Glossary

A selection of words, definitions and links
to understand precision medicine.
ACTIONABLE /DRIVER & PASSENGER / VUS

A mutation is said to be ‘actionable’ if it is associated with a treatment.

A mutation is said to be a ‘driver’ mutation if it plays a role in the progression of cancer.

A mutation is said to be a ‘passenger’ mutation if it has no impact on cancer.

A mutation is said to be ‘VUS’ (Variant of Unknown clinical Significance) if its impact is (still) unknown.

-> What is a mutation?

 

AMINO ACID

Basic building block of proteins.  A protein is composed of a succession of amino acids linked to one another. There are 20 amino acids symbolized by letters: A (Alanine), C (Cysteine), G (Glycine), T (Threonine), V (Valine), E (Glutamate), …

Each amino acid has specific physico-chemical properties: an amino-acid change in a protein can alter the protein’s 3D structure, and therefore its function too.

-> What is a protein?

ANTIBODY

Antibodies are proteins made by cells that belong to our immune system and known as B lymphocytes. Antibodies detect the presence of foreign agents (virus, bacteria…) or cancer cells. Once recognised, an immune reaction eliminates the intruder.

Certain antibodies are used as drugs, which target cancer cells (nivomulab).

APPROVED DRUG

A drug is always approved for a given disease – for lung cancer or even small cell lung cancer (SCLC) for example – following a detailed analysis of the quality, safety and efficiency of a treatment. See  ‘off label’ drug.

> Patient care

ATOM

The building block of matter. An atom is composed of a nucleus, itself composed of protons and neutrons around which revolve electrons.

-> What is molecular modelling?

BIOINFORMATICS

Bioinformatics is a field of the life sciences, which uses computer-based tools, mathematics and statistics to store, analyze, interpret and visualize biological data such as DNA sequences, the 3D structure of proteins and experimental results. Bioinformatics plays a key role in precision medicine.

-> About us

-> Video: Bioinformatics in Oncology

BRAF

The BRAF protein is involved in regulating cell division, and is frequently altered in cancer cells. Several drugs target the altered BRAF protein.

> An example of targeted chemotherapy

-> Choosing a treatment

BRCA1

The BRCA1 protein is involved in repairing DNA, and is frequently altered or absent in cancer cells.

CANCER

Cancer is a disease whose principle characteristic is the abnormal proliferation of cells in one part of our body.

> What is cancer?

CELL

A cell is the smallest unit required to build a living being. Their number varies from one species to another: bacteria are composed of only one cell, while there are 1,000 cells in C.elegans and about 100,000 billion (1014) in humans.

A tumour is composed of several billion cancer cells.

-> The biological concepts summed up in one drawing.

CHEMOTHERAPY

Chemotherapy uses different types of drugs to treat cancer. These drugs frequently block cell division.

> An example of targeted chemotherapy

-> Choosing a treatment

CHROMOSOME

A chromosome is compacted DNA which can be compared to a ball of compacted wool. In humans, chromosomes adopt the familiar X shape when cells are about to divide.

-> The biological concepts summed up in one drawing.

CLINICAL STUDY

Clinical studies involve many patients at a time. Their aim is to evaluate effectiveness and tolerance to certain treatments. Such studies require consent from the country’s authorities for health and ethics. The results of these studies are used to draw up files for national and international bodies to help validate the use of given drugs.

> Patient care

CNV/COPY NUMBER VARIATION

CNVs are mutations of a particular nature: whole pieces of a chromosome are either deleted or present in multiple copies in a genome. When parts of a chromosome are present in multiple copies, then certain genes are also present in multiple copies – which can lead to the overexpression of certain proteins.

> What is a mutation?

DATABANK

A computerized encyclopaedia where data is organised according to a certain structure so that huge quantities of information can be stored in an effective way.

As an example, the UniProtKB databank indexes information on proteins from all organisms, and the Swiss Personalized Oncology databank indexes information on mutations found in cancer cells. These databanks are regularly updated and particularly important for finding information in the field of precision medicine.

-> What is DNA profiling?

DNA

DNA is a succession of 4 nucleotides linked to one another and symbolized by 4 letters: a (adenine), c (cytosine), g (guanine) and t (thymine).

The order of the nucleotides is very important and constitutes what is known as genetic information.

-> The biological concepts summed up in one drawing.

DNA PROFILING

In order to create the DNA profile of a tumour, scientists have to index and interpret all the mutations found in the DNA of  tumour cells.

-> What is DNA profiling?

> Video: Bioinformatics in Oncology

DRUG

Drugs treat the causes and/or attenuate a disease’s symptoms. More often than not, drugs are small molecules composed of several dozen atoms (aspirin and ibuprofen for example). Other drugs can be proteins, such as insulin or antibodies (like nivomulab). Drugs usually target proteins.

> What is a drug?

EGFR

The EGFR protein is involved in controlling cell growth and cell division, and is frequently altered in cancer cells.

-> Choosing a treatment

EVOLUTION

Evolution is used to designate the transformation of organisms (animals, plants, bacteria, viruses) over successive generations, and is the consequence of mutations in their genome.

Evolution is at the starting point of what creates new species.

> What is a mutation?

FUNCTION

A protein’s role in a cell or in an organism. As an example, insulin regulates the rate of sugar in the blood, BRAF is involved in controlling cell division, BRACA1 repairs damaged DNA and haemoglobin carries oxygen in the blood.

-> What is a protein?

GENE

A gene is a piece of DNA which, more often than not, carries the information needed to make a protein.

-> The biological concepts summed up in one drawing.

GENETIC CODE

The genetic code is almost universal and is used to translate a sequence of nucleotides (DNA, mRNA) into a sequence of amino acids (or protein).

-> The biological concepts summed up in one drawing.

GENETIC COUNSELLING

Genetic counselling is needed when a patient presents a hereditary (i.e. a germ-line) mutation. Medical specialists in genetics discuss the implications of germ-line mutations with the patient (and sometimes the patient’s family). These mutations found in reproductive cells can be the cause of genetic diseases that are likely to appear from generation to generation within the same family. Certain mutations responsible for cancer are germ-line.

> Patient care

 

GENETIC DISEASE

Disease of genetic origin, which can be transmitted down generations within a same family. A genetic disease is caused by one or several genes that carry pathogenic mutations.

> What is a mutation?

GENOME

The sum of DNA found in one cell. As a rule, every cell in an organism has the same genome.

 

IMMUNE SYSTEM

The immune system plays a key role in our organism’s defence. Many organs, tissues, cells and proteins are involved.

When a cancer cell appears, or an infectious agent enters our organism (virus, fungus, bacteria, parasite), the immune system recognises them as ‘foreign bodies’. Many reactions are set off to eliminate the invaders (immune response).

> An example of targeted immunotherapy

IMMUNOTHERAPY

Immunotherapy uses different types of drugs which stimulate the immune system to recognise and eliminate cancer cells of its own accord.

> An example of targeted immunotherapy

LYMPHOCYTE

Cell that plays a role in the immune response. There are different kinds of lymphocytes. B lymphocytes produce antibodies. Certain T lymphocytes, like the cytotoxic T lymphocytes for example, directly attack cancer cells or cells that have been infected by a virus.

> An example of targeted immunotherapy

MEK / MEK1

The MEK/MEK1 protein is involved in controlling cell division, and is frequently altered in cancer cells.

-> Choosing a treatment

MOLECULAR MODELLING

Molecular modelling is a body of bioinformatical and biophysical techniques that help to represent and visualize the shapes of molecules in space, in particular those of proteins.

Molecular modelling also simulates the way proteins move and behave.

-> What is molecular modelling?

> Video: Bioinformatics & Molecular Modelling 

MOLECULAR TUMOR BOARD

Name given to multidisciplinary forums involving oncologists, geneticists, pathologists, biologists and bioinformaticians, all of whom provide their opinion on the records of cancer patients. The objective is to gather each specialist’s expertise – in particular in their interpretation of complex genetic data – as well as the resources of public and private institutions in the country to ensure the most comprehensive and effective care possible to each individual patient.

> Patient care

> Video: The Molecular Tumour Board

MOLECULE

A molecule is an assembly of atoms. A drug is a small molecule (less than 100 atoms). DNA and proteins are large molecules (i.e. made up of several thousand atoms).

MUTATION

A mutation is a change of one or several nucleotides in a sequence of DNA.

Mutations arise spontaneously over the course of a lifetime and during cell division. They are more frequent when DNA is in contact with external aggressors such as UVs, tobacco or certain viruses.

Certain mutations involve chromosomal rearrangements where long segments of DNA are present in multiple copies or even altogether removed  from a chromosome (see CNV).

Depending on the effect a mutation has, researchers talk about variants, genetic variation, genetic variants, polymorphisms (or SNP for Single Nucleotide Polymorphism), molecular anomalies or molecular alterations.

-> What is a mutation?

NUCLEOTIDE

Building block of DNA and RNA. Nucleotides are molecules symbolized by letters. For DNA, the letters are a (adenine), t (thymine), g (guanine) and c (cytosine). For RNA, t is replaced by u (uracil).

-> The biological concepts summed up in one drawing.

‘OFF LABEL’ DRUG

An ‘off label’ – drug is a drug that has been approved for treating one given type of cancer but is prescribed to treat another type of cancer.

‘Off label’ drugs are only prescribed to patients that are part of a clinical trial.

> Patient care

ONCOLOGY

Field of medicine that studies and takes care of – from a diagnostic and therapeutic viewpoint – patients suffering from cancer (synonym: cancerology). Doctors working in this field are called oncologists.

> Patient care

PATHOLOGY

Field that studies and analyzes cell and tissue samples taken from biopsies, surgery or smear tests. The field of pathology helps to establish a diagnosis as well as evaluate a response to treatment.

Thanks to immunohistochemistry, researchers are able to ‘see’ proteins under the microscope that are present in tissue cells. This is achieved by way of coloured antibodies that bind specifically to these proteins.

> Video: The Institute of Pathology

PD1 / PD-L1

Proteins PD1 and PD-L1 are involved in immune tolerance. If the PD-L1 protein is expressed on the surface of cancer cells, the cells are able to shun the immune system. Several drugs target PD1 and PD-L1 (like nivomulab for example).

> An example of targeted immunotherapy

PRECISION MEDICINE

Precision medicine is a part of personalized medicine. It uses novel technologies to identify tailor-made therapeutic strategies adapted to a patient’s history and genetic data. The terms genomic medicine, personalized medicine, personalized genomic medicine, predictive medicine, individualized medicine and molecular medicine are also frequently used to characterize the evolution of this particular type of medicine.

> Patient care

PROTEIN

Proteins are essential components of life. They are made out of amino acids and have thousands of diverse functions, such as regulating cell division for example.

-> What is a protein?

RNA

RNA is like a photocopy of a stretch of DNA. Its chemical composition is close to that of DNA. More often than not, RNA acts as a ‘messenger’ (mRNA) which is an essential step in protein synthesis.

-> The biological concepts summed up in one drawing.

SEQUENCING

DNA sequencing entails the use of laboratory techniques to determine the order of nucleotides present in a stretch of DNA. It is also possible to sequence RNA.

-> What is DNA profiling?

SOMATIC / GERM-LINE

Germ-line mutations are necessarily found in the DNA of germ cells, and therefore hereditary and transmitted from generation to generation. Germ-line mutations play a key role in evolution. Germ-line mutations are involved in the development of about 10 % of cancers.

Somatic mutations occur spontaneously in the DNA of cells of an organism, and are therefore not inherited. About 90% of cancers are caused by an accumulation of somatic mutations.

> What is a mutation?

3D STRUCTURE

The shape a protein adopts in space is called its 3D structure. The 3D structure of a protein depends on the sequence of its amino acids, and is very important for the protein’s function. Different experimental techniques are used to locate the positions of a protein’s atoms in space. With the help of molecular modelling, this data is then used to represent the whole protein in space.

-> What is molecular modelling?

TISSUE / ORGAN

A tissue is a group of cells that each contribute to a specific common function. An organ is made up of different tissues. As an example, skin is made out of three different kinds of tissue known as the epidermis, the dermis and the hypodermis, each of which has a specific function.

 

 

TP53

The TP53 protein is a ‘tumour suppressor’, and is frequently altered in cancer cells. When TP53 is altered, tumours can develop. A drug able to target TP53 has not (yet) been found.

TUMOUR

An assembly of cells whose starting point is the abnormal proliferation of a cell that became cancerous.

> What is cancer?

VEGF

The VEGF protein is sometimes overexpressed on the surface of cancer cells. Overexpression of VEGF can induce the synthesis of blood vessels around the tumour, thus giving it better access to nutrients and oxygen. Several drugs target the VEGF protein.

-> Choosing a treatment

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