My Cancer Genome Glossary
An agent that enhances the activity or therapeutic effect of another pharmacologic substance without having much, if any, therapeutic impact by itself. (NCIT 2012)
- Allele-specific polymerase chain reaction
A method used in a clinical laboratory to detect single nucleotide variants. The method consists of real-time PCR with fluorescent reporter probes in which reporter probes for one wild type and one mutant are added to the reaction mixture. Following hybridization to the genomic DNA, polymerase extends the probes in a complementary fashion, releasing the reporter molecules for detection. Subsequent PCR cycles using the reporter probes result in amplified signals, allowing for precise measurement of one or both alleles of interest. Alternatively, routine fluorescent PCR coupled with capillary electrophoresis for detection is used. Similarly, the 3’ end of the mutant-specific primer is extended only in the presence of DNA with that mutation.
- Allosteric inhibitor
An inhibitor that functions by binding to a site on the target that is not the target's active site, such that the active site adopts an inactive conformation.
- Amplicon capture custom panel
Next-generation sequencing method of detecting substitutions, duplications, insertions, deletions, and indels. The method consists of multiplexed PCR amplification of regions of interest, followed by NGS and specialized bioinformatics analysis. Examples of amplicon capture technology include Ion Torrent AmpliSeq, Illumina TruSeq, Agilent HaloPlex, and RainDance. These tests are custom-designed to interrogate tissues for mutations of interest in specific genes, typically 1 to 100.
See gene amplification.
See tumor angiogenesis.
- Antibody therapy
See complete remission.
A term for diseases in which abnormal cells divide without control and can invade nearby tissues. Malignant cells can also spread to other parts of the body through the blood and lymph systems. There are several main types of malignancy. Carcinoma is a malignancy that begins in the skin or in tissues that line or cover internal organs. Sarcoma is a malignancy that begins in bone, cartilage, fat, muscle, blood vessels, or other connective or supportive tissue. Leukemia is a malignancy that starts in blood-forming tissue such as the bone marrow, and causes large numbers of abnormal blood cells to be produced and enter the blood. Lymphoma and multiple myeloma are malignancies that begin in the cells of the immune system. Central nervous system cancers are malignancies that begin in the tissues of the brain and spinal cord. (NCIT 2012)
- Catalytic inhibitor
An inhibitor that binds to the target's active site, making the target inactive.
The susceptibility of tumor cells to the cell-killing effects of anti-cancer drugs. (NCIT 2012)
The use of synthetic or naturally occurring chemicals for the treatment of diseases. Although this term is used to describe any therapy involving the use of chemical-based agents, it is particularly used to refer to the use of chemical-based agents to treat cancer. Antineoplastic chemotherapy works by arresting or killing the growth and spread of cancer cells. Chemotherapy may also include agents that enhance immune function or alter hormonal activity. (NCIT 2012)
Part of a cell that contains genetic information. Except for the sperm and eggs, all human cells contain 46 chromosomes. One of the bodies in the cell nucleus that is the bearer of genes, has the form of a delicate chromatin filament during interphase, contracts to form a compact cylinder segmented into two arms by the centromere during metaphase and anaphase stages of cell division, and is capable of reproducing its physical and chemical structure through successive cell divisions. (NCIT 2013)
- Clinical trial
A research study that prospectively assigns human participants or groups of humans to one or more health-related interventions to evaluate the effects on health outcomes. Interventions include but are not restricted to drugs, cells and other biological products, surgical procedures, radiologic procedures, devices, behavioral treatments, process-of-care changes, and preventive care. See also Phase I trial, Phase II trial, and Phase III trial. (NCIT 2012)
- Complete remission (CR)
The disappearance of all signs of cancer in response to treatment. This does not always mean the cancer has been cured. Also known as complete response. (NCIT 2012)
- Copy number
- Copy number polymorphism
Refers to the genetic trait involving the number of copies of a particular gene present in the genome of an individual. Genetic variants, including insertions, deletions, and duplications of segments of DNA, are also collectively referred to as copy number variants. Copy number variants account for a significant proportion of the genetic variation between individuals.
- DNA sequencing
See nucleic acid sequencing.
- Deleterious mutation
- Deletion mutation
- Dideoxy sequencing
See Sanger dideoxy sequencing.
See protein domain.
On protein sequences, downstream refers to locations nearer to the 3’ end of the sequence relative to a reference location. See also upstream.
- Driver mutation
Genetic mutations thought to play a key role in oncogenesis or tumor survival.
A type of insertion mutation where the inserted sequence repeats an adjacent sequence. Duplications can be a few to many nucleotides in length.
See fluorescence in situ hybridization.
- Fluorescence in situ hybridization
- Formalin-fixed paraffin-embedded biospecimen
A biospecimen processed by the most common method used for preserving tissue. A tumor tissue biospecimen is removed from the patient via biopsy or surgery, and the tissue is then sectioned, fixed using formalin, and embedded in paraffin.
- Frameshift mutation
An insertion or deletion involving a number of base pairs that is not a multiple of three, which consequently disrupts the triplet reading frame of a DNA sequence. Such mutations usually lead to the creation of a premature termination (stop) codon, and result in a truncated (shorter-than-normal) protein product. (NCIT 2012)
- Functional domain
A portion of a protein with a discrete physiological role.
- Fusion gene
A gene made by joining parts of two different genes. Fusion genes may occur naturally in the body by transfer of DNA between chromosomes. For example, the BCR-ABL gene found in some types of leukemia is a fusion gene. Fusion genes can also be made in the laboratory by combining genes or parts of genes from the same or different organisms. (NCIT 2012) Fusions can result from translocations, deletions, and inversions.
- Fusion protein
- Gain of function
- Gene amplification
An increase in the number of copies of a gene. There may also be an increase in the RNA and protein made from that gene. Gene amplification is common in cancer cells, and some amplified genes may cause cancer cells to grow or become resistant to anticancer drugs. Genes may also be amplified in the laboratory for research purposes. (NCIT 2012)
- Gene mutation
- Germline mutation
- Growth factor
Substances made by the body that function to regulate cell division and cell survival. Some growth factors are also produced in the laboratory and used in biological therapy. (NCIT 2012)
Heterodimerization involves a biophysical interaction between two dissimilar biological molecules or subunits, such as between two proteins. The interaction is often mediated by a biophysical interaction between one or more specific domains within each subunit and, typically, significantly influences the function of each subunit. (NCIT 2012)
Homodimerization involves a biophysical interaction between two identical biological molecules or subunits, such as proteins. The interaction is often mediated by a biophysical interaction between one or more specific domains within the subunits and, typically, significantly influences the function of the subunits. (NCIT 2012)
- Homonal agent
A drug used to change the level of one or more hormones. The treatment may include administration of hormones or hormone analogs to the patient, or decreasing the level of hormones in the body by using hormone antagonists. To slow or stop the growth of certain cancers (such as prostate and breast cancer), synthetic hormones or other drugs may be given to block the body's natural hormones. (NCIT 2013)
- Hybridization capture custom panel
Next-generation sequencing method of detecting substitutions, duplications, insertions, deletions, indels, exon and gene copy number changes, and select translocations. The method consists of hybridization capture of regions of interest, followed by NGS and specialized bioinformatics analysis. Genomic DNA fragments are hybridized in solution to sequence-specific capture probes corresponding to target regions of the genome. Examples of hybridization capture technology include Agilent SureSelect, Nimblegen SeqCap, and Illumina TruSeq. These tests are custom-designed to interrogate tissues for mutations of interest in specific genes, typically 50 to several thousand.
See immunohistochemistry staining method.
- Immunohistochemistry staining method
A technique used to identify specific molecules in different kinds of tissue. The tissue is treated with antibodies that bind the specific molecule. These are made visible under a microscope by using a color reaction, a radioisotope, colloidal gold, or a fluorescent dye. Immunohistochemistry is used to help diagnose diseases, such as cancer, and to detect the presence of microorganisms. It is also used in basic research to understand how cells grow and differentiate (become more specialized). (NCIT 2012)
Treatment that boosts or restores the ability of the immune system to fight cancer, infections, and other diseases. Also used to lessen certain side effects that may be caused by some cancer treatments. Agents used in immunotherapy include monoclonal antibodies, growth factors, and vaccines. These agents may also have a direct antitumor effect. (NCIT 2013)
- In situ
In its original place. For example, in carcinoma in situ, abnormal cells are found only in the place where they first formed. They have not spread. (NCIT 2012)
- In vitro
In the laboratory (outside the body). The opposite of in vivo (in the body). (NCIT 2012)
- In vivo
Located or occurring in the body. (NCIT 2012)
- Inframe mutation
- Insertion mutation
A structural change in genomic DNA where the 5' to 3' order of a nucleotide sequence is completely reversed to the 3' to 5' order relative to its adjacent sequences. This inversion is termed either pericentric, if it includes the centromere of a chromosome, or pancentric, if it excludes the centromere. An inversion mutation abnormality may be heritable or occur somatically. The preferred term is inversion mutation abnormality. (NCIT 2012)
A type of enzyme that causes other molecules in the cell to become active. Some kinases work by adding chemicals called phosphates to other molecules, such as sugars or proteins. Kinases are a part of many cell processes. Some cancer treatments target certain kinases that are linked to cancer. (NCIT 2012)
- Kinase inhibitor
An ion, molecule, or molecular group that binds to a substance to form a larger complex. (NCIT 2012)
- MALDI-TOF MS
See matrix-assisted laser desorption/ionization time of flight mass spectrometry.
See multiplex ligation-dependent probe amplification.
See mass spectrometry.
- Mass spectrometry
An analytical technique wherein ions are separated according to their ratio of charge to mass. From the mass spectrum produced, the atomic weight of the particle can be deduced. (NCIT 2013)
- Matrix-assisted laser desorption/ionization time of flight mass spectrometry
In MALDI-TOF, a laser pulse is fired into a protein or peptide sample contained in a light-absorbing matrix. A small explosion vaporizes and ionizes the sample. In the presence of a high electric field, peptide ions are accelerated down an evacuated flight tube. Because large particles travel more slowly than small ones, the masses of the ionized particles are determined by measuring their arrival time at the end of the tube. (NCIT 2013)
Embryonic tissue of mesodermal origin. Develops into connective tissue, blood vessels, and lymphatic tissue. (NCIT 2012)
The spread or migration of cancer cells from one part of the body (the organ in which it first appeared) to another. The secondary tumor contains cells that are like those in the original (primary) tumor. (NCIT 2012)
- Metastatic disease
Cancer in which tumors have spread beyond the organ in which the cancer originated.
- Missense mutation
Therapy with a single agent or using a single treatment modality.
- Multiplex ligation-dependent probe amplification
A method used in a clinical laboratory to detect exon and gene copy number. Depending on experimental design, can also detect SNVs. The method consists of a series of steps that begins with specially designed primers that hybridize to patient DNA. Following hybridization, the bound primers are enzymatically ligated and the ligation products are amplified using multiplex PCR. Amplified products are detected and analyzed by capillary electrophoresis.
See no evidence of disease.
- No evidence of disease
When diagnostic tests fail to detect presence of disease (NCIT 2012). This may occur after treatment, for example, and a patient's cancer is being assessed regarding the need for additional treatment. Abbreviated NED.
- Nonsense mutation
- Nucleic acid sequencing
The process of determining the sequence of purines and pyrimidines in nucleic acids and polynucleotides. (NCIT 2012)
See overall survival.
- Overall survival
The percentage of people in a study or treatment group who are alive for a certain period of time after they were diagnosed with or treated for a disease, such as cancer. The survival rate is often stated as a five-year survival rate, which is the percentage of people in a study or treatment group who are alive five years after diagnosis or treatment. The preferred term is survival rate. (NCIT 2012)
See protein overexpression.
See polymerase chain reaction.
See progressive disease.
See progression-free survival.
See partial remission.
- Partial remission
A decrease in the size of a tumor, or in the extent of cancer in the body, in response to treatment. Also known as partial response. (NCIT 2012)
- Partial response
See partial remission.
The pathologic, physiologic, or biochemical mechanism resulting in the development of a disease or morbid process. (NCIT 2012)
- Phase I trial
A clinical research protocol designed to test a new biomedical intervention in a small group of people for the first time. A Phase I trial can be to establish the toxicity of a new treatment with escalating intensity of the treatment administered and/or to determine the side effects of a new treatment for a particular indication in subjects. (NCIT 2012)
- Phase II trial
A clinical research protocol designed to study a biomedical or behavioral intervention in a larger group of people (several hundred), to evaluate the drug's effectiveness for a particular indication in patients with the disease or condition under study, and to determine the common short-term side effects and risks associated with the intervention. (NCIT 2012)
- Phase III trial
A clinical research protocol designed to investigate the efficacy of the biomedical or behavioral intervention in large groups of human subjects (from several hundred to several thousand), to confirm efficacy, to monitor adverse reactions to the new medication or treatment regimen with respect to long-term use and by comparing the intervention to other standard or experimental interventions as well as to a placebo. (NCIT 2012)
- Point mutation
- Polymerase chain reaction
A method for amplifying a DNA base sequence using multiple rounds of heat denaturation of the DNA and annealing of oligonucleotide primers complementary to flanking regions in the presence of a heat-stable polymerase. This results in duplication of the targeted DNA region. Newly synthesized DNA strands can subsequently serve as additional templates for the same primer sequences, so that successive rounds of primer annealing, strand elongation, and dissociation produce rapid and highly specific amplification of the desired sequence. PCR also can be used to detect the existence of the defined sequence in a DNA sample. (NCIT 2013)
The likely outcome or course of a disease; the chance of recovery or recurrence. (NCIT 2012)
- Progression-free survival
The length of time during and after treatment in which a patient is living with a disease that does not get worse. Progression-free survival may be used in a clinical study or trial to help find out how well a new treatment works. (NCIT 2012)
- Progressive disease
A disease process that is increasing in scope or severity. (NCIT 2012)
- Protein domain
- Protein kinase inhibitor
- Protein overexpression
A DNA sequencing method that uses a “sequencing by synthesis” strategy. The strand complementary to a template is synthesized a single base at a time through the sequential addition of individual solutions of each base. Incorporation of a base into the growing strand generates free pyrophosphate that is detected as light, as generated by a luciferase-catalyzed reaction.
See Response Evaluation Criteria in Solid Tumors.
See ribonucleic acid.
See response rate.
A compound with structural and biochemical properties related to those of rapamycin; an allosteric mTOR inhibitor.
- Receptor tyrosine kinase
- Response Evaluation Criteria in Solid Tumors
- Response rate
The percentage of patients whose cancer shrinks or disappears after treatment. See also complete remission (CR), partial remission (PR), stable disease (SD), and progressive disease (PD). (NCIT 2012)
- Ribonucleic acid
One of two types of nucleic acid made by cells. Ribonucleic acid contains information that has been copied from DNA (the other type of nucleic acid). Cells make several different forms of ribonucleic acid, and each form ahs a specific job in the cell. Many forms of ribonucleic acid have functions related to making proteins. Ribonucleic acid is also the genetic material of some viruses instead of NDA. Ribonucleic acid can be made in the laboratory and used in research studies. (NCIT 2013)
See stable disease.
See single nucleotide polymorphism.
See single nucleotide variant.
See structural variant.
- Sanger dideoxy sequencing
A standard method used in a clinical laboratory to detect unknown mutations including SNVs and small duplications, insertions, deletions, and indels of interest. The method is typically performed on PCR products. Sequencing primers hybridize to the PCR product and are extended using DNA polymerase, the four deoxynucleotides (dNTPs), and a mixture of fluorescently labeled dideoxynucleotides (ddNTPs). Each of the four ddNTPs is labeled with a different fluorescent dye. Random incorporation of the labeled ddNTPs results in termination of strands at each location along the sequence. The reaction primers can be extended by up to about 1,000 nucleotides. Capillary electrophoresis separates the strands by size, and the terminating nucleotides are measured using fluorescence spectroscopy. In a clinical laboratory, both the forward and reverse strands are sequenced.
- Sanger sequencing
See Sanger dideoxy sequencing.
A cancer of the bone, cartilage, fat, muscle, blood vessels, or other connective or supportive tissue. (NCIT 2012)
- Single base extension assay
A method used in a clinical laboratory to detect targeted SNVs. The method consists of multiplex PCR and multiplex primer base extension coupled with capillary electrophoresis (e.g., Life Technologies' SNaPshot® Multiplex System). Detects 1–100+ SNVs simultaneously. These tests are custom-designed to interrogate tissues for mutations of interest and are usually designed to look for common mutations that occur at specific hotspots.
- Single nucleotide polymorphism
- Single nucleotide variant
- Somatic mutation
- Squamous cell carcinoma
Cancer that begins in squamous cells, which are thin, flat cells that look like fish scales. Squamous cells are found in the tissue that forms the surface of the skin, the lining of the hollow organs of the body, and the passages of the respiratory and digestive tracts. (NCIT 2012)
- Stable disease
Cancer that is neither decreasing nor increasing in extent or severity. (NCIT 2012)
- Stage I
Invasive cancer confined to the original anatomic site of growth without lymph node involvement. (NCIT 2012)
- Stage II
Invasive cancer more extensive than stage I, usually involving local lymph nodes without spread to distant anatomic sites. (NCIT 2012)
- Stage III
Locally advanced cancer that has spread to nearby organs but not to distant anatomic sites. (NCIT 2012)
- Stage IV
Cancer that has spread to distant anatomic sites beyond its original site of growth. (NCIT 2012)
- Structural variant
A mutation occurring when one or more nucleotides is replaced by alternate nucleotides.
A molecule with which a protein interacts specifically. See also substrate domain.
- Substrate domain
A substrate domain is a protein region that physically interacts stereospecifically, and usually at high affinity, with a specific target substrate. In enzymes, the substrate domain is often, though not necessarily, coincident with the catalytic domain. Typically, substrate interaction results in some protein conformational alteration and functional modification. (NCIT 2012)
- Survival rate
See overall survival.
- Therapeutic antibodies
- Tool compound
A chemical similar enough in structure, pharmacodynamics, and bioavailability to be used in place of a compound under development as a drug in preclinical studies. Tool compounds may be more readily available than compounds actively being developed as drugs.
With respect to chromosomal changes, translocations involve the movement of a chromosomal section to a new location in the same or a different chromosome.
- Tumor angiogenesis
Tumor angiogenesis is the growth of new blood vessels that tumors need to grow. This is caused by the release of chemicals by the tumor. (NCIT 2012)
Abbreviated Tyr or Y. Tyrosine is naturally occurring and is synthesized in vivo from phenylalanine (NCIT 2012). In vivo, tyrosine plays a role in protein synthesis and serves as a precursor for the synthesis of catecholamines, thyroxine, and melanin (NCIT 2012). Tyrosine has a polar side group which can be phosphorylated on the hydroxyl moiety by a tyrosine kinase. Tyrosine phosphorylation is critical for many intracellular signal transduction cascades. The effect of tyrosine phosphorylation is usually a change in the activity or localization of the target protein. The preferred term is L-tyrosine (NCIT 2012).
- Tyrosine kinase
Kinases that phosphorylate protein tyrosine residues. These kinases play major roles in mitogenic signalling, and can be divided into two subfamilies: receptor tyrosine kinases, that have an extracellular ligand-binding domain, a single transmembrane domain, and an intracellular tyrosine kinase domain; and nonreceptor tyrosine kinases, which are soluble, cytoplasmic kinases. The preferred term is protein tyrosine kinase. (NCIT 2012) See also receptor tyrosine kinase.
- Tyrosine kinase inhibitor
On protein sequences, upstream refers to locations nearer to the 5’ end of the sequence relative to a reference location. See also downstream.
- Whole exome sequencing
- Whole genome sequencing
- Wild type