GENOME EXPLORER SYSTEM TO PROCESS AND PRESENT NUCLEOTIDE VARIATIONS IN GENOME SEQUENCE DATA

• US 20190311784A1
• Filed: 06/24/2019
• Published: 10/10/2019
• Est. Priority Date: 10/24/2012
• Status: Active Application

• Current Assignee: NantOmics, LLC (NantWorks, LLC)
• Original Assignee: NantOmics, LLC (NantWorks, LLC)
• Inventors: Adams, Julie, Buholzer, Mirko
• Application Number:
  US16/450,775
• Publication Number:
  US 20190311784A1
• Time in Patent Office: Days
• CPC Class Codes: G16B 20/00 ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• CPC Class Codes: G16B 20/10 Ploidy or copy number detection
• CPC Class Codes: G16B 20/20 Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16B 30/10 Sequence alignment; Homology search
• 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
• CPC Class Codes: G16B 50/10 Ontologies; Annotations

Abstract

This disclosure provides a technology for users to gain first-hand knowledge and experience with interpreting whole genomes. The technology graphically depicts variations in genome sequences in an expandable display, and provides a platform whereby the user may find and research the biological significance of such variants. The technology also provides a unique collaborative environment designed to capture and improve the collective knowledge of the participating community.

Claims

1. A server system for sharing variations in complex sequences between clients, the server system comprising one or more processors coupled with at least one memory storing instructions that, when executed by the one or more processors, cause the one or more processors to:

assemble a gene sequence map that shows a plurality of variations between a sample complex sequence for a test sample and a reference complex sequence for a reference sample;

provide, via a network, the gene sequence map to a plurality of clients;

cause a first client to display a first user interface that receives directions to make the gene sequence map available to other clients and that receives first information about one or more of the variations made available to the other clients;

cause one or more second clients to display at least one second user interface that receives reply information from the one or more second clients about the one or more variations made available; and

provide, to the first client, the reply information for the one or more variations.

2. The server system of claim 1, wherein the gene sequence map is provided to the plurality of clients with one or more links for the one or more variations to first information and reply information, each of the one or more links for a respective variation.

3. The server system of claim 1, wherein the first information about the one or more variations provided by the first client is made available to other clients with hyperlinks that link to an indication of the one or more variations on the gene sequence map.

4. The server system of claim 3, wherein the first information is displayed in a feed as one or more entries, the feed being available to a plurality of users, wherein each entry of the one or more entries corresponds to a respective variation.

5. The server system of claim 3, wherein the first information about the one or more variations is made available to the other clients by way of an information website on the Internet.

6. The server system of claim 5, wherein the server system is configured to compile reply information about the one or more variations from other users into an assessment as to whether the one or more variations are pathogenic or benign.

7. The server system of claim 1, wherein the at least one second user interface provides a hyperlink to a forum at which the reply information is provided by the one or more second clients, and wherein the hyperlink is provided on the gene sequence map at or near each one or more loci corresponding to the one or more of the variations.

8. The server system of claim 1, wherein the first user interface is configured to receive a selection of the one or more variations from amongst a set of variations on the gene sequence map.

9. The server system of claim 1, wherein the at least one memory stores instructions that, when executed by the one or more processors, further cause the one or more processors to:

transmit, via the network, the one or more variations to the one or more second clients displaying the at least one second user interface; and

receive, via the network, the reply information from the at least one second user interface.

10. The server system of claim 9, wherein the one or more variations are transmitted with the gene sequence map, and wherein the at least one second user interface is configured to receive a location marker on the gene sequence map with the reply information.

11. The server system of claim 1, wherein the reply information for the one or more variations is provided to the first client via the first user interface.

12. The server system of claim 1, wherein the one or more second clients have a level of access that provides authority to update an entry for the for the one or more variations.

13. A method for sharing variations in complex sequences between clients, the method comprising performing, by a server system:

assembling a gene sequence map that shows a plurality of variations between a sample complex sequence for a test sample and a reference complex sequence for a reference sample;

providing, via a network, the gene sequence map to a plurality of clients;

causing a first client to display a first user interface that receives directions to make the gene sequence map available to other clients and that receives first information about one or more of the variations made available to the other clients;

causing one or more second clients to display at least one second user interface that receives reply information from the one or more second clients about the one or more variations made available; and

providing, to the first client, the reply information for the one or more variations.

14. The method of claim 13, wherein the gene sequence map is provided to the plurality of clients with one or more links for the one or more variations to first information and reply information, each of the one or more links for a respective variation.

15. The method of claim 13, wherein the first information about the one or more variations provided by the first client is made available to other clients with hyperlinks that link to an indication of the one or more variations on the gene sequence map.

16. The method of claim 15, wherein the first information is displayed in a feed as one or more entries, the feed being available to a plurality of users, wherein each entry of the one or more entries corresponds to a respective variation.

17. A computer product comprising a non-transitory computer readable medium storing a plurality of instructions that when executed control a computer system to perform:

assembling a gene sequence map that shows a plurality of variations between a sample complex sequence for a test sample and a reference complex sequence for a reference sample;

providing, via a network, the gene sequence map to a plurality of clients;

causing a first client to display a first user interface that receives directions to make the gene sequence map available to other clients and that receives first information about one or more of the variations made available to the other clients;

causing one or more second clients to display at least one second user interface that receives reply information from the one or more second clients about the one or more variations made available; and

providing, to the first client, the reply information for the one or more variations.

18. The computer product of claim 17, wherein the gene sequence map is provided to the plurality of clients with one or more links for the one or more variations to first information and reply information, each of the one or more links for a respective variation.

19. The computer product of claim 17, wherein the first information about the one or more variations provided by the first client is made available to other clients with hyperlinks that link to an indication of the one or more variations on the gene sequence map.

20. The computer product of claim 19, wherein the first information is displayed in a feed as one or more entries, the feed being available to a plurality of users, wherein each entry of the one or more entries corresponds to a respective variation.