Glossary

Tumor Types & Biomarkers
Tumor Types & Biomarkers

Explore clinical guidelines on why, whom and how to test actionable biomarkers in lung, breast, ovarian and prostate cancers.
- Lung Tumor
  
  EGFR
  
  ERBB2 (HER2)
- Breast Tumor
  
  BRCA1/2
  
  ESR1
  
  HER2
  
  PIK3CA/AKT1/PTEN
- Ovarian Tumor
  
  HRD
- Prostate Tumor
  
  HRRm
  
  PTEN
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Glossary

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A

Actionable biomarker: Actionable biomarkers are genetic alterations that are functional in driving malignancy and may be targeted by a Food and Drug Administration (FDA) approved treatment regimen. They can also help determine a patient’s eligibility for clinical trials.^1,2
Actionable mutation: An alteration in deoxyribonucleic acid (DNA) which, if detected in a tumor, may affect a patient’s response to a certain treatment.³
Artificial intelligence (AI): The ability of a computer to perform functions that are usually thought of as intelligent human behavior, such as learning, reasoning, problem solving, and decision making.⁴
Assay: An analytic procedure for detecting or measuring the presence, amount, state, or functional activity of a biomarker. An assay is one component of a test, tool, or instrument.⁵
ATM (ataxia telangiectasia mutated): The ATM gene provides instructions for making a protein that assists cells in recognizing and repairing DNA double-strand breaks (DSB). ATM mutations can increase cancer susceptibility and may be a useful actionable biomarker for some targeted therapies.⁶ See also DNA DSB. See also targeted therapy.

B

Biomarker: A genetic characteristic or biological molecule which indicates disease or a condition. It can also be a sign of abnormal processes in the body. Biomarkers may be found in tissue, blood, or other bodily fluids. In patients with cancer, they can be measured to inform diagnosis and eligibility for targeted therapy.² See also prognostic biomarker and predictive biomarker. See also targeted therapy.
Biomarker testing: A laboratory method that uses a sample of tissue, blood, or other bodily fluid to identify molecular and genetic characteristics. It may be performed to identify a patient’s risk of developing cancer or other diseases, or to inform prognosis and treatment planning in those who already have a cancer diagnosis. Also called molecular profiling and molecular testing.⁷ See also biomarker.
BRCA1/2 (BReast CAncer susceptibility gene 1/2): Genes on chromosome 17/13 respectively that normally help to suppress cell growth. A person who inherits certain mutations in a BRCA1/2 gene has a higher risk of getting breast, ovarian, prostate, and other types of cancer.⁸
Broad molecular profiling: Molecular testing that identifies all recommended and emerging biomarkers in either a single assay or a combination of a limited number of assays.⁹

C

Carcinogenesis: The initiation of cancer formation.¹⁰
CDK12 (cyclin-dependent kinase 12): CDK12 is a transcriptional CDK with a specific role in regulating transcription of genes involved in cellular responses to DNA damage and stress. Genomic alterations in CDK12 have been detected in esophageal, stomach, breast, endometrial, uterine, ovarian, bladder, colorectal, and pancreatic cancers; therefore, CDK12 may have an important role as a clinical biomarker for treatment response and effective therapeutic target.¹¹
CHEK2 (Checkpoint kinase 2): The CHEK2 gene encodes the CHK2 protein, which is a vital factor that responds to DNA double-strand breaks (DSB). High CHK2 expression is tightly associated with adverse tumor features, such as the recurrence, progression, and metastasis of many malignant tumors; therefore, may be an important biomarker to determine prognostic value.¹²
Circulating tumor cell (CTC): CTCs are tumor cells which are shed into the blood from primary tumors or secondary lesions.¹³
Circulating tumor DNA (ctDNA): Fragments of tumor cell DNA which are released into the patient’s bloodstream.¹⁴ See also liquid biopsy
Clinical Laboratory Improvement Amendments (CLIA): The Clinical Laboratory Improvement Amendments of 1988 (CLIA) regulations include federal standards applicable to all US facilities or sites that test human specimens for health assessment or to diagnose, prevent, or treat disease.¹⁵
Companion diagnostic: A laboratory test, often an in vitro device (IVD), which is used in conjunction with a drug or biological product to determine a patient’s suitability for that treatment. Companion diagnostics are essential for safe and effective use of their corresponding targeted therapy.^16,17
Complementary diagnostic: A laboratory test which provides information about whether a patient may benefit from a certain targeted therapy but is not essential for administration of a particular drug.¹⁷
Computational pathology (CPATH): A branch of pathology that uses machine learning to extract and analyze complex data sets of digital pathology images for the study of disease.^18,19
Concordance (in the context of tumor tissue and circulating tumor DNA [ctDNA]): The level of agreement or consistency in molecular alterations between tumor tissue and ctDNA samples. This measure is used to assess the reliability of ctDNA testing compared to the gold standard of tissue testing for genetic alterations in a tumor.^20,21
Concurrent testing: The simultaneous sequencing of both liquid and tissue biopsy tumor samples. This may provide advantages in timely clinical treatment decision-making compared to single-modality testing.²²
Cytopathology: The study of disease at a cellular level.²³

D

Deep learning models: Deep learning models are trained to detect malignancies and classify histology subtypes.¹⁹
Deficient mismatch repair (dMMR): Describes cells that have mutations in certain genes that are involved in correcting mistakes made when DNA is copied in a cell. Mismatch repair deficient cells usually have many DNA mutations, which may lead to cancer. MMR deficiency is most common in colorectal cancer but it may also be found in cancers of the breast, prostate, bladder, and thyroid and in an inherited disorder called Lynch syndrome. Knowing if a tumor is MMR deficient may help plan treatment or predict how well the tumor will respond to treatment.²⁴
Digital pathology: A technology that involves digital acquisition, management, interpretation, and sharing of slides and data. Digital slides are created when glass slides are captured with a scanning device, to provide a high-resolution image that can be viewed on a computer screen or mobile device. These images can be examined by a pathologist on a computer in a manner similar to standard microscopy, where the image can be magnified and navigated spatially. Also called whole slide imaging (WSI) or virtual pathology.²⁵
Digitally guided microdissection: This technology allows the precise and fully automated dissection of the tumor area without wasting limited and valuable patient material.²⁶
Double-strand break (DSB): A DSB is a type of DNA damage that occurs when both strands of the double-stranded DNA are cleaved. DSBs mainly occur due to ionizing radiation exposure and can also form when replication forks encounter DNA lesions or repair intermediates. The processing and repair of DSBs can lead to mutations, loss of heterozygosity, and chromosome rearrangements that result in cell death or cancer.²⁷

E

EGFR (epidermal growth factor receptor) mutations: EGFR encodes a protein involved in cell growth and cell survival. EGFR mutations have been found in some types of cancer, including non-small cell lung cancer. These changes may cause cancer cells to grow and spread in the body. Checking for changes in the EGFR gene in tumor tissue may help plan cancer treatment.²⁸
Emerging biomarker: A genetic characteristic or biological molecule which is becoming more apparent to be associated with disease development/progression.^2,29
Endobronchial ultrasound (EBUS): EBUS is an advanced bronchoscopic technique employing a side-viewing ultrasound transducer (either convex or radial) combined with a fiberoptic bronchoscope. Clinicians can assess and sample lymph nodes within the proximal bronchial tree, the hilar regions, and anterosuperior mediastinum, as well as both endobronchial and peribronchial mass lesions. The convex EBUS scope allows for real-time ultrasound needle guidance. Newer scope types, including radial-EBUS, allow for more peripheral bronchial tree assessment with a 360-degree view.³⁰
ERBB2 (erythroblastic oncogene B): ERBB2 is the human derivative of HER2 which encodes the HER2 protein which plays an important role in cellular functions including adhesion, differentiation, growth, apoptosis, and migration. ERBB2 mutations and amplifications have emerged as oncogenic drivers and drug targets in non-small cell lung cancer.³¹

F

FANCA (Fanconi anemia, complementation group A): FANCA encodes a protein involved in the DNA damage repair (DDR) pathway. Alterations in the FANCA gene disrupt the DDR pathway in cells, acting as a driver toward tumorigenesis.³²
FDA-approved companion diagnostic: A companion diagnostic that provides important information for the safe and effective use of targeted therapies that is approved by the US Food and Drug Administration.³³ See also companion diagnostic.
Formalin-fixed paraffin-embedded (FFPE) tissue: Fixation of tissues in formalin followed by embedding in paraffin wax to make formalin-fixed, paraffin-embedded (FFPE) tissue blocks is a standard way to preserve tissues for diagnosis.³⁴

G

Gene: A gene is the basic unit of heredity. Genes are composed of DNA.³⁵
Gene expression: The process of activating or inactivating a gene in a cell in order to make ribonucleic acid (RNA) and proteins. Gene expression is measurable at the RNA level or via proteins.³⁶
Genetic (in relation to cancer genetics): Genetic information can identify people who have an increased risk of cancer. Sources of genetic information include DNA samples, family history of disease, findings from physical examinations, and medical records. Family history may identify people with a modest to moderately increased risk of cancer or may serve as the first step in the identification of an inherited cancer predisposition that confers a very high lifetime risk of cancer. For an increasing number of diseases, DNA-based testing can be used to identify a specific pathogenic variant as the cause of inherited risk and to determine whether family members have inherited the disease-related variant.³⁷ See also gene.
Genetic alteration: A change or modification in a gene(s) resulting in something that is different from the original. Various DNA and genetic alterations have now been identified and linked to cancer growth and spread.^38,39
Genetic counseling: The process of helping people with cancer and their families understand the genetics implications of the disease. Genetic counseling often involves interpreting family and medical histories to determine disease recurrence and educating people on testing, management and prevention strategies.⁴⁰
Genetic predisposition: An inherited increase in the risk of developing a disease or condition. A predisposition does not mean a person is certain to develop the disease they may be predisposed to.⁴¹
Genetic testing: Testing of a person’s blood or tissue to assess whether there are any changes to their genetic material in order to determine if they have a disease or condition or may be develop one in the future. Genetic testing can be useful for diagnosing disease, determining optimized treatment, or helping to prevent disease.⁴²
Genome: The entire set of DNA (deoxyribonucleic acid) in an organism.⁴³ See also gene.
Genomic instability: Alterations of the DNA that can include single nucleotide to whole chromosome changes. Genomic instability is a hallmark of cancer and a driver of tumorigenesis. The type of instability affects patient prognosis and management in cancer.⁴⁴
Genomic testing: A test to determine the specific genes in a cancer tumor and monitor how active they are or whether they are mutated. Genomic testing is useful in helping patients and oncologists decide on more targeted therapies for a specific type of cancer.⁴⁵
Germline variant: A genetic alteration in a reproductive cell (egg or sperm) which is incorporated into the DNA of every cell in the body of the offspring. A variant (or mutation) contained within the germline can be passed from parent to offspring, and is, therefore, hereditary. Also called germline mutation.⁴⁶ See also somatic variant.

H

HER2 (Human epidermal growth factor receptor 2): Human epidermal growth factor receptor 2 is one of a family of four membrane tyrosine kinases and an oncogene. It is overexpressed in around 15–30% of breast cancers and 10–30% of gastric/gastroesophageal cancers. This makes it an important prognostic and predictive biomarker to help oncologists determine better treatment pathways for their cancer patients.^47,48
Histology: The study of tissues and cells using a microscope.⁴⁹
Homologous recombination: A process of DNA repair or tolerance of complex damages to DNA whereby two strands of DNA exchange genetic information.⁵⁰
Homologous recombination deficiency (HRD): A phenotype that is characterized by the inability of cells to accurately repair DNA double-stranded breaks using the homologous recombination repair (HRR) pathway.⁵¹ For example, in ovarian cancers, HRD includes individual mutations in BRCA1/2 and the assessment of genomic instability. In certain cancers, HRD status may indicate potential beneﬁt of poly-ADP ribose polymerase (PARP) inhibitors.⁵²
Homologous recombination repair (HRR): A DNA repair pathway that acts on double-stranded DNA breaks and interstrand cross-links.^51,52

I

Immunohistochemistry (IHC): A laboratory method that uses antibodies to check for certain antigens (markers) in a sample of tissue. The antibodies are usually linked to an enzyme or a fluorescent dye. After the antibodies bind to the antigen in the tissue sample, the enzyme or dye is activated, and the antigen can then be seen under a microscope. Immunohistochemistry is used to help diagnose diseases, such as cancer. It may also be used to help tell the difference between different types of cancer.⁵³

K

KEAP1 (Kelch-like ECH-associated protein 1): An adaptor subunit of Cullin 3-based E3 ubiquitin ligase, which plays a role in metabolic reprogramming, ferroptosis, cell cycle and radiation-therapy resistance. KEAP1 decreases PD-L1 expression.⁵⁴
KRAS (Kirsten rat sarcoma virus): An oncogene encoding a protein that functions as a molecular switch that controls signaling cascades. It is commonly mutated in human cancer.⁵⁵

L

Liquid biopsy: A sample of blood, urine, or other bodily fluid that can be used for biomarker testing. In cancer, liquid biopsies may be used to analyze small pieces of DNA (deoxyribonucleic acid), RNA (ribonucleic acid), or other molecules released by tumor cells into a person’s bodily fluids. Unlike tissue biopsies, they allow multiple samples to be taken over time.⁵⁶ See also circulating tumor DNA (ctDNA) and tumor biopsy.

M

Machine learning: A subfield of artificial intelligence that gives computers the ability to learn through data without explicitly being programmed.¹⁸
Microdissection: A group of laboratory techniques in which a microscope is used to aid dissection, in order to isolate small amounts of histologically characterized tissues for subsequent analysis.⁵⁷
Microsatellite instability-high (MSI-H): Microsatellites are short, repeated DNA sequences. Instability occurs when testing shows mutations in 30% or more microsatellites. Microsatellite instability is known to occur in several cancers including colorectal, gastric and endometrial. Testing for MSI-H is useful to find the right treatment.⁵⁸
Minimal residual disease (MRD): The presence of a very small number of tumor cells that remain in the body during or after treatment. MRD can be identified only by highly sensitive laboratory methods. Also called measurable residual disease.⁵⁹
Molecular profiling/testing: See biomarker testing.
Multi-cancer early detection (MCED): An emerging type of blood-based analysis that can test for a variety of cancers all at once, rather than testing for only one cancer at a time.⁶⁰
Multidisciplinary team (MDT): A cross-functional group of specialist healthcare professionals, including the pathologist and genetic counselor, who are involved in cancer care, working collaboratively with the goal of improving treatment efficiency and outcomes for people with cancer.⁶¹

N

National Comprehensive Cancer Network^® (NCCN^®): NCCN is an alliance of 33 cancer centers in the United States, providing clinical practice guidelines appropriate for use by patients, clinicians and other healthcare decision-makers around the world.⁶²
Next-generation sequencing (NGS): A high-throughput DNA sequencing technology which can identify multiple genetic variants or mutations in one panel.⁶³ See single-gene testing.
Non-homologous end joining (NHEJ): A repair pathway for DNA double strand breaks in human cells. Aberrant NHEJ is a major source of genomic instability that can lead to cancer.⁶⁴ See genomic instability.
Novel biomarker: Emerging and novel biomarkers can help identify new patient subsets, complement established biomarkers and provide multidisciplinary teams (MDTs) with increasingly informed and efficient options in cancer treatment options.⁶⁵ See also biomarker.

O

Oncogenic driver: Oncogenic drivers are mutations predominantly found in genes encoding proteins that are linked to normal cell proliferation. Mutations in these genes can initiate and maintain the growth of cancer cells.⁶⁶

P

PALB2 (partner and localizer of BRCA2): PALB2 is important in repair mechanisms following DNA double-strand breaks. PALB2 is a tumor suppressor and participates in the maintenance of genome integrity. Mutations in PALB2 point to an increased risk of breast cancer.⁶⁷ See also double-strand break.
Pathology: The study of disease including its causes, development, and mechanism. Pathologists study samples such as blood or tissue obtained from a patient to determine the nature or seriousness of their illness.⁶⁸
Patient navigators: A person who helps guide a patient through various aspects of their disease or care journey. Patient navigators help with screening, diagnosis, treatment, and follow-up of a medical condition.⁶⁹
PD-L1 (programmed cell death ligand 1): PD-L1 acts like a “brake” to keep the body’s immune responses in check. PD-L1 can be present in normal cells and in higher-than-normal amounts on some types of cancer cells. Inhibiting PD-L1 has been shown to be effective in treating cancer.⁷⁰
Pharmacogenomics: An important aspect of precision medicine that explores how DNA affects a patient's response to a drug.⁷¹
Phenotype: A person’s physical, biochemical, and behavioral traits such as height, eye color, and the presence of certain diseases. This is based on genes and environmental factors.⁷²
PIK3CA/AKT1/PTEN (phosphoinositide 3-kinase/serine/threonine protein kinase 1/phosphatase and tensin homolog): Three genes within the phosphatidylinositol (PI3K)/serine/threonine protein kinase (AKT)/ mammalian target of rapamycin (mTOR) pathway, which are physiologically involved in cell metabolism, growth and apoptosis. During cancer development this pathway can become dysregulated by activating mutations in PIK3CA, AKT1, or inactivating alterations in PTEN, potentially resulting in endocrine- and anti-HER2-targeted agent resistance.⁷³
Precision medicine: A personalized approach to therapy selection based on the presence of tumor-specific actionable biomarkers. By matching the right treatment to the right patients at the right time, precision medicine presents a new era of oncology care which strives to optimize efficiency and therapeutic benefit.⁷⁴ This relies on biomarker testing.
Predictive biomarker: A genetic characteristic or biological molecule which identifies individuals who are more likely to respond to a certain targeted treatment.⁷⁵
Prognostic biomarker: A genetic characteristic or biological molecule which indicates an increased likelihood of a future clinical event, disease progression, or disease recurrence.⁷⁶ See also biomarker.
Proto-oncogene: Proto-oncogenes are a group of genes that cause normal cells to become cancerous when they are mutated. The mutated version of a proto-oncogene is called an oncogene. Often, proto-oncogenes encode proteins that function to stimulate cell division, inhibit cell differentiation, and halt cell death. Oncogenes typically exhibit increased production of these proteins, thus leading to increased cell division, decreased cell differentiation, and inhibition of cell death.⁷⁷

R

RAD51D (RAD51 paralog D)

A recombination repair protein that is an important regulator of DNA through double-strand break repair. Misregulation of RAD51D is linked to diseases such as cancer.⁷⁸

Radiomics

An emerging field with medical imaging that captures tissue and lesion features such as heterogeneity and shape which can help in clinical decision making of diseases such as cancer. Because tissue heterogeneity is of great importance in assessing cancer tissue, radiomics together with genomic analysis may be of value for prognostics.⁷⁹

Rapid on-site evaluation (ROSE)

A method to determine whether the quality of tissue specimens is sufficient for cytopathological diagnosis.^80,81 Carried out during the biopsy procedure, this involves a pathologist (typically a cytopathologist) producing quick staining of smears to evaluate sample adequacy.⁸¹

Reflexive testing

An approach to testing in which pathologists are responsible for initiating and controlling testing for a set of prespecified biomarkers, agreed upon within the context of the multidisciplinary team (MDT), but without the need for a formal request from an oncologist.⁸²

S

Single-gene testing

Testing to look for a genetic change in one gene which is typically used to determine a specific diagnosis. This is different to next-generation sequencing which allows for multiple genes to be tested at the same time.⁸³

See next-generation sequencing (NGS).

SMARCA4 (SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily a, member 4)

SMARCA4 encodes the transcription activator BRG1, which participates in the activation or repression of transcriptional processes in various types of cancer.⁸⁴

Somatic testing

Mutations in tumors can happen sporadically or acquired in either somatic cells or germ cells. Somatic testing checks for known somatic mutations within a tumor, which may include BRCA1/2 (BReast CAncer susceptibility gene 1/2), PIK3CA (phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha), and PTEN (phosphatase and tensin homolog) among many others, depending on the type of cancer.⁸⁵

Somatic variant

A genetic alteration that occurs after conception and is not present within the germline. Somatic variants can occur in any of the cells of the body except the germ cells (sperm and egg) and therefore are not passed on to offspring. Somatic variants may lead to cancer or other diseases. Also called somatic mutation.⁸⁶ See also germline variant.

Standardized testing protocol

For accurate and reliable biomarker testing, laboratories should have a quality assurance (QA) system in place and comply with relevant (inter)national standards such as from the International Organization for Standardization (ISO), the College of American Pathologists (CAP), or the Clinical Laboratory Improvement Amendments (CLIA). External quality assurance (EQA), as a component of QA, services diagnostic laboratories by assessment of their testing procedures compared with their peers and/or ‘designated true value’.⁸⁷

STK11 (serine/threonine kinase)

A protein kinase which is closely associated with the regulation of cell polarity and energy metabolism via inhibition of the mTOR signaling pathway.⁸⁸

Synoptic reporting

A systematic way of communicating pathology test results which involves presenting information as discrete data elements and associated responses.⁸⁹This method can improve completeness and accuracy of the report, and may aid in quicker, more reliable interpretation by clinicians.⁹⁰

T

Targeted therapy/treatment: A drug that is designed to interact and/or interfere with particular molecular components of a tumor.⁹¹ Eligibility for targeted therapies is determined via biomarker testing.⁹²
Telegenetics/Telehealth/Telemedicine: The use of technology such as video conferencing to provide genetic services remotely. Telegenetics is valuable for patients who may not be able to attend a clinic due to their condition or location.⁹³
Test Turnaround Times (TAT): Test turnaround time is the time it takes for a laboratory or diagnostic services test to be done. It is used as an indicator of laboratory performance.⁹⁴
Tumor biopsy: A procedure whereby a small sample of tissue is taken from a tumor and sent to a laboratory for analysis. Cancer is predominantly diagnosed through a biopsy. The specific method of the biopsy will depend on the type of cancer that is suspected.⁹⁵
Tumor Cell Content (TCC)/estimation: Refers to the number of cancer cells present in a tumor. The count of circulating tumor cells is a prognostic factor in many cancer types.⁹⁶
Tumor Mutational Burden (TMB): The total number of mutations that are detected in the DNA of cancer cells. Knowing the tumor mutational burden can be useful in planning the best treatment.⁹⁷

V

Variant of Unknown/Uncertain Significance (VUS): A variant of unknown/uncertain significance is a change in a gene’s DNA sequence that affects a person’s health in an unknown capacity. It is usually not known if the VUS increases a person’s risk of developing a disease such as cancer.⁹⁸

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Glossary

A

Actionable biomarker

Actionable mutation

Artificial intelligence (AI)

Assay

ATM (ataxia telangiectasia mutated)

B

Biomarker

Biomarker testing

BRCA1/2 (BReast CAncer susceptibility gene 1/2)

Broad molecular profiling

C

Carcinogenesis

CDK12 (cyclin-dependent kinase 12)

CHEK2 (Checkpoint kinase 2)

Circulating tumor cell (CTC)

Circulating tumor DNA (ctDNA)

Clinical Laboratory Improvement Amendments (CLIA)

Companion diagnostic

Complementary diagnostic

Computational pathology (CPATH)

Concordance (in the context of tumor tissue and circulating tumor DNA [ctDNA])

Concurrent testing

Cytopathology

D

Deep learning models

Deficient mismatch repair (dMMR)

Digital pathology

Digitally guided microdissection

Double-strand break (DSB)

E

EGFR (epidermal growth factor receptor) mutations

Emerging biomarker

Endobronchial ultrasound (EBUS)

ERBB2 (erythroblastic oncogene B)

F

FANCA (Fanconi anemia, complementation group A)

FDA-approved companion diagnostic

Formalin-fixed paraffin-embedded (FFPE) tissue

G

Gene

Gene expression

Genetic (in relation to cancer genetics)

Genetic alteration

Genetic counseling

Genetic predisposition

Genetic testing

Genome

Genomic instability

Genomic testing

Germline variant

H

HER2 (Human epidermal growth factor receptor 2)

Histology

Homologous recombination

Homologous recombination deficiency (HRD)

Homologous recombination repair (HRR)

I

Immunohistochemistry (IHC)

K

KEAP1 (Kelch-like ECH-associated protein 1)

KRAS (Kirsten rat sarcoma virus)

L

Liquid biopsy

M

Machine learning

Microdissection

Microsatellite instability-high (MSI-H)

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