Methods and systems for designing gene panels

A system for gene selection for a gene panel based on an association with a disease, comprising:

• a disease association database configured to store disease information for a plurality of diseases and gene information for a plurality of genes, the disease association database including disease associations between the diseases in the plurality of diseases and gene-disease associations between the diseases and associated genes in the plurality of genes, wherein the disease associations include a disease hierarchy comprising a plurality of hierarchical levels, wherein higher levels in the disease hierarchy represent broader disease classifications and lower levels in the disease hierarchy represent more specific disease classifications, wherein the gene-disease associations include a strength parameter for each gene-disease association, the disease association database stored in a memory;
• and
• a processor communicatively connected with the memory, the processor configured to:
• for a disease of interest at a higher level in the disease hierarchy, retrieve the gene-disease associations of genes associated with the diseases at a given level in the disease hierarchy from the disease association database, wherein the diseases at the given level have hierarchical relationships with the disease of interest at the higher level in the disease hierarchy,
• for each gene associated with the diseases at the given level, apply a weight to the strength parameter for each gene-disease association to form a weighted strength parameter of the gene-disease association,
• add the weighted strength parameters of the gene-disease associations to form a rank score for each gene associated with the diseases at the given level,
• apply a threshold to the rank scores to select the rank scores having values greater than or equal to the threshold to form selected rank scores, wherein a number of the selected rank scores is less than an initial number of the rank scores,
• rank the genes associated with the diseases at the given level based on the values of the selected rank scores, wherein the genes are ranked from a highest selected rank score to a lowest selected rank score, to provide ranked gene information,
• assign a rank order index to each ranked gene based on the value of the selected rank score for the ranked gene, and
• store in the memory a table of ranked genes linked with the disease of interest at the higher level in the disease hierarchy, the table including, a disease identifier for the disease of interest, gene symbols for the ranked genes corresponding to the selected rank scores, the selected rank scores and the rank order index, wherein the table of ranked genes is stored using a lower amount of the memory than the rank scores.

A kit comprising a set of primers associated with a set of genes in a gene panel, the set of genes selected for the gene panel by the steps of:

• for a disease of interest at a higher level in a disease hierarchy, retrieving gene-disease associations of genes associated with diseases at a given level in the disease hierarchy from a disease association database, the disease association database configured to store disease information for a plurality of diseases and gene information for a plurality of genes, the disease association database including disease associations between the diseases in the plurality of diseases and gene-disease associations between the diseases and associated genes in the plurality of genes, wherein the disease associations include the disease hierarchy comprising a plurality of hierarchical levels, wherein higher levels in the disease hierarchy represent broader disease classifications and lower levels in the disease hierarchy represent more specific disease classifications, wherein the gene-disease associations include a strength parameter for each gene-disease association, the disease association database stored in a memory, wherein the diseases at the given level have hierarchical relationships with the disease of interest at the higher level in the disease hierarchy;
• for each gene associated with the diseases at the given level, applying a weight to the strength parameter for each gene-disease association to form a weighted strength parameter of the gene-disease association;
• adding the weighted strength parameters of the gene-disease associations to form a rank score for each gene associated with the diseases at the given level;
• applying a threshold to the rank scores to select the rank scores having values greater than or equal to the threshold to form selected rank scores, wherein a number of the selected rank scores is less than an initial number of the rank scores;
• ranking the genes associated with the diseases at the given level based on the values of the selected rank scores, wherein the genes are ranked from a highest selected rank score to a lowest selected rank score, to provide ranked gene information;
• assigning a rank order index to each ranked gene based on the value of the selected rank score for the ranked gene;
• storing in the memory a table of ranked genes linked with the disease of interest at the higher level in the disease hierarchy, the table including, a disease identifier for the disease of interest, gene symbols for the ranked genes corresponding to the selected rank scores, the selected rank scores and the rank order index, wherein the table of ranked genes is stored using a lower amount of the memory than the rank scores;
• and
• selecting at least one of the ranked genes from the table of ranked genes for the set of genes in the gene panel in response to a selection of the disease of interest by a user.

A method of selecting genes for a gene panel, comprising:

• for a disease of interest at a higher level in a disease hierarchy, retrieving gene-disease associations of genes associated with diseases at a given level in the disease hierarchy from a disease association, the disease association database configured to store disease information for a plurality of diseases and gene information for a plurality of genes, the disease association database including disease associations between the diseases in the plurality of diseases and gene-disease associations between the diseases and associated genes in the plurality of genes, wherein the disease associations include the disease hierarchy comprising a plurality of hierarchical levels, wherein higher levels in the disease hierarchy represent broader disease classifications and lower levels in the disease hierarchy represent more specific disease classifications, wherein the gene-disease associations include a strength parameter for each gene-disease association, the disease association database stored in a memory, wherein the diseases at the given level have hierarchical relationships with the disease of interest at the higher level in the disease hierarchy;
• for each gene associated with the diseases at the given level, applying a weight to the strength parameter for each gene-disease association to form a weighted strength parameter of the gene-disease association;
• adding the weighted strength parameters of the gene-disease associations to form a rank score for each gene associated with the diseases at the given level;
• applying a threshold to the rank scores to select the rank scores having values greater than or equal to the threshold to form selected rank scores, wherein a number of the selected rank scores is less than an initial number of the rank scores;
• ranking the genes associated with the diseases at the given level based on the values of the selected rank scores, wherein the genes are ranked from a highest selected rank score to a lowest selected rank score, to provide ranked gene information;
• assigning a rank order index to each ranked gene based on the value of the selected rank score for the ranked gene;
• and
• storing in the memory a table of ranked genes linked with the disease of interest at the higher level in the disease hierarchy, the table including, a disease identifier for the disease of interest, gene symbols for the ranked genes corresponding to the selected rank scores, the selected rank scores and the rank order index, wherein the table of ranked genes is stored using a lower amount of the memory than the rank scores.