Sequence scheduling and sample distribution techniques

• US 9,989,544 B2
• Filed: 07/09/2015
• Issued: 06/05/2018
• 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:
  US14/795,285
• Publication Number:
  US 20150309058A1
• Time in Patent Office: 1,062 Days
• Field of Search: 700266, 702 19, 702 20, 702 22, 702 31, 702 32, 930 10, 506 43
• 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 computer system for assigning sequencing runs for biological samples, comprising:

a plurality of sequencing devices respectively configured to acquire sequence data indicative of nucleotide identities from a respective plurality of biological samples during a sequencing run and communicate information related to an availability to sequence at least one of the plurality of biological samples;

a memory circuit including executable application instructions stored therein; and

a processor configured to execute the application instructions stored in the memory circuit, wherein the application instructions comprise instructions for;

receiving information related to the availability of the plurality of sequencing devices;

receiving identification information for the plurality of biological samples, wherein the identification information comprises sample preparation information for each respective biological sample of the plurality of biological samples;

identifying a subset of the plurality of sequencing devices that have a sample preparation compatibility with an individual biological sample of the plurality of biological samples based on the sample preparation information;

assigning the individual biological sample to an individual sequencing device of the subset based at least in part on the information related to the availability and the sample preparation compatibility of each respective sequencing device of the plurality of sequencing devices; and

providing an indication that the individual sequencing device is available to sequence the individual biological sample based on the information related to the availability and the sample preparation compatibility.

2. The system of claim 1, wherein, when the individual biological sample of the plurality of biological samples has a high priority designation and no sequencing device is available, the application instructions comprise providing an override indication and assigning the individual biological sample to the individual sequencing device based on a determination that a sufficient percentage of sequence data has been acquired of an ongoing incomplete sequencing run.

3. The system of claim 1, wherein, when the individual biological sample of the plurality of biological samples has a high priority designation and no sequencing device is available, the application instructions comprise assigning the individual biological sample to the sequencing device based on a surface sample density of an ongoing sequencing run and providing an indication to add the individual biological sample to the ongoing sequencing run.

4. The system of claim 3, wherein the application instructions comprise providing an indication that the individual biological sample should be tagged to distinguish the biological sample from the ongoing sequencing run.

5. The system of claim 1, wherein the application instructions comprise determining an earliest possible availability for an unavailable sequencing device by determining of a percentage of sufficient completion of an ongoing incomplete sequencing run.

6. The system of claim 1, wherein the application instructions comprise assigning each of the plurality of biological samples to respective sequencing devices based at least in part on an estimated total processing load of the plurality of sequencing devices.

7. The system of claim 6, wherein the assigning comprises smoothing the processing load over a period of time.

8. The system of claim 6, wherein the assigning comprises increasing the processing load at particular times.

9. The system of claim 6, wherein the assigning comprises determining if the sequencing device is capable of performing analysis in the cloud.

10. The system of claim 1, wherein the application instructions comprise instructions for receiving information related to sequencing capabilities of the plurality of sequencing devices, wherein the sequencing capabilities relate to capabilities of operating according to one or more sequencing protocols.

11. The system of claim 10, wherein the instructions for assigning the individual biological sample to the individual sequencing device comprise determining a compatibility between a desired nucleotide sequencing assay type for the individual biological sample and the sequencing capabilities of the individual sequencing device.

12. The system of claim 1, wherein the application instructions comprise providing instructions to a sample loading system to load the individual biological sample into the assigned individual sequencing device when the assigned individual sequencing device is available.

13. The system of claim 1, wherein the memory circuit and the processor are disposed on one of the plurality of sequencing devices.

14. The system of claim 1, wherein the subset comprises sequencing devices of the plurality of sequencing devices from a particular manufacturer.

15. The system of claim 1, wherein the sample preparation information comprises sample tag information, and wherein the subset comprises sequencing devices of the plurality of sequencing devices configured to sequence multiple biological samples simultaneously when at least one of the multiple biological samples comprises the sample tag.

16. The system of claim 1, wherein the individual sequencing device is configured to simultaneously sequence a predetermined number of biological samples prepared according to a same sample preparation protocol subset.

17. The system of claim 1, wherein the individual sequencing device is available when the predetermined number of biological samples has not yet been loaded onto the individual sequencing device.

18. The system of claim 1, wherein the application instructions comprise instructions for identifying the subset of the plurality of sequencing devices further based on a compatibility between sequencing parameter information of the individual biological sample and sequencing capabilities of the plurality of sequencing devices.

19. The system of claim 1, wherein the application instructions comprise instructions for interrupting an ongoing sequencing run of the individual biological sample based on a presence of a homopolymer region of interest in the sequence data.

20. The system of claim 19, wherein the application instructions comprise instructions for reassigning the individual biological sample to another sequencing device of the subset after the interrupting based on the presence of a homopolymer region of interest in the sequence data.

21. The system of claim 1, wherein the application instructions comprise instructions for reassigning the individual biological sample to another sequencing device of the plurality of sequencing devices based on an analysis of the sequence data of other biological samples of the plurality of biological samples.