Glossary

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Term Definition
Acquired resistance Clinical scenario in which a cancer that has initially responded to therapy relapses or progresses over time
ALK Also known as anaplastic lymphoma kinase, it is a protein involved in cell growth
AMP Also known as anchor multiplex PCR, it is a form of targeted NGS that allows detection of gene rearrangements from low nucleic acid input sourced from formalin-fixed paraffin-embedded specimens
Antigen A foreign substance that induces an immune response in the body
Archer fusion A targeted sequencing technology, it requires a single read spanning two separate genes to be considered a fusion candidate
Basket trial A clinical trial in which patients are grouped primarily by genetic mutations that drive disease rather than by the disease site or histology
BDGF Also known as brain-derived growth factor, it is a member of the neutrophin family of growth factors
Break-apart assay Break-apart probes target two areas of a specific gene sequence
Breakthrough therapy United States Food and Drug Administration designation that expedites drug development based on preliminary clinical evidence indicating that the drug may demonstrate substantial improvement over existing therapies on one or more clinically significant endpoints
Chimeric oncoprotein A protein generated by the chromosome translocation of two genes in which the functional domains of two separate genes are fused together
Chromosomal rearrangement A chromosome abnormality involving a change in the structure of the native chromosome
ctDNA Also referred to as circulating tumour DNA, it is fragmented DNA derived from tumours that circulates in the bloodstream that is not associated with cells
Dimerisation When two monomers join to form a dimer
Driver genetic alteration Genetic changes that disrupt normal cellular processes and contribute to the initiation and progression of the malignant phenotype
Epitope The part of an antigen that the antibody attaches itself to
Exon DNA or RNA segment containing information coding for a protein or peptide sequence
Exosome Extracellular vesicles that are produced in the endosomal compartment of most eukaryotic cells
FISH Also known as fluorescence in situ hybridisation, it detects gene rearrangements in RNA/DNA that may generate a fusion transcript
Fusion protein A protein created by the joining of two or more genes that originally coded for separate proteins
Gene fusion rearrangements Process by which the complete or partial sequences of two or more distinct genes are fused into a single gene or transcript
Genetic profiling The analysis of DNA samples from an individual
Genomics The study of genes and their functions, and related techniques
IC50 The half maximal inhibitory concentration, which is a measure of the potency of a substance in inhibiting a specific biological or biochemical function
High-prevalence tumours Tumours with a high likelihood of NTRK gene rearrangements. These include tumours with certain histologies or specific molecular subgroups, such as pan-negative lung adenocarcinoma, wild-type and MSI-high colorectal carcinomas, IDH1 wild-type gliomas, pan-negative GIST and CD34-positive fibrosarcoma of soft tissue and bone.
IHC Also known as immunohistochemistry, it detects protein expression which may be attributable to a fusion event
Integrative Genomics Viewer A visualisation tool that allows for real-time exploration of genomics data
Intron A segment of DNA or RNA that does not code for proteins and interrupts the sequence of genes
Kinase domain A structurally conserved region of protein kinases that contains the catalytic function of these enzymes
Low-prevalence tumours Tumours with a low likelihood of NTRK gene rearrangements
MAPK Also known as mitogen-activated protein kinase, this is a family of serine/threonine protein kinases involved in cellular functions such as proliferation, differentiation, apoptosis, and survival
Microsatellite instability Predisposition to genetic mutation resulting from impaired DNA mismatch repair
Mismatch repair DNA repair system in which one member of a mismatched pair of bases is converted to the normally matched base
Molecular tumour board Multidisciplinary panel that provides opinion on the clinical implications of molecular pathology test results of patient tumours
Multiplex To allow large expansion of the number of targets and throughput of diagnostic testing
Multikinase inhibitor A small-molecule inhibitor of several kinases with potential antineoplastic activity
Nested RT-PCR Also known as nested polymerase chain reaction, it is a form of PCR that reduces non-specific binding due to amplification of unexpected primer binding sites
Neutrophin A family of proteins that signal cell survival, differentiation, growth cessation, and apoptosis, which involves binding to two classes cell surface receptors, one of which are TRKs
NGF Also known as nerve growth factor, it is a neurotrophic factor and neuropeptide involved in the regulation of growth, maintenance, proliferation, and survival of neurons
NGS Also known as next-generation sequencing, it detects known and novel fusions with breakpoints in DNA or RNA
NTRK gene Gene coding for the neurotrophic receptor tyrosine kinase
NTRK gene fusion Targetable driver genetic alterations that code for aberrant fusion proteins and drive tumourigenesis; these are formed by joining of the 3’ region of the NTRK gene, including the kinase domain, with the 5’ region of a different gene (i.e. the fusion partner) by intra- or inter-chromosomal rearrangement
Ommaya An intraventricular catheter system used for aspiration of cerebrospinal fluid
Oncogenic driver A genomic alteration that confers a selective growth advantage
Orphan drug A pharmaceutical agent that has been developed specifically to treat a rare medical condition
PI3K Also known as phosphoinositide 3-kinase, this enzyme is involved in signal transduction and controls cell growth and other cell functions, including cell survival
PKC Also known as protein kinase C, this family of protein kinases controls the function of other proteins via phosphorylation of serine and threonine amino acid residues
Plasticity Adaptability to environmental changes
Point mutation Mutation affecting only one or very few nucleotides in a gene sequence
Precision medicine Medical care that optimises the efficiency or therapeutic benefit for particular patients, particularly through the use genetic or molecular profiling
Primers Short single strand of RNA or DNA that serves as a starting point for DNA synthesis
Proliferation assay Assays typically used to measure the rate of DNA replication, analyse metabolic activity, and determine cell surface antigen recognitions
ROS1 A receptor tyrosine kinase with structural similarity to the anaplastic lymphoma kinase protein, its activation can lead to aberrant stimulation of signal transduction pathways
RT-PCR Also known as reverse-transcriptase polymerase chain reaction, it can be used to detect known fusion transcripts in RNA
Sensitivity Ability of a test to correctly identify those with the disease
Solvent-front substitution Mutations involving the kinase solvent front of driver kinases and associated with resistance to kinase inhibitor therapies
Somatic Referring to cells of the body rather than germ-line cells
Specificity Ability of a test to correctly identify those without the disease
Transcript Length of RNA or DNA that has been transcribed from a DNA or RNA template, respectively
Transcription Process in which a single strand of DNA is copied into a molecular of mRNA
Translation Process in which mRNA is decoded to produce a specific amino acid chain (protein)
TRK fusion cancers Group of cancers that are caused in part by the presence of NTRK gene fusions
TRK fusion protein The protein product of NTRK gene fusions, these proteins are constitutively active and result in cell growth, proliferation, and survival pathway activation
TRK inhibitors A type of tyrosine kinase inhibitor and a type of targeted therapy against TRK fusion proteins
TRK receptors Also known as tropomyosin receptor kinase receptor, these are a family of tyrosine kinases that regulates synaptic strength and plasticity in the mammalian nervous system
Tumour-agnostic treatment A drug treatment that is used to treat any kind of cancer, regardless of where in the body or what tissue it initiated from
Tyrosine kinase An enzyme that can transfer a phosphate group from ATP to a protein in a cell, it plays a critical activation and deactivation role in many cellular functions
Tyrosine kinase inhibitor Substance that blocks the action of tyrosine kinases
Whole transcriptome sequencing The use of next-generation sequencing (NGS) to reveal the presence and quantity of RNA in a biological sample
Xenograft Transplant of an organ, tissue, or cells to an individual of another species
xDFG motif substitution Mutations involving the xDFG motif of driver kinases and associated with resistance to kinase inhibitor therapies
Last update: 24 June 2019