Systems and methods for gene variant grouping and visualization

1 . A method for determining relationships between gene variants of a gene, the gene variants being related to one or more cancers and being correlated to a treatment response of the one or more cancers to one or more treatments, the method comprising:

accessing, using at least one processor, a database comprising information about the gene variants, the information including at least information indicative of a treatment response of a first gene variant of the gene variants to one or more treatments;

categorizing, using the at least one processor, the information about the gene variants within a plurality of groups by:

determining, based on the information about the gene variants, one or more attributes of respective mutations associated with the gene variants;

determining whether the information about the gene variants includes (1) information indicating a gene group, the gene group including a particular gene variant and (2) information indicating the gene group includes a particular group of the plurality of groups associated with an attribute of the particular gene variant; and

categorizing the gene variants within the plurality of groups based on determining the information indicates the determined one or more attributes and, each of the plurality of groups associated with an attribute of respective mutations associated with the gene variants;

generating, using the at least one processor, hierarchical relationships between each group of the plurality of groups, wherein the hierarchical relationships form a directed acyclic graph, the hierarchical relationships between each group indicating relationships between the attributes of respective mutations associated with the gene variants;

generating, using the at least one processor, a visualization of the hierarchical relationships between each group of the plurality of groups; and

displaying, on a user interface of a computing device, the visualization.

2 . The method of claim 1 , wherein the act of categorizing further comprises categorizing the information about the gene variants within the plurality of groups such that each member of a group of the plurality of groups is unique.

3 . The method of claim 1 , wherein categorizing further comprises:

selecting, based on the categorized information about the gene variants within a group of the plurality of groups, an owner member of the group, wherein the owner member comprises information about a group category.

4 . The method of claim 1 , wherein categorizing, using the at least one processor, the information about the gene variants further comprises:

determining, based on information associated with a second gene variant of the gene variants, whether the second gene variant is a specific fusion mutation; and

conditionally categorizing, based on determining that the second gene variant is a specific fusion mutation, the second gene variant as a member of a fusion group or a rearrange group by determining whether the information associated with the second gene variant includes information indicating that a gene group including the second gene variant includes a fusion group or a rearrange group.

5 . The method of claim 1 , wherein categorizing, using the at least one processor, the information about the gene variants further comprises:

determining, based on information associated with a second gene variant of the gene variants, whether the second gene variant is a fusion mutation; and

conditionally categorizing, based on determining that the second gene variant is a fusion mutation, the second gene variant as a member of a rearrange group by determining whether the information associated with the second gene variant includes information indicating that a gene group including the second gene variant includes a rearrange group.

6 . The method of claim 1 , wherein categorizing, using the at least one processor, the information about the gene variants further comprises:

determining, based on information associated with a second gene variant of the gene variants, whether the second gene variant is a non-specific mutation type;

determining, based on the information associated with the second gene variant, whether the second gene variant is a mutant;

determining whether the information associated with the second gene variant includes information indicating that a gene group including the second gene variant includes a mutant group; and

conditionally categorizing the second gene variant as a member of a mutant group if: (1) the second gene variant is not a non-specific mutation type, (2) the second gene variant is not a mutant, and (3) the information associated with the second gene variant includes information indicating that a gene group including the second gene variant includes a mutant group.

7 . The method of claim 1 , wherein categorizing, using the at least one processor, the information about the gene variants further comprises:

determining, based on information associated with a second gene variant of the gene variants, whether the second gene variant is a gene variant having an activating protein effect;

determining whether the information associated with the second gene variant includes information indicating that a gene group including the second gene variant includes an activating mutation (act mut) group; and

conditionally categorizing the second gene variant as a member of an act mut group if: (1) the second gene variant is a gene variant having an activating protein effect and (2) the information associated with the second gene variant includes information indicating that a gene group including the second gene variant includes an act mut group.

8 . The method of claim 1 , wherein categorizing, using the at least one processor, the information about the gene variants further comprises:

determining, based on information associated with a second gene variant of the gene variants, whether the second gene variant is a gene variant having an inactivating protein effect;

determining whether the information associated with the second gene variant includes information indicating that a gene group including the second gene variant includes an inactivating mutation (inact mut) group; and

conditionally categorizing the second gene variant as a member of an inact mut group if: (1) the second gene variant is a gene variant having an inactivating protein effect and (2) the information associated with the second gene variant includes information indicating that a gene group including the second gene variant includes an inact mut group.

9 . The method of claim 1 , wherein categorizing, using the at least one processor, the information about the gene variants further comprises:

determining, based on information associated with a second gene variant of the gene variants, whether the second gene variant is a positional mutation;

determining a codon position of the second gene variant based on the information associated with the second gene variant;

comparing the determined codon position of the second gene variant with a codon position of a proposed positional group; and

conditionally categorizing the second gene variant as a member of the proposed positional group if the determined codon position of the second gene variant is equal to the codon position of the proposed positional group.

10 . The method of claim 1 , wherein categorizing, using the at least one processor, the information about the gene variants further comprises:

determining whether a second gene variant is a V600E or V600K gene variant based on information associated with the second gene variant;

determining whether the information associated with the second gene variant includes information indicating that a gene group including the second gene variant includes a V600E or V600K group; and

conditionally categorizing the second gene variant as a member of a V600E or V600K group if: (1) the second gene variant is a V600E or V600K gene variant and (2) the information associated with the second gene variant includes information indicating that a gene group including the second gene variant includes a V600E or V600K group.

11 . The method of claim 1 , wherein categorizing, using the at least one processor, the information about the gene variants further comprises:

determining, based on information associated with a second gene variant of the gene variants, whether the second gene variant is a part of a gene-exon map;

(1) conditionally determining, based on the determination that the second gene variant is a part of the gene-exon map and the information associated with the second gene variant, if a codon position of the second gene variant is within a positional range of an exon in the gene-exon map;

(2) conditionally determining, based on the determination that the second gene variant is a part of the gene-exon map, if the information associated with the second gene variant comprises information indicative of the second gene variant belonging to an exon #indel group; and

conditionally categorizing, based on affirmative determinations in (1) and/or (2), the second gene variant as a member of an exon group and/or an exon indel group.

12 . The method of claim 1 , wherein categorizing, using the at least one processor, the information about the gene variants further comprises:

determining, based on information associated with a second gene variant, whether a second gene variant of the gene variants is a frameshift gene variant;

determining, based on the information associated with the second gene variant, a codon position of a second gene variant;

determining a codon position of a proposed frameshift group; and

conditionally categorizing the second gene variant as a member of the proposed frameshift group if the codon position of the second gene variant is equal to the codon position of the proposed frameshift group.

13 . A system for determining relationships between gene variants of a gene, the gene variants being related to one or more cancers and being correlated to a treatment response of the one or more cancers to one or more medications, the system comprising:

at least one processor; and

at least one computer memory storing instructions, that, when executed by the at least one processor, perform a method of:

accessing, using at least one processor, a database comprising information about the gene variants, the information including at least information indicative of a treatment response of a first gene variant of the gene variants to one or more treatments;

categorizing, using the at least one processor, the information about the gene variants within a plurality of groups by:

determining, based on the information about the gene variants, one or more attributes of respective mutations associated with the gene variants;

determining whether the information about the gene variants includes (1) information indicating a gene group, the gene group including a particular gene variant and (2) information indicating the gene group includes a particular group of the plurality of groups associated with an attribute of the particular gene variant; and

categorizing the gene variants within the plurality of groups based on determining the information indicates the determined one or more attributes and, each of the plurality of groups associated with an attribute of respective mutations associated with the gene variants;

generating, using the at least one processor, hierarchical relationships between each group of the plurality of groups, wherein the hierarchical relationships form a directed acyclic graph, the hierarchical relationships between each group indicating relationships between the attributes of respective mutations associated with the gene variants;

generating, using the at least one processor, a visualization of the hierarchical relationships between each group of the plurality of groups; and

displaying, on a user interface of a computing device, the visualization.

14 . The system of claim 13 , wherein the act of categorizing further comprises categorizing the information about the gene variants within the plurality of groups such that each member of a group of the plurality of groups is unique.

15 . The system of claim 13 , wherein categorizing further comprises:

selecting, based on the categorized information about the gene variants within a group of the plurality of groups, an owner member of the group, wherein the owner member comprises information about a group category.

16 . The system of claim 13 , wherein categorizing, using the at least one processor, the information about the gene variants further comprises:

determining, based on information associated with a second gene variant of the gene variants, whether the second gene variant is a specific fusion mutation; and

conditionally categorizing, based on determining that the second gene variant is a specific fusion mutation, the second gene variant as a member of a fusion group or a rearrange group by determining whether the information associated with the second gene variant includes information indicating that a gene group including the second gene variant includes a fusion group or a rearrange group.

17 . The system of claim 13 , wherein categorizing, using the at least one processor, the information about the gene variants further comprises:

determining, based on information associated with a second gene variant of the gene variants, whether the second gene variant is a fusion mutation; and

conditionally categorizing, based on determining that the second gene variant is a fusion mutation, the second gene variant as a member of a rearrange group by determining whether the information associated with the second gene variant includes information indicating that a gene group including the second gene variant includes a rearrange group.

18 . At least one non-transitory computer-readable storage medium storing processor-executable instructions that, when executed by at least one processor, cause the at least one processor to perform a method for determining relationships between gene variants of a gene, the gene variants being related to one or more cancers and being correlated to a treatment response of the one or more cancers to one or more medications, the method comprising:

accessing a database comprising information about the gene variants, the information including at least information indicative of a treatment response of a first gene variant of the gene variants to one or more treatments;

categorizing the information about the gene variants within a plurality of groups by:

determining, based on the information about the gene variants, one or more attributes of respective mutations associated with the gene variants;

determining whether the information about the gene variants includes (1) information indicating a gene group, the gene group including a particular gene variant and (2) information indicating the gene group includes a particular group of the plurality of groups associated with an attribute of the particular gene variant; and

categorizing the gene variants within the plurality of groups based on determining the information indicates the determined one or more attributes and, each of the plurality of groups associated with an attribute of respective mutations associated with the gene variants;

generating hierarchical relationships between each group of the plurality of groups, wherein the hierarchical relationships form a directed acyclic graph, the hierarchical relationships between each group indicating relationships between the attributes of respective mutations associated with the gene variants;

generating, using the at least one processor, a visualization of the hierarchical relationships between each group of the plurality of groups; and

displaying, on a user interface of a computing device, the visualization.