1. Enabling precision medicine in cancer
An open community-driven knowledge
management system
Sigve Nakken & Eivind Hovig, Norwegian Cancer Genomics Consortium (NCGC)
Department of Tumor Biology
Institute for Cancer Research
Oslo University Hospital
!
cancergenomics.no

2. Precision medicine in cancer - background
1. Most tumors are driven
by somatic DNA
alterations
2. Each tumor (patient)
has a unique set of
alterations
3. Drug response/
resistance are affected
by alteration profile

3. • Great improvements in
software workflows for
variant identification
• Bottleneck prior to clinical
application: interpretation
and prioritization of
clinically actionable
variants
• Knowledge management
challenge
- ongoing clinical trials
- electronic health records
- biomedical literature
- genomic variation databases
- drug-gene interaction resources
- cancer registries
Precision medicine in cancer - status & challenges
Good et al. Genome Biology, 2014

4. Open community-driven knowledge base
Integrated cancer
knowledge base
Drug &
pharmacogenomics
data
Clinical trials
Somatic DNA
variation databases
Biomedical literature
Gene & pathway
data
Cancer commons knowledge base !
Actionable genomic events for clinical decision support
Patient sequence
data
Patient health
records
Oncologists
Clinical scientists,
Bioinformaticians
• Semantic web technologies
• Ontologies for translational medicine
- Variation Ontology
- Disease Ontology
- Sequence Ontology
- Gene Ontology
- Translational Medicine Ontology
• Specification for curation of actionable
genomic events
- evidence level
- evidence type
- actionability direction