VarSome Clinical provides information acquired by the following drug-related resources:
Pharmacogenomics Knowledgebase (PharmGKB)
PharmGKB is a pharmacogenomics knowledge resource including clinical information such as clinical guidelines, drug labels, potentially clinically actionable gene-drug associations, and genotype-phenotype relationships. Information on the impact of human genetic variation on drug responses is aggregated through various approaches which include, among others: literature review for the annotation of genetic variants and gene-drug-disease relationships, curation of FDA labels, and drug dosing guidelines in a pharmacogenomic approach.
VarSome integrates information from PharmGKB that may concern:
- The relationship between a variant selected from the table and corresponding medications along with related supporting publications. This information, if available, is located in tabular format in the “PharmGKB” Tab under the Variants Table. An example is shown in the following screenshot.
This Table holds the Clinical Annotations of the variant which can be also accessed at the PharmGKB site through the respective ID (red arrow). The "Annotation" column refers to manually curated genotype-based summaries describing the phenotypic impact of the variant. The user can also see an overview of the corresponding Publication. If the corresponding data are available, the user may also see a table for chemical relations or disease relations.
- This section concerns the relations of the gene containing the variant with drug substances. All the information can be found under the "Genes" tab on the right menu of the Variant Table page. If the corresponding information is available the user may see a table for Guidelines, Chemical relations, Drug Label Annotations. The user can also see an overview of the corresponding Publication.
The gene-related tables are also available for the user during the report generation process which is described in more detail in the article Report Generation. The addition of the PharmGKB section in the clinical report will generate a table similar to the following example:
Precision Medicine Knowledgebase (PMKB)
PMKB is a knowledge database that presents clinical interpretations of cancer variants in a structured way. It allows user contributions in terms of browsing, submitting, and editing existing entries. In addition, all changes are reviewed by molecular pathologists and oncologists.
VarSome presents the information retrieved from PMKB in the "Genes" Tab on the right menu of the Variant Table page:
The aforementioned information is also available for the user during the report generation process which is described in more detail in the article Report Generation. The addition of the PMKB section in the clinical report will generate a table similar to the following example:
Drug-Gene Interaction Database (DGIdb)
DGIdb provides information about known or potential drug-gene interactions using expert curation and text-mining methods. The presented drug-gene interactions have been mined from DrugBank, therapeutic target database (TTD), PharmGKB, a list of targeted agents in lung cancer, and ClinicalTrials.gov. In addition, retrieved data from Gene Ontology, dGene, and “druggable genome” lists from Hopkins and Groom (2002) and Russ and Lampel (2005) are utilized for the categorization of the genes as potentially druggable.
VarSome presents the information retrieved from DGIdb at the bottom of the "Genes" Tab on the right menu of the Variant Table page:
VarSome Clinical retrieves information from DGIdb and makes it available in the Clinical Report. By adding the DGIdb section to your Clinical Report, the information will be shown in tabular form, as below. This table holds aggregated information from DGIdb on the interaction of the respective gene with different drug substances and the various attributes of the interaction.