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.

Genes

These are genes that are explicitly mentioned in one or more FDA labels or clinical trials as a biomarker eligibility criteria.

ALK

HGNC:427

BRAF

HGNC:1097

BRCA1

HGNC:1100

BRCA2

HGNC:1101

EGFR

HGNC:3236

ERBB2

HGNC:3430

ERBB3

HGNC:3431

ESR1

HGNC:3467

EZH2

HGNC:3527

FGFR2

HGNC:3689

FGFR3

HGNC:3690

FLT3

HGNC:3765

IDH1

HGNC:5382

IDH2

HGNC:5383

KIT

HGNC:6342

KRAS

HGNC:6407

MET

HGNC:7029

NPM1

HGNC:7910

NRAS

HGNC:7989

NTRK1

HGNC:8031

NTRK2

HGNC:8032

NTRK3

HGNC:8033

PDGFRA

HGNC:8803

PIK3CA

HGNC:8975

PTCH1

HGNC:9585

RET

HGNC:9967

ROS1

HGNC:10261

SMO

HGNC:11119

Proteins

These are proteins that are explicitly mentioned in one or more FDA labels or clinical trials as a biomarker eligibility criteria.

AFP

UniProtKB:P02771

CD20

UniProtKB:P11836

CD25

UniProtKB:P01589

CD30

UniProtKB:P28908

CD33

UniProtKB:P20138

CD117

UniProtKB:P10721

EGFR protein

UniProtKB:P00533

ER

UniProtKB:P03372

HER2

UniProtKB:P04626

PD-L1

UniProtKB:Q9NZQ7

Gene categories

Genomic instability

HRD

HRD: Homologous Recombination Deficiency

HR

HR: Hormone-receptor

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.

Low

An intermediate level of overexpression that for now is only clinically pertinent in breast cancer.

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.

Wild-type

XREF SO:0000817

An attribute describing sequence with the genotype found in nature and/or standard laboratory stock.