UNC Oncologist Explains How Molecular Testing Can Guide Cancer Treatment

A tissue biopsy is the gold standard for biopsy. It is typically performed as part of a cancer diagnosis and workup. In a tissue biopsy, a portion of a tumor, or a mass that potentially has cancer cells, is collected via a procedure. This procedure can vary based on the location and type of suspected cancer. Once the tissue is collected, a histology is performed, which is a variety of tests used to better characterize the disease and the genetic mutations they harbor.

“Another name for [genetic mutations] is actionable genomic alterations, which is a lot of words, but just describes that it’s a mutation you can do something with,” says Dr. Jared Weiss, a medical oncologist specializing in lung and head & neck cancers at UNC Lineberger Comprehensive Cancer Center.

All of these tests provide valuable information for the healthcare team, including effective treatment options, targeted cancer therapies, and the behavior of the cancer.

This information gathered from the biopsy tests is used in combination with other factors such as staging scans (like an MRI or CT Scan), blood work, and an individual’s overall health, among other things, to recommend treatment options. The information can also provide an overall picture of cancer prognosis, or the likely course of the disease based on known studies and experiences treating other patients with a similar disease. Molecular testing looks at specific pieces of the cells and their DNA to provide a more detailed view.

Molecular Testing

A broad term that uses the detection of individual molecules or pieces of cancer cells to better characterize a cancer, its behavior, and potential targeted (and more effective) treatment options.

Molecular testing can be used to look for inherited DNA mutations or DNA mutations specific to the cancer itself. It can also test for other molecules, such as proteins or receptors on cancer cells.

Molecular testing, when applied to DNA, is used to identify hereditary cancers (Germline mutations) or mutations in cancer DNA that are not inherited and developed spontaneously (these are called somatic mutations).

Identifying specific inherited DNA mutations is often done with a PCR test (polymerase chain reaction test detects genetic material) or NGS (next-generation sequencing), and this information is used to help with cancer screening, preventive measures, and treatment.

Identifying target DNA mutations, molecules present, or molecules absent in the cancer itself can also be used to further guide treatment options and potential targeted therapies and give a better picture of the behavior of the disease.

According to Dr. Jared Weiss of UNC Health, with these targeted therapies, which can be identified by molecular testing, “you get a treatment that is far more likely to work than chemotherapy.” Additionally, he says, “They last longer than chemotherapy for control, and they are less toxic in getting you there.”

Germline Mutations and Molecular Testing

Germline mutations in your DNA are present in a parent’s reproductive cells (egg or sperm) and are inherited.

With a germline mutation, every cell in your body will have this germline mutation in the DNA. Most mutations do not cause problems. However, specific mutations can cause hereditary cancer syndromes.

Hereditary cancer syndromes are a group of genetic defects, or changes in DNA, that lead to an increased risk of cancer when inherited.

When you or a family member are diagnosed with a cancer known to have a strong genetic component, it will often be recommended to undergo genetic testing.

The risk for cancer is often location-specific and highly dependent on the type of genetic defect, and therefore preventive measures can be taken in regard to cancer screening, early detection, and treatment.

This testing of inherited DNA changes that lead to higher rates of cancer is known as Germline testing and is a type of molecular test.

Common Germline Mutations increasing the risk of various types of cancer include: BRCA1, BRCA 2,  p53, APC, MLH1, MSH2, RET

Somatic Mutations and Molecular Testing

Somatic Mutations are changes in DNA that occur after conception and can happen to any cell in your body at any time. These somatic mutations cannot be passed from parents to children.

Most somatic mutations do not cause issues but can lead to cancer if specific portions of the DNA are changed.

Somatic mutations can happen for various reasons, many being caused by lifestyle factors that stress your body, such as smoking, sun exposure, and chemical exposure.

Typically, a piece of the cancer tissue must be biopsied to test for somatic mutations in the cancer.

Somatic testing of cancer DNA is another molecular test that is used to look for potential DNA mutations that provide information about the cancer behavior and potential targeted therapies towards these DNA mutations.

Common Molecular Testing Techniques

Next Generation Sequencing (NGS): Analyzes multiple parts of DNA simultaneously and is used to detect inherited (germline) and spontaneous (somatic) mutations. Areas of DNA analyzed can vary depending on the specific NGS test.

Polymerase Chain Reaction (PCR): Also analyzes genetic code, but it targets specific gene mutations or abnormalities. It is easily reproducible and cheap compared to NGS and is often utilized when testing for a limited number of genetic abnormalities.

Fluorescence in-situ Hybridization (FISH): Fluorescent probes, or molecules that light up, target portions of the DNA to identify large changes such as duplication, deletions, or movement of portions of DNA, which can aid in diagnosis, prognosis, and guiding treatment. FISH is simple and reliable but does not look at specific genetic changes in the DNA.

Flow Cytometry: A method that tests cells or pieces of cells suspended in a liquid as they flow through a machine which rapidly quantifies cells, various types of cells, as well as other biomarkers such as DNA. Flow cytometry is often used in the workup of leukemias and lymphomas.

Gene Expression Microarrays: Analyzes multiple portions of DNA with a set of known targets and measure the expression of these various, predetermined genes. These tests are often used to classify tumors into molecular subtypes that help determine the cancer’s behavior and guide treatment decisions, such as Oncotype DX, which is often used to determine the need for chemotherapy in breast cancer patients.

Immunohistochemical (IHC) staining: Specific antibodies are applied to a tissue sample that targets protein, DNA, or other molecules of interest. These antibodies stain the tissue sample and allow pathologists to determine the presence/absence and concentration of specific molecules in a tissue sample. The specific molecule tested varies based on the suspected cancer type and location.

Next Generation Sequencing (NGS)

There are several ways to perform DNA testing for specific mutations that can be inherited (Germline) or develop spontaneously (Somatic).

Cheap and easy PCR and IHC  tests are commonly used to test a single or few potential DNA mutations or molecular markers that are commonly seen in certain cancers.

NGS allows for multiple genes or parts of your DNA to be tested simultaneously for multiple cancer-causing mutations relatively quickly and accurately.

Although NGS is widely used and can identify well-known DNA mutations that can cause cancer, there is still much unknown about a multitude of DNA mutations and their risk of causing cancer, and they are often coined as “variants of uncertain significance”

Given their complexity, it is important to discuss the findings of these tests with geneticists who are experts in interpreting these results.

Types of NGS Testing On The Market

There are a number of tests you may encounter, depending on where you are getting treatment and what you are getting treatment for. Here are some of the common ones currently on the market:

• FoundationOne®CDx looks at 324 genes in solid tumors and says it can takes up to 12 days for results. Test results include microsatellite instability (MSI) and tumor mutational burden (TMB) to help inform immunotherapy decisions.
• OmniSeq Insight provides comprehensive genomic and immune profiling for all solid tumors. It looks for 523 different genes. Test results include microsatellite instability (MSI) and tumor mutational burden (TMB), as well as PD-L1 by immunohistochemistry (IHC).
• Cobas EGFR Mutation Test v2 identifies 42 mutations in exons 18, 19, 20 and 21 of the epidermal growth factor receptor (EGFR) gene. It is designed to test both tissue and plasma specimens with a single kit, and allows labs to run tissue and plasma on the same plate simultaneously.

You should ask your healthcare team if the brand of molecular testing they are doing is optimal for your cancer type.

Liquid Biopsy

Typically used as a supplement to tissue biopsy, a sample of blood is tested for circulating cells or pieces of cancer cells using molecular testing

Because there is no tissue to observe, no histology is performed.

Liquid biopsy is less invasive than tissue biopsy and can be considered as an alternative when repeat testing of your cancer is needed, and it is too cumbersome to undergo repeat procedures for tissue biopsy.

Liquid biopsy is typically performed when a patient has metastatic disease that is undergoing monitoring, or current therapy is not working, and a need for new targeted therapy is being explored.

The use of liquid biopsy in the early detection of cancers and recurrence is a field of active research.

Please consult your healthcare team on the role of liquid biopsy in your cancer care.

Types of Liquid Biopsy Testing On The Market

Several types of liquid biopsies have been approved by the U.S. Food and Drug Administration (FDA) including:

• The Cell Search Circulating Tumor Cell (CTC) Test is used for metastatic breast, prostate, and colon cancer to help monitor disease and provide a prognosis based on the levels of CTCs.
• Labcorp Plasma Focus is used for non-small cell lung cancer (NSCLC), colorectal, breast, esophageal, gastric, gastroesophageal junction carcinomas and melanoma through ctDNA. Results can come back in 7-10 days.
• Cobas EGFR Mutation Test v2 is used in non-small cell lung cancer (NSCLC) and detects a mutation in the EGFR gene through ctDNA which can help determine targeted treatment.
• Guardant 360 CDx is used in non-small cell lung cancer (NSCLC) and can help detect specific mutations in ctDNA to help guide treatment.
• FoundationOne Liquid CDx uses ctDNA to detect mutations in prostate, NSCLC, ovarian, and breast cancer to better tailor therapy.

When undergoing a liquid biopsy, a healthcare provider will take a sample of your blood, much like a complete blood count, which will be sent to an additional laboratory for testing. This is much less invasive and time-intensive than other biopsy procedures.

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