What Is Genomic Testing?

Aims and applications differ from genetic tests

Genomic testing is a type of test that looks at more than just your genes but the ways in which your genes interact and what those interactions mean to your health.

Genomic testing is often confused with genetic testing. The main difference is that genetic tests are designed to detect a single gene mutation (such as the BRCA1 and BRCA2 mutations associated with breast and ovarian cancer), while genomic tests look at all of your genes.

By taking a broader look at your genetic makeup—including how your genes are sequenced and how they influence each other—genomic testing can offer insights into how your body works on a molecular level and what that means in terms of disease risk, progression, or recurrence.

Genomic testing is commonly used in cancer treatment to determine how a tumor is likely to behave. This can help doctors predict how aggressive your cancer will be and whether it is likely to spread (metastasize) to other parts of the body.

Genomic testing is a central tool in the development of personalized medicine that aims to customize treatments, products, and practices to the individual.

Genetics vs. Genomics

While genetics and genomics are both associated with genes, they have entirely different aims and applications.

Genetics

Genetics is the study of the effects that genes have on an individual. Genes provide the body instructions on how to make proteins; the proteins, in turn, determine the structure and function of each cell of the body.

The genes are made up of building blocks, called DNA, that are arranged in a string called "bases." The order, or sequencing, of bases will determine which instructions are sent and when.

While many genes are coded to produce specific proteins, other non-coded genes regulate how and when the proteins are produced (essentially turning on and off certain genes).

Any aberration in how a gene works may influence the risk of certain diseases depending on which proteins are affected.

In some cases, a single gene mutation can confer to diseases such as cystic fibrosis, muscular dystrophy, and sickle cell disease.

Genetic tests can also look for any genetic mutation you may have inherited from your parents, either to confirm a diagnosis, predict future risk, or identify if you are a carrier.

Genomics 

Genomics is the study of the structure, function, mapping, and evolution of the complete set of DNA, including all of the genes. The genetic material plus all of the sequences are called the genome. The aim of genomics is to analyze the function and structure of a genome in order to:

  • Understand how complex biological systems, such as the cardiovascular system and endocrine (hormone) system, influence each other
  • Predict what problems may occur if genetic interactions interfere with normal biological functions

All told, there are between 20,000 to 25,000 different protein-coding genes and roughly 2,000 non-coded regulatory genes in the human genome.

Genomics is important because it helps us understand why some people are genetically predisposed to certain illnesses (even if we don’t understand how certain genes interact).

Rather than identifying a single genetic pathway, genomics evaluates the multitude of genetic variables that affect the development and/or treatment of a disease, such as cancer or diabetes.

Unlike genetics, genomics is not constrained to inheritable mutations. It identifies how your genetic makeup influences the course of a disease and, conversely, how environment, lifestyle, and drug treatments can trigger mutations that alter that course. By understanding these ever-changing variables, doctors can make more informed choices in treatment, often preemptively.

Role of Genomic Testing

Genomic testing is based on our current understanding of the human genome, a process which began with the collaborative Human Genome Project from 1990 to 2003.

In the convening years, scientists have been able to increasingly identify which genetic anomalies translate to not only the development of a disease but the characteristics of the disease. Doing so has provided insights into why some people develop more aggressive forms of cancer, live longer with HIV, or fail to respond to certain forms of chemotherapy.

While genetic tests can confirm or rule out a suspected genetic condition, genomics takes testing one step further by providing us:

  • Risk markers in order to screen for diseases
  • Prognostic markers to predict how fast a disease will progress, how likely it is to recur, and the likely outcome of a disease
  • Predictive markers to guide treatment choices and avoid toxicity
  • Response markers to determine the efficacy of various treatments

While genomics focuses on the implications of our genetic makeup irrespective of all other factors, it is not used in isolation.

The growing movement toward personalized medicine is changing how we approach diseases in general. Rather than a one-size-fits-all solution, personalized medicine takes into account the high variability in genetics, environment, and lifestyle to offer a more tailor-made solution for each individual.

How the Test Works

Genomic tests are typically offered as a panel of targeted genes, ranging from an analysis of genetic "hot spots" (well-established sites of mutation) to full gene sequencing. The tests are typically performed in a specialized lab certified under the Clinical Laboratory Improvement Amendments (CLIA) of 1988. Today, there are more over 500 CLIA-certified genetics labs in the United States.

Most tests require a blood or saliva sample or a swab of the inside of your cheek (known as a buccal smear). Depending on the aims of the test, it may only require a few drops of blood or several vials. A biopsy of a tumor or bone marrow may be needed for people with cancer.

Once the sample is obtained, it usually takes between one and four weeks to receive the results. Depending on the condition being treated, a genetic counselor may be on hand to help you understand the limitations of the test and what the results mean and don't mean.

Next-Generation Sequencing

Next-generation sequencing (NGS) is the primary tool for genomic testing. It is used to identify and evaluate the genetic sequence of millions of short DNA segments called "reads." The reads are then assembled into a complete sequence to determine which genetic variations (variants) are present and what they mean.

NGS is extremely flexible and can be used to sequence only a few genes, such as for a hereditary breast cancer panel, or the whole genome used typically for research purposes to screen for rare diseases. 

Since most variants have little or no known impact on human health, they will be filtered out to identify the few that are medically meaningful. These variants will then be scored on a five-point scale ranging from:

  1. Benign (not disease-causing)
  2. Likely benign
  3. Uncertain
  4. Likely pathogenic (disease-causing)
  5. Pathogenic

While most labs will report the pathogenic and likely pathogenic findings, some will also include the uncertain, likely benign, and benign findings as well. An interpretation from a certified geneticist would also be included.

Primary and Secondary Results

Results directly related to a suspected condition are referred to primary results, while those that are medically meaningful but unrelated are called secondary (or incidental) results. 

Secondary findings are often relevant and may reveal a person’s genetic risk of a future disease, carrier status, or pharmacogenetic findings (how your body processes a specific drug). In some cases, testing may also be performed on your parents to help identify which variants are shared and which are de novo (not inherited).

Genomic Testing in Cancer

The development of genomic testing occurred more or less in tandem with the rise of targeted cancer therapies. As scientists began to grasp how certain genetic variants turned normal cells into cancerous ones, they were able to develop tests to screen for specific variants and develop drugs to target those genes.

Today, genomic testing has become an increasingly integral part of the treatment and management of many different types of cancer, including breast cancer and lung cancer.

While genetic tests may help identify a person’s risk of cancer, genomic testing helps us identify the genetic markers associated with the characteristic of the disease. It allows us to predict the likely behavior of a tumor, including how fast it will grow and how likely it is to metastasize.

This is important given that the cells of a tumor are prone to rapid mutation. Even if a single genetic variant is responsible for the rise of a tumor, the disease itself can take many different courses, some aggressive and others not. While a genetic test may help identify the malignancy, a genomic test can identify the most effective ways to treat it.

Moreover, if a tumor suddenly mutates, a genomic test can spot whether the mutation is receptive to targeted therapy. One such example is the drug Nerlynx (neratinib) used to target and treat early-stage HER2-positive breast cancer.

Comparison of Genetic and Genomic Testing in Breast Cancer

Genetics

Genomics

The study of inherited genetic traits, including those associated with certain diseases.

The study of the activity and interaction of genes in the genome, including their role in certain diseases.

Genetics establish your risk of inheriting cancer from your parents.

Once you have cancer, genomics establishes how the tumor will behave.

The BRCA1 and BRCA2 test can predict your risk of getting breast or ovarian cancer.

The Oncotype DX and PAM50 breast cancer tests are used to profile a tumor and predict how you will respond to chemotherapy.

Once you know your risk of breast cancer, you can take steps to actively reduce your risk.

Based on the results of the genomic test, you and your doctor can decide which treatment options are most appropriate following surgery

 

Home Genomic Testing

Home genomic testing has already infiltrated our everyday lives, starting largely with the release of the direct-to-consumer 23andMe home genetic kit in 2007.

While some home genetic tests, like the AncestryDNA and National Geographic Geno 2.0 tests, were designed solely to trace a person’s ancestry, 23andMe offered consumers the chance to identify their risk of certain genetic health disorders.

It is a business model that has been fraught with challenges. In 2010, the U.S. Food and Drug Administration (FDA) ordered 23andMe and other manufacturers of health-related home genetic tests to stop selling the devices, which the regulator deemed were "medical devices" under federal law.

In April 2016, after years of negotiation with the FDA, 23andMe was granted the right to release their Personal Genome Service Genetic Health Risk test which is able to provide information on a person’s predisposition to the following 10 diseases:

  • Alpha-1 antitrypsin deficiency (a genetic disorder linked to lung and liver disease)
  • Celiac disease
  • Early-onset primary dystonia (an involuntary movement disorder)
  • Factor XI deficiency (a blood clotting disorder)
  • Gaucher disease type 1
  • Glucose-6-phosphate dehydrogenase deficiency (a red blood cell disorder)
  • Hereditary hemochromatosis (an iron overload disorder)
  • Hereditary thrombophilia (a blood clotting disorder)
  • Late-onset Alzheimer’s disease
  • Parkinson’s disease

The saliva-based tests offer the same level of accuracy as those used by doctors.

Despite the advantages of these products, there remain concerns among some advocates as to the potential risk of discrimination should genetic information be shared without a consumer’s authorization. Some point to the fact that the pharmaceutical giant GlaxoSmithKline (GSK) is already an investor in 23andMe and plans to use the test results of the five million-plus customers to design new pharmaceutical drugs.

To counter the criticism, 23andMe advised the FDA that the results would be "de-identified," meaning that the consumer’s identity and information would not be shared with GSK.

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