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
=Point mutations=
==D816V==
==D842V==
==G12C==
==L858R==
==T315I==
==T790M==
==V600E==
==V600K==
=Point mutation categories=
==G12==
==G13==
==V600==
=Gene regions=
==Exon 2==
==Exon 14==
==Exon 18==
==Exon 19==
==Exon 20==
=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-PDGFRA==
==PML-RARA==
=Chromosomal regions=
==1p19q==
==5q==
==17p==
=Chromosomal rearrangements=
==t(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.
===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
===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===
==Non-resistant==
==Resistant==
=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.
Category:Ontology pages