Methods and systems for using a cloud computing environment to configure and sell a biological sample preparation cartridge and share related data

• US 9,805,407 B2
• Filed: 03/08/2013
• Issued: 10/31/2017
• Est. Priority Date: 01/25/2013
• Status: Active Grant

• Current Assignee: Illumina Incorporated
• Original Assignee: Illumina Incorporated
• Inventors: Shen, Min-Jui Richard, Lin, Charles Hsuan
• Primary Examiner(s): LEVINE, ADAM L
• Application Number:
  US13/791,168
• Publication Number:
  US 20140214579A1
• Time in Patent Office: 1,698 Days
• CPC Class Codes: G06Q 30/0601 Electronic shopping [e-shopping]
• CPC Class Codes: G06Q 30/0609 Buyer or seller confidence or verification
• CPC Class Codes: G06Q 30/0621 Item configuration or customization
• CPC Class Codes: G06Q 30/0627 using item specifications
• CPC Class Codes: G06Q 30/0635 Processing of requisition or of purchase orders
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• 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: G16H 10/40 for data related to laboratory analysis, e.g. patient specimen analysis
• CPC Class Codes: G16H 40/20 for the management or administration of healthcare resources or facilities, e.g. managing hospital staff or surgery rooms

Abstract

The present disclosure provides a novel approach for shifting or distributing various information (e.g., protocols, analysis methods, sample preparation data, sequencing data, etc.) to a cloud-based network. For example, the techniques relate to a cloud computing environment configured to receive this information from one or more individual sample preparation devices, sequencing devices, and/or computing systems. In turn, the cloud computing environment may generate information for use in the cloud computing environment and/or to provide the generated information to the devices to guide a genomic analysis workflow. Further, the cloud computing environment may be used to facilitate the sharing of sample preparation protocols for use with generic sample preparation cartridges and/or monitoring the popularity of the sample preparation protocols.

Claims

1. A computer-implemented method for sharing and monitoring use of protocols for assays utilizing variable configuration sample preparation cartridges to prepare biological samples in a cloud computing environment, comprising:

receiving from a submitter, at a server, a protocol for an assay utilizing a variable configuration sample preparation cartridge to prepare a biological sample on the cloud computing environment, wherein the variable configuration sample preparation cartridge is structurally configured to be utilized with different protocols for assays that utilize the variable configuration sample preparation cartridge for preparing biological samples including the protocol, and the protocol comprises processor-executable instructions for automatic sample preparation by a sample preparation device utilizing the variable configuration sample preparation cartridge;

storing the protocol on a memory of the server;

monitoring, at a processor of the server, for a request from a requester for the protocol;

receiving, at the server, from the requester the request for the protocol;

crediting, at the processor, the submitter with a purchase credit from a supplier of the variable configuration sample preparation cartridge for at least one request for the protocol;

conferring, at the processor, a certified status to the protocol upon the processor determining that at least a number of requests for the protocol by requesters meets a specific criterion; and

communicating the protocol to the requester, the requester having access to the cloud computing environment based on purchase of the variable configuration sample preparation cartridge, wherein the processor-executable instructions of the protocol are configured to, when executed, cause the sample preparation device to operate on the variable configuration sample preparation cartridge.

2. The method of claim 1, comprising receiving, at the server, a rating for the protocol from the requester.

3. The method of claim 1, comprising receiving from the submitter, at the server, an analysis method for use with the protocol.

4. The method of claim 1, comprising receiving from the supplier, at the server, a validation of the protocol.

5. The method of claim 1, comprising receiving, at the server, a citation of a publication that cites, uses, or both cites and uses the protocol.

6. The method of claim 1, comprising:

automatically preparing the biological sample, at the sample preparation device, utilizing the variable configuration sample preparation cartridge based on the protocol such that only a subset of compartments or channels in the variable configuration sample preparation cartridge are used in preparing the biological sample according to the protocol.

7. The method of claim 1, wherein conferring, at the processor, the certified status to the protocol comprises the processor determining that a combination of the number of requests for the protocol by the requesters, ratings of the protocol by the requesters, a number of citations for the protocol, and validation of the protocol meets specific criteria.

8. The method of claim 1, comprising receiving, at the server, a second request for a second protocol different from the protocol, wherein the second protocol is configured to be used with the variable configuration sample preparation cartridge and wherein the second protocol comprises processor-executable instructions to use a different subset of compartments of the variable configuration sample preparation cartridge than those used the protocol.

9. The method of claim 1, comprising receiving, at the server, a second request for a second protocol different from the protocol, wherein the second protocol is configured to be used with the variable configuration sample preparation cartridge and wherein the second protocol comprises processor-executable instructions to program a grid of dynamic pads, wherein the instructions change a state of respective individual pads of the dynamic pads in the grid in a pattern that is different from the first protocol.

10. The method of claim 1, comprising providing to the requester the different protocols configured for use with the variable configuration sample preparation cartridge and wherein the request is a selection of the protocol from the different protocols.

11. The method of claim 1, wherein the different protocols comprise different instructions to program a grid of dynamic pads of the variable configuration sample preparation cartridge.

12. The method of claim 1, wherein the different protocols comprise different instructions to use subsets of channels or compartment of the variable configuration sample preparation cartridge.

13. A system for sharing and monitoring use of protocols for assays utilizing variable configuration sample preparation cartridges to prepare biological samples, comprising:

a cloud computing environment in communication with a plurality of computer systems, wherein the cloud computing environment comprises at least one server comprising at least one processor and a memory, the at least one server being configured to communicate with at least one of the computer systems to receive from a submitter a protocol for an assay that utilizes a variable configuration sample preparation cartridge to prepare a biological sample and to store the protocol on the memory, the variable configuration sample preparation cartridge being structurally configured to be utilized with different protocols for assays that utilize the variable configuration sample preparation cartridge for preparing biological samples including the protocol, and the protocol comprises processor-executable instructions for automatic sample preparation by a sample preparation device utilizing the variable configuration sample preparation cartridge, and the at least one processor being programmed to monitor for a request by a requester for the protocol, the at least one server being configured to receive from the requester the request for the protocol, and the at least one processor is programmed to credit the submitter of the protocol with purchase credit from a supplier of the variable configuration sample preparation cartridge for at least one request for the protocol, wherein the at least one processor is programmed to confer a certified status to the protocol upon the processor determining that at least a number of requests for the protocol by requesters meets a specific criterion, and wherein the at least one processor is programmed to communicate the protocol to the requester, the requester having access to the cloud computing environment based on purchase of the variable configuration sample preparation cartridge, wherein the processor-executable instructions of the protocol are configured to, when executed, cause the sample preparation device to operate on the variable configuration sample preparation cartridge.

14. The system of claim 13, wherein the at least one server is configured to receive a rating for the protocol from the requester.

15. The system of claim 13, wherein the at least one server is configured to receive from the submitter an analysis method for use with the protocol.

16. The system of claim 13, wherein the at least one server is configured to receive from the supplier a validation of the protocol.

17. The system of claim 13, wherein the at least one server is configured to receive a citation of a publication that cites, uses, or both cites and uses the protocol.

18. The system of claim 13, wherein the at least one server is configured to receive instructions from the supplier to confer the supplier supported status to the protocol.

19. The system of claim 13, wherein the at least one server is configured to provide to the requester an analysis method for use with the protocol.

20. The system of claim 13, comprising the sample preparation device, and wherein the at least one server is configured to provide the protocol to the sample preparation device, and the sample preparation device is configured to automatically prepare the biological sample utilizing the variable configuration sample preparation cartridge based on the protocol such that the processor-executable instructions of the protocol program a grid of dynamic pads, wherein the instructions change a state of respective individual pads of the dynamic pads in the grid.

21. The system of claim 13, comprising the variable configuration sample preparation cartridge.

22. A system for sharing and monitoring use of protocols for assays utilizing variable configuration sample preparation cartridges to prepare biological samples, comprising:

a cloud-based server in communication with a plurality of computer systems;

a memory component that receives from one or more submitters, at the cloud-based server, protocols for assays that utilize variable configuration sample preparation cartridges to prepare biological samples and stores the protocols, wherein the variable configuration sample preparation cartridges are structurally configured to be utilized with different protocols for assays that utilize a respective variable configuration sample preparation cartridge for preparing biological samples including the protocols, and the protocols comprise processor-executable instructions for automatic sample preparation by a sample preparation device utilizing the respective variable configuration sample preparation cartridge; and

a processor programmed to;

receive requests for one or more of the protocols from one or more requesters;

monitor a number of requests for each of the protocols; and

credit a submitter of a respective protocol with a purchase credit from a supplier of the variable configuration sample preparation cartridges for at least one request for the respective protocol;

confer a certified status to the respective protocol upon the processor determining that at least a number of requests for the respective protocol by the one or more requesters meets a specific criteria; and

communicate the protocol to the one or more requesters, the one or more requesters having access to the cloud computing environment based on purchase of the variable configuration sample preparation cartridge, wherein the processor-executable instructions of the protocol are configured to, when executed, cause the sample preparation device to operate on the variable configuration sample preparation cartridge.

23. The system of claim 22, comprising the sample preparation device, and wherein the processor is programmed to provide the respective protocol to the sample preparation device, and the sample preparation device is configured to automatically prepare the biological sample utilizing the respective variable configuration sample preparation cartridge based on the respective protocol.

24. The system of claim 22, comprising the respective variable configuration sample preparation cartridge.