The use of computing tools to manage and analyze genomic and molecular biological data.
Also known as biological material, this is a general term that applies to any material taken from a person (typically blood or tissue samples).
A set of biological techniques developed through basic research and now applied to research and product development.
The cancer Biomedical Informatics Grid, or caBIG™, is the network or grid connecting individuals and institutions involved with cancer research to enable them to share data and computer tools. caBIG™ is an initiative supported by the National Cancer Institute, National Institutes of Health.
Structural alterations in the native structure of a chromosome resulting from the breakage and rejoining of two separate parts of a chromosome.
One of the threadlike "packages" of genes located in the nucleus of a cell. Humans have 23 pairs: 46 chromosomes; 44 autosomes, and an X and Y chromosome.
Breakage and removal of a large segment of DNA from one chromosome, followed by the segment's attachment to a different chromosome.
Drugs that are being tested in clinical trials but are not yet approved by the Food and Drug Administration.
The analyses of chromosomal number and structure.
The chemical inside the nucleus of a cell that carries the genetic instructions, or code, for making and maintaining living organisms. DNA consists of two long chains of chemical groups or bases, twisted together in pairs to form a double helix. The bases are the "letters" that spell out the genetic code. In DNA, the code letters are A, T, G, and C which stand for the chemicals adenine, thymine, guanine, and cytosine, respectively.
Determination of the order of bases in a DNA molecule.
The study of heritable changes in gene function that occur without a change in the DNA sequence.
A hybrid gene created from the joining of two separate genes through the deletion or inversion of part of a chromosome or translocation.
The functional and physical unit of heredity passed from parent to offspring. Genes are pieces of DNA, and most genes contain the information for making a specific protein.
The process by which proteins are made by genes from the instructions encoded in DNA.
The study of genes and their effects on inheritance of specific traits and on other biological processes.
The complete genetic material of an organism—the entire DNA contained in an organism or a cell, which includes both the chromosomes within the cell nucleus and the DNA in cell mitochondria.
Proteins that are part of a large protein complex that pack DNA into compact structures, called chromatin.
A somatic cell with fewer than the normal 46 chromosomes
Computation method(s) to analyze a) molecular characterization data of cancer to predict targets (e.g., bioinformatics), b) results of small molecule screens in the context of molecular phenotype of the cancer models used (e.g., cheminformatics) to identify perturbagen(s), c) structure-function predictions of small molecules or d) any other computationally intense approach(es).
Type of protein participating in a modular regulatory structure (that is, tumor checkpoint), the aberrant activity of which is both necessary and sufficient for tumor cell state implementation and maintenance and which directly controls the transcriptional state of a tumor cell.
Any change in the DNA of a cell. Mutations may be caused by mistakes during cell division, or can be caused by exposure to DNA-damaging agents in the environment. Mutations can be harmful, beneficial, or have no effect. Certain mutations may lead to cancer or other diseases.
A mutation in a gene that results in a change to an amino acid sequence of the gene product (i.e. protein). Depending on the mutation and its location in the gene, these types of mutations have the potential to affect the function of the protein.
A gene, typically involved with normal cell growth, that may contribute to cancer initiation and progression when mutated.
A modality designed to disrupt a specific intracellular process (or processes), thereby providing information about the operation of pathways/networks within a cancer cell. Perturbagens may be chemical compounds (small molecules), or biologicals (antibodies, proteins), or multi-component tools (e.g., CRISPR genome modulators). Perturbagens may also serve as prototypes for therapeutic modalities.
Change of a single nucleotide.
A common variation in the sequence of DNA among individuals.
Somatic Cell Genetic Mutation
A mutation that is neither inherited nor passed to offspring. Also called acquired mutations.
A specific, distinct molecular alteration(s) within cancer cells that is/are necessary for cellular transformation, proliferation, and/or metastasis. It can be due, for example, to either a gene mutation(s) (gain or loss of function, or loss of product) or amplification of a gene (increasing the concentration of the product within the cells), or chimeric gene function resulting from translocation.
Targeted (Cancer) Therapy
Targeted cancer therapies use drugs that block the growth and spread of cancer by interfering with specific molecules involved in carcinogenesis (the process by which normal cells become cancer cells) and tumor growth.
Translation of novel findings obtained from basic research laboratories into testable hypotheses for evaluation in clinical trials in human subjects.
Tumor Board Review
A treatment planning approach in which a number of doctors who are experts in different specialties (disciplines) review and discuss the medical condition and treatment options of a patient. In cancer treatment, a tumor board review may include that of a medical oncologist (who provides cancer treatment with drugs), a surgical oncologist (who provides cancer treatment with surgery), and a radiation oncologist (who provides cancer treatment with radiation). Also called multidisciplinary opinion.
A small, autoregulated module comprising one or more master regulator (MR) proteins, the concerted activity of which is both necessary and sufficient for the implementation and maintenance of a tumor cell state.
Tumor Suppressor Gene
A gene that codes for a protein that plays a role in regulating cell growth. When tumor suppressors are mutated or altered to be non-functional, especially in combination with mutations in other proteins, cancer may initiate or progress.
Use of an independent patient cohort to determine the population frequency of mutation(s) in a given gene. These alterations are initially detected during the project’s discovery phase.
Confirmation of somatic mutation(s) observed in a patient case. In general, each case within a given patient cohort will have a different profile of somatic mutations.
A gene or gene product that is not mutated or altered.