Cancer Genomic Testing

Genomic testing or genomic assay is performed on a tumor sample taken during a biopsy to look for mutations (changes) in the genes that make the tumor up.

Genomic testing or genomic assay is performed on a tumor sample taken during a biopsy (or, less often, on a blood sample). It looks for mutations (changes) in the genes that make up a tumor.

  • Genomic testing can be performed on an existing sample or a new sample that can be obtained through a biopsy.
  • After the disease has spread, new samples may be especially useful in determining whether cancer's DNA has mutated.
  • Oncology practice and patient care rapidly change because of advances in cancer genomics. Although genomic testing appears to be promising, it is still being researched.

Various types of cancer genomic tests include:

  • Single biomarker:
    • This looks for a single point of interest in the genome. It is frequently used to screen or confirm the eligibility of the tumor cells to respond to a particular drug.
  • Biomarker panel:
    • Panels search for multiple known genomic changes at the same time. They could be used to look for the most common changes in the tumor type.
  • Whole-genome, exome, or transcriptome sequencing:
    • It detects all genomic changes in a tumor's DNA or RNA. This can include new mutations that have not been previously identified.

Genomic testing entails analyzing a person's tumor to determine its specific properties to develop a better treatment plan. It can indicate how aggressive the cancer is, who might benefit from immediate cancer treatment, and who might benefit from active surveillance. 

The following are the most commonly used genomic tests to guide cancer treatment:

Table. Common genomic tests to guide cancer treatment
Gene Most commonly seen in (cancer types)
Human epidermal growth factor receptor 2 gene
  • Breast
  • Stomach
  • Lung
  • Uterus
  • Ovary
Epidermal growth factor receptor gene
  • Lung
  • Head
  • Neck
  • Pancreas
Fibroblast growth factor receptor gene
  • Bile duct (cholangiocarcinoma)
  • Breast cancer
  • Gastric cancer and other types of cancer
Mesenchymal epithelial transition gene
  • Lung
  • Head
  • Neck
  • Liver
  • Gastric and other types of cancer
Rat sarcoma virus gene
  • Colorectal
  • Lung
  • Head and neck cancer
BRAF gene
  • Colorectal
  • Lung
  • Malignant melanoma
Anaplastic lymphoma kinase gene
  • Brain
  • Nerve
  • Lung cancer

How does genomics play a role in cancer care?

Cancer is a disease of the genome (DNA) and occurs when changes in a person's genome cause uncontrollable cell growth and division. These genomic changes can be inherited from the person’s parents or acquired at some point during their life.

Acquired genomic variants are the root cause of the vast majority of cancer. However, in approximately five percent of cases, the individual has inherited a variant that greatly increases their risk of cancer.

Inherited variants or germline variants

  • These variants are found in nearly all cells of a person, and some rare variants increase a person's risk of cancer. When a patient has this type of germline variant, it is critical to identify it through genomic testing.
  • Additional screening or prophylactic surgery may be offered to the patient with this type of variant. 
  • Patients with specific BRCA1 and BRCA2 gene variants may choose to have a preventative mastectomy or oophorectomy.
  • It is critical to consider implications for the patient's family because appropriate testing can identify other at-risk relatives who may be able to take precautions to reduce their risk of cancer.

Acquired variants or somatic variants

  • These variants are only found in cancer cells. These mutations are not inherited and cannot be passed down to children.
  • Somatic variants can be caused by environmental factors such as ultraviolet light, smoking, radiation, or alcohol, or they can be completely random.
  • Errors may be introduced each time a cell divides. Although there are numerous mechanisms within the cell to correct these errors, they are occasionally overlooked.

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How will genomic assay help in advanced cancer treatment?

If a genomic assay reveals that cancer has certain mutations, the patient may be able to participate in clinical trials for new medicines that target those mutations.

Alternatively, the patient may be able to obtain a medicine that is not approved by the U.S. Food and Drug Administration for cancer but is approved to target that mutation in another type of cancer.

  • Oncologists encourage many people with metastatic cancer to undergo genomic testing. They believe it will be especially useful in matching people with clinical trials testing new treatments.
  • If the patient has several clinical trials to choose from, knowing the mutational profile of the tumor can help them narrow down their options.
  • Cancer that has progressed on standard treatments becomes stable and even shrinks when patients enter a clinical trial for a targeted therapy based on genomic markers.
  • However, oncologists caution that genomic tests are not yet considered standard of care.

To summarize, cancer treatment is not a one-size-fits-all proposition. Even if two people have the same tumor site, they may respond differently to treatment plans. Treatment must be truly personalized to provide the best possible care for oncology patients. That is where genomics is leading.

The study of a tumor site's genetic makeup is known as genomics. Genomic testing can help a care team better understand cancer by examining the specific genetic mutations at work. As a result, patients and doctors can benefit from a more personalized treatment plan and more informed decision-making.

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Medically Reviewed on 10/27/2021
References
Image Source: Bill Oxford / Getty Images

What Is Genomic Testing in Cancer? https://www.webmd.com/cancer/cancer-genomes-21/what-is-genomic-testing

What is Genomic Testing? https://blog.dana-farber.org/insight/2018/11/what-is-genomic-testing/

QUESTIONS TO ASK ABOUT GENOMIC TUMOR TESTING: https://www.jax.org/news-and-insights/2017/january/questions-to-ask-about-genomic-tumor-testing#

Genomics and Cancer Treatment: https://www.yalemedicine.org/conditions/cancer-genomics