MedGenome OncoMDΒΆ

If licensed, SVS includes annotating variants against MedGenome’s Oncology Mutation Database (OncoMD). OncoMD is a comprehensive knowledge base of cancer-specific genetic alterations, and by incorporating it into SVS, users can access up to 2 million plus annotated cancer variants. Not only does this addition allow users to quickly prioritize actionable variants, but also make clinical decisions based on the sensitivity of variants to approved drugs and enrollment to open clinical trials. See MedGenome OncoMD for specifics on the provided data.

Note

To add MedGenome OncoMD annotation to your license for SVS contact support@goldenhelix.com.

To access these annotations go to DNA-Seq > Annotate and Filter Variants then selecting the source(s) from the Secure Annotations/OncoMD location of the Data Source Library.

Available annotations include the following sources:

  • OncoMD Clinical Trials - List of open clinical trials for each Gene, along with cancer type, drug tested, status of trial and location.
  • OncoMD Drugs Targeting Mutation - This is a list of approved Drug for Mutations along with the response rate.
  • OncoMD Functional Validation of Variants - Provides information on Biochemical Assay, Cell based Assay Symbol, Effect of mutation on protein function, Mechanism of Action and MOA Validation along with PubMed IDs.
  • OncoMD Gene Info - Provides gene description and function in cancer information.
  • OncoMD Studies with Variant - List of studies associated with each Mutation along with the PubMedIDs, title of the published paper, type of study- e.g whole exome sequence etc and number of samples in each study.
  • OncoMD Variant Summary - Aggregate information about studies citing this variant, the number of samples it was observed in and which types of cancers.

Note

Annotation with the the OncoMD Gene Info and OncoMD Clinical Trials sources requires gene information that contains a GeneID field for your variants, you will be prompted to select a gene source on the options dialog, for example RefSeq Genes 105v2, NCBI.