Article by Sharon Rosen
Imagine scanning a page for errors manually one letter at a time, versus using a faster tool like spell check. That’s the difference between the first DNA sequencing methods and the new computerized machines known as next generation sequencing. It’s revolutionizing health care.
Next generation sequencing technology enables geneticists to examine all of your 22,000 genes at once. So finding a change in a gene, called a genetic variation, which causes a patient’s disease, can be done much faster and cheaper. In contrast, older sequencing methods only focus on one or a few genes at a time.
“This new technology is constantly evolving. It’s becoming faster and cheaper so more patients can benefit from individualized care. It used to take us months or even years to identify genetic causes of disease, Now we can get results back in a matter of weeks,” says Matthew Ferber, Ph.D., director, Clinical Genome Sequencing Laboratory in the Department of Laboratory Medicine and Pathology and one of the founding members of the Rare and Undiagnosed Disease Service for the Mayo Clinic Center for Individualized Medicine.
This new technology has transformed care for patients with many conditions.
“There are many genetic conditions where the diagnosis can be suspected based on clinical grounds and confirmed by a single gene analysis or other conventional tests. But when it comes to complicated cases with multiple issues, it becomes tedious, labor intensive and prohibitively expensive to establish a correct diagnosis by conventional testing. In these cases, next generation sequencing technology has become a game changer. In addition to significantly decreasing cost and time of testing, it also empowers clinicians with different diagnostic choices, from a specific group of disorders and custom panels to whole exome sequencing, that ultimately improves patient care,” says Pavel Pichurin, M.D., assistant professor of Medical Genetics at Mayo Clinic.
Finding answers for patients with undiagnosed genetic diseases
One of the areas where next generation sequencing has made the biggest impact is in the diagnosis of rare genetic diseases.
“Many patients, who are often children with very complex symptoms, and their families, will spend years searching for a diagnosis. These families spend tens of thousands of dollars on traditional tests that do not provide answers. Using whole exome sequencing, a form of next generation sequencing that enables us to look at all 22,000 genes in the human genome, we can make a diagnosis for 30 percent of these patients,” says Dr. Ferber. “While we cannot cure most rare genetic diseases, we can provide patients with information for future family planning and advice on how to better manage and monitor their symptoms.”
Providing a focused tool to identify disease
Next generation sequencing also offers the opportunity to examine a select group of genes, called targeted panel testing. This type of testing is used to diagnose and develop individualized treatments for many conditions, including:
- Neurological diseases
- Heart disease
- Many types of cancer
Dr. Ferber highlights the impact of targeted panel genetic testing by explaining how it is used to diagnose hereditary colorectal cancer.
“In 2012, we developed a targeted panel to examine 17 genes associated with hereditary colorectal cancer. Next generation sequencing technology enabled us to look at all 17 genes at the same time and find the genetic variant causing the disease faster. This is important for cancer families whose survival may depend upon prophylactic surgery, or heightened surveillance,” says Dr. Ferber.
Results from targeted panel testing can guide care not only for the patient but their family members as well:
- Physicians may be able to identify a genetic variant for which there is a targeted therapy.
- Family members of patients with inherited cancers can be tested to identify others at risk for developing the disease.
- Family members, who discover they have the same gene mutation but have not developed the disease, may choose pre-emptive screening, treatment or surgery.
Dr. Ferber explains that there are still cases where the older DNA sequencing methods, which look at one gene at a time, can be useful. In cases where physicians are fairly certain that a specific gene may be causing a disorder, single gene testing is still the best tool. At a cost of approximately $1,500, single gene test results are provided to patients within a week.
Choosing the right test for each patient
According to Dr. Ferber, the key to the successful use of genetic testing is to pick the right test for each patient.
“If you are a patient who may need genetic testing to diagnose your condition, talk with your physician and a genetics team that includes a genetic counselor or medical geneticist. At Mayo, we have a multidisciplinary clinical genomics team that ensures that the right genetic test method is selected for each patient and the test results are interpreted accurately,” says Dr. Ferber.