Childhood cancer is not one disease but instead multiple different entities. What makes most of these different entities childhood cancer is they are thought to be malignancies occurring due to changes in normal human developmental programs. Pediatric cancers differ from each other not only by the tissue in which they appear, but also how aggressive they are, likelihood to respond to different types of drugs, and risk of cancer recurrence. For example, certain types of cancers tend to have a poor response to conventional chemotherapy, but other cancers are exquisitely sensitive. Researchers have found that certain types of leukemias that are resistant to chemotherapy harbor a genetic abnormality termed the Philadelphia chromosome. This subgroup responds better to a different class of drugs which can be given in the form of a pill and when combined with chemotherapy is often considered as curative therapy. This approach of tailoring therapy according to the genetic and molecular characteristics of the cancer is called precision medicine.

Precision medicine and genetics hold the promise of changing the way cancer is diagnosed, treated, and monitored. While we still have a long way to go, advancements have been rapid and produced a major positive impact on the field of childhood cancer.

At the heart of precision medicine is the idea of biomarkers—measurable biological identifiers that can predict medical phenomena such as how aggressively a cancer grows/behaves. In this chapter, we introduce key concepts in biomarker testing that are relevant to pediatric cancer. We hope that after reading this chapter, you will become more familiar and comfortable with the basic terminology that is becoming part of the routine practice of pediatric oncology.

To better understand the terms throughout this chapter, we provide a brief overview of the human genome. More comprehensive background can be found in the reference section.

The genetic information in our cells is coded by the DNA molecule, which is composed of four chemical building blocks, abbreviated by the letters A, C, G and T. Each cell contains two copies of each building block, one copy inherited from the mother and one from the father. This creates a three-billion letter DNA strand. The DNA molecules making up the strand are packaged into 23 pairs of very long pieces called chromosomes. Each of the 46 chromosomes contains genes, which are stretches of letters within the DNA that encode the instructions to make proteins. The DNA regions that do not contain genes are called non-coding regions. There are approximately 20,000 genes in the human genome, however, not all of them are active in every cell at any given time. Many factors determine whether a gene will be active or not in a particular cell, and whether its corresponding protein will be produced. For example, some non-coding regions control gene activity and can turn a gene on or off. In addition, a chemical modification around a gene or within it, called methylation, can alter the gene activity.

Once a gene becomes active, its DNA letters are copied to another molecule called RNA in a process named transcription. Levels of RNA molecules from a given gene can be measured and indicate how active the gene is. Each RNA molecule is then further translated into a protein which is the main building block of cells.

Cancer cells arise from normal cells by modifying the structure and/or number of genes that control cell growth, cell death, ability to spread to other parts of the body, and other important processes that give the cancer cells survival advantage and makes them hard to destroy. The modified genes and their products, namely RNA and proteins, can be used as biomarkers in pediatric cancer as described below. Many of the genes involved in childhood cancer control the normal process of fetal development which make them quite distinct from adult cancers.

A biomarker is a characteristic of the body that can be measured as an indicator of a normal or abnormal biological process. There are several types of biomarkers including molecular, radiographic, and physiologic. For example, blood glucose (sugar) is a molecular biomarker, tumor size is a radiographic biomarker, and blood pressure is a physiologic biomarker.

Molecular biomarkers play a major role in precision medicine and in pediatric cancer in particular. Since cancer cells modify DNA and as a result their RNA and proteins, both the DNA and its products can be used as biomarkers to help identify individuals at risk of developing cancer, help define the type of cancer, help understand the mechanism by which it arose, determine how aggressive it is, and predict how likely the response to certain classes of drugs. Molecular biomarkers are also used in cancer research, mainly in drug development, as discussed below.

Categories of biomarkers in cancer medicine

Biomarkers are routinely used in clinical practice in the following important ways:

• to help identify people genetically predisposed to a type of cancer,
• to help in diagnosis,
• to guide therapy,
• to monitor response to therapy,
• to guide drug dosing,
• in post-treatment surveillance (monitoring),
• to aid in cancer research and new drug development.

These seven categories are explained below. The categories are not mutually exclusive, and a biomarker can fall into multiple categories depending on the context it is used.

Indicator of cancer predisposition

Although the majority of cancers arise spontaneously, several genetic mutations can be inherited and increase the risk of developing cancer. For example, individuals carrying a mutated retinoblastoma (RB1) gene are at increased risk of developing retinoblastoma, a type of cancer arising in the retina of the eye at a very young age. Children with a family history of retinoblastoma can be tested for the presence of a RB1 mutation and should obtain frequent eye screening that enables earlier detection of this cancer. In this case, RB1 is used as a biomarker for cancer predisposition. Many other cancer predisposition gene mutations have been discovered over the past decades.

Biomarkers help in diagnosis

The gold standard for diagnosing cancer is by observation of malignant cells under the microscope which is performed by a pathologist, a medical doctor with specialized training in identifying abnormal cells and cell activity. Pathologists look at the size, shape, and number of cells to help determine whether a cell is cancerous and identify the type of cancer. In addition, the cells are stained for different types of proteins that are specific to the suspected cancer. This process allows the pathologist to increase the accuracy of the diagnosis.

Neuroblastoma is a pediatric cancer of the peripheral nervous system that expresses a protein called PHOX2B. This protein is not found in healthy tissues after birth and can be used as a specific biomarker for the diagnosis of neuroblastoma. Occasionally, the origin and type of tumor can be difficult to determine only from the way the cells appear under the microscope. In these situations, testing for specific genes known to be altered can aid in diagnosing the type of cancer. For example, a class of pediatric tumors, called NTRK-fusion positive tumors, are characterized by an alteration in one of three genes in the Neurotrophic Tyrosine Receptor Kinase (NTRK) family. The DNA coding for this gene is fused to another DNA molecule and form a fusion gene. This group of tumors can appear almost anywhere in the body, and is therefore difficult to make a diagnosis based solely on the cellular appearance. In this case, the NTRK gene is used as a diagnostic marker and also as a biomarker for very specific treatments designed to “turn off” these unusually “turned on” fusion genes that instruct a cell to continue to grow (see below).

Biomarkers that guide therapy

Biomarkers can also help clinicians choose the appropriate therapy for a child’s cancer. For example, and as described above, NTRK-fusion cancers are treated with drugs that were developed to inhibit the protein which is the product of the fusion NTRK- gene. One such drug is called Larotrectinib and allows for a more effective and less toxic treatment for this group of cancers. Here, the NTRK-fusion gene serves as a biomarker to guide therapy.

The Philadelphia chromosome that was described earlier is another example of a biomarker used to guide therapy. Currently, clinicians routinely test for the presence of the BCR-ABL1 fusion gene (the medical term for the Philadelphia chromosome) in patients with acute lymphoblastic leukemia. A positive test warrants the incorporation of drugs that inhibit the action of the fusion protein. Other examples of biomarkers used to guide therapy include the same fusion protein BCR-ABL1 in chronic myeloid leukemia (CML) and mutated BRAF in pediatric brain tumors called gliomas. Both of these cancers can be targeted with drugs known to inhibit the corresponding abnormal gene product.

A large clinical effort to use various genetic biomarkers to guide therapy is exemplified by the Molecular Analysis for Therapy Choice (MATCH) trial. This is a clinical trial in which patients with cancer are assigned to receive a treatment tailored to the genetic characteristics of their type of cancer. A sample of the patient’s tumor is then subjected to genetic analysis (see below) and if a genetic change matches a drug being used in the trial, the patient may receive the treatment with that drug if eligible. In this case, the genetic changes of the cancer are biomarkers that guide specific drug therapy.

Finally, genetic analysis of pediatric tumors may identify mutations that match to an FDA-approved drug for the same mutation found in adult cancers. Clinicians may recommend "off label" drug treatment for children when a clinical trial is not available.

Prognostic marker

A prognostic marker is a biomarker used to predict the course of disease, also known as prognosis. The products of certain genes (e.g., RNA and proteins mentioned above) and the quantity in tumors can be used as a biomarker to determine how aggressive the tumor is. For example, the gene MYCN is amplified in a subset of neuroblastomas. That is, the cancer cells have multiple DNA copies, usually hundreds, of the gene MYCN instead of the normal two copies. The presence of MYCN amplification in neuroblastoma tends to require more intense therapy. Prognostic biomarkers are used to stratify patients in clinical trials and/or assign appropriate treatment.

Biomarkers that monitor response to therapy

Biomarkers can be used to determine if a patient responds to therapy. In acute lymphoblastic and other leukemias, a bone marrow aspirate and biopsy are performed during treatment to measure a set of cell surface markers present on the leukemic cells collectively known as minimal residual disease (MRD). The absence of MRD suggests that therapy was successful in eliminating the cancer cells. In solid cancers, technology now allows detection of genetic mutations in blood samples or from the fluid removed from a spinal tap, also called liquid biopsies. The detection of circulating tumor DNA (ctDNA) is increasingly being used to monitor response to therapy and also to detect gene mutation-drug matches, especially when performing a tumor biopsy might be dangerous to the patient.

Biomarkers that guide drug dosing

Certain genes in our DNA are responsible for the way our body responds to drugs. Changes in these genes can result in accumulation of several drugs in the body and lead to side effects. Measuring the presence of the changes in these genes can help physicians decrease the dose of a drug and prevent accumulation. Such genes are considered biomarkers for drug dosing. For example, an enzyme called thiopurine methyltransferase (TPMT) is required for metabolizing the drug mercaptopurine used in leukemia therapy. High levels of mercaptopurine result in decreased white blood cells leading to increased susceptibility of infections. Individuals with DNA changes in the gene coding for TPMT are unable to metabolize mercaptopurine appropriately and need dose reduction of this drug. In this case, the gene TPMT is considered a biomarker for drug dosing.

Biomarkers in post-treatment surveillance

Following completion of cancer therapy, patients usually undergo routine surveillance studies, such as magnetic resonance imaging (MRI) or positron emission tomography (PET) scans, to ensure that the cancer does not recur. These studies can only detect tumors that are large enough to be seen by the naked eye.

The emerging group of biomarkers mentioned above called ctDNA or liquid biopsies are based on the DNA content of cancer are released into the bloodstream. Levels of cancer cell-free DNA can be monitored before, during, and after therapy and be used to detect disease recurrence earlier than current imaging methods.

Cancer researchers use biomarkers routinely during drug development. The process of drug development is long and complex, including multiple steps before a drug is approved to treat human patients. It may take a decade or more from the start of the process until the drug is approved and costs around 1 billion dollars. Unfortunately, approximately 5% of drugs developed make it to the final stage of FDA approval.

While detailed discussion of drug development is beyond the scope of this chapter, we briefly review the main steps and provide examples of biomarkers used throughout the process.

Preclinical laboratory studies

Drug development starts with target identification in the laboratory. The target, usually a protein, should play an important and unique role in the cancer cell life. Biomarkers can help identify molecular pathways, that is, a group of genes that acts together and contributes to the development or maintenance of a specific cancer. By narrowing down the list of genes of interest, the process of identifying potential targets becomes more efficient and biologically sound.

Once a target is identified, thousands of compounds are typically screened for potential drug candidates against the target. Biomarkers can aid in selecting the most promising compound (known as lead compound) and gain insight into its mechanism of action. The lead compound then undergoes a battery of laboratory tests. Biomarkers can help to assess the safety and efficacy of the drug, to understand the drug mechanism of action and aid in dose selection.

An example of a preclinical tool that can be used to predict response to therapy is called the Avatar system. In this system, a small piece of a patient’s tumor is injected into a mouse lacking an immune system, also known as patient-derived xenograft (PDX). The tumor is allowed to grow in the mouse and subsequently reinjected into multiple mice. These PDXs have become a major tool for testing candidates’ drugs as they reflect the genetics of patient tumors seen in the clinic. While this in vivo approach is promising, it should be noted that the process of establishing a PDX is long, expensive, and does not always mimic the tumor heterogeneity in the human cancer. Some investigators are attempting to establish Avatar systems to individualize drug selection, but this remains unproven and very much a subject of ongoing research studies.

A faster and cheaper way to perform drug testing is to use cell cultures (in vitro). In this approach cancer cells from patients are grown in a plastic plate to which drugs are added and tested for efficacy. The main drawback of this approach is that cancer cells do not grow in the artificial conditions of cell cultures which include oxygen levels, nutrients and exposure to plastic. Another difference is that cancer cells in the body are typically surrounded by normal cells termed a microenvironment. Despite these limitations, cell culture studies can be a useful screen and provide valuable information.

Clinical research steps

The steps following preclinical or laboratory studies are known collectively as clinical research. The main purpose of clinical research is to test safety and efficacy of the selected drug in humans.

Phase 1 of clinical trial is aimed at assessing the safety of the drug in humans and also collect data on the appropriate dosing. It typically consists of a relatively small number patients, especially in childhood cancer where many drugs have already been studied in adult trials. Approximately 70% of drugs tested in Phase 1 trial move to the Phase 2 clinical trial in which the efficacy and side effects of the drug are evaluated. About 33% of Phase 2 trials move to the Phase 3 trial. The goal of Phase 3 trials is to test the efficacy of the drug and compare it to current therapies for the specific type of cancer. These studies enroll several hundreds to thousands of patients and can continue for many years. Phase 3 trials also provide new safety data about the drug that was not detected in previous phases. Roughly 25 to 30% of the drugs that enter Phase 3 trials are approved by the FDA for marketing and move to Phase 4 trial or a post market safety monitoring phase.

Biomarkers play an important role in clinical trials and help select patients for enrollment into clinical trials, stratify patients into a subgroup of treatment, guide dose selection, help in assessment of safety and evaluation of drug efficacy, and help to monitor side effects. For example, the presence of NTRK-fusion gene can be a biomarker for selection of patients into a clinical trial that tests the efficacy of Larotrectinib in NTRK-fusion positive tumors. The levels of liver enzymes (aminotransferase) are typically used as safety biomarkers for drugs that can cause liver injury, such as Larotrectinib. The presence of NTRK-fusion gene in cell-free DNA blood samples can be used as biomarkers for response to therapy.

In this section we describe in more detail the types of tests used to measure cancer biomarkers in the clinical setting. The ideal biomarker is one that is always positive for a specific type of cancer but negative for all others, allows for treating that type of cancer, and is low cost, and fast to identify in a test. It is important to note that similar to other tests in medicine, no such perfect test exists.

Biochemical testing

This type of testing measures the level of a biomarker, usually a protein, that is secreted by the tumor cells into the blood or other body fluids such as urine or cerebral spinal fluid. The physician orders the test and the appropriate sample is collected from the patient. Testing for the majority of biochemical biomarkers does not require insurance approval. The result of the test is reported as a number and is interpreted as abnormal if outside of the normal range of expected values. For example, the protein alpha-fetoprotein (AFP) is usually secreted by a pediatric liver tumor called hepatoblastoma. High levels of this protein can be used to aid in diagnosis, prognosis, and response to therapy.

Another example of a biochemical biomarker is urine catecholamines. These molecules are secreted by the sympathetic nervous systems and can be detected in the urine. High levels of these molecules aid in the diagnosis, response to therapy, and prediction of relapse in neuroblastoma. See Table 1 for biochemical biomarkers used in pediatric cancers.

Table 1. Biochemical biomarkers used in pediatric cancers

Biochemical biomarker	Type of biomarker	Type of pediatric cancer
AFP	Diagnosis, response to therapy, post-treatment surveillance	hepatoblastoma, GCT
LDH	Response to therapy, post-treatment surveillance	GCT, non-Hodgkin lymphoma, osteosarcoma
bHCG	Diagnosis, response to therapy, post-treatment surveillance	GCT
ESR	Response to therapy	Hodgkin lymphoma
Uric acid	Diagnosis of tumor lysis syndrome, guide therapy, response to therapy	ALL, AML
Urine catecholamines	Diagnosis, post-treatment surveillance	neuroblastoma
ALL, acute lymphoblastic leukemia; AML, acute myeloid leukemia; GCT, germ cell tumors

Immunohistochemical staining

Immunohistochemical staining (IHC) testing uses antibodies to detect biomarkers, usually proteins, that are inside or on the surface of cancer cells in a tissue on microscope slides. The cancer tissue is taken via biopsy or surgical removal, prepared (either frozen or paraffin embedded) and stained using an antibody directed at the protein of interest. The pathologist then confirms the presence or absence of the protein under the microscope.

The protein PHOX2B, which was discussed above in the context of diagnostic biomarkers, is detected using IHC staining. Additional diagnostic biomarkers detected by IHC staining include myogenin for rhabdomyosarcoma, CD99 for Ewing sarcoma, CD19 for B acute lymphoblastic leukemia and others.

Genetic testing

Genetic testing is based on methods that measure changes in the DNA. The changes can be in the number or structure of chromosomes, genes and/or non-coding regions. The broader definition of genetic testing also encompasses changes in the number or structure of RNA molecules which are derived from DNA. Types of genetic tests can be broadly classified as sequencing-based methods and non-sequencing-based methods. Described below are the most common types of genetic testing encountered in pediatric cancer with examples for each type of test.

Non-sequencing based methods

Cancer cells usually change the size, number, and shape of chromosomes. The methods below differ not only by the way they detect chromosomal changes, but also the minimal size of the change that can be detected.

Karyotype. This test produces an image of the cancer cells’ chromosomes and allows the detection of large chromosomal abnormalities. It requires growing the cancer cells in culture and typically takes 1 to 2 weeks to result.

Karyotyping is used as a prognostic biomarker in acute lymphoblastic leukemia. Specifically, patients with leukemia cells showing low number of chromosomes (less than 40 chromosomes on karyotype, also called hypodiploid) tend to be harder to treat than patients with high number of chromosomes (hyperdiploid).

Fluorescence in situ hybridization (FISH). This test uses a fluorescent probe that binds to specific regions of chromosomes and can detect regions where part of the chromosome is amplified, deleted, or fused to another chromosome (an aberration referred to as chromosomal translocation). This test can detect smaller changes than karyotype, is low cost and takes approximately 1 to 2 days for results. The disadvantage of this test is that it requires prior knowledge of the changed region in the DNA.

FISH is used to detect biomarkers in many types of childhood cancers including acute lymphoblastic leukemia, acute myeloid leukemia, neuroblastoma, Ewing sarcoma, rhabdomyosarcoma, neuroblastoma, and others (See Table 2).

Table 2. Genetic biomarkers used in pediatric cancers

Genetic biomarker	Type of test	Type of biomarker	Type of pediatric cancer
hyperdiploid, hypodiploid	Karyotype	prognostic	ALL
BCR-ABL	FISH	diagnostic, guide therapy	CML, ALL
MYCN	FISH	diagnostic, prognostic	neuroblastoma, medulloblastoma
ESWR1-FLI1	FISH	diagnostic	Ewing sarcoma
FOXO1-PAX3	FISH	diagnostic, prognostic	alveolar rhabdomyosarcoma
1p loss, 11q loss, 17q gain	SNP array	prognostic, guide therapy	neuroblastoma
1p and 16q loss, 1q gain	SNP array	prognostic, guide therapy	Wilms tumor
FLT3	DNA sequencing	prognostic, guide therapy	AML
BRAF	DNA sequencing	guide therapy	LGG, LCH, melanoma
ALK	DNA sequencing	guide therapy	neuroblastoma, IMT
NTRK-fusion	RNA sequencing	diagnostic, guide therapy	NTRK-fusion positive cancers
ALL, acute lymphoblastic leukemia; AML, acute myeloid leukemia; CML, chronic myeloid leukemia; LGG, low grade glioma; LCH, Langerhans cell histiocytosis; IMT, Inflammatory myofibroblastic tumor; NTRK, Neurotrophic Tyrosine Receptor Kinase (NTRK) q = the long arm of the chromosome p = the short arm of the chromosome

Single Nucleotide Polymorphism Microarray (SNP array). Occasionally, only small regions of the chromosome are amplified or lost and the orientation of the DNA letters can be inverted. Such changes cannot be detected using Karyotype or FISH. In such cases, a SNP array can help detect biomarkers by analyzing tumor DNA with hundreds of thousands of DNA polymorphisms or spelling changes in DNA that vary based on race and ethnicity. This allows for the detection of gains or losses of chromosomal regions without any prior knowledge of where these exist. SNP arrays are used to detect prognostic biomarkers in neuroblastoma and Wilms tumor.

Sequencing-based methods

Sequencing is the process of determining the sequence of letters of a DNA or RNA molecule. DNA and RNA sequencing technologies continue to evolve to allow for faster, cheaper, and more accurate results. The traditional sequencing method referred to as Sanger sequencing or First-Generation Sequencing is clinically used to determine the sequence of a single gene. First Generation Sequencing is accurate but time consuming. Next Generation Sequencing (NGS) is a technology that allows the sequencing of many genes or all of the gene in parallel. The following are sequencing-based genetic tests and their use in pediatric cancer.

Single gene test. This test is used to detect a change in a gene that is known to be modified in a type of cancer and for which a targeted therapy exists. For example, the gene ALK is mutated in approximately 15–25% of neuroblastomas. The presence of an ALK mutation may warrant the addition of an ALK-inhibitor to a treatment, and this is currently being tested in clinical trials. With the evolution of NGS, single gene testing is largely being replaced by NGS multigent strategies.

Targeted genetic panel. This test relies on NGS technology and is performed on a set of genes that are known to contribute to a specific type of cancer of a group of cancers. The number of genes included in a panel varies depending on the type of cancer and laboratory that performs the test, but typically is in the range of several hundred.

Germline testing. Most cancers are not inherited. However, well described cancer predisposition syndromes exist and offer an opportunity for biomarker testing. Liquid biopsies or ctDNA is a sequenced-based genetic testing that is performed on a normal tissue, most often on blood or saliva, to detect a change in a gene or other regions in the DNA that affect all the cells of the body and could give rise to cancer.

Your oncologist may decide to order germline testing if other family members had cancer at a young age, if the cancer originates on both sides of the body (for example, in both eyes or both kidneys), and/or if your child has concerning features on physical exam. With the increased use of NGS on tumor tissue, it is now not uncommon to uncover a potentially concerning genetic predisposition mutation even if no family history exists. This typically leads to a referral to a genetic counselor for a discussion of the test result, potential confirmation testing, and further counseling as to what this means for the patient and family members.

Various tests ordered for you/your family

Depending on the type of cancer your oncologist suspects, he/she may choose to order single gene or a genetic panel test and recommend testing other family members. However, there are occasions when neither a single gene nor genetic panel testing reveal the cause of familial cancer. In these situations, your oncologist may decide to test all the genes or the entire genome.

Whole exome sequencing (WES). Each gene is composed of DNA regions that are protein coding, called exons, and non-protein-coding regions, called introns. WES is a NGS test which sequences all the genes, which comprise approximately 1% to 5% of the genome.

Whole genome sequencing (WGS). Remember that most of the genome contains sequences that do not code for protein. Growing evidence suggests that the non-coding regions of DNA play an important role in cancer development and maintenance. When WES testing does not discover the etiology of cancer, your oncologist/geneticist may recommend WGS testing. Currently this is very rarely pursued, but may be ordered with increasing frequency as we understand more about the noncoding genome.

RNA sequencing. This test provides the sequences of the genes that are active in the cancer. Remember that the DNA of active genes is copied into RNA molecules. These molecules can be sequenced (by converting them to a DNA molecule and using DNA sequencing technologies) and reveal a group of genes that act in concert in a particular type of cancer, called a gene signature. While still uncommon in pediatric cancers, the use of signatures to classify cancer types and predict outcome is becoming more clinically useful in adult cancers. In pediatric cancers, the use of RNA sequencing is mostly for detecting gene fusions. The advantages of using RNA sequencing over FISH for the detection of gene fusion is that RNA sequencing does not require knowing both partners of the fusion and it can detect novel fusions. NTRK-fusion positive cancers are diagnosed using RNA sequencing.

Informed consent

Typically, the physician ordering the test would be your oncologist. However, in some institutions your oncologist may refer you to a geneticist who will order the test.

Prior to collecting a sample for genetic testing, the ordering physician will ask you to sign a document that gives patient consent to perform the test known as informed consent. This document states that the test is voluntary and that the patient or patient’s parent if the child is under 18 fully understands and agrees to the test. Your physician should discuss the risks, benefits, and limitations of the test prior to signing the consent form.

Turnaround time for results

Turnaround time for results depend on the laboratory where the test is performed. Typically, single gene testing can take up to a week for results, whereas most current NGS assays take 2 to 4 weeks for results.

Tissue banking

You may elect to store the cancer tissue of your child for the purpose of basic science and clinical research. Tissue banks are repositories that collect and store biological samples and associated clinical data. Importantly, some clinical trials require that your child’s tumor tissue be collected and stored in a central biobank. You will also be asked to sign a consent to allow a local or remote biobank to collect and store your child’s sample. The name of your child will remain undisclosed.

Interpreting the results

The ordering physician should deliver and explain the results of the genetic testing. It is important to know that the results of genetic testing are not always straightforward, especially sequencing-based methods. For example, the sequence of a gene of interest may reveal a change from the normal sequence, but it does not necessarily mean that the change (often termed variant) causes a change in the function of the gene resulting in cancer.

In addition, when performing WES or WGS, unexpected secondary findings for which the test was not initially indicated may be found. For example, a WES test may reveal a change in a gene that causes heart disease. A thorough discussion with your oncologist prior to undergoing the test should include any potential secondary results, their significance and future actions that would need to be taken.

Clinical trials

Website: https://clinicaltrials.gov
https://www.cancer.gov/research/infrastructure/clinical-trials/featured/nci-match

Drug development

Website: https://www.fda.gov/
Search: drug development approval process, patient focused drug development guidance series
https://www.fda.gov/drugs/development-approval-process-drugs

Genetic testing in cancer

Website: https://www.cancer.gov/
Search: genetics, genetic testing, causes and preventions
https://www.cancer.gov/about-cancer/causes-prevention/genetics/genetic-testing-fact-sheet

Genetic panels

Website: https://www.chop.edu
Search: cancer-panels
https://www.chop.edu/cancer-panels

NTRK-fusion positive cancers

Website: https://www.bayer.com/
Search: trk-fusion-cancer
https://www.bayer.com/en/pharma/trk-fusion

US Food and Drug Administration (FDA)

Website: https://www.fda.gov/
Search: patients/drug-development-process, step-3 clinical research
https://www.fda.gov/drugs/development-approval-process-drugs

National Cancer Institute–Children’s Oncology Group; Pediatric MATCH Trial (revised June 2023)

Website: https://www.cancer.gov
Search: clinical trials, nci supported, nci match

http://www.cancer.gov/about-cancer/treatment/clinical-trials/
Search: nci-supported/nci-match

https://www.cancer.gov/news-events/cancer-currents-blog/
Search: new-nci-precision-medicine-trials; nci-supported/pediatric match/pediatric match infographic

Pediatric MATCH

NCI-COG Pediatric MATCH (Molecular Analysis for Therapy Choice), also known as Pediatric MATCH, is an international pediatric precision medicine cancer treatment trial that explores whether targeted therapies can be effective for children, adolescents and young adults with solid tumors that harbor specific gene mutations. Pediatric MATCH is a phase 2 trial that investigates different study drugs, each targeting a defined set of gene mutations, in order to match patients with therapies aimed at the molecular abnormalities in his or her tumor.

Children’s Oncology Group

The Children’s Oncology Group (COG), a National Cancer Institute supported clinical trials group, is the world’s largest organization devoted exclusively to childhood and adolescent cancer research. The COG unites more than 10,000 experts in childhood cancer at more than 200 leading children’s hospitals, universities, and cancer centers across North America, Australia, and New Zealand in the fight against childhood cancer.

Today, more than 90% of 16,000 children and adolescents diagnosed with cancer each year in the United States are cared for at Children’s Oncology Group member institutions. COG’s unparalleled collaborative efforts provide the information and support needed to answer important clinical questions in the fight against cancer.

The Children’s Oncology Group has nearly 100 active clinical trials open at any given time. These trials include front-line treatment for many types of childhood cancers, studies aimed at determining the underlying biology of these diseases, and trials involving new and emerging treatments, supportive care, and survivorship.

The Children’s Oncology Group research has turned children’s cancer from a virtually incurable disease 50 years ago to one with a combined 5-year survival rate of 80% today. Our goal is to cure all children and adolescents with cancer, reduce the short and long-term complications of cancer treatments, and determine the causes and find ways to prevent childhood cancer.

More Resources

Extended and updated list of references and resources:
https://www.alexslemonade.org/childhood-cancer/guides/resource-links

biomarker (tumor marker)

a measurable biological identifier that can predict medical phenomena such as how aggressively a cancer grows. There are several types of biomarkers including molecular, radiographic, and physiologic.

biomarker testing

a method to look for genes, proteins, and other substances (called biomarkers or tumor markers) that can provide information about cancer. Each person’s cancer has a unique pattern of biomarkers. Some biomarkers affect how certain cancer treatments work.

chromosomes

a threadlike structure of nucleic acids and protein found in the nucleus of most living cells, carrying genetic information in the form of genes.

clinical research

medical research that involves enrolling volunteers to take part in studies (clinical trials) that monitor an individual’s progress during and after cancer treatment. The main purpose of clinical research is to test safety and efficacy of a selected drug. These studies help doctors and researchers learn more about specific diseases and find new medications or treatments to improve health care for people in the future.

gene signature or gene expression signature

a single or combined group of genes in a cell with a uniquely characteristic pattern of gene expression that demonstrates an altered or unaltered biological process or medical condition or disease.

genetic testing

examining one’s DNA, the chemical database that carries instructions for your body’s functions. Such testing can reveal changes (mutations) in genes that may cause illness or disease.

germline testing

sequenced-based genetic testing that is performed on a normal tissue, most often on blood or saliva, to detect a change in a gene or other regions in the DNA that affect all the cells of the body and could give rise to cancer.

human genome

the entire set of DNA instructions found in a cell. In humans, the genome consists of 23 pairs of chromosomes located in the cell’s nucleus.

ideal biomarker

the goal of the "ideal" biomarker includes all of the following 4 characteristics: shows positive result for a specific type of cancer and negative result for all others (cancer-specific); allows for treatment of that specific cancer; low cost to test; and rapid results from a test.

karyotyping

a test that produces an image of the cancer cells’ chromosomes and allows the detection of large chromosomal abnormalities. It requires growing the cancer cells in culture and typically takes 1 to 2 weeks to result.

liquid biopsies or ctDNA

blood samples or fluids removed from a spinal tap that are used to detect genetic mutations in solid cancers.

informed consent

a document that must be signed by a patient or parent if the child is under age 18 giving consent to perform any genetic testing including collecting all samples for the genetic testing. Before signing this informed consent, patient and family must be informed of risks, benefits and limitations of the test. If patient results are to be included in a clinical trial, the patient or parent must agree to the results to be included in the specific study and any future follow-up required.

minimal residual disease (MRD)

a small number of cancer cells left in the body after treatment. These cells have the potential to come back and cause relapse.

Molecular Analysis for Therapy Choice (MATCH) trial

international pediatric precision medicine cancer treatment trial that explores whether targeted therapies can be effective for children, adolescents and young adults with solid tumors that harbor specific gene mutations. Pediatric MATCH is a phase 2 trial that investigates different study drugs, each targeting a defined set of gene mutations, in order to match patients with therapies aimed at the molecular abnormalities in his or her tumor.

molecular pathways

a group of genes that act together and contribute to the development or maintenance of a specific cancer.

Philadelphia chromosome

a defect in chromosome 22 of leukemia cancer cells where part of the chromosome is amplified, deleted or fused to another chromosome; scientific name is BCR-ABL1 fusion gene.

NTRK-fusion positive tumors/cancers

a group of pediatric tumors that can appear almost anywhere in the body, and therefore are difficult to make a diagnosis based solely on the cellular appearance.

non-coding regions

DNA regions that do not contain genes.

prognostic marker

a biomarker that helps predict the course of the disease and outcome.

pathologist

a medical doctor with specialized training in identifying abnormal cells and cell activity.

precision medicine

tailoring cancer therapy according to the genetic and molecular characteristics of the specific cancer using genetics testing and molecular biomarkers.

prognosis

a prediction of the probable course and outcome of the disease (how aggressive the tumor/cancer is) and the prospects of recovery.

tissue banks

repositories that collect and store biological samples and associated clinical data.

variantc

a change in the normal sequencing of a gene.