Ontario Molecular Pathology Research Network

Allele

fr: allèle

One of two or more versions of a gene or DNA sequence at a particular region on a chromosome. A person has two alleles for each gene, one inherited from each parent.

Example: The patient’s genetic profile exhibited a variation in the BRCA1 gene, with one allele carrying a pathogenic mutation associated with an increased risk of hereditary breast cancer.

Relevant Lessons:

• Clinical Reports Summary Page

Amino Acid

fr: acide aminé

An amino acid is the basic molecule that serves as the building blocks for proteins. There are 20 different amino acids. Some amino acids can be synthesized in the body; however, others (essential amino acids) must be obtained from a person’s diet.

Example: A DNA mutation caused an amino acid change that disrupted the normal function of the protein.

Relevant Lessons:

• Clinical Reports Summary Page

Angiogenesis

fr: Angiogenèse

Angiogenesis is the process of new capillaries forming out of preexisting blood vessels in your body. It’s normally a helpful, important process that supports wound healing and supplies oxygen-rich blood to your organs and tissues. But in people with cancer, angiogenesis supports tumor growth and spread by feeding tumors with oxygen and nutrients.

Example: Angiogenesis plays a crucial role in the metastatic process by promoting the growth of new blood vessels that supply nutrients and oxygen to secondary tumors, enabling their continued expansion and progression.

Relevant Lessons:

• Metastasis Video

Autosomal

fr: autosomique

Is associated with any of the 22 numbered pairs of chromosomes found in most human cells. Autosomal chromosomes are numbered 1-22. The sex chromosomes (X and Y chromosomes) determine whether an individual is male or female and are not considered autosomal chromosomes.

Example: The BRCA1 gene is located on chromosome #17. Variants in BRCA1 are transmitted in an autosomal dominant pattern within a family.

Relevant Lessons:

• Clinical Reports Summary Page

Benign

fr: bénigne (feminine), bénin (masculine)

Not cancer. Benign tumors may grow larger but do not spread to other parts of the body.

Also called nonmalignant.

Example: Based on its appearance and the absence of abnormal cancer biomarkers, the pathologist determined that the tumor was benign.

Relevant Lessons:

• Clinical Reports Summary Page

Bioinformatics

fr: Bioinformatique

Bioinformatics is a field of study that analyzes biological data by combining biology, computer science, mathematics and statistics.

Example: In the clinical trial study, the researchers used bioinformatics to predict the efficiency and effectiveness of precision medicine based on a patient’s genotype.

Relevant Lessons:

• What is Molecular Pathology Infographic

Biomarkers

fr: Biomarqueurs

A biological molecule found in blood, other body fluids, or tissues that is a sign of a normal or abnormal process, or of a condition or disease. A biomarker may be used to see how well the body responds to a treatment for a disease or condition. Also called molecular marker and signature molecule.

Example: In molecular pathology, researchers are actively exploring the identification and validation of specific biomarkers that can serve as indicators of disease presence, progression, or response to treatment, providing valuable insights into personalized medicine.

Relevant Lessons:

• Biomarker Storybook
• What does a molecular pathologist do?
• What is Molecular Pathology infographic

Carcinoma

fr: carcinome

Cancer that begins in a part of the skin or in the layer of cells that covers internal organs.

Example: The biopsy confirmed the diagnosis of invasive ductal carcinoma of the breast.

Relevant Lessons:

• Clinical Reports Summary Page

Carrier

fr: porteur

An individual who has one copy of a variant allele that is associated with a recessive genetic disorder. Carriers do not exhibit symptoms of the disorder.

Example: Genetic counseling identified the patient as a carrier of a hereditary cancer susceptibility gene.

Relevant Lessons:

• Clinical Reports Summary Page

Cellular Biomarker

fr: Biomarqueurs cellulaires

Indicators related to cell structure, function, or activity. Cellular Biomarkers are used to see if there are any abnormal cellular activities or structures indicative of cancer.

Example: Antigen Kiel (Ki-67) protein expression is a cellular biomarker associated with active cell division and used for predicting tumor aggressiveness in various cancers.

Relevant Lessons:

• Social Media Biomarkers Campaign

Chromosome

fr: chromosome

A structure found inside the nucleus of a cell. A chromosome is made up of proteins and DNA organized into genes. Each cell normally contains 23 pairs of chromosomes.

Example: The oncologist explained that the cancer cells exhibited an abnormal number of chromosomes, which could influence the tumor’s behavior and response to treatment.

Relevant Lessons:

• Clinical Reports Summary Page

Circulating Tumor Cells (ctc)

fr: cellules tumorales circulantes (ctc)

Circulating tumor cells (CTCs) are tumor cells that become dislodged from the primary tumor. These cells enter the bloodstream and if they land in favourable sites, they could form metastases.

Example: By analyzing circulating tumor cells isolated from the patient’s blood sample, we can gain insights into the molecular characteristics of the cancer without the need for a more invasive tissue biopsy.

Relevant Lessons:

• Liquid Biopsy Infographic

Clinical Trials

fr: essai clinique

A clinical trial is a research study involving human participants that evaluates the safety and/or effects of one or more interventions on health outcomes. Interventions include, but are not limited to, drugs, vaccines, radiopharmaceuticals, cells and other biological products, surgical procedures, radiologic procedures, devices, genetic therapies, natural health products, process-of-care changes, preventive care, manual therapies, and psychotherapies.

Example: Next-generation sequencing detected an ALK gene rearrangement. While the patient is eligible for ALK inhibitors, participation in a clinical trial targeting ALK fusions is also recommended.

Relevant Lessons:

• Clinical Trial Video

Control Group

fr: contrôle

In a clinical trial, the control group refers to patients who do not receive the new treatment being studied. Patients in group are compared to patients who receive the new treatment, to see if the new treatment works.

Example: The clinical trial incorporated a control group that received a standard treatment , enabling researchers to compare the effects of the experimental drug.

Relevant Lessons:

• Clinical Trial Video

Copy Number Variation (CNV)

fr: Variation du nombre de copies

CNV refers to a type of genetic variation where the number of copies of a particular segment of DNA varies from one individual to another. These variations can range from small deletions or duplications to larger structural changes in the genome.

Example: Researchers are investigating how copy number variation contributes to the growth and spread of cancer cells, aiming to develop targeted therapies in future.

Relevant Lessons:

• Abbreviations in Molecular Pathology

Circulating Tumor DNA (ctDNA)

fr: ADN tumoral circulant (ADNc)

Circulating tumor DNA (ctDNA) is found in the bloodstream and refers to DNA that comes from cancerous cells and tumors. Most DNA is inside a cell’s nucleus. As a tumor grows, cells die and are replaced by new ones. The dead cells get broken down and their contents, including DNA, are released into the bloodstream. ctDNA are small pieces of DNA, usually comprising fewer than 200 building blocks (nucleotides) in length.

Example: Circulating tumor DNA (ctDNA) refers to small pieces of DNA from cancer cells that end up in the bloodstream. DNA is normally inside a cell’s nucleus but as tumour cells die, their DNA gets broken down and released into the bloodstream.

Relevant Lessons:

• Liquid Biopsy Infographic

Diagnostic Biomarker

fr: Biomarqueurs diagnostiques

Indicates the presence or absence of a disease or condition. Answers the question of which type of cancer is present and at what stage is it.

Example: Increased levels of Carbohydrate Antigen (CA 19-9) are diagnostic biomarkers used in pancreatic cancer detection and monitoring.

Relevant Lessons:

• Social Media Biomarker Series

Digital Pathology

fr: pathologie numérique

Pathologists examine tissue on glass slides using a powerful microscope. In digital pathology, the glass slides are scanned into a computer, where they can be viewed by the pathologist using specialized software.

Example: Digital pathology enables pathologists to analyze tissue samples using computer technology, streamlining the diagnostic process and facilitating collaboration among healthcare professionals.

Relevant Lessons:

• What is Molecular Pathology Infographic

DNA Methylation

fr: méthylation de l’ADN

DNA methylation works by adding a chemical modification to DNA. Typically, this group is added to specific places on the DNA, where it blocks the proteins that attach to DNA to “read” the gene. This chemical group can be removed through a process called demethylation. Typically, methylation turns genes “off” and demethylation turns genes “on.

Example: Upon studying the disease at the molecular level, unusual DNA methylation was found suggesting that possible changes in gene activity is linked to the development of the illness.

Relevant Lessons:

• Clinical Reports Summary Page

DNA Mutation

fr: Mutation de l’ADN

A mutation is a change in the DNA sequence. A mutation is also called a “variant.”

Example: A DNA mutation in the BRCA1 disrupted the normal function of the gene and contributed to cancer development.

Relevant Lessons:

• Clinical Reports Summary Page

DNA Sequencing

fr: séquençage ADN

Sequencing DNA means determining the order of the four chemical building blocks – called “bases” – that make up the DNA molecule. The sequence tells scientists the kind of genetic information that is carried in a particular DNA segment.

Example: DNA sequencing has played a crucial role in uncovering the genetic variations associated with the rare disease, aiding researchers in pinpointing potential therapeutic targets.

Relevant Lessons:

• Clinical Reports Summary Page

Dominant

fr: dominant

A person receive two versions of each gene, known as alleles, from each parent. If the alleles of a gene are different, one allele may be preferentially expressed compared to the other – this is the dominant gene. The effect of the other allele, called recessive, is masked.

Example: The patient’s family tree showed patterns of autosomal dominant inheritance, suggesting a hereditary cause of the disease.

Relevant Lessons:

• Clinical Reports Summary Page

Epigenetics

fr: épigénétique

Epigenetics is the study of how your behaviors and environment can cause changes that affect the way your genes work. Unlike genetic changes, epigenetic changes are reversible and do not change your DNA sequence, but they can change how your body reads a DNA sequence.

Example: Epigenetic changes were detected in the MGMT gene, which made the patient’s tumour respond more strongly to chemotherapy.

Relevant Lessons:

• Clinical Reports Summary Page

Exons

fr: éxome

Exons are the genome’s protein-coding regions and are collectively known as the exome.

Example: By analyzing the exome of tumour tissues, researchers identified key mutations in genes associated with DNA repair pathways, offering valuable information about the genomic landscape of the cancer and potential targets for precision therapies.

Relevant Lessons:

• Clinical Reports Summary Page

Flow Cytometry

fr: cytométrie en flux

A lab test used to analyze cells or tiny particles. During the process, a sample of cells or particles is suspended in fluid and injected into a flow cytometer machine. Approximately 10,000 cells can be analyzed and processed by a computer in less than one minute.

Example: Flow cytometry showed a decrease in the leukemia cells after initial treatment.

Relevant Lessons:

• Clinical Reports Summary Page

Formalin-Fixed Paraffin-Embedded (FFPE)

fr: Fixé au Formol et Intégré en Paraffine

FFPE refers to a method of preserving tissue samples for histological analysis. Tissue samples are fixed in formalin, dehydrated, and embedded in paraffin wax, allowing them to be stored for long periods while preserving cellular structure.

Example: The pathologist examined the Formalin-Fixed Paraffin-Embedded tissue samples under the microscope to determine the stage and grade of the patient’s cancer.

Relevant Lessons:

• Abbreviations in Molecular Pathology

Frameshift Mutation

fr: mutation de décalage de cadre

A type of insertion or deletion of DNA bases in a gene that affects the “reading frame” of the gene’s instructions to shift and leads to incorrect protein production. Also called frameshift variant.

Example: A frameshift mutation in the MLH1 gene leads to a shortened protein and loss of mismatch repair function.

Relevant Lessons:

• Clinical Reports Summary Page

Genotype

fr: Génotype

The genotype represents the genetic blueprint of an organism. It encompasses the entire selection of genetic information inherited from one’s ancestors.

Example: A research study focused on understanding the genotype of cancer cells, revealing specific genetic alterations that contribute to the uncontrolled growth and survival of the malignant cells.

Relevant Lessons:

• Clinical Reports Summary Page

Germline

fr: Lignée germinale

Germline DNA refers to tissue derived from reproductive cells (egg or sperm) that become incorporated into the DNA of every cell in the body of the offspring. A germline mutation may be passed from parent to offspring. Also called constitutional DNA.

Example: A germline mutation in the BRCA1 gene was identified. This pathogenic variant is associated with an increased risk of hereditary breast and ovarian cancer syndrome.

Relevant Lessons:

• Clinical Reports Summary Page

Heterozygous

fr: hétérozygote

Refers to having inherited different versions (alleles) of a gene from each biological parent. Thus, an individual who is heterozygous for a gene has two different versions of that gene.

Example: DNA sequencing identified a heterozygous BRCA2 variant gene that is associated with an increased risk of hereditary breast and ovarian cancer syndrome.

Relevant Lessons:

• Clinical Reports Summary Page

Histology

fr: histologie

The study of tissues and cells under a microscope.

Example: The histology showed the presence of abnormal cell patterns characteristic of pancreatic cancer.

Relevant Lessons:

• Clinical Reports Summary Page

Histopathology

fr: histopathologie

Is the diagnosis and study of diseases of tissues and involves examining tissues and/or cells under a microscope. Pathologists are experts in histopathology.

Example: Histopathology of the excised mass revealed a poorly differentiated adenocarcinoma.

Relevant Lessons:

• Clinical Reports Summary Page

Homozygous

fr: homologue

Homozygous refers to having inherited the same versions (alleles) of a genomic marker from each biological parent. An individual who is homozygous for a gene has two identical versions of that gene.

Example: A germline homozygous mutation in the DNA repair gene led to colon cancer development in the patient.

Relevant Lessons:

• Clinical Reports Summary Page

Imaging Biomarker

fr: Biomarqueurs d’imagerie

Imaging Biomarkers are observable through imaging techniques like Magnetic resonance imaging (MRI), Computed Tomography (CT) scans, or Positron Emission Tomography (PET) scans. They are used to determine the location, size, and extent of the cancerous growth within the body.

Example: Prostate-specific membrane antigen (PSMA) PET scans use radioactive chemicals to detect PSMA on prostate cancer cells. PSMA PET is an imaging biomarker that can be used to look for prostate cancer metastasis.

Relevant Lessons:

• Social Media Biomarker Series

In Silico Analysis

fr: Analyse in silico

In silico studies are biological experiments carried out entirely on a computer, or via a computer simulation

Example: In in silico analysis showed that the DNA variant would lead to a defective protein.

Relevant Lessons:

• Clinical Reports Summary Page

Inherited

fr: hérité

Refers to a trait or variants encoded in DNA and passed from parent to offspring during reproduction.

Example: The increased risk of developing certain types of cancer can be influenced by inherited genetic mutations, as individuals may inherit genetic predispositions that make them more susceptible to the disease.

Relevant Lessons:

• Clinical Reports Summary Page

Intronic Region

fr: région intronique

Introns are sections of an RNA transcript, or the DNA encoding it, that are cut out before the RNA molecule makes a protein. The sections of DNA (or RNA) that code for proteins is called exons.

Example: Researchers focused on the intronic region to study non-coding segments of the gene, revealing important information about regulatory elements and their influence on genetic processes

Relevant Lessons:

• Clinical Reports Summary Page

Loss of Heterozygosity (LOH)

fr: Perte d’hétérozygotie

LOH refers to the loss of one allele at a specific genetic locus, resulting in a region of DNA becoming homozygous. LOH can occur through various mechanisms, including deletion, mutation, or chromosomal rearrangement, and is often associated with tumor suppressor gene inactivation.

Example: The presence of loss of heterozygosity in the tumor samples indicated a potential genetic driver of the patient’s cancer, guiding treatment decisions towards therapies targeting specific mutated genes.

Relevant Lessons:

• Abbreviations in Molecular Pathology

Malignant

fr: maligne (feminine), malin (masculine)

A term used to describe cancer. Malignant cells grow in an uncontrolled way and can invade nearby tissues and spread to other parts of the body through the blood and lymphatic systems

Example: The pathology report confirmed the presence of malignant cells in the tissue, underscoring the urgency for a comprehensive and aggressive approach to treatment.

Relevant Lessons:

• Clinical Reports Summary Page

Metabolic Biomarker

fr: Biomarqueurs métaboliques

Reflect changes in chemical pathways in the body. Metabolic biomarkers are used to determine if there any metabolic abnormalities indicating the presence or aggressiveness of cancer.

Example: Increased levels of lactate in tumor tissues serve as metabolic biomarkers indicating tumor aggressiveness and poor prognosis in various cancers.

Relevant Lessons:

• Social Media Biomarker Series

Microsatellite Instability (MSI)

fr: Instabilité des microsatellites

MSI is a condition characterized by the accumulation of errors in microsatellite DNA sequences, which are short repetitive sequences scattered throughout the genome.

Example: Microsatellite instability, characterized by errors in the repetition of short DNA sequences, is a hallmark of certain types of cancer, including colorectal cancer, and can influence prognosis and treatment options for affected patients.

Relevant Lessons:

• Abbreviations in Molecular Pathology

Monitoring Biomarker

fr: Surveillance des biomarqueurs

Monitoring biomarkers track disease progression or treatment response over time. These biomarkers tries to answer the question of how is the cancer progressing or responding to treatment over time?

Example: Circulating tumor DNA (ctDNA) levels are monitoring biomarkers used to track disease progression and treatment response in advanced cancers.

Relevant Lessons:

• Social Media Biomarker Series

Nucleotide

fr: Nucléotide

A molecule that is the basic building block of the nucleic acids DNA and RNA. A nucleotide is made up of a nitrogen-containing base (adenine, guanine, thymine, and cytosine in DNA, and adenine, guanine, uracil, and cytosine in RNA), a phosphate group, and a sugar molecule (deoxyribose in DNA, and ribose in RNA). DNA and RNA are polymers made up of many nucleotides.

Example: DNA sequencing was used to identify the precise nucleotide that was mutated in the BRCA1 gene.

Relevant Lessons:

• Clinical Reports Summary Page

Patient Partner

fr: patient partenaire

Patient partners have lived experience as a cancer patient, family member or caregiver. Patient partners bring their insight and perspective to a research project or organization.

Example: The hospital implemented a patient engagement initiative, appointing a patient partner to work closely with healthcare professionals, sharing their experiences and perspectives to improve the overall quality of care and services.

Relevant Lessons:

• Being an active participant in your cancer care

Phenotype

fr: Phénotype

The phenotype constitutes the visible aspects of a person resulting from the instruction in their genome. In essence, the genotype serves as the underlying script, dictating what should be expressed at the phenotype (visible) level.

Example: In a recent study of breast cancer, the triple-negative phenotype was associated with tumors lacking expression of estrogen receptors, progesterone receptors, and HER2, influencing the prognosis and treatment approach for patients with this specific cancer phenotype.

Relevant Lessons:

• Clinical Reports Summary Page

Predictive Biomarker

fr: Biomarqueurs prédictifs

Predicts response to treatment or therapy and tries to answer the question of how likely is it that a specific treatment or therapy will be effective?

Example: Epidermal Growth Factor Receptor (EGFR) mutation status in non-small cell lung cancer is used as a predictive biomarker, as it predicts response to targeted therapies against EGFR.

Relevant Lessons:

• Social Media Biomarker Series

Prognostic Biomarker

fr: Biomarqueurs pronostiques

Provides information about disease progression and outcome. Answers the question of what is the likely course of the disease and what are the expected outcomes?

Example: Elevated levels of circulating tumor cells (CTCs) are prognostic biomarkers associated with poor survival outcomes in various cancers.

Relevant Lessons:

• Social Media Biomarker Series

Promoter Region

fr: région promotrice

A region of DNA before the first exon of a gene that tells the cell when the gene should be made in a process called transcription.

Example: DNA methylation in the promoter region prevented the gene from being expressed in the patient’s tumour.

Relevant Lessons:

• Clinical Reports Summary Page

Protein Biomarker

fr: Biomarqueurs protéiques

Proteins detected in biological samples like blood, urine, or tissues. Protein biomarkers are used to see if there are any abnormal levels of specific proteins associated with cancer present in the body.

Example: Carbohydrate Antigen (CA-125) is a protein biomarker used for monitoring ovarian cancer progression and response to treatment.

Relevant Lessons:

• Social Media Biomarker Series

Recessive

fr: récessif (masculine), récessive (feminine)

Individuals inherit two versions of each gene, known as alleles, from each parent. In the case of a recessive trait, the alleles of the trait-causing gene are the same, and both (recessive) alleles must be present to express the trait. A recessive allele does not produce a trait at all when only one copy is present. This contrasts to a dominant trait, which requires that only one of the two alleles be present to express the trait.

Example: While most cancer-related mutations are dominant and lead to abnormal cell growth, recessive mutations require both copies of a gene to be altered before contributing to the development of the disease.

Relevant Lessons:

• Clinical Reports Summary Page

Refractory Cancer

fr: épisode réfractaire

Refractory cancer is cancer that fails to respond to treatment or continues to progress despite treatment. Refractory cancer may also be called resistant cancer.

Example: Despite undergoing multiple rounds of treatment, the patient’s cancer remained refractory, posing significant challenges for the medical team in finding an effective therapeutic approach.

Relevant Lessons:

• Being an active participant in your cancer care

Risk Biomarker

fr: Biomarqueurs de risque

Risk biomarkers are derived from genetic material such as DNA or RNA. They answer the question of is there a genetic predisposition to cancer, and if so, which specific gene variants are present?

Example: Variants in the BRCA1 and BRCA2 genes are genetic biomarkers associated with increased risk of hereditary breast and ovarian cancer.

Relevant Lessons:

• Social Media Biomarker Series

Single Nucleotide Polymorphism/ Single Nucleotide Variant (SNP, SNV)

fr: Polymorphisme nucléotidique unique/ Variante nucléotidique unique

SNPs and SNVs are variations in a single nucleotide at a specific position in the genome.

Example: The presence of specific single nucleotide polymorphisms within certain genes has been linked to an increased risk of developing certain types of cancer, highlighting the importance of genetic variation in cancer susceptibility and progression.

Relevant Lessons:

• Abbreviations in Molecular Pathology

Somatic

fr: somatique

Cells that are not part of the germline are called somatic cells, and any changes to the DNA that occur within these cells are known as somatic variants. Somatic variants are not present in every cell in the body, and are not passed from parent to child.

Example: DNA sequencing of the BRAF gene revealed a somatic variant. Targeted therapy with a BRAF inhibitor should be considered.

Relevant Lessons:

• Clinical Reports Summary Page

The Cancer Genome Atlas (TCGA)

fr: L’Atlas du génome du cancer

TCGA is a comprehensive database that catalogues genomic, transcriptomic, and epigenomic data from thousands of cancer patients across different cancer types. It serves as a valuable resource for cancer research and personalized medicine initiatives.

Example: The Cancer Genome Atlas (TCGA) project has provided researchers with a comprehensive database of genomic alterations across various cancer types, revolutionizing our understanding of cancer biology and informing the development of personalized cancer treatments.

Relevant Lessons:

• Abbreviations in Molecular Pathology

Therapeutic Biomarker

fr: Biomarqueurs thérapeutiques

Monitors and predicts the effect of treatment and answers the question of how is the current treatment working for the patient.

Example: Carcinoembryonic Antigen (CEA) is used as a therapeutic biomarker to monitor treatment response in colorectal cancer. Decreasing CEA levels means that the cancer is responding to therapy.

Relevant Lessons:

• Social Media Biomarker Series

Tumour Mutational Burden (TMB)

fr: Charge mutationnelle tumorale

TMB is a measure of the total number of mutations present in the DNA of tumor cells. It is used as a biomarker to assess the overall mutational load of a tumor and may correlate with response to immunotherapy and prognosis in certain cancers.

Example: The tumor mutational burden is being increasingly recognized as a predictive biomarker for response to certain immunotherapy treatments in cancer patients.

Relevant Lessons:

• Abbreviations in Molecular Pathology

Variant Allele Frequency (VAF)

fr: Variante de fréquence des allèles

VAF is the proportion of sequencing reads that contain a specific genetic variant relative to the total number of reads covering that position. It provides information about the abundance of a variant within a sample.

Example: In analyzing the genetic makeup of the tumor, researchers observed a high variant allele frequency, indicating a significant proportion of mutated alleles present in the tumor sample compared to normal tissue.

Relevant Lessons:

• Abbreviations in Molecular Pathology