Genome explorer system to process and present nucleotide variations in genome sequence data
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.
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:
receive, over a network from a first client, a sample complex sequence for a test sample, wherein the sample complex sequence includes at least 1,000 genes;
determine, by the one or more processors of the server system, a plurality of variations by comparing the sample complex sequence for the test sample to a reference complex sequence for a reference sample, wherein the reference complex sequence including the at least 1,000 genes;
assemble, by the one or more processors, a gene sequence map that is a graphical depiction showing the plurality of variations between the sample complex sequence for the test sample and the reference complex sequence for the reference sample along a DNA structure;
provide, via the network, the gene sequence map to a plurality of clients;
cause the first client to display a first user interface that receives directions to make the gene sequence map for the sample complex sequence available to other clients and that receives first information about one or more of the variations of the plurality of 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, privately to the first client or to a portion of the plurality of clients selected by the first client, the reply information for the one or more variations over the network.
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 the first information and the 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 the 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 at least one memory stores instructions that, when executed by the one or more processors, further cause the one or more processors to:
granting access to the reply information for the one or more variations to the first client or to the portion of the plurality of clients selected by the first client over the network,
wherein the one or more second clients have a level of access that provides authority to update an entry for the one or more variations.
13. A method for sharing variations in complex sequences between clients, the method comprising performing, by one or more processors of a server system:
receiving, over a network from a first client, a sample complex sequence for a test sample, wherein the sample complex sequence includes at least 1,000 genes;
determining a plurality of variations by comparing the sample complex sequence for the test sample to a reference complex sequence for a reference sample, wherein the reference complex sequence including the at least 1,000 genes;
assembling a gene sequence map that is a graphical depiction showing the plurality of variations between the sample complex sequence for the test sample and the reference complex sequence for the reference sample along a DNA structure;
provide, via the network, the gene sequence map to a plurality of clients;
cause the first client to display a first user interface that receives directions to make the gene sequence map for the sample complex sequence available to other clients and that receives first information about one or more of the variations of the plurality of 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, privately to the first client or to a portion of the plurality of clients selected by the first client, the reply information for the one or more variations over the network.
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 the first information and the 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 13 , further comprising:
granting access to the reply information for the one or more variations to the first client or to the portion of the plurality of clients selected by the first client over the network.
17. A computer product comprising a non-transitory computer readable medium storing a plurality of instructions that when executed control one or more processors of a computer system to perform:
receiving, over a network from a first client, a sample complex sequence for a test sample, wherein the sample complex sequence includes at least 1,000 genes;
determining a plurality of variations by comparing the sample complex sequence for the test sample to a reference complex sequence for a reference sample, wherein the reference complex sequence including the at least 1,000 genes;
assembling a gene sequence map that is a graphical depiction showing the plurality of variations between the sample complex sequence for the test sample and the reference complex sequence for the reference sample along a DNA structure;
provide, via the network, the gene sequence map to a plurality of clients;
cause the first client to display a first user interface that receives directions to make the gene sequence map for the sample complex sequence available to other clients and that receives first information about one or more of the variations of the plurality of 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, privately to the first client or to a portion of the plurality of clients selected by the first client, the reply information for the one or more variations over the network.
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 the first information and the 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 17 , wherein the non-transitory computer readable medium is further configured to perform:
granting access to the reply information for the one or more variations to the first client or to the portion of the plurality of clients selected by the first client over the network.