Biomarker Glossary
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AntibodyA protein made by plasma cells (a type of white blood cell) in response to exposure to an antigen - a substance, such as a protein, that causes the body to make a specific immune response). Each antibody binds to one specific antigen. Antibody binding “marks" a protein as “foreign”, alerting the immune response. For example, the “coat” proteins of viruses, such as the influenza virus) are recognized by antibodies.
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BiomarkerA biomarker is any molecule that can be measured in the blood, other bodily fluids, or tissues, and which can provide useful information about a person’s health status. Biomarkers can also be called “molecular markers”, “tumor markers” or “signature molecules”.1 The presence/ levels of specific genes or proteins are common biomarkers.
Biomarker TestingBiomarker testing is a way to assess biomarkers that can provide information about your health status, including cancer. Biomarker testing may allow your physicians to match your treatment plan more precisely to your cancer.

Test results may take several weeks to be received by your doctor.2 All biomarker laboratory results are recorded in a biomarker testing report. It is a good idea to get a copy of this report, for your own information and to have it available to show to other doctors, if necessary.
Biopsyan examination of tissue removed from a living body to discover the presence, cause, or extent of a disease.
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cfDNACirculating free DNA molecules are degraded DNA fragments released to the blood plasma. cfDNA can be used to describe various forms of DNA freely circulating in the bloodstream, including circulating tumor DNA, cell-free mitochondrial DNA, and cell-free fetal DNA.

Because some tumors shed cells and genetic material into blood, it may be possible to examine genetic biomarkers in blood samples. Although these "liquid biopsies" are not yet routinely used, they have several potential advantages. Because they don’t involve surgery, they can be done more frequently than standard biopsies. They can also be performed when surgical biopsies cannot, such as when tumors are difficult to reach or patients can’t tolerate surgery.
Circulating tumor DNA (ctDNA)is found in the bloodstream and refers to DNA derived from cancer cells. As a tumor grows, some of its cells die and disintegrate, releasing small fragments of DNA into the blood.
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DNADNA, or deoxyribonucleic acid, is the hereditary material in humans and all other cellular organisms. DNA is the biochemical substance which makes up the genes.
Driver MutationA “driver” mutation is a mutation that causes a cancer cell to grow and divide. “Driver” mutations usually occur in “oncogenes”, genes which play important roles in normal cell proliferation but which, when mutated, can drive cancer growth.
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Genesare specific segments of DNA, often encoding the information for synthesis of a protein; the genome is the complete genetic material of an organism, comprising tens of thousands of genes as well as large amounts of DNA that do not encode specific genes.
Gene and GenomeAll of the genetic information in a cell is in the form of DNA (deoxyribonucleic acid) or RNA (ribonucleic acid, which is derived from DNA information). A gene is the segment of DNA which gives instructions for the formation of a gene product, and the complete genetic information of a cell comprises its “genome”. The DNA is packaged in chromosomes. 8
GeneticsGenetics is the study of genes, which are inherited from the parents and may be passed on through the generations. Every cell in the body contains DNA - the genome (although the nucleus and DNA may be lost during the maturation of certain cell types, such as red blood cells). Genes carry instructions for certain traits, such as eye colour —or, perhaps, a stronger likelihood of development of certain cancers. However, the effects of specific genes may depend very strongly on interactions with other genes and with the environment.
Genetic Testing or Germline TestingGenetic testing for an inherited mutation (also called "germline genetic testing") looks at DNA (e.g., in blood or saliva samples) to identify mutations that can predispose a person to diseases such as cancer. 5
GenomicsGenomics refers to the study of entire genomes.
Genomic SequencingDetermination of the entire genetic makeup of a cell. This method can be used to find changes in specific parts of the genome. The results of genomic sequencing may also be used to diagnose and treat disease. 6 (Compare with “whole exome sequencing”, which examines only a small portion of the entire genome.) (Also called Whole Genome Sequencing).
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ImmunohistochemistryImmunohistochemistry is staining that uses antibodies to identify the expression of specific proteins by cells (especially, cancer cells). Positive staining for the KIT and DOG1 proteins is a diagnostic marker of GIST. After your pathologist has confirmed your GIST diagnosis, the pathologist will send the results to your oncologist.
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KITKIT is a proto-oncogene, meaning that overexpression of, or mutations in the gene for, this protein can lead to cancer.
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Molecular ProfilingA laboratory method that uses a sample of tissue, blood, or other body fluid to identify specific genes, proteins, or other molecules that may be signs of disease. Molecular profiling may be done as an add-on to other investigative procedures, such as biopsies, to help diagnose some types of cancer. It may also be used to help plan treatment, find out how well treatment is working, or predict whether cancer will come back or spread to other parts of the body.
MutationMutations are changes in genes, which may relate to the development of cancer. Mutations can be inherited (“germline”) or they may occur during the division and growth of your body’s cells (“somatic”). Somatic mutations cannot be passed on to your children (see below).
Mutational TestingMutational testing is a type of biomarker testing that involves DNA sequencing of genes. The information gathered can help to determine a diagnosis and predict the course of your disease and its response to treatment.
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Next Generation Sequencing“Next generation sequencing” (NGS, NextGenSeq) refers to any of several methods for sequencing DNA, developed in the 2000s, technical breakthroughs which have made DNA sequencing far faster and less expensive than the older methods (such as “Sanger sequencing”) that were used in the Human Genome Project prior to 2000.
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PCR/amplicifationPolymerase chain reaction (PCR) is an amplification technique for cloning specific segments of genome, rapidly generating large numbers of copies of its DNA. The invention of the PCR technique was one of the most important advances in modern science; without PCR, techniques like mutational analysis and ctDNA analysis (see below) would be almost impossibly difficult.
PDGFRAThe PDGFRA gene provides instructions for making a protein called Platelet-Derived Growth Factor Receptor Alpha (PDGFRA). Both KIT and PDGFRA belong to a large family of proteins called Receptor Tyrosine Kinases (RTKs)
Protein ExpressionGenes encode proteins, but different cell types (liver cells, white blood cells, neurons, etc.) synthesize (“express”) different sets of proteins. Protein Expression refers to these patterns of proteins in particular cells.
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RNARibonucleic acid, or RNA, is the intermediate “messenger” molecule that transmits the instructions held in the DNA (in the cell’s nucleus) to the machinery that makes the cell’s proteins.
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SequencingDNA sequencing refers to determining the exact sequence of nucleotides (the “bases” A, C, G, and T), in a DNA molecule.
Somatic MutationAn alteration in DNA that arises in a body cell that is not a “germ cell” (egg or sperm cell). Sometimes, these alterations can cause cancer or other diseases. 3
Somatic Mutation TestingTesting for mutations that drive disease processes that are not inherited.
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TMB or Tumor Mutational BurdenEvery cell contains mutations, most of which have no major consequences. “Mutational burden” denotes the extent of mutations (e.g., in the DNA of a cancer cell).
Tissue BiopsiesMany different biopsy techniques can be used to obtain tumor tissue. The choice of technique is determined by the location and size of the tumor, as well as the patient's overall health. The patient's healthcare team will discuss the best options with the patient as well as the risks and benefits of the procedures.
Tumor Profiling/Mutation ProfilingThis term may be used to describe a comprehensive analysis of changes in a set of genes.
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Whole Exome SequencingA laboratory process that is used to determine the nucleotide sequence primarily of the exonic (or protein-coding) regions of an individual’s genome and related sequences, representing approximately 1% of the complete DNA sequence. It is also called WES and WXS. WES can be a cost-effective alternative to sequencing the entire genome, since mutations in protein-coding regions are most likely to affect health and disease.
References
1. https://www.cancer.gov/about-cancer/treatment/types/biomarker-testing-cancer-treatment#:~:text=Biomarker%20testing%20is%20a%20way,how%20certain%20cancer%20treatments%20work.
2. https://www.cancer.net/navigating-cancer-care/diagnosing-cancer/reports-and-results/reading-pathology-report.
3. https://www.cancer.gov/publications/dictionaries/cancer-terms/def/somatic-mutation
4. https://www.cancer.gov/publications/dictionaries/cancer-terms/def/molecular-profiling
5. https://www.facingourrisk.org/info/hereditary-cancer-and-genetic-testing/genetic-testing/what-is-genetic-testing
6. https://www.cancer.gov/publications/dictionaries/cancer-terms/def/genomic-sequencing
7. https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/whole-genome-sequencing
8. https://byjus.com/biology/difference-between-gene-and-genome/
9. https://www.cancercenter.com/diagnosing-cancer/genetic-and-genomic-testing
10. https://www.cancer.gov/about-cancer/diagnosis-staging/diagnosis/tumor-markers-fact-sheet