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

• US 20040072195A1
• Filed: 04/01/2003
• Published: 04/15/2004
• Est. Priority Date: 01/25/2002
• Status: Abandoned Application

• Current Assignee: Applied Biosystems LLC (Thermo Fisher Scientific Incorporated)
• Original Assignee: Applied Biosystems LLC (Thermo Fisher Scientific Incorporated)
• Inventors: Livak, Kenneth J., Lucero, Michael, Stevens, Junko, Hunkapiller, Michael W., Eddins, Susan K., Gilbert, Dennis A.
• Application Number:
  US10/404,640
• Publication Number:
  US 20040072195A1
• Time in Patent Office: Days
• US Class Current: 435/6
• 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: G01N 35/00732 Identification of carriers, materials or components in automatic analysers
• CPC Class Codes: G01N 35/1002 Reagent dispensers
• 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 25/20 Polymerase chain reaction [PCR]; Primer or probe design; Probe optimisation
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• 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

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. A method for facilitating genetic analysis:

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

providing to the user (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.

2. The method of claim 1, wherein the one or more assays each comprises a homogeneous reaction mixture.

3. The method of claim 2, wherein the homogeneous reaction mixture comprises components for conducting a fluorogenic 5′

nuclease assay.

4. The method of claim 1, wherein the information is provided on a disk.

5. The method of claim 4, wherein the disk is a compact disk (CD).

6. The method of claim 1, wherein the information is provided via a computer network.

7. The method of claim 6, wherein the information is transmitted to the user via electronic mail.

8. The method of claim 6, wherein the information is provided via a file transfer protocol (FTP).

9. The method of claim 1, wherein the information is comprised, at least in part, of American Standard Code for Information Interchange (ASCII) formatted text.

10. The method of claim 1, wherein at least one of the one or more assays and the information are shipped to the user together in a single package.

11. 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 first laboratory instrument; and

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

12. The method of claim 11, wherein each of the plurality of assays comprises a homogeneous reaction mixture.

13. The method of claim 12, wherein the homogeneous reaction mixture comprises components for conducting a fluorogenic 5′

nuclease assay.

14. The method of claim 11, wherein the information is provided on a compact disk (CD).

15. The method of claim 11, wherein the instrument is a thermal cycler and the thermal cycler is configured to perform a real-time polymerase chain reaction.

19. The method of claim 11, wherein the information is comprised, at least in part, of American Standard Code for Information Interchange (ASCII) formatted text.

20. The method of claim 11, wherein at least one of the plurality of assays and the information are shipped to the user together in a single package.

21. The method of claim 11, wherein each of the plurality of assay mixtures is contained in a single tube.

22. The method of claim 11, wherein the requesting step is carried out via the Internet.

23. The method of claim 11, further comprising a second laboratory instrument and a computer system adapted for electronic communication with the second instrument.

24. The method of claim 23, wherein the first instrument is a liquid-handling robot.

25. The method of claim 23, wherein the second instrument is a sequence detection system.

26. The method of claim 23, further comprising the step of transferring at least a portion of the electronic information from the computer that is in communication with the first instrument to the computer that is in communication with the second instrument after the assay mixtures have been processed by the first instrument.

27. The method of claim 26, further comprising the step of transferring at least a portion of the electronic information from the computer that is in communication with the second instrument to a computer that can be used to analyze the results of assay manipulation by the first or second instruments.

16. The method of claim 111, wherein the information is provided via a computer network.

17. The method of claim 16, wherein the information is transmitted by the supplier via electronic mail.

18. The method of claim 16, wherein the information is downloaded by the user from a server.

28. A method for facilitating genetic analysis, comprising:

receiving a request for a plurality of assay mixtures for genetic analysis from a user; 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.

29. The method of claim 28, wherein the plurality of assay mixtures and the information is supplied to the user together, at the same time.

30. The method of claim 28, wherein the information is provided on a removable disk.

31. The method of claim 30, wherein the removable disk comprises a compact disk (CD).

32. The method of claim 28, wherein the information is provided via a computer network.

33. The method of claim 28, wherein each of the plurality of assay mixtures comprises a homogeneous reaction mixture.

34. The method of claim 33, wherein each homogeneous reaction mixture comprises a fluorogenic 5′

nuclease assay.

35. The method of claim 28, wherein each of the plurality of assay mixtures is contained in a single tube.

36. The method of claim 28, wherein the program storage device comprises a removable disk.

37. The method of claim 28, further comprising providing a web site configured for receiving requests from users for assay mixtures for genetic analysis.

38. A method, comprising:

providing a program storage device readable by a computer system, embodying a program of instructions executable by the computer system for genetic analysis;

uploading electronic information relating to a plurality of assay mixtures from a data storage device to the computer system;

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

transferring the file to the thermal cycler for implementation.

39. The method of claim 38, wherein the method further comprises:

monitoring for electronic information ready for uploading.

40. The method of claim 38, wherein the method further comprises:

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

41. The method of claim 38, wherein the method further comprises:

building an assay information database.

42. The method of claim 38, wherein the method further comprises:

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

43. The method of claim 38, wherein the method further comprises:

generating or updating an activity log.

44. The method of claim 38, wherein the method further comprises:

outputting the instructions to a printer for printing.

45. The method of claim 38, wherein the method further comprises:

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

46. The method of claim 38, wherein the data storage device is a removable disk.

47. The method of claim 38, wherein the thermal cycler is adapted to perform a real-time polymerase chain reaction.