a cross-sectional view, taken along line 6B in Fig. 3B, of an entire process tube strip 100 positioned in the carrier tray 300 after securing the process tubes 102 in the carrier tray 300.
• the cross- sectional diameter of the elliptical port 306 in the y direction can be larger than the diameter of the protrusion 212.
• Fig. 7 is a close-up view of two of the process tubes 102 shown in Fig. 6A and corresponds to the process tubes 102 of Fig. 5 after securing the process tubes 102 in the carrier tray 300.
• the cross-sectional diameter of the elliptical port in the x direction can be smaller than the diameter of the protrusion 212.
• the annular ledge 204 is sufficiently wide at at least two points around the port 306 that the annular ledge 204 cannot pass through the port 306.
• the annular ledge 204 can have a sufficiently large diameter to cover all points around the port 306.
• the annular ledge 204 can have a larger diameter than the width and length diameters of the port 306.
• the height of the securement region 200 (from the lower surface 210 of the annular ledge 204 to a location on the upper slope 214 of the protrusion 212) corresponds approximately to the height of the port 306, between the port top edge 318 and the port bottom edge 319.
• the neck 228 of the process tube 102 can have a smaller outside diameter than the diameter of the port 306, creating a gap 324 between the process tube 102 and the port interior wall 314.
• the outside diameter of the neck 228 can be a fixed circular diameter.
• the width of the gap 324 can vary between the length side (y direction) and width side (x direction) of the port 306.
• the size of the gap 324 on each length side of the port 306 can be approximately twice the size of the gap on each width side of the port 306.
• the gap 324 provides a point of adjustment for the process tube 102 in the securement region 200.
• the gap 324 exists primarily between the neck 228 of the process tube 102 and the port interior wall 316, but the gap 324 also exists along a portion of the upper slope 214 of the protrusion 212 and along a portion of the lower surface 210 of the annular ledge 204.
• the gap 324 is enlarged slightly at the top portion of the securement region 200 because the rounded corners of the port top edge 318 provide additional distance between the port 306 and the neck 228 of the process tube 102.
• the gap 324 can provide the process tube 102 some degree of freedom of movement within the port 306 of the carrier tray 300, even when the process tube 102 is secured in the port 306.
• the process tube 102 can be adjusted in the port 306 while being maintained securely in the port 306 because the point of contact between the upper slope 214 of the protrusion 212 and the port bottom edge 319 can adjust as the process tube 102 needs to tilt.
• the locations of the points of contact between the securement region 200 of the process tube 102 and the port 306 of the carrier tray 300 will adjust. For example, when the process tube tilts to one side, a point of contact on one side of the process tube 102 between the upper slope 214 and port bottom edge 319 moves near the top of the upper slope 214; on the other side of the tube, another point of contact moves to be near the bottom of the upper slope 214 (near the apex 215).
• the gap 324 allows the process tube 102 to adjust when placing a plurality of process tubes into the carrier tray 100 as part of a process tube strip 100. Because of possible manufacturing variations of the carrier trays 300 and the process tubes 102, each carrier tray 300 may be sized slightly differently and each process tube 102 may fit in the carrier trays 300 differently.
• process tubes 102 are often attached together as part of a process tube strip 102 when inserted in the carrier tray 300, it is possible that, without mitigating considerations, the manufacturing variations of the carrier tray 300 and process tubes 102 could prevent accurate placement of an entire process tube strip 100 in a carrier tray 300.
• accurate insertion of a process tube 102 at one end of a process tube strip 100 into the carrier tray 300 could prevent accurate insertion of the process tubes 102 at the other end of the process tube strip 100 into the carrier tray 300 because the process tubes 102 could be misaligned in either the x direction (lateral) or y direction (front to back).
• the present disclosure addresses these issues in a number of ways, including allowing the process tubes 102 to tilt and adjust in the port 306 when the process tube strip 100 is being maneuvered and inserted in the carrier tray 300.
• the process tubes 102 can tilt and adjust in the port 306 because the gaps 324 allow for such motion.
• the elliptical shape of the ports 306 also enhances the adjustment available in the y direction.
• the connector tabs 104 connecting the process tubes 102 are thin and pliable enough to allow maneuverability and adjustment between the individual process tubes 102 when inserting them in the carrier tray 300.
• the connector recess 232 (seen in Fig. 2B) on the connector tab 104 allows increased flexibility between the individual process tubes 102 when inserting them in the ports 306.
• the gaps 324, the elliptical-shaped ports 306, and the connector tabs 104 afford the process tube 102 the capacity to adjust and always lay flat on the carrier tray 300 when inserting a process tube strip 100 into the carrier tray 300. Furthermore, the capacity of a process tube 102 to tilt or adjust in the carrier tray 300 facilities insertion of the process tube 102 into a heater of the thermal cycler, as discussed below in more detail.
• the process tubes 102 can undergo processing in preparation for use in a thermal cycler. Liquid reagents can be inputted into the secured process tubes 102.
• the process tubes 102 in the carrier tray 300 can be subjected to heat or other processes for drying or lyophilization in order to dry the liquid reagents in the process tubes 102.
• the process tubes 102 can also be hot stamped to mark the process tubes 102, indicating the type of reagents added to the process tubes 102.
• the hot stamping can be in the form of a color stamped on the top ring 202 and/or the annular ledge 204.
• the process of applying force to securing the process tubes 102 in the ports 306 of the carrier tray 300, the process of inputting liquid reagents into the secured process tubes 102, the process of drying the liquid reagents in the process tubes 102, and the process of hot stamping the process tubes 102 in carrier tray 300 can all be automated and performed at the site of manufacture and assembly of the process tubes 102 and carrier trays 300.
• the assembled carrier trays 300 containing the prepared process tubes 102 can then be shipped to the end user for additional processing such as depositing extracted nucleic acid samples in the process tubes 102 prior to running amplification assays on the samples the process tubes 102 in a thermal cycler.
• the addition of the extracted nucleic acid samples to the process tubes 102 acts to reconstitute the dried reagents to allow the reagents to associate with the nucleic acid samples in the reconstituted solution.
• an end user can remove one or more process tube strips 100 from a single-color carrier tray 300 and exchange them with differently colored process tube strips 100 in a different carrier tray 300 to achieve the desired number and type of reagents for a given amplification assay.
• the force necessary to remove the process tube strip 100 can be approximately half of the force required to insert it.
• the insertion force for a process tube strip 100 can have a range of approximately 0.7 lbs. force to 1.7 lbs. force and the removal force for the process tube strip 100 can have a range of approximately 0.3 lbs. force to 0.8 lbs force.
• the insertion force for a process tube strip 100 can be approximately 1 lb.
• the force and the removal force for the process tube strip 100 can be approximately 0.5 lb. force.
• the force necessary to secure a process tube strip 100 in the ports 306 can be approximately 1.18 lbs. force and the force necessary to remove the process tube strip is 0.60 lbs. force.
• the insertion and removal forces prescribed for the process tube strips 100 insure that a process tube strip 100 is not overly difficult to insert or remove from the carrier tray 300 and also prevent the process tube strips 100 from falling out of the carrier tray under normal handling conditions.
• the same carrier tray 300 housing the process tubes 102 in which the mixing of reagents and nucleic acid samples occurs can be input directly into the thermal cycler.
• the end user is not required to do the mixing of reagents and nucleic acid in one tube and then transport that mixed solution to another tube, or even move the first tube to another tray.
• the process tubes 102 containing the reagents and secured in the carrier tray 300 can receive the samples, e.g., nucleic acid samples, and, then without removing the process tubes 102 from the carrier tray 300, can be input into the thermal cycler for amplification assays.
• solid reagents may be added to the process tubes 102 in addition to, or instead of, the liquid reagents. It is also contemplated that empty process tubes 102 and carrier trays 300 can be supplied to the end user and the end user can deposit the solid or liquid reagents in the process tubes 102 prior to adding the nucleic acid samples.
• the securement force can be applied simultaneously to multiple (or all) process tubes 102 in the carrier tray 300.
• the securement force can be applied separately to individual process tubes 102 one at a time, as needed.
• the securement force can be applied in an automated manner and can be conducted concurrently along with the automated steps of filling the process tubes 102 with reagents and hot stamping the process tubes 102.
• the same apparatus can be used to hot stamp and apply the securement force to the process tubes 102.
• separate apparatuses can be used for hot stamping and applying the securement force.
• the securement force can first be applied to secure the process tubes 102 in the ports 306 of the carrier tray 300 prior to hot stamping the top ring 202 of the process tubes 102.
• the automated hot stamping apparatus may stick to the top ring 202 of the process tubes 102 when applying pressure to the top ring 202. Because of the novel way in which the process tubes 102 are secured in the carrier tray 300 in the embodiments described herein, a process tubes 102 are not pulled up and out of the carrier tray 300 when the hot stamping apparatus pulls apart from the process tube 102 being stamped.
• the process tubes 102 are secured in the carrier tray 300, the process tubes 102 can be transported without risk of the process tubes 102 falling out of the carrier tray 300.
• the embodiments disclosed herein also advantageously overcome other issues that present in other PCR tube trays, such as bunching of tubes on one side of the tray or tubes falling out of alignment in the tray.
• Fig. 8 is an isometric view of an exemplary heater assembly 400 to be used in a thermal cycler (not shown). Amplification assays (such as PCR or isothermal amplification) can be performed in the thermal cycler.
• the heater assembly 400 is part of temperature cycling- subsystem of the thermal cycler and can work in conjunction with other subsystems of the thermal cycler, such as a detection subsystem.
• the exemplary heater assembly 400 shown in Fig. 8 is a 96-well assembly containing 96 heater wells 402, although other assemblies are contemplated (e.g., 48-well assemblies, etc.).
• the heater assembly 400 includes a flat top surface 404 between the heater wells 402, and a side surface 410.
• Each heater well 402 is conical in shape and is comprised of an interior wall 406and a well bottom 412.
• the heater wells 402 in the heater assembly 400 are arranged in an array of 8 rows and 12 columns to correspond to the spatial arrangement of process tubes 102 in a carrier tray 300.
• Each heater well 402 can receive a process tube 102.
• the carrier tray 300 can be placed directly over the heater assembly 400 in the thermal cycler in order to place all process tube 102 in the carrier tray 300 into the heater assembly 400 simultaneously.
• Not shown in Fig. 8 is the casing around the heater assembly 400 or the necessary circuitry to provide heat to the heater wells 402.
• each carrier tray 300 may be sized slightly differently and each process tube 102 may fit in the carrier trays 300 differently. If the process tubes 102 were rigidly attached to the carrier tray 300, the manufacturing tolerances could prevent all of the process tubes in a 96- tube carrier tray 300 from accurately being placed in the heater wells 402. For example, fitting a process tube 102 in a heater well 402 on one side of the heater assembly 400 may prevent a process tube 102 on the other side of the heater assembly 400 from being accurately and securely placed into its respective heater well 402.
• the process tubes 102 are able to float or adjust slightly when secured in the carrier tray 300 because of the gap 324 between the port interior wall 316 and the securement region 200 of the process tube 102.
• the connector recess 232 (seen in Fig. 2B) on the connector tab 104 also allows flexibility between the individual process tubes 102 when inserting them in the heater wells 402. Allowing the process tubes 102 to float within ports 306 of the carrier tray 300 permits the process tubes 102 to adjust position to fit accurately and securely into the heater wells 402 of the heater assembly 400.
• Fig. 9 is a cross-sectional view of two exemplary process tubes 102 positioned in heater wells 402 of the heater assembly 400.
• the body 218 of the process tube 102 comes in physical contact with, and is mated to, the interior wall 406 of the heater well 402.
• the heater well 402 is deeper than the body 218 of the process tube 102, such that when the process tube 102 is secured in a port 306 of the carrier tray 300 and the carrier tray 300 is positioned over the heater assembly 400, the base 220 of the process tube 102 does not extend to the well bottom 412. In this manner, a gap 414 is created between the base 220 of the process tube 102 and the well bottom 412.
• the gap 414 ensures that the body 218 of the process tube 102 remain in physical contact with the well interior wall 406; if the base 220 of the process tube 102 were to bottom out in the heater well bottom 412 first, before the body 218 contacts the well interior wall 406, a gap could exist between the wall 406 and the body 218 of the process tube 102 and cause poor heat transfer between the heater well 402 and the process tube 102.
• the gap 414 below the process tube 102 ensures that a gap does not exist between the wall 406 and the body 218 of the process tube 102.
• the heater well 402 can surround the body 218 of the process tube 102 and provide uniform heating to the contents of the process tube 102 during the thermal cycling steps of the amplification assay. When the process tube 102 is placed in the heater well 402, the heater well 402 can surround the body 218 of the process tube to a location just below the lower slope 216 of the protrusion 212.
• This example illustrates a specific process for preparing a carrier tray 300 with process tubes 102 to be provided to an end user.
• the process tubes of the process tube strips are secured in the ports of the carrier tray by applying a force to the top ring of the process tube.
• Each process tube in the carrier tray is filled with the same specific liquid reagents.
• the carrier tray is heated to dry the reagents in the process tubes.
• the process tubes are hot stamped with specific colors to indicate the assay for which they will be used.
• the carrier tray is stacked and packaged with other carrier trays having the same or different reagents and shipped to the end user.
• the end user can use the entire carrier tray as is, or may depopulate the carrier tray and repopulate the carrier tray or trays with a mix of individual process tube strips or tubes of various reagent types.
• This example describes the test procedure and results of a test to determine the force necessary to secure the process tube strips 100 in the ports 306 of the carrier tray 300 and the force necessary to subsequently remove the process tube strips 100 from the ports 306.
• Table 1 shows the force necessary to insert and secure all the process tubes 102 of a process tube strip 100 in a carrier tray 300. As shown, the average insertion force to secure the process tube strips 100 in the carrier tray 300 was 1.18 lbs force and the average removal force was 0.60 lbs force.

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• 2013
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