Single-tube, ready-to-use assay kits and methods using same

• US 20030175774A1
• Filed: 01/02/2003
• Published: 09/18/2003
• Est. Priority Date: 01/25/2002
• Status: Abandoned Application

• Current Assignee: Dennis A. Gilbert, Junko Stevens, Kenneth J. Livak, Michael Lucero, Michael W. Hunkapiller, Susan K. Eddins
• Original Assignee: Dennis A. Gilbert, Junko Stevens, Kenneth J. Livak, Michael Lucero, Michael W. Hunkapiller, Susan K. Eddins
• Inventors: Livak, Kenneth J., Lucero, Michael, Stevens, Junko, Hunkapiller, Michael W., Eddins, Susan K., Gilbert, Dennis A.
• Application Number:
  US10/335,690
• Publication Number:
  US 20030175774A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: B01L 2300/021 Identification, e.g. bar codes
• CPC Class Codes: B01L 3/545 for laboratory containers
• CPC Class Codes: B01L 3/5453 for test tubes
• CPC Class Codes: C12Q 1/6858 Allele-specific amplification
• CPC Class Codes: C12Q 2547/101 by confinement to a single tube/container
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: G01N 35/00663 of consumables
• CPC Class Codes: G06Q 30/0621 Item configuration or customization
• CPC Class Codes: G06Q 30/0633 Lists, e.g. purchase orders, compilation or processing
• CPC Class Codes: G06Q 30/0641 Shopping interfaces
• CPC Class Codes: G06Q 50/22 Social work or social welfare, e.g. community support activities or counselling services
• CPC Class Codes: G16B 25/00 ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
• CPC Class Codes: G16B 25/10 Gene or protein expression profiling; Expression-ratio estimation or normalisation
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16B 30/10 Sequence alignment; Homology search
• CPC Class Codes: G16B 30/20 Sequence assembly
• CPC Class Codes: G16B 35/00 ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides
• CPC Class Codes: G16B 35/20 Screening of libraries
• CPC Class Codes: G16B 45/00 ICT specially adapted for bioinformatics-related data visualisation, e.g. displaying of maps or networks
• CPC Class Codes: G16B 50/00 ICT programming tools or database systems specially adapted for bioinformatics
• CPC Class Codes: G16B 50/10 : Ontologies; Annotations
• CPC Class Codes: G16C 20/60 : In silico combinatorial chemistry
• CPC Class Codes: G16H 10/40 : for data related to laboratory analysis, e.g. patient specimen analysis

Abstract

An assay kit is provided that includes assay reagents stored in a single-tube container, and a data storage medium containing information about the contents of the container. Methods are provided for using the data provided with the kit to direct instruments and/or processes, for example, to control an instrument to perform amplification and/or sequencing reactions.

Claims

1. An assay kit comprising:

a container, the container containing a mixture having reagents adapted to perform an allelic discrimination or expression analysis reaction when admixed with at least one target polynucleotide sequence, and

a data storage medium containing data about the contents of the first container.

2. The assay kit of claim 1, further comprising a second container that contains assay reagents.

3. The assay kit of claim 1, wherein the container has a machine-readable label that provides information about the contents of the container.

4. The assay kit of claim 1, further comprising at least one first probe, wherein the at least one first probe has a first marker dye.

5. The assay kit of claim 1, wherein the container is sealed.

6. The assay kit of claim 1, wherein the kit further comprises a target polynucleotide.

7. The assay kit of claim 1, wherein the reagents utilize fluorogenic 5′

nuclease chemistry during the performance of the reaction.

8. The assay kit of claim 1, wherein the mixture further comprises a DNA polymerase, one or more polynucleotide monomers, at least one salt, and a buffer.

9. The assay kit of claim 8, wherein the polynucleotide monomers are peptide nucleic acids.

10. The assay kit of claim 1, wherein the container is a tube.

11. The assay kit of claim 5, wherein the sealed container is sealed with a removable cap.

12. The assay kit of claim 1, wherein the data storage medium is a compact disk (CD) and the data is electronically formatted.

13. The assay kit of claim 1, wherein the data includes sequence information about at least one of at least one first probe and at least one primer.

14. The assay kit of claim 4, wherein the data includes information about the first marker dye.

15. The assay kit of claim 4, wherein the data includes information that is capable of controlling at least one scientific laboratory instrument.

16. The assay kit of claim 15, wherein the at least one instrument is an instrument designed to perform at least one of a polymerase chain reaction and a polynucleotide sequencing reaction.

17. The assay kit of claim 15, wherein the data storage medium is a compact disk (CD) and the data is electronically formatted.

18. The assay kit of claim 1, wherein the data storage medium contains a software program that can be utilized with data contained on the data storage medium to control at least one scientific or laboratory instrument.

19. The assay kit of claim 18, wherein the software program is adapted to receive output data from at least one scientific or laboratory instrument.

20. The assay kit of claim 1, further comprising a second data storage medium, and the second data storage medium contains a software program that can be utilized to control at least one scientific or laboratory instrument.

21. The assay kit of claim 20, wherein the software program is adapted to receive output data from at least one instrument.

22. The assay kit of claim 1, wherein the data storage medium is separate from the container.

23. The assay kit of claim 1, wherein the data storage medium is affixed to the container.

24. The assay kit of claim 23, wherein the data storage medium includes an optically detectable code.

25. The assay kit of claim 23, wherein the data storage medium is the form of a 2-dimensional barcode.

26. The assay kit of claim 1, wherein the data storage medium is etched in the container.

27. A method of performing an assay, comprising:

providing an assay kit according to claim 1, using the data to control an instrument to process the assay reagents, and performing an assay.

28. The method of claim 27, further comprising processing the data with a software program to control the instrument.

29. A method comprising:

providing the assay kit of claim 1;

and

shipping the assay kit to a customer.

30. The method of claim 29, wherein the assay kit comprises reagents for conducting a homogeneous assay.

31. A genetic-analysis kit, comprising:

a first container;

a reaction mixture held in the first container, the reaction mixture being adapted for allelic discrimination or expression analysis;

a data storage medium including information in electronic form thereon, the information pertaining at least in part to the reaction mixture; and

a second container holding the first container and the data storage medium for transport as a unit.

32. The kit of claim 31, wherein the first container comprises a tube.

33. The kit of claim 31, wherein the second container comprises a package.

34. The kit of claim 31, wherein the data storage medium comprises a disk.

35. The kit of claim 34, wherein the disk comprises a removable disk.

36. The kit of claim 31, wherein the reaction mixture comprises a homogeneous reaction mixture.

37. The kit of claim 36, wherein the homogeneous reaction mixture comprises components for conducting a fluorogenic 5′

nuclease assay.

38. The kit of claim 31, wherein the information is comprised, at least in part, of American Standard Code for Information Interchange (ascii)-formatted text.

39. The kit of claim 31, wherein the data storage medium further includes machine-readable code thereon.

40. A method for facilitating genetic analysis:

receiving from a user a request for one or more genetic-analysis assays; and

providing to the customer (i) the one or more assays, with each assay being provided in a single-tube format, and (ii) information relating to the one or more assays, with the information being in electronic form.

41. The method of claim 40, wherein the one or more assays each comprises a homogeneous reaction mixture.

42. The method of claim 41, wherein the homogeneous reaction mixture comprises components for conducting a fluorogenic 5′

nuclease assay.

43. The method of claim 40, wherein the information is provided on a disk.

44. The method of claim 43, wherein the disk is a removable disk.

45. The method of claim 40, wherein the information is provided via a computer network.

46. The method of claim 45, wherein the information is transmitted to the customer via electronic mail.

47. The method of claim 45, wherein the information is provided via a file transfer protocol (FTP).

48. The method of claim 40, wherein the information is comprised, at least in part, of ascii-formatted text.

49. The method of claim 40, wherein at least one of the one or more assays and the information are shipped to the customer together in a single package.

50. A method for genetic analysis, comprising:

requesting a plurality of assay mixtures for genetic analysis from a supplier;

receiving from the supplier (i) the plurality of assay mixtures, and (ii) information, in electronic form, pertaining to each assay mixture;

transferring at least a portion of the electronic information to a computer system adapted for electronic communication with a thermal cycler; and

employing the computer system and at least a portion of the information, instructing the operation of the instrument, whereby each of the assay mixtures is analyzed.

51. The method of claim 50, wherein each of the plurality of assays comprises a homogeneous reaction mixture.

52. The method of claim 51, wherein the homogeneous reaction mixture comprises components for conducting a fluorogenic 5′

nuclease assay.

53. The method of claim 50, wherein the information is provided on a removable disk.

54. The method of claim 50, wherein the thermal cycler is configured to perform a real-time polymerase chain reaction.

55. The method of claim 50, wherein the information is provided via a computer network.

56. The method of claim 55, wherein the information is transmitted by the supplier via electronic mail.

57. The method of claim 55, wherein the information is downloaded by the customer from a server.

58. The method of claim 50, wherein the information is comprised, at least in part, of American Standard Code for Information Interchange (ASCII)-formatted text.

59. The method of claim 50, wherein at least one of the plurality of assays and the information are shipped to the user together in a single package.

60. The method of claim 50, wherein each of the plurality of assay mixtures is contained in a single tube.

61. The method of claim 50, wherein the requesting step is carried out via the Internet.

62. A method for facilitating genetic analysis, comprising:

receiving a request for a plurality of assay mixtures for genetic analysis from a customer; and

supplying to the user (i) the plurality of assay mixtures, (ii) information, in electronic form, pertaining to each assay mixture, and (iii) a program storage device readable by a computer system, embodying a program of instructions executable by the computer system to perform method steps for genetic analysis, the method steps comprising (a) transferring at least a portion of the electronic information to a memory of the computer system, (b) employing at least a portion of the information, generating instructions for the operation of a thermal cycler adapted to perform real-time polymerase chain reaction, and (c) sending the instructions to the thermal cycler whereby the thermal cycler acts upon the assay mixtures.

63. The method of claim 62, wherein the plurality of assay mixtures and the information is supplied to the user together, at the same time.

64. The method of claim 62, wherein the information is provided on a removable disk.

65. The method of claim 64, wherein the removable disk comprises a compact disk (CD).

66. The method of claim 62, wherein the information is provided via a computer network.

67. The method of claim 62, wherein each of the plurality of assay mixtures comprises a homogeneous reaction mixture.

68. The method of claim 67, wherein each homogeneous reaction mixture comprises a fluorogenic 5 nuclease assay.

69. The method of claim 62, wherein each of the plurality of assay mixtures is contained in a single tube.

70. The method of claim 62, wherein the program storage device comprises a removable disk.

71. The method of claim 62, further comprising providing a web site configured for receiving requests from customers for assay mixtures for genetic analysis.

72. A program storage device readable by a computer system, embodying a program of instructions executable by the computer system for genetic analysis, the method steps comprising:

(i) uploading electronic information relating to a plurality of assay mixtures from a data storage device to the computer system,

(ii) employing the information, generating a file containing instructions for operation of a thermal cycler; and

(iii) tranferring the file to the thermal cycler for implementation.

73. The device of claim 72, wherein the method steps further comprise:

monitoring for electronic information ready for uploading.

74. The device of claim 72, wherein the method steps further comprise:

receiving a results file from the thermal cycler, and causing the results file to be saved.

75. The device of claim 72, wherein the method steps further comprise:

building an assay information database.

76. The device of claim 72, wherein the method steps further comprise:

generating plate documents and providing the plate documents in the file for transfer to the thermal cycler.

77. The device of claim 72, wherein the method steps further comprise:

generating or updating an activity log.

78. The device of claim 72, wherein the method steps further comprise:

outputting the instructions to a printer for printing.

79. The device of claim 72, wherein the method steps further comprise:

determining errors in the information or instructions that could adversely impact analysis of the assay mixtures.

80. The device of claim 72, wherein the data storage device is a removable disk.

81. The device of claim 72, wherein the thermal cycler is adapted to perform a real-time polymerase chain reaction.