Methods and systems for using a cloud computing environment to share biological related data

• US 10,217,156 B2
• Filed: 10/03/2017
• Issued: 02/26/2019
• 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:
  US15/723,918
• Publication Number:
  US 20180158126A1
• Time in Patent Office: 511 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 of a cloud-computing environment, a protocol for an assay utilizing a variable configuration sample preparation cartridge to prepare a biological sample, 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;

conferring, at the server, a certification to the protocol upon a processor of the server determining that a quality of the protocol meets a specific criterion; and

communicating the protocol to a requester based at least in part on the certification, the requester having access to the cloud computing environment based on obtaining 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, wherein the quality is based at least in part on the rating.

3. The method of claim 1, comprising receiving, at the server, a validation for the protocol, wherein the quality is based at least in part on the validation.

4. The method of claim 1, comprising receiving, at the server, a number of requests for the protocol, wherein the quality is based at least in part on the number of requests being above a threshold.

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, wherein the quality is based at least in part on the citation.

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

7. The method of claim 1, wherein the different protocols comprise different instructions to program a grid of dynamic pads.

8. 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 of a cloud-computing environment, a protocol for an assay utilizing a variable configuration sample preparation cartridge to prepare a biological sample, 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;

receiving, at the server, information indicative of a certification of the protocol; and

communicating the protocol to a requester, the requester having access to the cloud computing environment based on obtaining 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.

9. The method of claim 8, wherein the different protocols comprise different instructions to use subsets of channels or compartments of the variable configuration sample preparation cartridge.

10. The method of claim 8, wherein the different protocols comprise different instructions to program a grid of dynamic pads.

11. The method of claim 8, wherein the protocol is compatible with the variable configuration sample preparation cartridge of a particular supplier.

12. The method of claim 8, wherein the protocol is compatible with the sample preparation device of a particular supplier.

13. The method of claim 8, wherein the information is received from a supplier of the variable configuration sample preparation cartridge.

14. The method of claim 8, wherein the information is received from a supplier of the sample preparation device.