Biomarkers

The purpose of this page is to create a reference controlled vocabulary for biomarker-specified concepts. It is not meant for any other purpose at this time.

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

XREF SO:0001872

A region of a chromosome, where the chromosome has undergone a large structural rearrangement that altered the genome organization. There is no longer synteny to the reference genome.

fusion

XREF SO:0000806

translocation

XREF SO:0000199

A region of nucleotide sequence that has translocated to a new position. The observed adjacency of two previously separated regions.

Methylation

XREF GO:0006306

The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine.

Hypermethylation

XREF GO:0044026 An increase in the epigenetic methylation of cytosine and adenosine residues in DNA.

Hypomethylation

XREF GO:0044028 An decrease in the epigenetic methylation of cytosine and adenosine residues in DNA.

Regulated

XREF SO:0000471

The gene product is involved in its own transcriptional regulation.

Positive

XREF SO:0000475

The gene product is involved in its own transcriptional regulation, where it increases transcription.

Negative

XREF SO:0000473

The gene product is involved in its own transcriptional regulation where it decreases transcription.

Functional mutations

Gain-of-function

Synonyms: GOF

XREF SO:0002053

A sequence variant whereby new or enhanced function is conferred on the gene product.

Loss-of-function

Synonyms: LOF

XREF SO:0002054 A sequence variant whereby the gene product has diminished or abolished function.

Germline

XREF SO:0001778

A germline mutation, or germinal mutation, is any detectable variation within germ cells. Mutations in these cells are the only mutations that can be passed on to offspring, when either a mutated sperm or oocyte come together to form a zygote.

Somatic

Synonyms: tumor, acquired

XREF SO:0001777

An alteration in DNA that occurs after conception and is not present within the germline. Somatic variants can occur in any of the cells of the body except the germ cells (sperm and egg) and therefore are not passed on to children.