Sequence scheduling and sample distribution techniques

• US 9,116,139 B2
• Filed: 11/05/2012
• Issued: 08/25/2015
• Est. Priority Date: 11/05/2012
• Status: Active Grant

• Current Assignee: Illumina Incorporated
• Original Assignee: Illumina Incorporated
• Inventors: Kain, Robert C., Dickinson, Alexander G., Shen, Min-Jui Richard, Eltoukhy, Helmy A., Garcia, Francisco Jose
• Primary Examiner(s): Sasaki, Shogo
• Application Number:
  US13/668,686
• Publication Number:
  US 20140127792A1
• Time in Patent Office: 1,023 Days
• Field of Search: 700/266, 702/19, 702/20, 702/22, 702/31, 702/32, 930/10, 506/43
• US Class Current: 1/1
• CPC Class Codes: B01J 19/00 Chemical, physical or physico-chemical processes in general; Their relevant apparatus
• CPC Class Codes: G01N 35/00871 Communications between instruments or with remote terminals
• CPC Class Codes: G01N 35/0092 Scheduling

Abstract

A technique is disclosed for sample management for use in conjunction with sequencing devices that sequence biological samples, e.g., DNA and RNA. A sequencing device or a network of sequencing devices may be scheduled according to the characteristics of the samples in queue and the capabilities and availability of sequencing devices. Biological samples may be automatically queued and loaded via a sample distribution system. A sample distribution system may be used to reduce operator intervention.

Claims

1. A sequencing device, comprising:

a sample device configured to receive a biological sample and process the biological sample during a sequencing run;

a detection module coupled to the sample device, wherein the detection module comprises detection circuitry configured to acquire sequence data representative of nucleotide identities from the biological sample during the sequencing run; and

at least one processor programmed to;

receive the sequence data as the sequencing run is in progress;

determine the nucleotide identities of the biological sample based on the sequence data;

generate one or more files comprising the nucleotide identities;

analyze the nucleotide identities to determine if the acquired sequence data from the biological sample is sufficient; and

provide an indication that the sequencing device is available in response to determining that the sequence data from the biological sample is sufficient to determine a characteristic of the biological sample, wherein the indication is provided while the detection module is acquiring additional sequence data from the biological sample during the sequencing run and before the sequencing run is complete;

wherein the processor is programmed to reassign the detection module to sequence a second biological sample after sufficient sequence data from the biological sample has been acquired and before the sequencing run is complete.

2. The sequencing device of claim 1, wherein the processor is programmed to receive instructions to communicate the nucleotide identities to a cloud-based computing environment.

3. The sequencing device of claim 1, wherein the sequencing device is communicatively coupled to a network of sequencing devices.

4. The sequencing device of claim 3, wherein the network of sequencing devices comprises a distributed control system for controlling the sequencing devices.

5. The sequencing system of claim 3, wherein the network of sequencing devices comprises a central control system for controlling the sequencing devices.

6. The sequencing device of claim 1, wherein the sample device comprises a housing having a sample input port configured to receive the biological sample.

7. The sequencing device of claim 1, wherein the processor is programmed to determine that the acquired sequence data is sufficient to assemble a genome of the biological sample.

8. The sequencing device of claim 1, wherein the acquired sequence data comprises an incomplete set of nucleotide identity files of the biological sample.

9. The sequencing device of claim 1, wherein the processor is programmed to determine that the acquired sequence data is sufficient based on a presence of a minimum file set in the acquired sequence data.

10. The sequencing device of claim 1, wherein the processor is programmed to determine that the acquired sequence data is sufficient based on a determination of a percentage completion of the sequencing run.

11. The sequencing device of claim 10, wherein the percentage completion associated with sufficient acquired sequence data is associated with an organism of origin of the biological sample.

12. The sequencing device of claim 1, wherein the processor is programmed to provide instructions to the detection module to interrupt the sequencing run before the sequencing run is complete in response to determining that the sequence data is sufficient.

13. A sequencing device, comprising:

a sample device configured to receive a biological sample and process the biological sample during a sequencing run;

a detection module coupled to the sample device, wherein the detection module comprises detection circuitry configured to acquire sequence data representative of nucleotide identities from the biological sample during the sequencing run; and

at least one processor programmed to;

receive the sequence data as the sequencing run is in progress;

determine the nucleotide identities of the biological sample based on the sequence data;

generate one or more files comprising the nucleotide identities;

analyze the nucleotide identities to determine if the acquired sequence data from the biological sample is sufficient; and

provide an indication that the sequencing device is available in response to determining that the sequence data from the biological sample is sufficient to determine a characteristic of the biological sample, wherein the indication is provided while the detection module is acquiring additional sequence data from the biological sample during the sequencing run and before the sequencing run is complete;

wherein the processor is programmed to determine a priority of a second biological sample in queue behind the biological sample and to provide instructions to the detection module to interrupt the sequencing run before the sequencing run is complete in response to determining that the sequence data is sufficient and that the priority of the second biological sample is higher than a priority of the biological sample.

14. The sequencing device of claim 13, wherein the processor is programmed to receive instructions to communicate the nucleotide identities to a cloud-based computing environment.

15. The sequencing device of claim 13, wherein the sequencing device is communicatively coupled to a network of sequencing devices.

16. The sequencing device of claim 15, wherein the network of sequencing devices comprises a distributed control system for controlling the sequencing devices.

17. The sequencing system of claim 15, wherein the network of sequencing devices comprises a central control system for controlling the sequencing devices.

18. The sequencing device of claim 13, wherein the sample device comprises a housing having a sample input port configured to receive the biological sample.

19. The sequencing device of claim 13, wherein the processor is programmed to determine that the acquired sequence data is sufficient to assemble a genome of the biological sample.

20. The sequencing device of claim 13, wherein the acquired sequence data comprises an incomplete set of nucleotide identity files of the biological sample.

21. The sequencing device of claim 13, wherein the processor is programmed to determine that the acquired sequence data is sufficient based on a presence of a minimum file set in the acquired sequence data.

22. The sequencing device of claim 13, wherein the processor is programmed to determine that the acquired sequence data is sufficient based on a determination of a percentage completion of the sequencing run.

23. The sequencing device of claim 22, wherein the percentage completion associated with sufficient acquired sequence data is associated with an organism of origin of the biological sample.

24. A sequencing device, comprising:

a sample device configured to receive a biological sample and process the biological sample during a sequencing run;

a detection module coupled to the sample device, wherein the detection module comprises detection circuitry configured to acquire sequence data representative of nucleotide identities from the biological sample during the sequencing run; and

at least one processor programmed to;

receive the sequence data as the sequencing run is in progress;

determine the nucleotide identities of the biological sample based on the sequence data;

generate one or more files comprising the nucleotide identities;

analyze the nucleotide identities to determine if the acquired sequence data from the biological sample is sufficient; and

provide an indication that the sequencing device is available in response to determining that the sequence data from the biological sample is sufficient to determine a characteristic of the biological sample, wherein the indication is provided while the detection module is acquiring additional sequence data from the biological sample during the sequencing run and before the sequencing run is complete;

wherein the processor is programmed to determine a priority of a second biological sample in queue behind the biological sample and to provide instructions to the detection module to permit the sequencing run to run to completion in response to determining that the sequence data is sufficient and that the priority of the second biological sample is lower than a priority of the biological sample.

25. The sequencing device of claim 24, wherein the processor is programmed to receive instructions to communicate the nucleotide identities to a cloud-based computing environment.

26. The sequencing device of claim 24, wherein the sequencing device is communicatively coupled to a network of sequencing devices.

27. The sequencing device of claim 26, wherein the network of sequencing devices comprises a distributed control system for controlling the sequencing devices.

28. The sequencing system of claim 26, wherein the network of sequencing devices comprises a central control system for controlling the sequencing devices.

29. The sequencing device of claim 24, wherein the sample device comprises a housing having a sample input port configured to receive the biological sample.

30. The sequencing device of claim 24, wherein the processor is programmed to determine that the acquired sequence data is sufficient to assemble a genome of the biological sample.

31. The sequencing device of claim 24, wherein the acquired sequence data comprises an incomplete set of nucleotide identity files of the biological sample.

32. The sequencing device of claim 24, wherein the processor is programmed to determine that the acquired sequence data is sufficient based on a presence of a minimum file set in the acquired sequence data.

33. The sequencing device of claim 24, wherein the processor is programmed to determine that the acquired sequence data is sufficient based on a determination of a percentage completion of the sequencing run.

34. The sequencing device of claim 33, wherein the percentage completion associated with sufficient acquired sequence data is associated with an organism of origin of the biological sample.