Biomarkers

Alterations

SNV

XREF SO:0001483

SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist.

Substitution

XREF SO:1000002

A sequence alteration where the length of the change in the variant is the same as that of the reference.

Structural variant

XREF SO:0001537

A sequence variant that changes one or more sequence features.

Copy number variation

XREF SO:0001019 A variation that increases or decreases the copy number of a given region.

Amplification

XREF SO:0001880 A sequence variant, caused by an alteration of the genomic sequence, where the structural change, an amplification of sequence, is greater than the extent of the underlying genomic features.

Deletion

XREF SO:0000159 The point at which one or more contiguous nucleotides were excised.

Expression

XREF GO:0010467

The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.

Overexpression

XREF GO:0010628

Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.

Underexpression

XREF GO:0010629

Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.

Normal expression

This is expression level as expected for a given gene in a given cellular context

Rearrangement

Synonyms: fusion, translocation

Functional mutations

Gain-of-function

Synonyms: GOF

Loss-of-function

Synonyms: LOF

Somatic

Synonyms: tumor, acquired