US 20050063806 A1
A device for transporting cartridges comprises a housing for holding a plurality of cartridges in a temperature controlled environment. A transport system is also provided and has a grasping mechanism for grasping one of the cartridges. The transport system is further used to remove the cartridge from the housing and to place the cartridge into a scanner.
36. A holder for an array unit having a planar substrate and an array of chemical moieties on a surface of the substrate, the holder comprising: a body with a retaining mechanism which releasably retains an array unit in a seated position, such that an array unit can be repeatedly inserted into and removed from the seated position in which it is retained in the holder; a machine readable holder identifier which includes data on a characteristic of the holder or seated array.
37. A holder according to
38. A holder according to
39. A holder according to
40. A holder according to
41. A holder according to
42. A holder according to
43. A holder according to
44. A holder according to
45. A holder according to
46. A holder according to
47. A holder according to
48. A holder according to
49. A holder according to
50. A method of reading an array of chemical moieties on a substrate of an array unit, the method comprising: seating the array unit in a holder, which holder carries a holder identifier; mounting the holder with seated array unit into an array reader; reading the holder identifier and retrieving data on a position or dimension of the seated array unit based on the read holder identifier; and reading the array.
51. A method according to
52. A method according to
53. A method according to
54. A method according to
55. A holder according to
56. A holder according to
57. A method according to
58. A method according to
59. A method according to
60. A method comprising forwarding data representing a result of a reading obtained by the method of
61. A method according to
62. A method comprising receiving data representing a result of a reading obtained by the method of
63. A method of reading an array of chemical moieties on a substrate of an array unit, the method comprising: seating the array unit in a holder, which holder carries a holder identifier; reading the holder identifier and retrieving a characteristic of the holder or seated array based on the read holder identifier; and when the retrieved characteristic does not meet a predetermined condition, rejecting the seated array unit for reading or generating an operator alert.
64. A method according to
65. An apparatus for reading an array of chemical moieties on a substrate of an array unit, the apparatus comprising: a receptacle into which is mountable a holder carrying a seated array unit, which holder carries a holder identifier; a reader system to read the holder identifier and data from different chemical moieties of the array; and a processor which retrieves data on a characteristic of the holder or seated array based on the read holder identifier.
66. An apparatus according to
67. An apparatus according to
68. An apparatus according to
69. An apparatus according to
70. An apparatus according to
71. An apparatus according to
72. An apparatus according to
73. An apparatus according to
74. An apparatus according to
75. An apparatus according to
76. An apparatus according to
77. An apparatus according to
78. A computer program product for use with an apparatus of
79. A computer program product according to
80. A computer program product according to
This application is a continuation in part application of and claims the benefit from U.S. Provisional Patent Application No. 60/217,246, filed Jul. 10, 2000, the complete disclosure of which is herein incorporated by reference.
This invention relates generally to the field of automation, and in particular to the use of automated equipment to transfer items. More specifically, the invention relates to the automated transfer of array cartridges into and out of an imaging apparatus.
1. Polymer Arrays
Methods for using arrays of polymers to identify receptors with specific affinities for one of the polymers in the array are known. For example, one method uses immobilized antibodies to analyze binding to peptide ligands or vice-versa. Another type of method uses immobilized oligonucleotides to analyze hybridization to a target nucleic acid. For instance, U.S. patent application Ser. No. 08/624,312, filed Mar. 26, 1996, the complete disclosure of which is herein incorporated by reference, describes apparatus and methods for carrying out repeated hybridizations of a target nucleic acid to an array of nucleic acid probes. Such polymer arrays are described in, e.g., U.S. Pat. No. 5,143,854 and published PCT Application Nos. WO90/15070 and WO92/10092, the complete disclosures of which are herein incorporated by reference. These polymer arrays are nucleic acid arrays which include a plurality of different polynucleotides coupled to a substrate in different known locations.
In one exemplary arrangement, such arrays are packaged within a housing or cartridge, like those described in, e.g., U.S. Pat. No. 5,945,334, and in copending U.S. patent application Ser. Nos. 08/624,312, previously incorporated by reference, 08/528,173, filed Sep. 19, 1995, and published PCT Application No. WO95/33846. The disclosures of all of these references are herein incorporated by reference. In brief, such a cartridge may be constructed of a body having a reaction cavity or hybridization chamber. The array or substrate is mounted over the cavity on the body such that the front side of the array substrate, e.g., the side upon which the polynucleotides are situated, is in fluid communication with the cavity. The cartridge includes inlet and outlet ports to allow various fluids to be introduced into and removed from the hybridization chamber.
Imaging the polymer arrays may be accomplished, for example, by placing the cartridges into a scanning device, such as the GeneArray scanner, available from Affymetrix, Inc. Techniques for imaging polymer arrays are described in U.S. Pat. Nos. 5,834,758 and 5,578,832, the complete disclosures of which are herein incorporated by reference.
In many cases, it is desirable to maintain the cartridges in a temperature controlled environment. Hence, a need exists for equipment and techniques to transfer cartridges from a temperature controlled environment for placement into the scanner in an organized and efficient manner, and for the return of the cartridges to the temperature controlled environment following imaging. Hence, the invention is related to apparatus and methods to facilitate imaging of array cartridges in such a manner.
In one embodiment, a device for transporting cartridges comprises a housing for holding a plurality of cartridges in a temperature controlled environment. The device further includes a transport system having a grasping mechanism to grasp one of the cartridges, to remove the cartridge from the housing and to place the cartridge into a scanner. In this way, each cartridge remains within a temperature controlled environment until ready for scanning. At such time, the transport system is employed to remove the cartridge from the housing and to place the removed cartridge into the scanner.
In one aspect, the device further includes a heating station for heating a cartridge (to prevent fogging) prior to insertion into the scanner. As such, the grasping mechanism may be configured to place the grasped cartridge at the heating station prior to placement into the scanner. In one specific aspect, the heating station may include a fan that is disposed to blow ambient air onto the cartridge to heat the cartridge.
In another aspect, the device may also include a holding station to hold a cartridge after being removed from the scanner. In this way, a cartridge that is removed from the scanner may be positioned near the scanner during a cycle where another cartridge is removed from the heating station and placed into the scanner. The cartridge that is held in the holding station may then be placed back into the housing. In this manner, the throughput of the device may be increased by reducing the amount of travel by the grasping system while the scanner is idle, i.e. awaiting a new cartridge.
Conveniently, a rack system may be rotatably disposed within the housing and may include a plurality of racks for holding the cartridges. In one aspect, a plurality of carriers may be provided, with each carrier holding multiple cartridges. In this way, a carrier of cartridges may conveniently be placed into the housing and coupled to the rack system simply by inserting the carrier into one of the racks. Conveniently, a belt may be coupled to the rack system, and a motor may be used to rotate the belt, thereby rotating the rack system. By rotating the rack system, one or more carriers may be aligned with an opening in the housing to facilitate removal of the cartridges. In a particular aspect, the carriers may each have a bottom end and an open top end, and a plurality of slots for receiving the cartridges in a parallel arrangement. When inserted into the slots, the cartridges extend above the top ends of the carriers to facilitate easy gasping and removal from the carriers. Further, the rack system may be configured to maintain the top ends of the carriers generally horizontal during rotation. In this way, the cartridges will not fall out of the carriers when rotated within the housing. Such a feature may be accomplished by use of belts that maintain alignment of the individual racks during rotation by the motor.
In another aspect, the device may include a barcode reader that is disposed within the housing. In this way, barcode labels on the cartridges may be read as they are removed from and/or placed into the housing. In one aspect, the grasping mechanism comprises a pair of fingers that are movable toward and away from each other to grasp and release the cartridges. In still another aspect, the transport system may comprise a horizontal lead screw and a first motor to rotate the horizontal lead screw. With such a configuration, the grasping mechanism may be coupled to the horizontal lead screw such that rotation of the lead screw translates the grasping mechanism horizontally. Further, a vertical lead screw may be provided along with a second motor to rotate the vertical lead screw. The grasping mechanism may be coupled to the vertical lead screw such that rotation of the lead screw translates the grasping mechanism vertically. A controller may then be employed to operate the motors and the grasping mechanism when transporting the cartridges. Conveniently, the housing may include a lid, and an electric motor may be used to open the lid, such as when receiving a signal from the controller. In this way, the housing may remain closed until a cartridge is removed from or placed into the housing. Alternatively, the lid may be slid open and closed by some interaction of the horizontal travelling system and the lid, i.e. the interaction could push the lid to the side.
The invention further provides an alignment mechanism for aligning a scanner with transporting device, such as the transporting device just described. The alignment mechanism comprises a clamping plate that may be clamped to a portion of the scanner. For example, the alignment mechanism may be clamped to a pair of feet on the bottom of the scanner. An adjustment plate is slidably coupled to the clamping plate and has at least one connector that may be connected to the transporting device, thereby coupling the scanner to the transporting device. An alignment fixture is removably coupled to the adjustment plate and includes an arm that is adapted to be aligned with an entry port of the scanner. In this way, the scanner may be moved relative to the transport device until the alignment fixture is aligned with the entry port. A securing mechanism may then be operated to secure the adjustment plate to the clamping plate, thereby fixing the position of the scanner relative to the transporting device. The alignment fixture may then be removed from the adjustment plate. Alternatively, the transporting device and the scanner may be aligned without the use of an alignment mechanism. Hence, the invention is not intended to be limited for use only with an alignment mechanism.
The invention further provides a method for transporting cartridges. According to the method, a plurality of cartridges are placed into a temperature controlled housing. One of the cartridges is grasped and removed from the housing with a grasping mechanism, moved to the scanner and then placed into the scanner. The grasping mechanism is then opened to deposit the cartridge into the scanner.
In one step, the cartridges are rotated within the housing to align groups of the cartridges with an opening in the housing to facilitate removal of the cartridges. In another step, each cartridge is placed in a warming station prior to being deposited into the scanner. For example, ambient air may be blown onto the cartridge to warm the cartridge and preventing fogging of the cartridge when within the scanner. After scanning, the cartridge is removed from the scanner and placed back into the housing, and another cartridge is placed into the scanner.
In an alternative aspect, to increase throughput the cartridge may be placed in a holding station after removal of the cartridge from the scanner. For example, one cartridge may be placed into the scanner prior to replacing a removed cartridge that is held within the holding station back into the housing. In this way, the grasping mechanism may return to the warming station to find a new cartridge for the scanner after removing a cartridge from the scanner. The grasping mechanism may then deposit the new cartridge into the scanner and return the cartridge that is held at the holding station back to the housing. While at the housing, another cartridge may then be removed and placed into the warming station to complete the cycle. In this way, the amount of travel of the grasping mechanism is minimized while the scanner is sitting idle, i.e. awaiting another cartridge, to increase throughput.
In another step, a barcode label on the cartridge may be read upon removal of the cartridge from the housing to keep track of which cartridges have been removed and scanned. In yet another step, the housing is aligned with the scanner and the housing is secured to the scanner prior to use.
In an alternative embodiment, a method for transporting cartridges comprises placing a plurality of cartridges into a carrier such that the cartridges extend above the carrier. One of the cartridges is removed from the carrier with a grasping mechanism and is moved to the scanner. The cartridge is placed into the scanner, and the grasping mechanism is released to deposit the cartridge into the scanner.
The invention provides for the transport of cartridges into an imaging device or scanner where the probe arrays are imaged. The invention may be used with essentially any type of imaging device or scanner where cartridges are inserted and processed. Conveniently, such scanners may utilize the imaging techniques described in U.S. Pat. Nos. 5,834,758 and 5,578,832, previously incorporated by reference, when imaging the probe arrays. However, the invention may be utilized with other types of scanners as well.
The cartridges used with the invention may be utilized in performing a variety of procedures, including, for example, hybridization reactions and, more specifically, nucleic acid hybridizations, extension or amplification reactions using tethered probes as template or primer sequences, screening of receptors against arrays of small molecules, peptides or peptideomimetics, carbohydrates, and the like. Cartridges suitable for performing such procedures are described in U.S. Pat. No. 5,945,334 and in co-pending U.S. application Ser. Nos. 08/624,312 and 08/528,173 and PCT Application No. WO95/33846, previously incorporated herein by reference. However, it will be appreciated that the invention is not intended to be limited to only these specific types of cartridges.
Referring now to
Cartridge 10 includes a pair of sides 26 and 28, a top 30 and a bottom 32. Extending from side 28 is an edge 34 that permits insertion of cartridge 10 into a carrier in only one orientation as described hereinafter.
Referring now to
As best shown in
As also shown in
Alignment mechanism 78 comprises a clamping plate 84, an adjustment plate 86, and an alignment fixture 88. Clamping plate 84 and adjustment plate 86 are also illustrated in
Adjustment plate 86 is coupled to clamping plate 84 so as to permit adjustment plate 86 to be moved relative to clamping plate 84. More specifically, a pair of tightening screws 96 and 98 are provided to secure clamping plate 84 to adjustment plate 86. Screws 96 and 98 are screwed into blocks 87 and 89 (see
Referring now to
Transport device 106 comprises a base 107 that may be coupled to adjustment plate 86 simply by sliding base 107 over adjustment plate 86. Transport device 106 further comprises a housing 108 that defines an interior 110. Housing 108 is constructed of an insulating material, such as styrofoam, to help maintain a temperature controlled environment within interior 110. Hidden from view is a thermal Peltier cooling device to provide a chilled environment within interior 110. Merely by way of example, interior 110 may be maintained at a temperature in the range from about 5° C. to about 25° C., and more preferably at about 15° C. Also hidden from view is a fan that is disposed within interior 110 to circulate air within interior 110 to maintain a generally constant temperature throughout interior 110.
Disposed within interior 110 is a rack system 112 that is configured to hold a plurality of carriers which each include multiple cartridges as described hereinafter. Conveniently, an opening 114 is provided in housing 108 to facilitate insertion and removal of the carriers. Although not shown, a cover will be placed over opening 114 when in use to maintain the temperature controlled environment within interior 110. Housing 108 further includes a top opening 116 to provide access into interior 110 when removing individual cartridges for scanning as described hereinafter.
Each rack 124 comprises a pair of arms 128 and 130. Arm 128 includes a hole 132 and arm 130 includes a hole 134. Each rack 124 is configured to hold a carrier 36 as previously described in connection with
Hence, rack system 112 permits multiple cartridges to be held within interior 110 and provides a convenient way to advance the cartridges until they are aligned with opening 116 where they will be retrieved from housing 110 as described hereinafter. Further, by using standard carriers, multiple sets of cartridges may easily be inserted into housing 110 simply by inserting the carriers through opening 114 in housing 108 and sliding the carriers between arms 128 and 130 of racks 124 until knobs 54 and 56 fit into holes 132 and 134.
As also shown in
An alternative belt arrangement is shown in
Referring now to
In operation, motor 158 is actuated to turn lead screw 156. This in turn moves grasping mechanism 160 horizontally side to side depending on the direction of rotation of lead screw 156. Motor 176 is operated to rotate lead screw 164 to raise or lower grasping fingers 166 and 168 depending on the direction of rotation of lead screw 164. Solenoid 170 may be actuated to move fingers 166 and 168 relative to each other to grasp or release a cartridge depending on the direction of movement of solenoid 170. Conveniently, transport device 106 may include a printed circuit board having controlling circuitry to operate the various motors and solenoid. Wiring 178 permits an electrical connection between the PC board and the components of grasping mechanism 160. Similarly, wiring 180 provides the appropriate electrical connection between the PC board and solenoid 170. Similar wiring may be employed for motor 158. A power supply 185 is also provided to supply power to the various electrical components of transport device 106. As best shown in
As previously described, lead screws may be employed to horizontally and vertically translate grasping mechanism 160. However, it will be appreciated that other translation mechanisms may be used as well. For example, a system of belts could also be employed.
Referring back to
Cartridge transport device 106 further includes a warming station 192 for warming cartridge 10 after being removed from housing 110. Warming of cartridge 10 is desirable in that it helps to eliminate condensation on the cartridge before it enters into scanner 70. Warming station 192 includes a fan 194 that is employed to blow ambient air across cartridge 10 to warm cartridge 10 before entering scanner 70.
Disposed adjacent entry port 76 is a holding station 196 that is employed to hold one of cartridges 10 after it has been removed from scanner 70. Holding station 196 is optional and serves to increase the throughput of cartridges that are scanned with scanner 70 as described hereinafter.
In operation, rack system 112 is employed to align a set of cartridges 10 which are held within a carrier 36 with opening 116. Grasping mechanism 160 is then positioned over opening 116 using lead screw 156. Grasping mechanism 160 is lowered into housing 110 using lead screw 164 until grasping fingers 166 and 168 are disposed on either side of one of the cartridges 10. Solenoid 170 is then actuated to move grasping fingers 166 and 168 together to grasp the cartridge. The cartridge is then raised from housing 110 by rotating lead screw 164 in the opposite direction. Conveniently, cartridge 10 may include a barcode label which identifies the particular cartridge. Further, a barcode reader (not shown) may be disposed within housing 110 to read the barcode label as the cartridge is being removed from housing 108. Use of carriers 36 is advantageous in that they properly align the cartridges so that the label may be read by the barcode reader and so that the cartridges will be in the proper orientation when being inserted into entry port 76 of scanner 70.
After cartridge 10 has been removed from housing 108, it is taken to warming station 192 where it is warmed by air produced from fan 194. After sufficient warming, cartridge 10 is again grasped by grasping mechanism 160 and moved into entry port 76 of scanner 70. Following scanning, grasping mechanism 160 is employed to remove cartridge 10 from scanner 70. Grasping mechanism 160 may then be moved back over opening 116, to place cartridge 10 back into housing 108 after lid 188 has been opened.
Alternatively, to reduce the cycle time, the cartridge may be placed into holding station 196 after exiting scanner 70. In this way, after depositing cartridge 10 in holding station 196, grasping mechanism 160 may be moved back to warming station 194 to remove a cartridge that had previously been placed into warming station 194. Cartridge 10 is then removed from warming station 194 and placed into entry port 76 of scanner 70 allowing scanning to commence. Grasping mechanism 160 then grasps the cartridge that is held within holding station 196 and returns it back to housing 108. Grasping mechanism 160 then removes another cartridge from housing 108 and places it into the empty warming station. Grasping mechanism 160 is then moved back to warming station 194 where the above described process is repeated. In this way, the operation of grasping mechanism 160 is partially overlapped with scanning to increase the number of cartridges that may be scanned within a given time period.
The PC board may be configured to control all of the operations so that scanning takes place in a fully automated manner. Conveniently, a computer having a display screen may be coupled to the PC board and may include a networking interface to permit convenient interaction with the scanner and transport device. Further, the host computer may include appropriate display screens to permit manual operation of any of the above steps and to permit tracking of a specific cartridge based on the barcode information.
Referring now to
Also coupled to scanner 70 is a track 216 to which a carrier frame 218 is coupled. Frame 218 is configured to hold a carrier 36 which in turn holds a set of cartridges 10 as shown. Frame 218 is slidable along track 216 to permit carrier 36 to be moved relative to arms 212 and 214 when an appropriate cartridge needs to be removed from or inserted into carrier 36. Conveniently, a motor (not shown) may be used to translate frame 218 horizontally along track 216. Although shown holding two carriers 36, it will be appreciated that in operation only a single carrier 36 may be used.
In operation, carrier 36 is moved along track 216 until a first one of the cartridges 10 is aligned with arms 212 and 214. Shaft 206 is then rotated to lower arms 212 and 214 until positioned about the first cartridge. Shaft 208 may then be rotated to move arms 212 and 214 close together until they grasp the cartridge. Carrier 36 may then be moved along track 216 so as to be clear of entry port 76. Lead screw 206 is rotated to lower cartridge 10 into entry port 76. Shaft 208 is rotated to release arms 212 and 214. Following scanning, the reverse procedure is followed to remove cartridge 10 from scanner 70 and to place it back into carrier 36. The process is then repeated for the remaining cartridges within carrier 36.
Hence, the invention provides exemplary techniques for transporting cartridges to and from a scanner. Conveniently, the invention may utilize standardized carriers that hold a number of cartridges that may be stored in a cool chamber. A two-axis robot may be employed to move the cartridges to and from the scanner, a warming station, and a holding station. A local operator interface and network connection may be provided to a host work station to facilitate operation of the transport system.
Use of the cartridge carriers is advantageous in that they provide a standardized way to hold the multiple cartridges. Further, the cartridge carriers may include keyed slots to prevent reverse installation. Use of the housing having a chilled chamber permits storage of the cartridges for several hours prior to scanning. However, it will be appreciated that in some embodiments, a temperature controlled chamber may not be needed. Following removal, the warming station may be used to eliminate condensation on the cartridge before its insertion into the scanner. Also, use of the robot allows automated movement of the cartridges between the carriers and the various stations in the scanner. Conveniently, a barcode scanner may be employed to identify the cartridge contents to the host computer. In one aspect, a connection may be made to the transport system using a network interface, and a local user interface may be incorporated to facilitate loading and unloading of the cartridges. Further, a non-intrusive alignment mechanism may be used to non-intrusively couple to the scanner. The alignment mechanism may then be used as the sole contact for alignment between the cartridge loader and the scanner. Conveniently, the cartridge loader may be configured to be relatively small in size so as to fit on a bench top and be installable by a single person.
The invention has been described in detail for purposes of clarity of understanding. However, it will be appreciated that certain changes and modifications may be practiced within the scope of the appended claims.