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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.