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Publication numberUS20060246576 A1
Publication typeApplication
Application numberUS 11/388,762
Publication dateNov 2, 2006
Filing dateMar 23, 2006
Priority dateApr 6, 2005
Also published asCN1847848A, CN1847848B, CN1876800A, CN201006877Y, CN201040757Y, US8796186, US20060234371, US20100069265, US20100081583
Publication number11388762, 388762, US 2006/0246576 A1, US 2006/246576 A1, US 20060246576 A1, US 20060246576A1, US 2006246576 A1, US 2006246576A1, US-A1-20060246576, US-A1-2006246576, US2006/0246576A1, US2006/246576A1, US20060246576 A1, US20060246576A1, US2006246576 A1, US2006246576A1
InventorsMohsen Shirazi
Original AssigneeAffymetrix, Inc.
Export CitationBiBTeX, EndNote, RefMan
External Links: USPTO, USPTO Assignment, Espacenet
Fluidic system and method for processing biological microarrays in personal instrumentation
US 20060246576 A1
Abstract
A fluidic system and method for processing biological sensors. The fluidic system includes a fluidic component including at least a first container and a second container. The first container is capable of holding a first volume of a first fluid, and the second container is capable of holding a second volume of a second fluid. Additionally, the fluidic system includes a support component configured to support at least the first container and the second container. The first container and the second container are substantially stationary with respect to the support component. Moreover, the fluidic system includes a transport component configured to move a first sensor, with respect to the support component, into the first container and in contact with the first volume of the first fluid, and move a second sensor, with respect to the support component, into the second container and in contact with the second volume of the second fluid. The first sensor and the second sensor are moved substantially simultaneously.
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Claims(55)
1. A fluidic system for processing biological sensors, the fluidic system comprising:
a fluidic component including at least a first container and a second container, the first container capable of holding a first volume of a first fluid, the second container capable of holding a second volume of a second fluid;
a support component configured to support at least the first container and the second container, the first container and the second container being substantially stationary with respect to the support component;
a transport component configured to:
move a first sensor, with respect to the support component, into the first container and in contact with the first volume of the first fluid;
move a second sensor, with respect to the support component, into the second container and in contact with the second volume of the second fluid;
wherein the first sensor and the second sensor are moved substantially simultaneously.
2. The fluidic system of claim 1 wherein the fluidic system is configured to process the first sensor and the second sensor so that the processed first sensor and the processed second sensor are ready for scan.
3. The fluidic system of claim 1 wherein:
when the first sensor is inside the first container and in contact with the first volume of the first fluid, the first volume of the first fluid remains completely within the first container;
when the second sensor is inside the second container and in contact with the second volume of the second fluid, the second volume of the second fluid remains completely within the second container.
4. The fluidic system of claim 1 wherein the first sensor is attached to a first support member.
5. The fluidic system of claim 4 wherein the first support member is a peg.
6. The fluidic system of claim 4 wherein the second sensor is attached to a second support member.
7. The fluidic system of claim 6 wherein each of the first support member and the second support member is a part of a plate.
8. The fluidic system of claim 1 wherein:
the first sensor is associated with a sensor length, a sensor width, and a sensor thickness;
the sensor length is equal to or shorter than 10 mm;
the sensor width is equal to or narrower than 10 mm;
the sensor thickness is equal to or thinner than 1000 μm.
9. The fluidic system of claim 1 wherein the first sensor is a biological sensor.
10. The fluidic system of claim 9 wherein the biological sensor includes a microarray.
11. The fluidic system of claim 1 wherein the first volume of the first fluid sensor is equal to or smaller than 5 ml.
12. The fluidic system of claim 1 wherein the support component is further configured to support, directly, at least the first container and the second container.
13. The fluidic system of claim 1 wherein the support component is further configured to support, indirectly through another object, at least the first container and the second container.
14. The fluidic system of claim 1 wherein the first fluid and the second fluid are the same or different in kind.
15. The fluidic system of claim 1 wherein the first volume and the second volume are the same or different in size.
16. The fluidic system of claim 1 wherein each of the first container and the second container is a well.
17. The fluidic system of claim 1 wherein the first container and the second container are two of a plurality of containers, the plurality of containers being attached, directly or indirectly, to a common component.
18. The fluidic system of claim 17 wherein the plurality of containers are arranged in one or more rows and one or more columns.
19. A fluidic system for processing biological sensors, the fluidic system comprising:
a fluidic component including at least a first container and a second container, the first container capable of holding a first volume of a first fluid, the second container capable of holding a second volume of a second fluid;
a support component including a panel for supporting at least the first container and the second container, the first container and the second container being substantially stationary with respect to the panel;
a transport component including a gripper and at least one motor;
wherein:
the gripper is capable of gripping the first sensor and the second sensor substantially simultaneously and of releasing the first sensor and the second sensor substantially simultaneously;
the at least one motor is configured to move the gripped first sensor, with respect to the panel, into the first container and in contact with the first volume of the first fluid;
the at least one motor is further configured to move the gripped second sensor, with respect to the panel, into the second container and in contact with the second volume of the second fluid;
wherein the first sensor and the second sensor are moved substantially simultaneously.
20. The fluidic system of claim 19 wherein the gripper includes an actuator.
21. The fluidic system of claim 20 wherein the actuator is a pneumatic actuator.
22. The fluidic system of claim 20 wherein the actuator is an electrical actuator.
23. The fluidic system of claim 19 wherein:
the at least one motor is capable of moving the gripped first sensor in at lest six directions;
each of the six directions is opposite to another direction of the six directions and is perpendicular to four directions of the six directions;
the four directions of the six directions are different from the another direction.
24. The fluidic system of claim 19 wherein the fluidic component is at least partially enclosed by a cover.
25. The fluidic system of claim 19 wherein:
the first container and the second container are attached to an object associated with a temperature;
the object includes a heater configured to heat up the first volume of the first fluid and the second volume of the second fluid;
the object further includes a thermometer configured to measure the temperature.
26. The fluidic system of claim 19, and further comprising a temperature controller coupled to the heater and the thermometer and configured to heat the temperature to a predetermined value.
27. The fluidic system of claim 19 wherein the transport component is coupled to a processing system, the processing system configured to provide instructions to the transport component for gripping, releasing, or moving the first sensor and the second sensor.
28. The fluidic system of claim 27 wherein the processing system includes a computer.
29. The fluidic system of claim 19 wherein the fluidic system is configured to process the first sensor and the second sensor so that the processed first sensor and the processed second sensor are ready for scan.
30. The fluidic system of claim 19 wherein:
when the first sensor is inside the first container and in contact with the first volume of the first fluid, the first volume of the first fluid remains completely within the first container;
when the second sensor is inside the second container and in contact with the second volume of the second fluid, the second volume of the second fluid remains completely within the second container.
31. The fluidic system of claim 19 wherein the first sensor is attached to a first support member.
32. The fluidic system of claim 31 wherein the first support member is a peg.
33. The fluidic system of claim 31 wherein the second sensor is attached to a second support member.
34. The fluidic system of claim 32 wherein each of the first support member and the second support member is a part of a plate.
35. The fluidic system of claim 19 wherein:
the first sensor is associated with a sensor length, a sensor width, and a sensor thickness;
the sensor length is equal to or shorter than 10 mm;
the sensor width is equal to or narrower than 10 mm;
the sensor thickness is equal to or thinner than 1000 μm.
36. The fluidic system of claim 19 wherein the first sensor is a biological sensor.
37. The fluidic system of claim 36 wherein the biological sensor includes a microarray.
38. The fluidic system of claim 19 wherein the first volume of the first fluid sensor is equal to or smaller than 5 ml.
39. The fluidic system of claim 19 wherein the support component is further configured to support, directly, at least the first container and the second container.
40. A method for processing biological sensors, the method comprising:
performing a hybridization process on at least a first sensor and a second sensor;
after the hybridization process, transferring the first sensor and the second sensor into a fluidic system, the fluidic system including at least a first container and a second container, the first container holding a first volume of a first fluid, the second container holding a second volume of a second fluid;
moving the first sensor into the first container and in contact with the first volume of the first fluid;
moving the second sensor into the second container and in contact with the second volume of the second fluid;
wherein the moving the first sensor and the moving the second sensor are performed substantially simultaneously.
41. The method of claim 40 wherein:
the fluidic system includes a support component configured to support at least the first container and the second container, the first container and the second container being substantially stationary with respect to the support component;
the moving the first sensor includes moving the first sensor with respect to the support component;
the moving the second sensor includes moving the second sensor with respect to the support component.
42. The method of claim 40, and further comprising after the moving the first sensor and the moving the second sensor, processing the first sensor and the second sensor so that the processed first sensor and the processed second sensor are ready for scan.
43. The method of claim 42 wherein the processing the first sensor and the second sensor includes performing at least a low stringency wash, at least a high stringency wash, and at least a stain process to the first sensor and the second sensor.
44. The method of claim 42, and further comprising:
transferring the processed first sensor and the processed second sensor out of the fluidic system;
performing a scanning process on the processed first sensor and the processed second sensor.
45. The method of claim 44 wherein between the transferring the first sensor and the second sensor-into a fluidic system and the transferring the processed first sensor and the processed second sensor out of the fluidic system:
the first volume of the first fluid is not in contact with any sensor other than the first sensor;
the second volume of the second fluid is not in contact with any sensor other than the second sensor.
46. The method of claim 44 wherein between the transferring the first sensor and the second sensor into a fluidic system and the transferring the processed first sensor and the processed second sensor out of the fluidic system:
the first container is not provided with any volume of any fluid that is different from the first volume of the first fluid and is not provided by the first sensor;
the second container is not provided with any volume of any fluid that is different from the second volume of the second fluid and is not provided by the second sensor.
47. The method of claim 40 wherein:
the moving the first sensor includes when the first sensor is inside the first container and in contact with the first volume of the first fluid, keeping the first volume of the first fluid completely within the first container;
the moving the second sensor includes when the second sensor is inside the second container and in contact with the second volume of the second fluid, keeping the second volume of the second fluid completely within the second container.
48. The method of claim 40 wherein the first sensor is attached to a first support member.
49. The method of claim 48 wherein the first support member is a peg.
50. The method of claim 48 wherein the second sensor is attached to a second support member.
51. The method of claim 50 wherein each of the first support member and the second support member is a part of a plate.
52. The method of claim 40 wherein the first sensor is a biological sensor.
53. The method of claim 52 wherein the biological sensor includes a microarray.
54. The method of claim 40 wherein the first fluid and the second fluid are the same or different.
55. The method of claim 40 wherein the first volume and the second volume are the same or different in size.
Description
    CROSS-REFERENCES TO RELATED APPLICATIONS
  • [0001]
    This application claims priority to U.S. Provisional Application No. 60/669,130, filed Apr. 6, 2005, which is incorporated by reference herein.
  • STATEMENT AS TO RIGHTS TO INVENTIONS MADE UNDER FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT
  • [0002]
    Not applicable.
  • REFERENCE TO A “SEQUENCE LISTING,” A TABLE, OR A COMPUTER PROGRAM LISTING APPENDIX SUBMITTED ON A COMPACT DISK.
  • [0003]
    Not applicable.
  • BACKGROUND OF THE INVENTION
  • [0004]
    The present invention relates in general to biological microarray techniques. More particularly, the invention provides a fluidic system and method for processing biological microarrays. Merely by way of example, the invention is described as it applies to personal instrumentation, but it should be recognized that the invention has a broader range of applicability.
  • [0005]
    A biological microarray often includes nucleic acid probes that are used to extract sequence information from nucleic acid samples. The nucleic acid samples are exposed to the nucleic acid probes under certain conditions that would allow hybridization. Afterwards, the biological microarray is processed and scanned to determine to which probes the nucleic acid samples have hybridized. Based on such determination, the sequence information is obtained by comparing patterns of hybridization and non-hybridization. As an example, the sequence information can be used for sequencing nucleic acids, or diagnostic screening for genetic diseases or for the presence of a particular pathogen or a strain of pathogen.
  • [0006]
    The processing of the biological microarray prior to scanning is often performed by a fluidic system. For example, the fluidic system includes a fluidic station. The fluidic station can wash and stain the microarray. With the advancement of the microarray design, the fluidic station often needs to be modified in order to improve automation and lower cost.
  • [0007]
    Hence it is highly desirable to improve fluidic techniques for processing microarrays.
  • BRIEF SUMMARY OF THE INVENTION
  • [0008]
    The present invention relates in general to biological microarray techniques. More particularly, the invention provides a fluidic system and method for processing biological microarrays. Merely by way of example, the invention is described as it applies to personal instrumentation, but it should be recognized that the invention has a broader range of applicability.
  • [0009]
    According to one embodiment of the present invention, a fluidic system for processing biological sensors includes a fluidic component including at least a first container and a second container. The first container is capable of holding a first volume of a first fluid, and the second container is capable of holding a second volume of a second fluid. Additionally, the fluidic system includes a support component configured to support at least the first container and the second container. The first container and the second container are substantially stationary with respect to the support component. Moreover, the fluidic system includes a transport component configured to move a first sensor, with respect to the support component, into the first container and in contact with the first volume of the first fluid, and move a second sensor, with respect to the support component, into the second container and in contact with the second volume of the second fluid. The first sensor and the second sensor are moved substantially simultaneously.
  • [0010]
    According to another embodiment, a fluidic system for processing biological sensors includes a fluidic component including at least a first container and a second container. The first container is capable of holding a first volume of a first fluid, and the second container is capable of holding a second volume of a second fluid. Additionally, the fluidic system includes a support component including a panel for supporting at least the first container and the second container. The first container and the second container are substantially stationary with respect to the panel. Moreover, the fluidic system includes a transport component including a gripper and at least one motor. The gripper is capable of gripping the first sensor and the second sensor substantially simultaneously and of releasing the first sensor and the second sensor substantially simultaneously. The at least one motor is configured to move the gripped first sensor, with respect to the panel, into the first container and in contact with the first volume of the first fluid. The at least one motor is further configured to move the gripped second sensor, with respect to the panel, into the second container and in contact with the second volume of the second fluid. The first sensor and the second sensor are moved substantially simultaneously.
  • [0011]
    According to another embodiment, a method for processing biological sensors includes performing a hybridization process on at least a first sensor and a second sensor, and after the hybridization process, transferring the first sensor and the second sensor into a fluidic system. The fluidic system includes at least a first container and a second container, the first container holds a first volume of a first fluid, and the second container holds a second volume of a second fluid. Additionally, the method includes moving the first sensor into the first container and in contact with the first volume of the first fluid, and moving the second sensor into the second container and in contact with the second volume of the second fluid. The moving the first sensor and the moving the second sensor are performed substantially simultaneously.
  • [0012]
    Many benefits are achieved by way of the present invention over conventional techniques. Certain embodiments of the present invention provide an automated fluidic system. Some embodiments of the present invention provide a low-cost fluidic system. Certain embodiments of the present invention can improve throughput of the fluidic system. For example, a plurality of biological sensors, such as microarrays, is processed in parallel. Some embodiments of the present invention can reduce cross-contamination between different processes performed on one or more biological sensors. For example, at a given process, different sensors are washed, stained, and/or held in different wells. In another example, a given sensor is washed, stained, and/or held in different wells for different processes respectively. In yet another example, each well is used for at most a single process for at most a single sensor, such as a microarray.
  • [0013]
    Depending upon embodiment, one or more of these benefits may be achieved. These benefits and various additional objects, features and advantages of the present invention can be fully appreciated with reference to the detailed description and accompanying drawings that follow.
  • BRIEF DESCRIPTION OF THE DRAWINGS
  • [0014]
    FIGS. 1-4 show a simplified fluidic system for processing biological sensors according to an embodiment of the present invention;
  • [0015]
    FIGS. 5(A) and (B) show a simplified well strip in fluidic system for processing biological sensors according to an embodiment of the present invention;
  • [0016]
    FIG. 6 is a simplified diagram showing temperature as function of time for well strip in fluidic system for processing biological sensors according to an embodiment of the present invention;
  • [0017]
    FIGS. 7(A) and (B) show a simplified gripper in fluidic system for processing biological sensors according to an embodiment of the present invention;
  • [0018]
    FIG. 8 shows a simplified fluidic system for processing biological sensors according to another embodiment of the present invention;
  • [0019]
    FIG. 9 shows a simplified fluidic method for processing biological sensors that is performed by fluidic system 100 or 800 according to an embodiment of the present invention;
  • [0020]
    FIGS. 10(A)-(V) are simplified diagrams showing movement of one or more sensors made by fluidic system 100 or 800 according to an embodiment of the present invention;
  • [0021]
    FIGS. 11(A) and (B) are simplified microarrays on pegs that can be processed by fluidic system 100 or 800 according to an embodiment of the present invention;
  • DETAILED DESCRIPTION OF THE INVENTION
  • [0022]
    The present invention relates in general to biological microarray techniques. More particularly, the invention provides a fluidic system and method for processing biological microarrays. Merely by way of example, the invention is described as it applies to personal instrumentation, but it should be recognized that the invention has a broader range of applicability.
  • I. General Description
  • [0023]
    The present invention cites certain patents, applications and other references. When a patent, application, or other reference is cited or repeated below, it should be understood that it is incorporated by reference in its entirety for all purposes as well as for the proposition that is recited.
  • [0024]
    As used in this application, the singular form “a,” “an,” and “the” include plural references unless the context clearly dictates otherwise. For example, the term “an agent” includes a plurality of agents, including mixtures thereof.
  • [0025]
    An individual is not limited to a human being but may also be other organisms including but not limited to mammals, plants, bacteria, or cells derived from any of the above.
  • [0026]
    Throughout this disclosure, various aspects of this invention can be presented in a range format. It should be understood that the description in range format is merely for convenience and brevity and should not be construed as an inflexible limitation on the scope of the invention. Accordingly, the description of a range should be considered to have specifically disclosed all the possible subranges as well as individual numerical values within that range. For example, description of a range such as from 1 to 6 should be considered to have specifically disclosed subranges such as from 1 to 3, from 1 to 4, from 1 to 5, from 2 to 4, from 2 to 6, from 3 to 6 etc., as well as individual numbers within that range, for example, 1, 2, 3, 4, 5, and 6. This applies regardless of the breadth of the range.
  • [0027]
    The practice of the present invention may employ, unless otherwise indicated, conventional techniques and descriptions of organic chemistry, polymer technology, molecular biology (including recombinant techniques), cell biology, biochemistry, and immunology, which are within the skill of the art. Such conventional techniques include polymer array synthesis, hybridization, ligation, and detection of hybridization using a label. Specific illustrations of suitable techniques can be had by reference to the example herein below. However, other equivalent conventional procedures can, of course, also be used. Such conventional techniques and descriptions can be found in standard laboratory manuals such as Genome Analysis: A Laboratory Manual Series (Vols. I-IV), Using Antibodies: A Laboratory Manual, Cells: A Laboratory Manual, PCR Primer: A Laboratory Manual, and Molecular Cloning: A Laboratory Manual (all from Cold Spring Harbor Laboratory Press), Stryer, L. (1995) Biochemistry (4th Ed.) Freeman, New York, Gait, “Oligonucleotide Synthesis: A Practical Approach” 1984, IRL Press, London, Nelson and Cox (2000), Lehninger, Principles of Biochemistry 3rd Ed., W.H. Freeman Pub., New York, N.Y. and Berg et al. (2002) Biochemistry, 5th Ed., W.H. Freeman Pub., New York, N.Y., all of which are herein incorporated in their entirety by reference for all purposes.
  • [0028]
    The present invention can employ solid substrates, including arrays in some preferred embodiments. Methods and techniques applicable to polymer (including protein) array synthesis have been described in U.S. Ser. No. 09/536,841, WO 00/58516, U.S. Pat. Nos. 5,143,854, 5,242,974, 5,252,743, 5,324,633, 5,384,261, 5,405,783, 5,424,186, 5,451,683, 5,482,867, 5,491,074, 5,527,681, 5,550,215, 5,571,639, 5,578,832, 5,593,839, 5,599,695, 5,624,711, 5,631,734, 5,795,716, 5,831,070, 5,837,832, 5,856,101, 5,858,659, 5,936,324, 5,968,740, 5,974,164, 5,981,185, 5,981,956, 6,025,601, 6,033,860, 6,040,193, 6,090,555, 6,136,269, 6,269,846 and 6,428,752, in PCT Applications Nos. PCT/US99/00730 (International Publication Number WO 99/36760) and PCT/US01/04285 (International Publication Number WO 01/58593), which are all incorporated herein by reference in their entirety for all purposes.
  • [0029]
    Patents that describe synthesis techniques in specific embodiments include U.S. Patent Nos. 5,412,087, 6,147,205, 6,262,216, 6,310,189, 5,889,165, and 5,959,098.
  • [0030]
    Nucleic acid arrays are described in many of the above patents, but the same techniques are applied to polypeptide arrays.
  • [0031]
    Nucleic acid arrays that are useful in the present invention include those that are commercially available from Affymetrix (Santa Clara, Calif.) under the brand name GeneChip®. Example arrays are shown on the website at affymetrix.com.
  • [0032]
    The present invention also contemplates many uses for polymers attached to solid substrates. These uses include gene expression monitoring, profiling, library screening, genotyping and diagnostics. Gene expression monitoring and profiling methods can be shown in U.S. Pat. Nos. 5,800,992, 6,013,449, 6,020,135, 6,033,860, 6,040,138, 6,177,248 and 6,309,822. Genotyping and uses therefore are shown in U.S. Ser. Nos. 15 10/442,021, 10/013,598 (U.S. Patent Application Publication 20030036069), and U.S. Pat. Nos. 5,856,092, 6,300,063, 5,858,659, 6,284,460, 6,361,947, 6,368,799 and 6,333,179. Other uses are embodied in U.S. Pat. Nos. 5,871,928, 5,902,723, 6,045,996, 5,541,061, and 6,197,506.
  • [0033]
    The present invention also contemplates sample preparation methods in certain preferred embodiments. Prior to or concurrent with genotyping, the genomic sample may be amplified by a variety of mechanisms, some of which may employ PCR. See, e.g., PCR Technology: Principles and Applications for DNA Amplification (Ed. H.A. Erlich, Freeman Press, NY, N.Y., 1992); PCR Protocols: A Guide to Methods and Applications (Eds. Innis, et al., Academic Press, San Diego, Calif., 1990); Mattila et al., Nucleic Acids Res. 19, 4967 (1991); Eckert et al., PCR Methods and Applications 1, 17 (1991); PCR (Eds. McPherson et al., IRL Press, Oxford); and U.S. Pat. Nos. 4,683,202, 4,683,195, 4,800,159 4,965,188, and 5,333,675, and each of which is incorporated herein by reference in their entireties for all purposes. The sample may be amplified on the array. See, for example, U.S. Pat. No. 6,300,070 and U.S. Ser. No. 09/513,300, which are incorporated herein by reference.
  • [0034]
    Other suitable amplification methods include the ligase chain reaction (LCR) (e.g., Wu and Wallace, Genomics 4, 560 (1989), Landegren et al., Science 241, 1077 (1988) and Barringer et al. Gene 89:117 (1990)), transcription amplification (Kwoh et al., Proc. Natl. Acad. Sci. USA 86, 1173 (1989) and WO88/10315), self-sustained sequence replication (Guatelli et al., Proc. Nat. Acad. Sci. USA, 87, 1874 (1990) and WO90/06995), selective amplification of target polynucleotide sequences (U.S. Pat. No. 6,410,276), consensus sequence primed polymerase chain reaction (CP-PCR) (U.S. Pat. No. 4,437,975), arbitrarily primed polymerase chain reaction (AP-PCR) (U.S. Pat. Nos. 5,413,909, 5,861,245) and nucleic acid based sequence amplification (NABSA). (See, U.S. Pat. Nos. 5,409,818, 5,554,517, and 6,063,603, each of which is incorporated herein by reference). Other amplification methods that may be used are described in U.S. Pat. Nos. 5,242,794, 5,494,810, 4,988,617 and in U.S. Ser. No. 09/854,317, each of which is incorporated herein by reference.
  • [0035]
    Additional methods of sample preparation and techniques for reducing the complexity of a nucleic sample are described in Dong et al., Genome Research 11, 1418 (2001), in U.S. Pat. No. 6,361,947, 6,391,592 and U.S. Ser. Nos. 09/916,135, 09/920,491 (U.S. Patent Application Publication 20030096235), Ser. No. 09/910,292 (U.S. Patent Application Publication 20030082543), and Ser. No. 10/013,598.
  • [0036]
    Methods for conducting polynucleotide hybridization assays have been well developed in the art. Hybridization assay procedures and conditions will vary depending on the application and are selected in accordance with the general binding methods known including those referred to in: Maniatis et al. Molecular Cloning: A Laboratory Manual (2nd Ed. Cold Spring Harbor, N.Y., 1989); Berger and Kimmel Methods in Enzymology, Vol. 152, Guide to Molecular Cloning Techniques (Academic Press, Inc., San Diego, Calif., 1987); Young and Davism, P.N.A.S. 80: 1194 (1983). Methods and apparatus for carrying out repeated and controlled hybridization reactions have been described in U.S. Pat. Nos. 5,871,928, 5,874,219, 6,045,996 and 6,386,749, 6,391,623 each of which are incorporated herein by reference.
  • [0037]
    The present invention also contemplates signal detection of hybridization between ligands in certain preferred embodiments. See U.S. Pat. Nos. 5,143,854, 5,578,832; 5,631,734; 5,834,758; 5,936,324; 5,981,956; 6,025,601; 6,141,096; 6,185,030; 6,201,639; 6,218,803; and 6,225,625, in U.S. Ser. No. 10/389,194 and in PCT Application PCT/US99/06097 (published as WO99/47964), each of which also is hereby incorporated by reference in its entirety for all purposes.
  • [0038]
    Methods and apparatus for signal detection and processing of intensity data are disclosed in, for example, U.S. Pat. Nos. 5,143,854, 5,547,839, 5,578,832, 5,631,734, 5,800,992, 5,834,758; 5,856,092, 5,902,723, 5,936,324, 5,981,956, 6,025,601, 6,090,555, 6,141,096, 6,185,030, 6,201,639; 6,218,803; and 6,225,625, in U.S. Ser. Nos. 10/389,194, 60/493,495 and in PCT Application PCT/US99/06097 (published as WO99/47964), each of which also is hereby incorporated by reference in its entirety for all purposes.
  • [0039]
    The practice of the present invention may also employ conventional biology methods, software and systems. Computer software products of the invention typically include computer readable medium having computer-executable instructions for performing the logic steps of the method of the invention. Suitable computer readable medium include floppy disk, CD-ROM/DVD/DVD-ROM, hard-disk drive, flash memory, ROM/RAM, magnetic tapes and etc. The computer executable instructions may be written in a suitable computer language or combination of several languages. Basic computational biology methods are described in, e.g. Setubal and Meidanis et al., Introduction to Computational Biology Methods (PWS Publishing Company, Boston, 1997); Salzberg, Searles, Kasif, (Ed.), Computational Methods in Molecular Biology, (Elsevier, Amsterdam, 1998); Rashidi and Buehler, Bioinformatics Basics: Application in Biological Science and Medicine (CRC Press, London, 2000) and Ouelette and Bzevanis Bioinformatics: A Practical Guide for Analysis of Gene and Proteins (Wiley & Sons, Inc., 2nd ed., 2001). See U.S. Pat. No. 6,420,108.
  • [0040]
    The present invention may also make use of various computer program products and software for a variety of purposes, such as probe design, management of data, analysis, and instrument operation. See, U.S. Pat. Nos. 5,593,839, 5,795,716, 5,733,729, 5,974,164, 6,066,454, 6,090,555, 6,185,561, 6,188,783, 6,223,127, 6,229,911 and 6,308,170.
  • [0041]
    Additionally, the present invention may have preferred embodiments that include methods for providing genetic information over networks such as the Internet as shown in U.S. Ser. Nos. 10/197,621, 10/063,559 (United States Publication No. 20020183936), Ser. Nos. 10/065,856, 10/065,868, 10/328,818, 10/328,872, 10/423,403, and 60/482,389.
  • II. Definitions
  • [0042]
    An “array” is an intentionally created collection of molecules which can be prepared either synthetically or biosynthetically. The molecules in the array can be identical or different from each other. The array can assume a variety of formats, e.g., libraries of soluble molecules; libraries of compounds tethered to resin beads, silica chips, or other solid supports.
  • [0043]
    Nucleic acid library or array is an intentionally created collection of nucleic acids which can be prepared either synthetically or biosynthetically and screened for biological activity in a variety of different formats (e.g., libraries of soluble molecules; and libraries of oligos tethered to resin beads, silica chips, or other solid supports). Additionally, the term “array” is meant to include those libraries of nucleic acids which can be prepared by spotting nucleic acids of essentially any length (e.g., from 1 to about 1000 nucleotide monomers in length) onto a substrate. The term “nucleic acid” as used herein refers to a polymeric form of nucleotides of any length, either ribonucleotides, deoxyribonucleotides or peptide nucleic acids (PNAs), that comprise purine and pyrimidine bases, or other natural, chemically or biochemically modified, non-natural, or derivatized nucleotide bases. The backbone of the polynucleotide can comprise sugars and phosphate groups, as may typically be found in RNA or DNA, or modified or substituted sugar or phosphate groups. A polynucleotide may comprise modified nucleotides, such as methylated nucleotides and nucleotide analogs. The sequence of nucleotides may be interrupted by non-nucleotide components. Thus the terms nucleoside, nucleotide, deoxynucleoside and deoxynucleotide generally include analogs such as those described herein. These analogs are those molecules having some structural features in common with a naturally occurring nucleoside or nucleotide such that when incorporated into a nucleic acid or oligonucleoside sequence, they allow hybridization with a naturally occurring nucleic acid sequence in solution. Typically, these analogs are derived from naturally occurring nucleosides and nucleotides by replacing and/or modifying the base, the ribose or the phosphodiester moiety. The changes can be tailor made to stabilize or destabilize hybrid formation or enhance the specificity of hybridization with a complementary nucleic acid sequence as desired.
  • [0044]
    Biopolymer or biological polymer: is intended to mean repeating units of biological or chemical moieties. Representative biopolymers include, but are not limited to, nucleic acids, oligonucleotides, amino acids, proteins, peptides, hormones, oligosaccharides, lipids, glycolipids, lipopolysaccharides, phospholipids, synthetic analogues of the foregoing, including, but not limited to, inverted nucleotides, peptide nucleic acids, Meta-DNA, and combinations of the above. “Biopolymer synthesis” is intended to encompass the synthetic production, both organic and inorganic, of a biopolymer.
  • [0045]
    Related to a bioploymer is a “biomonomer” which is intended to mean a single unit of biopolymer, or a single unit which is not part of a biopolymer. Thus, for example, a nucleotide is a biomonomer within an oligonucleotide biopolymer, and an amino acid is a biomonomer within a protein or peptide biopolymer; avidin, biotin, antibodies, antibody fragments, etc., for example, are also biomonomers. initiation Biomonomer: or “initiator biomonomer” is meant to indicate the first biomonomer which is covalently attached via reactive nucleophiles to the surface of the polymer, or the first biomonomer which is attached to a linker or spacer arm attached to the polymer, the linker or spacer arm being attached to the polymer via reactive nucleophiles.
  • [0046]
    Complementary: Refers to the hybridization or base pairing between nucleotides or nucleic acids, such as, for instance, between the two strands of a double stranded DNA molecule or between an oligonucleotide primer and a primer binding site on a single stranded nucleic acid to be sequenced or amplified. Complementary nucleotides are, generally, A and T (or A and U), or C and G. Two single stranded RNA or DNA molecules are said to be complementary when the nucleotides of one strand, optimally aligned and compared and with appropriate nucleotide insertions or deletions, pair with at least about 80% of the nucleotides of the other strand, usually at least about 90% to 95%, and more preferably from about 98 to 100%. Alternatively, complementarity exists when an RNA or DNA strand will hybridize under selective hybridization conditions to its complement. Typically, selective hybridization will occur when there is at least about 65% complementary over a stretch of at least 14 to 25 nucleotides, preferably at least about 75%, more preferably at least about 90% complementary. See, M. Kanehisa Nucleic Acids Res. 12:203 (1984), incorporated herein by reference.
  • [0047]
    Combinatorial Synthesis Strategy: A combinatorial synthesis strategy is an ordered strategy for parallel synthesis of diverse polymer sequences by sequential addition of reagents which may be represented by a reactant matrix and a switch matrix, the product of which is a product matrix. A reactant matrix is a 1 column by m row matrix of the building blocks to be added. The switch matrix is all or a subset of the binary numbers, preferably ordered, between 1 and m arranged in columns. A “binary strategy” is one in which at least two successive steps illuminate a portion, often half, of a region of interest on the substrate. In a binary synthesis strategy, all possible compounds which can be formed from an ordered set of reactants are formed. In most preferred embodiments, binary synthesis refers to a synthesis strategy which also factors a previous addition step. For example, a strategy in which a switch matrix for a masking strategy halves regions that were previously illuminated, illuminating about half of the previously illuminated region and protecting the remaining half (while also protecting about half of previously protected regions and illuminating about half of previously protected regions). It will be recognized that binary rounds may be interspersed with non-binary rounds and that only a portion of a substrate may be subjected to a binary scheme. A combinatorial “masking” strategy is a synthesis which uses light or other spatially selective deprotecting or activating agents to remove protecting groups from materials for addition of other materials such as amino acids.
  • [0048]
    Effective amount refers to an amount sufficient to induce a desired result.
  • [0049]
    Genome is all the genetic material in the chromosomes of an organism. DNA derived from the genetic material in the chromosomes of a particular organism is genomic DNA.
  • [0050]
    A genomic library is a collection of clones made from a set of randomly generated overlapping DNA fragments representing the entire genome of an organism. Hybridization conditions will typically include salt concentrations of less than about 1M, more usually less than about 500 mM and preferably less than about 200 mM. Hybridization temperatures can be as low as 5.degree. C., but are typically greater than 22.degree. C., more typically greater than about 30.degree. C., and preferably in excess of about 37.degree. C. Longer fragments may require higher hybridization temperatures for specific hybridization. As other factors may affect the stringency of hybridization, including base composition and length of the complementary strands, presence of organic solvents and extent of base mismatching, the combination of parameters is more important than the absolute measure of any one alone.
  • [0051]
    Hybridizations, e.g., allele-specific probe hybridizations, are generally performed under stringent conditions. For example, conditions where the salt concentration is no more than about 1 Molar (M) and a temperature of at least 25 degrees Celsius (° C.), e.g., 750 mM NaCl, 50 mM NaPhosphate, 5 mM EDTA, pH 7.4 (5×SSPE) and a temperature of from about 25 to about 30° C.
  • [0052]
    Hybridizations are usually performed under stringent conditions, for example, at a salt concentration of no more than 1 M and a temperature of at least 25° C. For example, conditions of 5×SSPE (750 mM NaCl, 50 mM NaPhosphate, 5 mM EDTA, pH 7.4) and a temperature of 25-30° C. are suitable for allele-specific probe hybridizations. For stringent conditions, see, for example, Sambrook, Fritsche and Maniatis. “Molecular Cloning A laboratory Manual” 2nd Ed. Cold Spring Harbor Press (1989) which is hereby incorporated by reference in its entirety for all purposes above.
  • [0053]
    The term “hybridization” refers to the process in which two single-stranded polynucleotides bind non-covalently to form a stable double-stranded polynucleotide; triple-stranded hybridization is also theoretically possible. The resulting (usually) double-stranded polynucleotide is a “hybrid.” The proportion of the population of polynucleotides that forms stable hybrids is referred to herein as the “degree of hybridization.”
  • [0054]
    Hybridization probes are oligonucleotides capable of binding in a base-specific manner to a complementary strand of nucleic acid. Such probes include peptide nucleic acids, as described in Nielsen et al., Science 254, 1497-1500 (1991), and other nucleic acid analogs and nucleic acid mimetics.
  • [0055]
    Hybridizing specifically to: refers to the binding, duplexing, or hybridizing of a molecule only to a particular nucleotide sequence or sequences under stringent conditions when that sequence is present in a complex mixture (e.g., total cellular) DNA or RNA.
  • [0056]
    Isolated nucleic acid is an object species invention that is the predominant species present (i.e., on a molar basis it is more abundant than any other individual species in the composition). Preferably, an isolated nucleic acid comprises at least about 50, 80 or 90% (on a molar basis) of all macromolecular species present. Most preferably, the object species is purified to essential homogeneity (contaminant species cannot be detected in the composition by conventional detection methods).
  • [0057]
    Ligand: A ligand is a molecule that is recognized by a particular receptor. The agent bound by or reacting with a receptor is called a “ligand,” a term which is definitionally meaningful only in terms of its counterpart receptor. The term “ligand” does not imply any particular molecular size or other structural or compositional feature other than that the substance in question is capable of binding or otherwise interacting with the receptor. Also, a ligand may serve either as the natural ligand to which the receptor binds, or as a functional analogue that may act as an agonist or antagonist. Examples of ligands that can be investigated by this invention include, but are not restricted to, agonists and antagonists for cell membrane receptors, toxins and venoms, viral epitopes, hormones (e.g., opiates, steroids, etc.), hormone receptors, peptides, enzymes, enzyme substrates, substrate analogs, transition state analogs, cofactors, drugs, proteins, and antibodies. Linkage disequilibrium or allelic association means the preferential association of a particular allele or genetic marker with a specific allele, or genetic marker at a nearby chromosomal location more frequently than expected by chance for any particular allele frequency in the population. For example, if locus X has alleles a and b, which occur equally frequently, and linked locus Y has alleles c and d, which occur equally frequently, one would expect the combination ac to occur with a frequency of 0.25. If ac occurs more frequently, then alleles a and c are in linkage disequilibrium. Linkage disequilibrium may result from natural selection of certain combination of alleles or because an allele has been introduced into a population too recently to have reached equilibrium with linked alleles.
  • [0058]
    Mixed population or complex population: refers to any sample containing both desired and undesired nucleic acids. As a non-limiting example, a complex population of nucleic acids may be total genomic DNA, total genomic RNA or a combination thereof. Moreover, a complex population of nucleic acids may have been enriched for a given population but include other undesirable populations. For example, a complex population of nucleic acids may be a sample which has been enriched for desired messenger RNA (mRNA) sequences but still includes some undesired ribosomal RNA sequences (rRNA).
  • [0059]
    Monomer: refers to any member of the set of molecules that can be joined together to form an oligomer or polymer. The set of monomers useful in the present invention includes, but is not restricted to, for the example of (poly)peptide synthesis, the set of L-amino acids, D-amino acids, or synthetic amino acids. As used herein, “monomer” refers to any member of a basis set for synthesis of an oligomer. For example, dimers of L-amino acids form a basis set of 400 “monomers” for synthesis of polypeptides. Different basis sets of monomers may be used at successive steps in the synthesis of a polymer.
  • [0060]
    The term “monomer” also refers to a chemical subunit that can be combined with a different chemical subunit to form a compound larger than either subunit alone. mRNA or mRNA transcripts: as used herein, include, but not limited to pre-mRNA transcript(s), transcript processing intermediates, mature mRNA(s) ready for translation and transcripts of the gene or genes, or nucleic acids derived from the mRNA transcript(s). Transcript processing may include splicing, editing and degradation. As used herein, a nucleic acid derived from an mRNA transcript refers to a nucleic acid for whose synthesis the mRNA transcript or a subsequence thereof has ultimately served as a template. Thus, a cDNA reverse transcribed from an mRNA, an RNA transcribed from that cDNA, a DNA amplified from the cDNA, an RNA transcribed from the amplified DNA, etc., are all derived from the mRNA transcript and detection of such derived products is indicative of the presence and/or abundance of the original transcript in a sample. Thus, mRNA derived samples include, but are not limited to, mRNA transcripts of the gene or genes, cDNA reverse transcribed from the mRNA, cRNA transcribed from the cDNA, DNA amplified from the genes, RNA transcribed from amplified DNA, and the like.
  • [0061]
    Nucleic acid library or array is an intentionally created collection of nucleic acids which can be prepared either synthetically or biosynthetically and screened for biological activity in a variety of different formats (e.g., libraries of soluble molecules; and libraries of oligos tethered to resin beads, silica chips, or other solid supports). Additionally, the term “array” is meant to include those libraries of nucleic acids which can be prepared by spotting nucleic acids of essentially any length (e.g., from 1 to about 1000 nucleotide monomers in length) onto a substrate. The term “nucleic acid” as used herein refers to a polymeric form of nucleotides of any length, either ribonucleotides, deoxyribonucleotides or peptide nucleic acids (PNAs), that comprise purine and pyrimidine bases, or other natural, chemically or biochemically modified, non-natural, or derivatized nucleotide bases. The backbone of the polynucleotide can comprise sugars and phosphate groups, as may typically be found in RNA or DNA, or modified or substituted sugar or phosphate groups. A polynucleotide may comprise modified nucleotides, such as methylated nucleotides and nucleotide analogs. The sequence of nucleotides may be interrupted by non-nucleotide components. Thus the terms nucleoside, nucleotide, deoxynucleoside and deoxynucleotide generally include analogs such as those described herein. These analogs are those molecules having some structural features in common with a naturally occurring nucleoside or nucleotide such that when incorporated into a nucleic acid or oligonucleoside sequence, they allow hybridization with a naturally occurring nucleic acid sequence in solution. Typically, these analogs are derived from naturally occurring nucleosides and nucleotides by replacing and/or modifying the base, the ribose or the phosphodiester moiety. The changes can be tailor made to stabilize or destabilize hybrid formation or enhance the specificity of hybridization with a complementary nucleic acid sequence as desired.
  • [0062]
    Nucleic acids according to the present invention may include any polymer or oligomer of pyrimidine and purine bases, preferably cytosine, thymine, and uracil, and adenine and guanine, respectively. See Albert L. Lehninger, PRINCIPLES OF BIOCHEMISTRY, at 793-800 (Worth Pub. 1982). Indeed, the present invention contemplates any deoxyribonucleotide, ribonucleotide or peptide nucleic acid component, and any chemical variants thereof, such as methylated, hydroxymethylated or glucosylated forms of these bases, and the like. The polymers or oligomers may be heterogeneous or homogeneous in composition, and may be isolated from naturally-occurring sources or may be artificially or synthetically produced. In addition, the nucleic acids may be DNA or RNA, or a mixture thereof, and may exist permanently or transitionally in single-stranded or double-stranded form, including homoduplex, heteroduplex, and hybrid states.
  • [0063]
    An “oligonucleotide” or “polynucleotide” is a nucleic acid ranging from at least 2, preferable at least 8, and more preferably at least 20 nucleotides in length or a compound that specifically hybridizes to a polynucleotide. Polynucleotides of the present invention include sequences of deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) which may be isolated from natural sources, recombinantly produced or artificially synthesized and mimetics thereof. A further example of a polynucleotide of the present invention may be peptide nucleic acid (PNA). The invention also encompasses situations in which there is a nontraditional base pairing such as Hoogsteen base pairing which has been identified in certain tRNA molecules and postulated to exist in a triple helix. “Polynucleotide” and “oligonucleotide” are used interchangeably in this application.
  • [0064]
    Probe: A probe is a surface-immobilized molecule that can be recognized by a particular target. See U.S. Pat. No. 6,582,908 for an example of arrays having all possible combinations of probes with 10, 12, and more bases. Examples of probes that can be investigated by this invention include, but are not restricted to, agonists and antagonists for cell membrane receptors, toxins and venoms, viral epitopes, hormones (e.g., opioid peptides, steroids, etc.), hormone receptors, peptides, enzymes, enzyme substrates, cofactors, drugs, lectins, sugars, oligonucleotides, nucleic acids, oligosaccharides, proteins, and monoclonal antibodies.
  • [0065]
    Primer is a single-stranded oligonucleotide capable of acting as a point of initiation for template-directed DNA synthesis under suitable conditions e.g., buffer and temperature, in the presence of four different nucleoside triphosphates and an agent for polymerization, such as, for example, DNA or RNA polymerase or reverse transcriptase. The length of the primer, in any given case, depends on, for example, the intended use of the primer, and generally ranges from 15 to 30 nucleotides. Short primer molecules generally require cooler temperatures to form sufficiently stable hybrid complexes with the template. A primer need not reflect the exact sequence of the template but must be sufficiently complementary to hybridize with such template. The primer site is the area of the template to which a primer hybridizes. The primer pair is a set of primers including a 5′ upstream primer that hybridizes with the 5′ end of the sequence to be amplified and a 3′ downstream primer that hybridizes with the complement of the 3′ end of the sequence to be amplified.
  • [0066]
    Polymorphism refers to the occurrence of two or more genetically determined alternative sequences or alleles in a population. A polymorphic marker or site is the locus at which divergence occurs. Preferred markers have at least two alleles, each occurring at frequency of greater than 1%, and more preferably greater than 10% or 20% of a selected population. A polymorphism may comprise one or more base changes, an insertion, a repeat, or a deletion. A polymorphic locus may be as small as one base pair. Polymorphic markers include restriction fragment length polymorphisms, variable number of tandem repeats (VNTR's), hypervariable regions, minisatellites, dinucleotide repeats, trinucleotide repeats, tetranucleotide repeats, simple sequence repeats, and insertion elements such as Alu. The first identified allelic form is arbitrarily designated as the reference form and other allelic forms are designated as alternative or variant alleles. The allelic form occurring most frequently in a selected population is sometimes referred to as the wildtype form. Diploid organisms may be homozygous or heterozygous for allelic forms. A diallelic polymorphism has two forms. A triallelic polymorphism has three forms. Single nucleotide polymorphisms (SNPs) are included in polymorphisms.
  • [0067]
    Receptor: A molecule that has an affinity for a given ligand. Receptors may be naturally-occurring or manmade molecules. Also, they can be employed in their unaltered state or as aggregates with other species. Receptors may be attached, covalently or noncovalently, to a binding member, either directly or via a specific binding substance. Examples of receptors which can be employed by this invention include, but are not restricted to, antibodies, cell membrane receptors, monoclonal antibodies and antisera reactive with specific antigenic determinants (such as on viruses, cells or other materials), drugs, polynucleotides, nucleic acids, peptides, cofactors, lectins, sugars, polysaccharides, cells, cellular membranes, and organelles. Receptors are sometimes referred to in the art as anti-ligands. As the term receptors is used herein, no difference in meaning is intended. A “Ligand Receptor Pair” is formed when two macromolecules have combined through molecular recognition to form a complex. Other examples of receptors which can be investigated by this invention include but are not restricted to those molecules shown in U.S. Pat. No. 5,143,854, which is hereby incorporated by reference in its entirety.
  • [0068]
    “Solid support”, “support”, and “substrate” are used interchangeably and refer to a material or group of materials having a rigid or semi-rigid surface or surfaces. In many embodiments, at least one surface of the solid support will be substantially flat, although in some embodiments it may be desirable to physically separate synthesis regions for different compounds with, for example, wells, raised regions, pins, etched trenches, or the like. According to other embodiments, the solid support(s) will take the form of beads, resins, gels, microspheres, or other geometric configurations. See U.S. Pat. No. 5,744,305 for exemplary substrates.
  • [0069]
    Target: A molecule that has an affinity for a given probe. Targets may be naturally occurring or man-made molecules. Also, they can be employed in their unaltered state or as aggregates with other species. Targets may be attached, covalently or noncovalently, to a binding member, either directly or via a specific binding substance. Examples of targets which can be employed by this invention include, but are not restricted to, antibodies, cell membrane receptors, monoclonal antibodies and antisera reactive with specific antigenic determinants (such as on viruses, cells or other materials), drugs, oligonucleotides, nucleic acids, peptides, cofactors, lectins, sugars, polysaccharides, cells, cellular membranes, and organelles. Targets are sometimes referred to in the art as anti-probes. As the term targets is used herein, no difference in meaning is intended. A “Probe Target Pair” is formed when two macromolecules have combined through molecular recognition to form a complex.
  • III. Specific Embodiments
  • [0070]
    FIGS. 1-4 show a simplified fluidic system for processing biological sensors according to an embodiment of the present invention. These diagrams are merely examples, which should not unduly limit the scope of the claims. One of ordinary skill in the art would recognize many variations, alternatives, and modifications. The system 100 includes a fluidic component 110, a support component 120, and an electrical and mechanical component 130. Although the above has been shown using a selected group of components for the system 100, there can be many alternatives, modifications, and variations. For example, some of the components may be expanded and/or combined. Other components may be inserted to those noted above. Depending upon the embodiment, the arrangement of components may be interchanged with others replaced. Further details of these components are found throughout the present specification and more particularly below.
  • [0071]
    The fluidic component 110 includes at least some containers. Each of these containers includes one or more fluids for processing at least one biological sensor. For example, each container is a well. In another example, the wells are grouped into one or more plate and/or one or more strip. As shown in FIGS. 1-4, the wells are grouped into at least a well plate 112 and a well strip 114. In one embodiment, the well plate 112 includes 96 wells, and the well strip 114 includes 4 wells. In another embodiment, each well contains one or more fluids, and different wells contain the same or different fluids. In yet another embodiment, different wells have the same or different depths.
  • [0072]
    FIGS. 5(A) and (B) show a simplified well strip 114 in fluidic system 100 for processing biological sensors according to an embodiment of the present invention. These diagrams are merely examples, which should not unduly limit the scope of the claims. One of ordinary skill in the art would recognize many variations, alternatives, and modifications. The well strip 114 includes a plurality of tubes 510, a heater 512, and a thermometer 514 such as a thermocouple. Although the above has been shown using a selected group of components for the well strip 114, there can be many alternatives, modifications, and variations. For example, some of the components may be expanded and/or combined. Other components may be inserted to those noted above. Depending upon the embodiment, the arrangement of components may be interchanged with others replaced. Further details of these components are found throughout the present specification and more particularly below.
  • [0073]
    The plurality of tubes 510 provides a plurality of wells for the one or more sensors. For example, each of the plurality of tubes 510 includes at least one fluid. The fluid is heated by the heater 512, and the temperature of the fluid is monitored, directly or indirectly, by the thermocouple 514. In response, the thermocouple 514 sends a signal to a temperature controller. In one embodiment, the temperature controller is also a component of the fluidic system 100. The temperature controller processes the received signal in light of a target temperature and adjusts the power of the heater 512 in order to achieve the targeted temperature for the fluid. As shown in FIG. 1, the targeted temperature is provided to the fluidic system 100 by the user through a temperature interface 140 according to an embodiment of the present invention. The temperature interface 140 is a component of the fluidic system 100.
  • [0074]
    FIG. 6 is a simplified diagram showing temperature as function of time for well strip 114 in fluidic system 100 for processing biological sensors according to an embodiment of the present invention. This diagram is merely an example, which should not unduly limit the scope of the claims. One of ordinary skill in the art would recognize many variations, alternatives, and modifications. As shown in FIG. 6, a curve 610 represents the temperature measured by the thermometer 514 as a function of time. Curves 620 represent temperatures for fluids in the plurality of tubes 510, such as wells, as functions of time. The temperatures for fluids have been measured by other thermometers, such as thermocouples, in the plurality of tubes. Curves 620 show that at a given time the fluid temperatures in different tubes are close to each other, and the fluid temperatures stabilize at about 50° C. after a period of time.
  • [0075]
    As shown in FIGS. 1-4, the fluidic component 110 also includes holder strips 116 and 118. In one embodiment, the holder strip 116 is used to transport the one or more sensors to the fluidic system 100 after a hybridization process is performed. For example, the holder strip 116 is a hybridization tray. In another embodiment, the holder strip 118 is used to transport the one or more sensors out of the fluidic system 100. For example, the holder strip 118 includes at least a cuvette holder.
  • [0076]
    The support component 120 includes at least a panel 122. For example, the panel 122 is placed horizontally. As shown in FIGS. 1-4, the fluidic component 110 is placed on the panel 122. For example, the fluidic component 110 is fixed at a predetermined position, directly or indirectly, on the panel 122. In another example, the one or more wells of the fluidic component are substantially perpendicular to the panel 122.
  • [0077]
    As shown in FIGS. 1-4, the well plate 112 includes a plurality of wells arranged into a plurality of rows and a plurality of columns. For example, the number of rows is equal to or larger than the number of columns. In another example, each of the plurality of rows extends from a first side of the well plate to a second side of the well plate. In one embodiment, the well strip 114 and two holder strips 116 and 118 all are placed next to the first side of the well plate 112. In yet another example, the plurality of rows is perpendicular to the plurality of columns. Additionally, the well strip 114 includes a row of wells. The holder strips 116 and 118 each include a row of wells capable of holding the one or more sensors. In one embodiment, the plurality of rows is parallel to the rows of wells for the well strip 114 and the holder strips 116 and 118. In another embodiment, the plurality of columns is parallel to the rows of wells for the well strip 114 and the holder strips 116 and 118.
  • [0078]
    According to an embodiment, the well plate 112, the well strip 114, the holder strip 116, and/or the holder strip 118 include a plurality of wells. At least one of the plurality of wells contains one or more fluids. For example, the volume of the one or more fluids in each well is equal to or smaller than 3 ml or 5 ml. In one embodiment, the volume of the one or more fluids for low stringency wash or stain is about 1.9 ml, and for high stringency wash is about 3.7 ml. In another embodiment, different wells have the same or different depths.
  • [0079]
    The electrical and mechanical component 130 can move each of the one or more sensors from one position to another position. For example, the one or more sensors are not parts of the electrical and mechanical component 130. In another example, the electrical and mechanical component 130 is used as a transport component. In yet another example, the movement of the sensors can be made in one, two, or three dimensions. In yet another example, the movement of the sensors is made at various speed. As shown in FIGS. 1-4, the electrical and mechanical component 130 moves each of the one or more sensors from one well to another well of the fluidic component 110. Additionally, the electrical and mechanical component 130 can move each of the one or more sensors within a corresponding well of the fluidic component 110, and/or move each of the one or more sensors into and/or out of a corresponding well of the fluidic component 110.
  • [0080]
    According to an embodiment of the present invention, the electrical and mechanical component 130 includes at least a gripper 132, and motors 134, 136, and 138. Additionally, the motors 134, 136, and 138 each can move one or more sensors in two opposite directions of one dimension. For example, the motor 134 can move the one or more sensors in two opposite directions that are perpendicular to the panel 122. In another example, the motors 136 and 138 can move the one or more sensors in directions that are parallel to the panel 122. In one embodiment, the motor 136 can move the one or more sensors in directions that are parallel to the well strip 114. In another embodiment, the motor 138 can move the one or more sensors in directions that are perpendicular to the well strip 114.
  • [0081]
    Additionally, the electrical and mechanical component 130 includes other components. For example, the electrical and mechanical component 130 includes at least a high-voltage power supply and a low-voltage power supply. In one embodiment, the power suppliers are used to provide voltages at predetermined values and/or within predetermined ranges to, for example, the motors 134, 136, and 138. In another embodiment, the power suppliers receive 115-votage AC power from an external source.
  • [0082]
    FIGS. 7(A) and (B) show a simplified gripper 132 in fluidic system 100 for processing biological sensors according to an embodiment of the present invention. These diagrams are merely examples, which should not unduly limit the scope of the claims. One of ordinary skill in the art would recognize many variations, alternatives, and modifications. The gripper 132 includes an actuator 710, and two arms 720 and 730. Although the above has been shown using a selected group of components for the gripper 132, there can be many alternatives, modifications, and variations. For example, some of the components may be expanded and/or combined. Other components may be inserted to those noted above. Depending upon the embodiment, the arrangement of components may be interchanged with others replaced. Further details of these components are found throughout the present specification and more particularly below.
  • [0083]
    The actuator 710 is used to move the arms 720 and 730. In one embodiment, the actuator 710 is an electrical actuator. In another embodiment, the actuator 710 is a pneumatic actuator. For example, the pneumatic actuator receives a gas at a first pressure from a gas regulator, and the gas regulator converts the gas at a second pressure to the gas at the first pressure. In another example, the gas is clean dry air. As shown in FIG. 1, the first pressure is monitored by a pressure meter 150, which is a component of the fluidic system 100. Additionally, the arm 720 includes a plurality of fingers, such as fingers 722, 724, 726, and 728, as shown in FIG. 7(A). Similarly, the arm 730 also includes a plurality of fingers. As shown in FIG. 7(B), the gripper 132 is used to grip the one or more sensors. For example, the one or more sensors are not parts of the system 100.
  • [0084]
    As discussed above and further emphasized here, FIGS. 1-4 are merely examples, which should not unduly limit the scope of the claims. One of ordinary skill in the art would recognize many variations, alternatives, and modifications. For example, the well plate 112 can be replaced by a well strip with a single row or a single column. In another example, the strips 114, 116, and/or 118 can be replaced by a plate with a plurality of rows and a plurality of columns. In yet another example, one or more additional plates, and/or one or more additional strips can be included in the fluidic component 110.
  • [0085]
    FIG. 8 shows a simplified fluidic system for processing biological sensors according to another embodiment of the present invention. This diagram is merely an example, which should not unduly limit the scope of the claims. One of ordinary skill in the art would recognize many variations, alternatives, and modifications. The system 800 includes a fluidic component, a support component, and an electrical and mechanical component. The fluidic component, the support component, and the electrical and mechanical component are either the same as or modified from the fluidic component 110, the support component 120, and the electrical and mechanical component 130 respectively.
  • [0086]
    For example, the fluidic component of the system 800 is either partially or completely enclosed by a cover 810. In another example, the fluidic component of the system 800 includes a well plate, a well strip, and two holder strips. The well plate includes a plurality of wells arranged into a plurality of rows and a plurality of columns. For example, the number of rows is equal to or larger than the number of columns. In another example, each of the plurality of columns extends from a first side of the well plate to a second side of the well plate. In one embodiment, the well strip and two holder strips all are placed next to the first side of the well plate. In yet another example, the plurality of rows is perpendicular to the plurality of columns. Additionally, the well strip includes a row of wells, and each of the holder strips includes a row of wells that are capable of holding the one or more sensors. In one embodiment, the plurality of rows is parallel to the rows of wells for the well strip and the holder strips. In another embodiment, the plurality of columns is parallel to the rows of wells for the well strip and the holder strips.
  • [0087]
    As discussed above and further emphasized here, a fluidic system for processing biological sensors according to certain embodiments of the present invention includes a fluidic component, a support component, and an electrical and mechanical component. For example, the fluidic system is the system 100 or 800. In another example, the electrical and mechanical component can move each of one or more sensors within a corresponding well of the fluidic component, and/or move each of the one or more sensors into and/or out of a corresponding well of the fluidic component. In another example, the fluidic component includes a well plate, a well strip, and two holder strips. In one embodiment, one holder strip is used to transport the one or more sensors to the fluidic system after a hybridization process is performed. In another embodiment, another holder strip is used to transport the one or more microarrays out of the fluidic system.
  • [0088]
    According to an embodiment of the present invention, the movement of the one or more sensors into, within, and/or out of the fluidic system 100 or 800 is controlled by instructions received by the electrical and mechanical component from a processing system. For example, the processing system is external to the fluidic system. In another example, the processing system is a component of the fluidic system. In one embodiment, the processing system includes a computer or a processor. For example, the computer or the processor is directed by a code. In another example, the computer or the processor is directed by instructions included by a computer-readable medium in a computer program product.
  • [0089]
    FIG. 9 shows a simplified fluidic method for processing biological sensors that is performed by fluidic system 100 or 800 according to an embodiment of the present invention. This diagram is merely an example, which should not unduly limit the scope of the claims. One of ordinary skill in the art would recognize many variations, alternatives, and modifications. The method 900 includes a process 910 for low stringency wash, a process 920 for high stringency wash, a process 930 for Streptavidin Phycoerythrin (SAPE) stain, a process 940 for low stringency wash, a process 950 for antibody (AB) stain, a process 960 for low stringency wash, a process 970 for SAPE stain, and a process 980 for low stringency wash. Although the above has been shown using a selected sequence of processes, there can be many alternatives, modifications, and variations. For example, some of the processes may be expanded and/or combined. Other processes may be inserted to those noted above. Depending upon the embodiment, the specific sequence of processes may be interchanged with others replaced. Further details of these processes are found throughout the present specification and more particularly below.
  • [0090]
    At each of the processes 910, 940, and 960 for low stringency wash, each of the one or more sensors is washed in a plurality of wells at room temperature. For example, the plurality of wells includes two wells. In another example, the plurality of wells includes four wells. For each well, the corresponding sensor is mixed with the fluid in the well for a plurality of times. For example, the plurality of times includes 23 times within 3 minutes. In another example, the plurality of times includes 36 times within 2 minutes.
  • [0091]
    At the process 920 for high stringency wash, each of the one or more sensors is washed in at least one well. Within each well, the fluid is at an elevated temperature, and the corresponding sensor is mixed with the fluid for a period of time. For example, the elevated temperature is 48° C., and the period of time is 25 minutes. In another example, the elevated temperature is 41° C., and the period of time is also 25 minutes.
  • [0092]
    At each of the processes 930 and 970 for SAPE stain, each of the one or more sensors is stained in at least one well at room temperature. For each well, the corresponding sensor is mixed with the fluid for a period of time. As an example, example, the period of time is 10 minutes.
  • [0093]
    At the process 950 for AB stain, each of the one or more sensors is stained in at least one well at room temperature. For each well, the corresponding sensor is mixed with the fluid for a period of time. As an example, the period of time is 10 minutes.
  • [0094]
    As discussed above and further emphasized here, the processes 910, 920, 930, 940, 950, 960, 970, and 980 are all performed by the fluidic system 100 or 800 according to an embodiment of the present invention. Prior to the process 910, the one or more sensors are processed for hybridization. For example, the hybridization process is performed at 48° C. for 16 hours. Following the process 980, the one or more sensors are scanned.
  • [0095]
    FIGS. 10(A)-(V) are simplified diagrams showing movement of one or more sensors made by fluidic system 100 or 800 according to an embodiment of the present invention. This diagram is merely an example, which should not unduly limit the scope of the claims. One of ordinary skill in the art would recognize many variations, alternatives, and modifications.
  • [0096]
    According to one embodiment, each of FIGS. 10(A)-(V) shows the well plate 112, the well strip 114, and the holder strip 116 and 118. For example, the well plate includes 96 wells that are arranged into rows 1-12 and columns A-H. The row 1 is intended for SAPE stain, the row 3 is intended for AB stain, and rows 5-12 are intended for low stringency wash. In another example, the well strip 112 is intended for high stringency wash. In yet another example, the holder strip 116 is a hybridization tray that is intended to transport the one or more sensors to the fluidic system 100 after a hybridization process is performed. In yet another embodiment, the holder strip 118 includes a cuvette holder and is intended to transport the one or more microarrays out of the fluidic system 100.
  • [0097]
    In order to describe movement of the one or more sensors, when a well is being used or after a well has been used, the well is marked with a square with hatch pattern. As shown in FIG. 10(A), the one or more sensors are transported to the fluidic system 100 by the holder strip 116. Afterwards, the one or more sensors are processed with low stringency wash according to the process 910 as shown in FIGS. 10(B)-(E). Each sensor is washed in four wells in rows 12, 11, 10, and 9 respectively. At each well, the sensor is agitated substantially parallel to the well depth in order to achieve a plurality of times of mixture with the fluid within the well. After the process 920, the one or more sensors are moved to the well strip 114 and processed with high stringency wash as shown in FIG. 10(F).
  • [0098]
    FIG. 10(G) shows the one or more sensors are moved from the well strip 114 to the row 1 of the well plate 112. At the row 1, the one or more sensors are stained with SAPE according to the process 930. At the process 940, another low stringency wash is performed on the one or more sensors as shown in FIGS. 10(H)-(K). Each sensor is washed in four wells in rows 8, 7, 6, and 5 respectively. At each well, the sensor is agitated substantially parallel to the well depth in order to achieve a plurality of times of mixture with the fluid within the well.
  • [0099]
    Following the process 940, the one or more sensors are moved to the row 3 of the well plate 112 as shown in FIG. 10(L). At the row 3, the one or more sensors are stained with AB according to the process 950. Afterwards, the one or more sensors are processed with low stringency wash according to the process 960 as shown in FIGS. 10(M)-(P). Each sensor is washed in four wells in rows 12, 11, 10, and 9 respectively, and none of these four wells has been used at the process 910. At each well, the sensor is agitated substantially parallel to the well depth in order to achieve a plurality of times of mixture with the fluid within the well.
  • [0100]
    FIG. 10(Q) shows the one or more sensors are moved from the row 9 to the row 1 of the well plate 112. At the row 1, the one or more sensors are stained with SAPE according to the process 970. None of the wells used in the process 970 has been used in the process 930. At the process 980, another low stringency wash is performed on the one or more sensors as shown in FIGS. 10(R)-(U). Each sensor is washed in four wells in rows 8, 7, 6, and 5 respectively, and none of these four wells has been used at the process 940. At each well, the sensor is agitated substantially parallel to the well depth in order to achieve a plurality of times of mixture with the fluid within the well. After the process 980, the one or more sensors are placed into the holder strip 118 as shown in FIG. 10(V). These sensors can be transported from the fluidic system 100 to a scanner.
  • [0101]
    As discussed above and further emphasized here, the fluidic system 100 or 800 can be used to process biological sensors according to certain embodiments of the present invention. As an example, the processing is performed according to the method 900. In another example, the biological sensors can be various types. See U.S. patent application Ser. Nos. 10/826,577 filed Apr. 16, 2004 and Ser. No. 11/243,621 filed Oct. 4, 2005, each of which is incorporated by reference herein. In yet another example, each of the one or more biological sensors is a biological microarray. In one embodiment, the biological microarray has a sensor length, a sensor width, and a sensor thickness. For example, the sensor length is equal to or shorter than 10 mm, the sensor width is equal to or narrower than 10 mm, and the sensor thickness is equal to or thinner than 1000 μm. In another example, the sensor length is equal to about 6.3 mm, the sensor width is equal to about 6.3 mm, and the sensor thickness is equal to about 700 μm.
  • [0102]
    In one embodiment, each biological sensor is a biological microarray. In another embodiment, each biological sensor is attached to a support component. For example, the support component is a peg. FIGS. 11(A) and (B) are simplified microarrays on pegs that can be processed by fluidic system 100 or 800 according to an embodiment of the present invention. These diagrams are merely examples, which should not unduly limit the scope of the claims. One of ordinary skill in the art would recognize many variations, alternatives, and modifications. As shown in FIG. 11(A), a biological microarray is attached to one peg, and each biological microarray can be manipulated individually by the fluidic system 100 or 800. As shown in FIG. 11(B), a plurality of biological microarrays is attached to a plurality of pegs respectively, and the plurality of pegs is connected by a base component. For example, the plurality of pegs includes four pegs, and the plurality of biological microarrays includes four microarrays. In another example, the plurality of pegs includes eight pegs, and the plurality of biological microarrays includes eight microarrays. In yet another example, the plurality of microarrays is manipulated together by the fluidic system 100 or 800.
  • [0103]
    Also as discussed above and further emphasized here, the fluidic system 100 or 800 can be used to process biological sensors ready for scan according to certain embodiments of the present invention. In one embodiment, the processing is performed according to the method 900. In another embodiment, the scanner for scanning the processed biological sensors can be of various types. For example, the scanner is made by Axon. Alternatively, see U.S. Provisional Application Ser. Nos. 60/648,309 filed Jan. 27, 2005 and 60/673,969 filed Apr. 22, 2005, each of which is incorporated by reference herein.
  • [0104]
    According to another embodiment of the present invention, a fluidic system for processing biological sensors includes a fluidic component including at least a first container and a second container. The first container is capable of holding a first volume of a first fluid, and the second container is capable of holding a second volume of a second fluid. Additionally, the fluidic system includes a support component configured to support at least the first container and the second container. The first container and the second container are substantially stationary with respect to the support component. Moreover, the fluidic system includes a transport component configured to move a first sensor, with respect to the support component, into the first container and in contact with the first volume of the first fluid, and move a second sensor, with respect to the support component, into the second container and in contact with the second volume of the second fluid. The first sensor and the second sensor are moved substantially simultaneously. For example, the fluidic system is implemented according the system 100 and/or the system 800.
  • [0105]
    According to yet another embodiment, a fluidic system for processing biological sensors includes a fluidic component including at least a first container and a second container. The first container is capable of holding a first volume of a first fluid, and the second container is capable of holding a second volume of a second fluid. Additionally, the fluidic system includes a support component including a panel for supporting at least the first container and the second container. The first container and the second container are substantially stationary with respect to the panel. Moreover, the fluidic system includes a transport component including a gripper and at least one motor. The gripper is capable of gripping the first sensor and the second sensor substantially simultaneously and of releasing the first sensor and the second sensor substantially simultaneously. The at least one motor is configured to move the gripped first sensor, with respect to the panel, into the first container and in contact with the first volume of the first fluid. The at least one motor is further configured to move the gripped second sensor, with respect to the panel, into the second container and in contact with the second volume of the second fluid. The first sensor and the second sensor are moved substantially simultaneously. For example, the fluidic system is implemented according the system 100 and/or the system 800.
  • [0106]
    According to yet another embodiment, a method for processing biological sensors includes performing a hybridization process on at least a first sensor and a second sensor, and after the hybridization process, transferring the first sensor and the second sensor into a fluidic system. The fluidic system includes at least a first container and a second container, the first container holds a first volume of a first fluid, and the second container holds a second volume of a second fluid. Additionally, the method includes moving the first sensor into the first container and in contact with the first volume of the first fluid, and moving the second sensor into the second container and in contact with the second volume of the second fluid. The moving the first sensor and the moving the second sensor are performed substantially simultaneously. For example, the fluidic system is implemented according the system 100 and/or the system 800.
  • [0107]
    The present invention has various applications. For example, the fluidic system 100 or the fluidic system 800 is used as a fluidic station. In one embodiment, the fluidic station, as shown in FIG. 1, has a footprint of 19.5-inch width and 17.5-inch depth. Additionally, the fluidic station has a height of 15 inch. In another example, certain embodiments of the present invention are used for personal and portable instruments as well as methods for processing biological microarrays.
  • [0108]
    The present invention has various advantages. Certain embodiments of the present invention provide an automated fluidic system. Some embodiments of the present invention provide a low-cost fluidic system. Certain embodiments of the present invention can improve throughput of the fluidic system. For example, a plurality of biological sensors, such as microarrays, is processed in parallel. Some embodiments of the present invention can reduce cross-contamination between different processes performed on one or more biological sensors. For example, at a given process, different sensors are washed, stained, and/or held in different wells. In another example, a given sensor is washed, stained, and/or held in different wells for different processes respectively. In yet another example, each well is used for at most a single process for at most a single sensor, such as a microarray.
  • [0109]
    Although specific embodiments of the present invention have been described, it will be understood by those of skill in the art that there are other embodiments that are equivalent to the described embodiments. Accordingly, it is to be understood that the invention is not to be limited by the specific illustrated embodiments, but only by the scope of the appended claims.
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Classifications
U.S. Classification435/287.2, 435/287.3
International ClassificationC12M1/34
Cooperative ClassificationG01N2035/1048, G01N2035/00158, G01N2035/0498, B01L9/52, G01N35/028, B01L9/523, G01N2035/0425, G01N2035/00356, G01N1/312, G01N35/0099
European ClassificationG01N35/02P, G01N35/00R
Legal Events
DateCodeEventDescription
Jul 3, 2006ASAssignment
Owner name: AFFYMETRIX, INC., CALIFORNIA
Free format text: ASSIGNMENT OF ASSIGNORS INTEREST;ASSIGNOR:SHIRAZI, MOHSEN;REEL/FRAME:018021/0789
Effective date: 20060605