My Cancer Genome Glossary
A
- Adjuvant:
An agent that enhances the activity or therapeutic effect of another pharmacologic substance without having much, if any, therapeutic impact by itself. (NCIT, 2012)
- 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.
- Amplification:
See gene amplification.
- Angiogenesis:
See tumor angiogenesis.
- Antibody therapy:
Treatment with injections of antibodies to directly destroy specific, usually cancerous, cells or to stimulate the immune system to destroy those cells. (NCIT, 2012)
- Biomarker:
“a characteristic that is objectively measured and evaluated as an indicator of normal biological processes, pathogenic processes, or pharmacologic responses to a[n] … intervention.” Example: cholesterol level. (Biomarkers Definitions Working Group, 2001; IOM, 2010)
- Cancer:
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.
- Chemosensitivity:
The susceptibility of tumor cells to the cell-killing effects of anticancer drugs. (NCIT, 2012)
- Chemotherapy:
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)
- 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)
- Codon:
In DNA or RNA, a sequence of 3 consecutive nucleotides that codes for a specific amino acid or signals the termination of gene translation (stop or termination codon). (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)
- CR:
See complete remission.
- Deleterious mutation:
A mutation that is documented to be associated with risk of disease. (NCIT, 2012)
- Deletion mutation:
Absence of a segment of DNA; may be as small as a single base or as large as a whole chromosome. (NCIT, 2012)
- DNA sequencing:
See nucleic acid sequencing.
- Domain:
See protein domain.
- Downstream:
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:
“Driver mutations are those that are causally implicated in oncogenesis or tumor survival. Such mutations have been positively selected during carcinogenesis and often show a recurrent pattern within or across tumor types. This is in contrast with passenger events, which arise from the background mutation rate and do not contribute to oncogenesis.” (JCO/ASCO Glossary, 2012)
- Exon:
The sequence of DNA present in mature messenger RNA, some of which encodes the amino acids of a protein. Most genes have multiple exons with introns between them. (NCIT, 2012)
- FISH:
See fluorescence in situ hybridization.
- Fluorescence in situ hybridization:
A physical mapping approach that uses fluorescent tags to detect hybridization of probes within metaphase chromosomes or less condensed somatic interphase chromatin. This technique can be used for identification of chromosomal abnormalities and for gene mapping. (NCIT, 2012)
- 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)
- Fusion:
See fusion gene.
- 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.
- Gene:
A functional unit of heredity which occupies a specific position on a particular chromosome and serves as the template for a product that contributes to a phenotype or a biological function. (NCIT, 2012)
- 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:
The result of any gain, loss or alteration of the sequences comprising a gene, including all sequences transcribed into RNA. (NCIT, 2012)
- Genome:
The complete genomic content of an organism, and possibly the full DNA sequence of that organism. It is contained in a set of chromosomes in eukaryotes, a single chromosome in bacteria, or a DNA or RNA molecule in viruses. (NCIT, 2012)
- Germline mutation:
A gene change in the body's reproductive cells (egg or sperm) that becomes incorporated into the DNA of every cell in the body of offspring; germline mutations are passed on from parents to offspring. (NCIT, 2012)
- 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)
- GTPase:
Proteins that hydrolyze guanine triphosphate to yield guanine diphosphate. This is a class of proteins that belongs to a family of high energy phosphate hydrolases. Members of this family play major roles in biological signal transduction pathways. (NCIT, 2012)
- Heterodimerization:
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:
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)
- IHC:
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)
- 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:
Any point mutation occuring within the protein-coding region of a gene, and which results in a retention of the reading frame of the encoded protein. (NCIT, 2012)
- Inversion:
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)
- Kinase:
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)
- Ligand:
An ion, molecule, or molecular group that binds to a substance to form a larger complex. (NCIT, 2012)
- Mesenchyme:
Embryonic tissue of mesodermal origin. Develops into connective tissue, blood vessels, and lymphatic tissue. (NCIT, 2012)
- Metastasis:
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:
A point mutation occurring within the protein-coding region of a gene, and which codes for a different amino acid than expected. (NCIT, 2012)
- Monotherapy:
Therapy with a single agent or using a single treatment modality.
- Mutation:
See gene mutation.
- NED:
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:
A mutation that alters the genetic code in a way that causes the premature termination of a protein. The altered protein may be partially or completely inactivated, resulting in a change or loss of protein function. (NCIT, 2012)
- Nucleic acid sequencing:
The process of determining the sequence of purines and pyrimidines in nucleic acids and polynucleotides. (NCIT, 2012)
- Oncogene:
A gene that is a mutated (changed) form of a gene involved in normal cell growth. Oncogenes may cause the growth of cancer cells. Mutations in genes that become oncogenes can be inherited or caused by being exposed to substances in the environment that cause cancer. (NCIT, 2012)
- OS:
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)
- 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.
- Pathogenesis:
The pathologic, physiologic, or biochemical mechanism resulting in the development of a disease or morbid process. (NCIT, 2012)
- PD:
See progressive disease.
- PFS:
See progression-free survival.
- 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)
- Phosphorylation:
The creation of a phosphate derivative of an organic molecule. This is usually achieved by transferring a phosphate group from ATP via the action of a kinase. (NCIT, 2012)
- PR:
See partial remission.
- Prognosis:
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:
A specific physical region or amino acid sequence in a protein which is associated with a particular function or corresponding segment of DNA. (NCIT, 2012)
- Rapalogue:
A compound with structural and biochemical properties related to those of rapamycin; an allosteric mTOR inhibitor.
- Receptor tyrosine kinase:
A class of membrane receptors that contain protein tyrosine kinase activity. This enzymatic activity is integral to the function of the receptor as a signal transducer; the phosphorylation event alters the functional activity of its protein substrate. (NCIT, 2012)
- RECIST:
See Response Evaluation Criteria in Solid Tumors.
- Response Evaluation Criteria in Solid Tumors:
Standard parameters to be used when documenting response of solid tumors to treatment; a set of published rules that define when cancer patients improve ("respond"), stay the same ("stable"), or worsen ("progression") during treatments. (from RECIST via NCIT, 2012)
- 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)
- RR:
See response rate.
- Sarcoma:
A cancer of the bone, cartilage, fat, muscle, blood vessels, or other connective or supportive tissue. (NCIT, 2012)
- SD:
See stable disease.
- Sensitivity:
See chemosensitivity.
- Somatic mutation:
An alteration in DNA that occurs after conception. Somatic mutations 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. These alterations can (but do not always) cause cancer or other diseases. (NCIT, 2012)
- 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)
- Substrate:
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.
- Translocation:
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)
- Tyrosine:
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.
- Upstream:
On protein sequences, upstream refers to locations nearer to the 5’ end of the sequence relative to a reference location. See also downstream.
- Wild type:
The naturally occuring, normal, non-mutated version of a gene or genome. (NCIT, 2012). When referred to in reference to mutation testing findings, wild type refers to no mutations being detected; there may be mutations in the gene or genome that were not tested or detected.