Genomic & Tumor DNA sequencing and Chemo-Sensitivity Tests

What is clinical tumor DNA sequencing?

When mammalian cells are exposed to DNA-damaging carcinogens, cancer can develop. When the immune system does not work well, random DNA mutations can develop into malignant tumors. Each person’s cancer has a unique combination of genetic changes. In this perspective, tumor DNA sequencing is a test to identify these unique DNA changes. Especially in the primary tumor. A few oncologists recommend to also test metastasis DNA.

In some cases, knowledge of the genetic alterations  can help determine a treatment plan. Some treatments, in particular, some targeted therapies, are effective only for people whose cancer cells have specific genetic alterations that cause the cells to grow out of control (these are sometimes called “driver” mutations). For example, mutations in the EGFR gene that make cells divide rapidly are found in some people’s lung cancer cells. A patient whose lung cancer cells harbor an EGFR mutation may respond to treatment with drugs called EGFR inhibitors. Clinical tumor DNA sequencing can reveal whether a patient’s lung tumor has an EGFR mutation. Tumor DNA sequencing is at the crux of precision medicine: care tailored to the molecular characteristics of each patient’s disease.

Tumor DNA sequencing Options

Tumor DNA sequencing is most common for patients with cancer types that may be susceptible to treatment with a targeted therapy. These patients are commonly tested for the genetic mutation the therapy targets. For example, genetic testing is a routine part of care for colorectal and lung cancer.

In addition, some oncologists may recommend tumor DNA sequencing for patients with advanced cancer that is not responding to standard treatment or for which no standard treatment is available. This may help identify other treatments that might be effective given the cancer’s genetic makeup.

In other cases, tumor DNA sequencing may be available for patients who are participating in a clinical trial that includes a sequencing test. Several ongoing precision medicine trials, such as NCI-MATCH and NCI-COG Pediatric MATCH, are using tumor DNA sequencing to assign patients to investigational treatments based on the genetic alterations in their tumors.

How is tumor DNA sequencing done?

A sample of the tumor is removed and, in some cases, a sample of  healthy cells as well. They may obtain these samples during surgery, if it is part of the treatment plan. In other cases, biopsies are done.

These samples will be sent to a specialized lab, where researchers will isolate the DNA and then use a machine called a DNA sequencer to “read” it. They will then analyze the sequence of  the DNA to determine if there are any genetic alterations that make the tumor susceptible to certain treatments. They may also examine the DNA sequence of healthy cells to determine if the patient has any inherited, or germline, mutations that increase risks of cancer and can also influence treatment decisions.

RNA analysis is also starting to be considered.

Based on the tumor’s unique genetic alterations, the specialized lab may generate a report that lists treatments the tumor is likely to respond to.

What kinds of sequencing tests are available?

The Government’s FDA Approved Two Genomic Profiling Tests for Cancer that can identify different cancer-associated genetic alterations. DNA sequencing tests can have a broad or a targeted focus. Targeted DNA sequencing tests, also called multigene panels, are the most frequently used sequencing test for patient care. These tests analyze specific “driver” mutations. Some targeted sequencing tests analyze alterations that are common in a single cancer type, whereas others analyze alterations that may be found in many cancer types.

Broad DNA sequencing tests analyze the sequence of large regions of DNA rather than specific mutations. For example, whole-genome sequencing reads the sequence of all of the DNA in your cells—what’s known as the genome. Another broad test, called whole-exome sequencing, reads the sequence of all of the patient’s genes, known as the exome. Most cancer-causing DNA changes occur in genes, but DNA changes outside of genes can also drive cancer growth. Because whole genome and whole exome tests have not been directly compared, it is not clear if one type of test is more beneficial to patients.

In addition, a quantitative mRNA expression test can also gather information about what treatments may work best for you. For example, one quantitative mRNA test commonly used for cancer care analyzes 21 different genes that can cause breast cancer and predicts whether a patient with breast cancer is likely to benefit from chemotherapy treatment.

What do the results of a tumor DNA sequencing test mean?

Multigene panel tests indicate whether the patient has a genetic alteration in the tumor that can be targeted by an existing therapy. Because broad tumor DNA sequencing tests analyze more regions of DNA, they may be more difficult to interpret. For example, they may identify genetic alterations that do not cause cancer (benign) or whose effects are not known (of unknown significance). Alterations that are benign or of unknown significance do not aid patient care.

Tumor DNA sequencing tests may also uncover the presence of inherited alterations that increase cancer risk (hereditary cancer syndromes) or that are associated with diseases or conditions other than cancer. These are known as incidental, or secondary, findings. Finding that a patient carries an inherited genetic alteration may have implications for the patient and his or her family. Genetic counselors are usually hired to help interpret the results of DNA sequencing tests.

Discussion

What are the limitations of tumor DNA sequencing tests?

Genetic testing is still in its infancy, one patient I know had multiple genetic testing from six different DNA sequencing companies and they were all dissimilar. The biggest problem with DNA sequencing is based on unreliability, given the dynamic and changing nature of genetic expression. The genetic alterations in a tumor that changes over time only captures a “snapshot” of the alterations present at one point in time. This means that the results of a sequencing test obtained a few months ago may not accurately reflect the genetic alterations present in the patient’s cancer cells when he or she will be ready for the treatment. Furthermore, most companies will only test the primary tumor. Yet, most patients dont die from the primary tumor. They succomb to metastasic tumors and those tend to have a different genetic make-up. Worse, from the Institute’s holistic viewpoint, most genetic alternations in the cell’s nucleus are a function of the cross-talk with mitochondria’s genome, which, to my knowledge is never tested. Lastly, even the mitochondria’s genome can change, given one’s lifestyle, food, climate and other factors. Therefore, the ACR Institute can’t recommend these expensive tests, unless the patient is commited to a chemotherapeutic approach, in which case the best of these tests may be useful. However, even here,  not every patient will benefit, DNA alteration that is driving the growth of the tumor may not even have been identified. Or the Lab may find such an alteration but it cannot be targeted by existing therapies. And even if the patient has an alteration that can be targeted by an existing therapy, other unique aspects of the patient’s biology (such as how your body breaks down a drug or the immune system responds to the immune checkpoint inhibitors) can influence how the patient can actually respond to the therapy.

Another limitation is that tumors are composed of cancer cells with varied, or heterogeneous, genetic alterations. Therefore, a small sample of cancer cells obtained from a biopsy may not accurately represent a heterogeneous tumor. This could mean that DNA sequencing tests may identify a potential treatment that can act against some, but not all, of your cancer cells. Cancer cells that are not targeted by the treatment have the potential to continue growing, causing the tumor to come back. Furthermore, cancer stem cells are not even targeted. More often than not, these Master cells just spur the regrowth of the tumor the targeted therapy will have shrunk.

How much does tumor DNA sequencing cost?

The cost of tumor DNA sequencing varies by the type of test. For example, one commercial test that analyzes genetic alterations in more than 300 genes for patients with solid tumors, currently costs around 6 thousand dollars.

Clinical whole-exome sequencing tests cost between $1,000 and $5,000, and whole-genome sequencing could cost over $10,000. However, biotechnology companies are constantly developing faster and cheaper sequencing techniques that could eventually bring the price down.

Insurance coverage of tumor DNA sequencing depends on the patient’s insurance provider and the type of cancer. Insurance providers typically cover a DNA sequencing test if there is sufficient evidence to support that the test is necessary to guide patient treatment. Tests without sufficient evidence to support their utility may be considered experimental and are likely not covered by insurance.

Many clinical trials involve tumor DNA sequencing. If the patient participates in one of these clinical trials, the cost of tumor sequencing might be covered.