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Table 2 A draft proposal for the minimal data needed for curation of evidence of a clinically actionable genomic event: types of events

From: Organizing knowledge to enable personalization of medicine in cancer

Event type Description Example
Single nucleotide variant (SNV) Single nucleotide alterations BRAF c.1799 T > A (V600E)
Small insertion or deletion (Indel) Small numbers of nucleotides deleted or inserted PTEN c.800delA (K267fs*9)
Copy number variation (CNV) Large-scale (for example, chromosomal) or focal changes in copy-number status such as amplifications and deletions ERBB2 amplification
Structural variation (SV) Large-scale (for example, chromosomal) rearrangements such as translocations or inversions FLT3 internal tandem duplication
Chimeric transcript Aberrant expression of messenger RNA involving distant intra- or inter-chromosomal gene pairs BCR-ABL fusion
Epigenetic modification Alterations at the epigenetic level such as DNA methylation or histone modifications TERT promoter hypermethylation
Expression biomarker Significantly increased or decreased expression of RNA or protein High SPARC expression
  1. Note: Certain types of events are by their nature non-specific in the genomic sense. For example, there can be an almost infinite number of ways to truncate and thereby destroy function of a protein, such as the retinoblastoma protein. Many specific deletions in the RB1 gene might be grouped together under a common generic event for `RB1 loss’ with a consistent interpretation. Therefore, hierarchical relationships must be supported and ontologies may need to be modified or developed specifically for this domain space.