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
ALK
HGNC:427
BRAF
HGNC:1097
CD25
HGNC:6008
CD30
HGNC:11923
CD33
EGFR
HGNC:3236
ER
FGFR2
HGNC:3689
FGFR3
HGNC:3690
FLT3
HER2
HGNC:3430
IDH1
IDH2
KIT
KRAS
PD-L1
HGNC:17635
PDGFRA
HGNC:8803
PIK3CA
ROS1
Point mutations
D816V
D842V
L858R
T315I
T790M
V600E
V600K
Point mutation categories
V600
Gene regions
Exon 18
Exon 19
Gene categories
BRCA
Genomic instability
dMMR
HRD
HRD: Homologous Recombination Deficiency
MSI-H
HR
HR: Hormone-receptor
NTRK
PDGFR
Somatostatin receptor
Gene rearrangements
BCR-ABL1
FIP1L1-PDGFRα
PML-RARα
Chromosomal regions
1p19q
5q
17p
Chromosomal rearrangements
15;17
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.
Frameshift
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.
Insertion
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
Unknown
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.
Activating
Loss-of-function
Synonyms: LOF
XREF SO:0002054 A sequence variant whereby the gene product has diminished or abolished function.
Inactivating
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.