Molecular Medicine



  • A

    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
    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
    Treatment with injections of antibodies to directly destroy specific, usually cancerous, cells or to stimulate the immune system to destroy those cells. (NCIT 2012)

    The American Society of Clinical Oncology (ASCO) is a network of oncology professionals dedicated to providing resources for education, policy, clinical research, and improving the care of cancer patients. As part of this goal, ASCO develops and publishes clinical practice guidelines to support doctors in evidence-based care. More information about the ASCO guidelines can be found here.

  • B
    “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)

    The British National Formulary (BNF) is a publication of the British Medical Association and the Royal Pharmaceutical Society that provides guidelines for prescribing and administering medicines available through the United Kingdom Nutritional Health Service. More information about the BNF can be found here.

  • C
    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​​)​​​ is the website of the National Cancer Institute (NCI), the principal agency for cancer research within the U.S. government. Information about cancer prevention, screening, diagnosis, treatment, and research is published on as part of NCI’s mandate to disseminate information about cancer and cancer research. This includes clinical trials currently running at the NIH Clinical Center and elsewhere. More information about can be found here.

    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​​)
    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 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
    The number of molecules of a particular type on or in a cell or part of a cell. Usually applied to specific genes or to plasmids within a bacterium. (NCIT 2013​​)
    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.
    See complete remission​. is an online clinical trials registry maintained by the United States National Library of Medicine at the National Institutes of Health. Clinical trial information is submitted and updated by the sponsor or principal investigator of the study, often to fulfill regulatory requirements for clinical trial registration. The registry contains both interventional and observational clinical trials conducted in all 50 U.S. states and in 210 countries. More information about can be found here.

  • D

    dbNSFP is a database for functional prediction and annotation of non-synonymous single nucleotide variants in the human genome. For more details about dbNSFP, please see the following publications: Liu et al., 2015, and Liu et al., 2011.

    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​)
    Dideoxy sequencing
    See Sanger dideoxy sequencing.


    DNA Sequencing
    See nucleic acid 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.
  • E

    The European Medicines Agency (EMA) is an agency that oversees medicinal product regulation and approves (or “licenses”) drugs in a centralized manner for use within the European Union.  Additionally, the EMA develops guidelines and regulations to facilitate drug development and access and monitors drug safety across the lifecycle of the drug. Before approving a drug, the EMA completes a review of safety and efficacy evidence to determine whether the drug is safe and effective for its intended use. Once approval has been granted, the centralized marketing authorization is valid in all European Union member states, Iceland, Norway, and Liechtenstein. More information about the EMA can be found here.

    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​)
  • F

    The U.S. Food and Drug Administration (FDA) is an agency within the United States government that oversees regulation of a broad range of products that includes human and veterinary drugs, medical devices (including companion diagnostics), dietary supplements, tobacco products, cosmetics, and some foods. FDA approval is required for drugs to be marketed within the United States. Before approving a drug, the FDA reviews evidence to determine whether the drug is safe and effective for its intended use. Companion diagnostics, which are used to ensure safe and effective use of one or more drugs, undergo a similar approval process. More information about FDA review processes can be found here.

    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​​)​​
    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.
    See fusion gene and fusion protein.
    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
    A protein in which the coding region of two genes have become inframe and co-continuous. Fusions proteins can be formed by chromosomal breakage and/or recombination and also can be experimentally created using recombinant DNA techniques. (NCIT 2013​)
  • G
    Gain of function
    Occurs when a genetic mutation causes a protein to acquire new biochemical capabilities. These new functions can result in oncogenesis, cell survival, or cell proliferation.
    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​​)
    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​​)
    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​​)​​
  • H
    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​)

    The Human Genome Variation Society (HGVS) nomenclature system is an internationally accepted standard for sequence variant description in molecular diagnostics. The HGVS system is described in more detail on its website and in the following publication: den Dunnen et al., 2016.

    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​)
    Hormonal 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.
  • I
    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​)
    “The occurrence of a combination of a deletion and insertion” (HGVS 2013). Commonly referred to as a class of mutations that includes insertion , deletion mutations, and mutation events where both an insertion and a deletion have occurred (NCIT 2013​​).
    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​​)​​
    See indel.
    Insertion mutation
    Any rearrangement to the genomic content that adds one or more extra nucleotides into the DNA. Insertions may be reversible, particularly if caused by transposable elements. They may alter the reading frame of a gene, or may cause large scale additions of genomic DNA. (NCIT 2013​​)
    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​​)

    The International System for Human Cytogenetic Nomenclature (ISCN) system is an international standard for cytogenetic alteration description. The ISCN system is described in the following reference manual: McGowan-Jordan J, Simons A, Schmid M. ISCN 2016: An International System for Human Cytogenomic Nomenclature (2016). Switzerland: Karger Publishers; 2016.

  • K
    The appearance of the chromosomal makeup of a somatic cell in an individual or species, including the number, arrangement, size, and structure of the chromosomes. (NCIT 2013​​)
    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
    See protein kinase inhibitor.
  • L
    An ion, molecule, or molecular group that binds to a substance to form a larger complex. ​(NCIT 2012​​)
  • M
    See matrix-assisted laser desorption/ionization time of flight 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.

    The Medicines and Healthcare Products Regulatory Agency (MHRA) is a licensing body in the United Kingdom that oversees regulation of drug and medical device licensing and marketing, sampling drugs to determine if they meet quality standards, and regulating blood and blood products. Additionally, the MHRA monitors drug safety across the lifecycle of the drug and approves clinical trials within the United Kingdom. Prior to Brexit, the MHRA enforced EMA drug licensing regulations in the United Kingdom and evaluated applications for drugs to be evaluated for a United Kingdom-specific approval. Before approving a drug, the MHRA completes a review of safety and efficacy evidence to determine whether the drug is safe and effective for its intended use. More information about the MHRA can be found here.

    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​​)​​
    See multiplex ligation-dependent probe amplification.​
    Therapy with a single agent or using a single treatment modality​.​​
    See mass spectrometry.
    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 gene mutation.
  • N

    The National Comprehensive Cancer Network (NCCN) is a nonprofit organization of 28 cancer centers focused on improving patient care, research, and education. Towards this goal, the NCCN publishes guidelines for cancer treatment that provide recommendations for cancer prevention, diagnosis, and treatment. These guidelines are the source of many therapeutic assertions on and can be accessed here.

    NCI Thesaurus

    The NCI Thesaurus (NCIt) is a website published monthly by the National Cancer Institute that provides definitions, synonyms, and other information on cancers and related diseases, single agents (drugs) and related substances, and other topics related to cancer. Reference terminology and biomedical ontologies within the NCIt are widely used by the NCI and within the biomedical community. More information about the NCIt can be found at its website.

    See no evidence of disease.

    The National Institute for Health and Care Excellence (NICE) is a part of the Department of Heath in the United Kingdom that generates guidelines and advice for health, public health, and social health practitioners in the National Health Services. Additionally, NICE provides information services and develops quality standards and performance metrics to improve quality of care. NICE guidelines are developed on the basis of safety, efficacy, and economic considerations and determine which medicines are widely available through the National Health Services. While medicines recommended by NICE are typically approved (or “licensed”) by the MHRA, NICE will sometimes recommend “off-label” prescription when there is good evidence for a medicine’s use. More information about NICE guidelines can be found here.

    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 sequence
    The process of determining the sequence of purines and pyrimidines in nucleic acids and polynucleotides. (NCIT 2012)
  • O
    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​​)​​

    OncoTree is an open-source disease ontology developed by Memorial Sloan Kettering Cancer Center to facilitate standardization of cancer diagnoses. The OncoTree ontology is primarily used by precision oncology research projects that standardize cancer diagnoses associated with patient samples by annotating the samples with the appropriate OncoTree code. The OncoTree disease ontology can be accessed at the OncoTree website.

    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.
  • P
    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​)​​​
    See polymerase chain reaction.
    See progressive disease.​​
    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​​)​​
    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​)​​
    Point mutation
    An alteration in a DNA sequence caused by the substitution of a single nucleotide for another nucleotide. (NCIT 2013​)
    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​​)
    See partial remission.​​
    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​)
    Protein kinase inhibitor
    Any substance that inhibits a protein kinase, an enzyme that catalyzes the addition of a phosphate group to a protein and is active in many diverse signaling pathways. (NCIT 2013​)
    Protein overexpression
    Synthesis of excess polypeptide within the cell. Overexpression is often due to the amplification or deregulation of the gene which encodes the gene product. Overexpression of certain proteins or other substances may play a role in cancer development. (NCIT 2013​​)
    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.
  • R
    A compound with structural and biochemical properties related to those of rapamycin; an allosteric mTOR inhibitor.
    Any process affecting a DNA sequence that results in the gain, loss or exchange of DNA between chromosomes and/or autonomous replicons. (NCIT 2013​​)
    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​)​​
    See Response Evaluation Criteria in Solid Tumors​.

    The Reference Sequence (RefSeq) database is a collection of taxonomically diverse and non-redundant DNA, RNA, and protein sequences published and maintained by the National Center for Biotechnology Information (NCBI). RefSeq genomic sequences are drawn from selected entries in GenBank. RNA transcript and protein records in RefSeq are generated using computation, manual curation, and propagation from annotated genomes submitted to members of the International Nucleotide Sequence Database Collaboration. More information about RefSeq can be found here.

    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. (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​​)​​​
    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 ribonucleic acid.​
    See response rate
  • S
    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​)
    See chemosensitivity
    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
    A variation of a single nucleotide at a specific location of the genome due to base substitution, present at an appreciable frequency between individuals of a single interbreeding population. (NCIT 2013​)
    Single nucleotide variant
    A variation of a single nucleotide at a specific location of the genome due to base substitution, including somatic variants such as point mutations in cancers.

    The Scottish Medicines Consortium (SMC) is an organization that reviews new medicines that have been approved by the MHRA or EMA. SMC acceptance is based upon safety, efficacy, and economic considerations. Medicines must be approved by the SMC to be routinely prescribed in Scotland. More information about the SMC can be found here.


    SNOMED Clinical Terms (SNOMED CT) is a collaboratively developed multilingual health terminology distributed by the U.S. National Library of Medicine. SNOMED CT is used as a global language for health terms in over 50 countries and has been designated as a U.S national standard for the electronic exchange of clinical health information. More information about SNOMED CT can be found here.

    See single nucleotide polymorphism.
    See single nucl​eotide variant.
    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)
    Structural variant
    A large structural anomaly of genetic material such as a translocation or inversion that results from breakpoints between multiple chromosomes or within a single chromosomes. These often result in fusion genes and associated fusion proteins.
    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.
    See structural variant.
  • T
    Test Term

    this is a test.

    Therapeutic antibodies
    Antibodies made in another animal or in the laboratory to directly destroy specific, usually cancerous, cells or to stimulate the immune system to destroy those cells. (NCIT 2013​​)
    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
    Any substance that inhibits tyrosine kinase may result in inhibition of cell growth and cell proliferation. (NCIT 2013​​)
  • U
    UMIN Clinical Trials Registry

    The University Hospital Medical Information Network (UMIN) Clinical Trials Registry is a clinical trials registry focused on Japanese trials. Like, trials registered with UMIN may be either observational or interventional. More information about the UMIN Clinical Trials Registry can be found here.


    The Universal Protein Resource (UniProt) is a set of databases that serve as a comprehensive resource for protein sequence and annotation data. The UniProt databases contain both manually and computationally annotated protein sequences, as well as clustered sets of reference sequences and proteomes for selected species with fully sequenced genomes. UniProt is generated and maintained by the UniProt consortium, which consists of the European Bioinformatics Institute, the Swiss Institute of Bioinformatics, and the Protein Information Resource. More details about Uniprot can be found at its website.

    On protein sequences, upstream refers to locations nearer to the 5’ end of the sequence relative to a reference location. See also downstream.
    Universal Transcript Archive

    The Universal Transcript Archive (UTA) is a collection of transcript versions from multiple sources aligned to reference sequences developed by Reece Hart and maintained by Andreas Prlic. This database facilitates transcript analysis for genetic variants. The UTA is described here  in more detail.

  • W

    The World Health Organization (WHO) is an agency of the United Nations focused on international health. As part of this goal, WHO publishes classifications of cancer types and standards for cancer prevention, detection, and treatment. More information about WHO can be found here.

    WHO Classification

    The World Health Organization (WHO) Classification of Tumors is a set of reference manuals for tumor classification. Tumors in related anatomical systems are collected in volumes prepared by internationally recognized experts and published by the International Agency for Research on Cancer. Historically, these manuals focused on histological classification of tumors; recent editions also incorporate advances in molecular classification. More information about each volume in the WHO Classification of Tumors can be found here.

    Whole exome sequencing
    A procedure that can determine the DNA sequence for all of the exons in an individual. (NCIT 2013​​)
    Whole geome sequencing
    A procedure that can determine the sequence for nearly the entire genome of an individual. (NCIT 2013​​)
    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.​​