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Table 1 A draft proposal for the minimal data needed for curation of evidence of a clinically actionable genomic event: evidence details

From: Organizing knowledge to enable personalization of medicine in cancer

Data type Description Example
Gene Gene implicated (Entrez gene id) ESR1 (2099)
Event (gene-level or variant-level) Genomic event such as SNV, indel, CNV, chimeric transcript, structural variation, epigenetic alteration, expression change, etc. See Table 2 for more details chr6:g.152419922 T > A (Y537S)
Disease Specific disease or disease subtype that is associated with this event and its clinical implication (Disease Ontology Identifier) Estrogen-receptor positive breast cancer (DOID:0060075)
Evidence type Category of clinical action implicated by event. See Table 3 for more details Predictive
Evidence level Levels of evidence for clinical actionability. See Table 3 for more details Level B - clinical evidence
Evidence direction A positive or negative value indicating whether the evidence statement supports or refutes a clinical association with the event Positive - the evidence supports the association
Treatment (FDA status) For predictive evidence, indicates the therapy for which sensitivity or resistance is indicated Hormone therapy resistance
Actionability direction Positive or negative association with treatment or diagnostic/prognostic end point Negative - mutation is associated with resistance to therapy
Text summary (wiki-like) Human readable interpretation. Free-form text summary of this event’s effect on cancer and potential clinical interpretations. This interpretation is the synthesis of all other information about an event and its relevance to clinical action and should be the living product of active discussion Studies suggest ligand-binding-domain ESR1 mutants mediate clinical resistance to hormonal therapy and suggest that more potent estrogen receptor antagonists may be of substantial therapeutic benefit
Source Literature where the event is described/explored (PubMed id) PMID: 24185512
  1. Note: Example data were drawn from a single study describing evidence for the clinical relevance of ESR1 Y537S mutations.