The eDyNAmiC team is supported through the Cancer Grand Challenges initiative. Learn more here

The eDyNAmiC team is supported through the Cancer Grand Challenges initiative. Learn more here

Glossary

  • A piece of DNA or RNA that is the source and/or product of amplification or replication events. It can be formed artificially or naturally.
  • A computational approach for mapping the fine structure of amplicons in cancer cell lines.
  • Refers to a sequence of amino acids, the building blocks of protein, arranged in a specific order: aspartic acid (Asp), glutamic acid (Glu), and alanine (Ala).
  • Techniques for studying chromatin accessibility and nucleosome positioning.
  • An enzyme found in cells that plays a crucial role in energy transfer. It helps break down a molecule called ATP (adenosine triphosphate) to release energy that cells need to function.
  • A cycle of events in which chromosomes break and fuse repeatedly.
  • A strategic collaboration with the Broad Institute (Boston, MA, USA) and other institutes that leverages the expertise and infrastructure available at each institution to catalyse a new wave of precision cancer medicines. https://depmap.org/portal/
  • Any gene (or genes) harboured on the sequence of an extrachromosomal DNA (ecDNA) element.
  • Appears as a constricted region of a chromosome and plays a key role in helping the cell divide up its DNA during division (mitosis and meiosis).
  • The extent to which proteins are able to interact with chromatinised DNA, which is regulated through nucleosome occupancy and other factors occluding access to DNA.
  • Techniques for studying the three-dimensional structure of chromatin.
  • Thread-like structures in the nucleus of cells that contain genes and genetic information.
  • A catastrophic event involving numerous structural rearrangements of a chromosome.
  • Refers to a situation where multiple genes are amplified or multiplied in a cell simultaneously. This process can occur in cancer cells and is often associated with the overproduction of certain proteins that promote cancer growth or progression.
  • Specific DNA sequences within the genome that play a pivotal role in governing gene expression. These enhancers are stretches of DNA that can augment the transcription of genes, impacting the timing and intensity of a particular gene's expression.
  • Derived from the bacterial immune defence system, stands for clustered regularly interspaced short palindromic repeats and CRISPR-associated protein 9. This technique enables precise editing of DNA sequences and has been adapted for various genome editing applications.
  • Developed by the Chang lab is a method that enhances the isolation of megabase-sized extrachromosomal DNA (ecDNA) from cancer cells and patient tissue, aiding in research related to cancer genomics.
  • The study of chromosomes and their relationship to human diseases.
  • Despite their name are not linked to cell death. They constitute a family of proteins fundamental to cellular functions, especially in RNA metabolism, regulating RNA dynamics within cells.
  • Small fragments of extrachromosomal DNA (ecDNA), which have been observed in a large number of human tumors including breast, lung, ovary, colon, and most notably, neuroblastoma.
  • A protein on cells that helps them grow. A mutation in the gene for EGFR can make it grow too much, which can cause cancer.
  • The study of changes in gene expression or cellular phenotype caused by mechanisms other than changes in the underlying DNA sequence.
  • DNA that exists outside the normal chromosomes in a cell that encodes oncogenes. ecDNAs lack centromeres and telomeres and must rely on unknown mechanisms to ensure transmission into daughter cells during cell division.
  • A protein, also known as STRAP, that is involved in diverse cellular processes, including signalling pathways related to cell growth, proliferation, and survival.
  • Describes a specific increase in the copy number of a particular DNA segment or region within a chromosome, focusing on a localised area instead of amplifying the entire chromosome.
  • Refers to the various components or parts that constitute an organism's genetic material.
  • The complete collection of genes or genetic material present in a cell or organism.
  • Chemical alterations on histone proteins that can influence gene regulation.
  • Sections on chromosomes that display a uniformly stained appearance when observed under a microscope. These regions are significant as they often indicate genetic irregularities such as additional copies of genes or gene sequences.
  • The genetic variation present within a tumour.
  • A cellular process in which a single cell divides twice to produce four cells, each containing half the original amount of genetic information.
  • A field of biology studying the comprehensive analysis of small molecules, known as metabolites, within cells, tissues, or biological systems.
  • Small nuclear structures present in the cytoplasm containing damaged DNA fragments that were not incorporated into the main nucleus after mitosis.
  • A cellular process wherein replicated genetic information in a single cell divides into two identical nuclei.
  • Abbreviation for messenger RNA. This type of RNA (ribonucleic acid) molecule plays a vital role in gene expression by carrying genetic information from the cell's nucleus DNA to the ribosomes in the cytoplasm, where proteins are produced.
  • Short for the mechanistic target of rapamycin, a protein kinase that regulates cellular processes in response to various signals, such as nutrient availability, energy levels, and stress. It acts as a central regulator of cell growth, proliferation, metabolism, and survival.
  • The abbreviation for mechanistic target of rapamycin complex 1, primarily regulating processes related to cell growth and metabolism.
  • The outcome of a mutagenic process involving some form of DNA damage, subsequently influenced by DNA repair and/or replicative machinery.
  • Refers to a family of proto-oncogenes encoding transcription factors that regulate the expression of numerous genes. Overexpression or dysregulation of MYC proteins is often associated with cancer, leading to uncontrolled cell growth and tumour development.
  • A gene that encodes the protein N-Myc and is a member of the MYC family of proto-oncogenes, implicated in tumour formation and progression.
  • Primarily a childhood cancer that arises from immature nerve cells, commonly found in the adrenal glands but can occur in various areas like the abdomen, chest, neck, or near the spine.
  • Refers to a gene associated with neuroblastoma, a childhood cancer originating from immature nerve cells.
  • " Chromosomal structural units consisting of DNA wrapped around histone proteins."
  • Genes with the potential to cause cancer by promoting cell growth and division.
  • A gene or genetic alteration observed alongside a primary genetic change but does not significantly contribute to disease development or progression.
  • The process of deducing haplotype information of a sequence from genomic data.
  • Customising cancer treatments for individual patients based on their specific genetic characteristics.
  • The comprehensive study of proteins in a biological system.
  • Large genomic alterations encompassing deletions, duplications, insertions, inversions, and translocations that describe different combinations of DNA gains, losses, or rearrangements.
  • TCA (tricarboxylic acid) cycle, also known as the Krebs cycle or citric acid cycle, is a crucial part of cellular respiration and is pivotal in producing ATP, the cell's energy currency.
  • A region of repetitive DNA sequences at the end of a chromosome. Telomeres protect the ends of chromosomes from becoming frayed or tangled. With each cell division, telomeres shorten until the cell can no longer divide successfully, leading to cell death.
eDyNAmiC
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