Why Genetic Testing is Important for Cystic Fibrosis

Genetic tests find changes, called mutations, in genes that cause disease. These tests can be a helpful tool in confirming a disease diagnosis. Different types of mutations may cause a single disease. Some drugs are more effective for certain types of mutations and some drugs only work on certain mutation types. Knowing what type of mutation is present may predict how a person will respond to certain drugs. In deciding to have or not have a genetic test, it is helpful to understand a little about how genes work, what types of mutations genes may carry, and how genetic testing is performed.

Background
Cells are specialized small units that make up all living things, and the human body contains trillions of cells. There are many different types of human cells, including brain cells, liver cells, and muscle cells. Every cell contains 20,000 to 25,000 genes. Genes, made up of DNA, are the “blueprints” of the cell and tell our body how to make proteins. Proteins form the structure of the cells and perform most important functions in the human body. Proteins produce traits – such as eye color, foot size, and height –and can be passed from parent to child.

In cystic fibrosis (CF), the CFTR gene is important because it makes a protein that functions as a channel that allows fluids to move across cell membranes. It is most important in cells that are specialized to produce tears, saliva, digestive enzymes, sweat, and mucus. These channels affect the water levels in the cell and the ability of mucus to move in the body, which acts to protect and lubricate the organs, digestive and reproductive systems of the body.

A change or mutation in the genetic blueprint can lead to a loss of the CFTR protein. A mutation may also result in production of a protein that is short and/or does not work properly so that it does not serve its purpose as a channel across the cell membrane. Several types of mutations within the DNA of the CFTR gene can lead to cystic fibrosis. They include:

• Deletion – a part of the DNA blueprint for CFTR is missing. The deletion of three DNA bases, DeltaF508, is the most common mutation in CFTR.
• Duplication –a piece of DNA in the CFTR gene is repeated.
• Insertion– an extra piece of DNA is added to the CFTR gene.
• Missense – a segment of the genetic code is changed (one or more bases are substituted), which leads to an error in the CFTR protein.
• Nonsense – a segment of the genetic code is changed and is read as a premature “stop signal” in the gene, so that cells stop making the CFTR protein or make an incomplete protein. Nonsense mutations cause approximately 10% of CF cases.

Potential Uses of Cystic Fibrosis Genetic Testing
Genetic testing can help confirm whether or not someone has cystic fibrosis and can indicate the specific type of genetic mutation (deletion, duplication, insertion, missense, or nonsense) that is causing it. This knowledge may make a person eligible to participate in a clinical trial of a drug designed to overcome a specific type of mutation.

For example, PTC Therapeutics is developing an investigational drug called ataluren (PTC124®). This drug is designed to allow the cells to override the premature stop signal caused by a nonsense mutation in the CFTR gene. Ataluren is now being studied in clinical trials in patients with cystic fibrosis who have the disease due to a nonsense mutation. These trials are taking place at many clinics around the world. If these trials show positive results, ataluren may be approved by regulatory agencies and be made available to treat patients who have cystic fibrosis due to a nonsense mutation.

Knowing the type of CFTR mutation may help patients and families choose between clinical trials or treatment options. Carefully choosing a treatment plan not only increases the chance of success, but also avoids exposure to a drug that may have little or no chance for benefit and may unnecessarily expose patients to harmful side effects.

CFTR gene testing can be performed on individuals who are suspected of having cystic fibrosis, on siblings of those with cystic fibrosis and on mothers and fathers who believe they may be carriers of the disease and are concerned they might pass it on to their children. Carrier testing is especially important for couples of northern European and Ashkenazi Jewish descent, as the frequency of the CFTR mutation is higher in these populations. It is also important to note that in individuals with other ancestry, the mutations are often different and routine testing may not be as reliable as in the Caucasian population.

Performing Cystic Fibrosis Genetic Testing
To perform the gene test for cystic fibrosis, a single routine blood sample is required. In most cases, a primary doctor can order the test. To arrange for testing, the doctor can contact a gene testing laboratory (see below) to get instructions on the type of blood collection tube to use and the details of where to send the blood sample. Often the doctor’s office staff can also provide information on the cost of the test and whether health insurance will pay for it.

Once the sample is sent to the gene-testing laboratory, the laboratory will check to see if a mutation is present in the CFTR DNA. The laboratory will also test for the type of mutation and its location within the CFTR gene. There are over 1000 known mutations in the CFTR gene. Because the CFTR gene is large and mutations have been found in most regions of the gene, testing will usually be performed in a multi-step process. If there is a specific mutation already known to run in the family, it is only necessary to check family members for the familial mutation. If there is no known mutation, a mutation panel designed to look for common mutations is generally recommended. This panel checks for the most common CF mutations found in the Caucasian population and is less expensive than full-length gene sequencing. If the results of this test are negative or the patient has non-Caucasian ancestry, the healthcare provider will then consider a second test. This may include gene scanning to look for regions where the mutation may be located and gene sequencing or sequence analysis that looks for insertions, missense, and nonsense mutations.

If the sequencing test is negative the healthcare provider may recommend a test that looks for large deletions and duplications in the CFTR gene. These types of gene changes are difficult to detect with gene sequencing and a different technology is used. Usually laboratories charge separately for each test.
Genetic test results are sent back to the doctor who ordered the test. Depending upon the laboratory and whether more than one test is required, the results are normally available in 2 to 8 weeks.

Deciding Whether to Have CFTR Genetic Testing
As noted above, genetic testing can have advantages. However, in some situations, the knowledge that comes with testing may bring concerns. Family members may differ in their responses to genetic test results. These differing responses may result in changes in relationships among family members. Choices regarding reproductive decision-making and options for prenatal testing are things that every family should consider before having testing. Insurance companies vary on coverage for genetic testing and families should consider the cost of testing. It is important for each family to consider the advantages and disadvantages of the test before it is performed. It is also important to consider that with CF testing, the effectiveness of testing will vary due to ethnicity, as different mutations are more common in different ethnic groups.

Genetic Testing Resources
Physicians who treat cystic fibrosis will generally be aware of laboratories that perform genetic testing. Laboratories that perform testing may also be located through GeneTests (www.genetests.org), a website sponsored by the United States National Institutes of Health. Once on this website, click on the Laboratory Directory link at the top of the page to find a list of genetic testing laboratories. Note that since listing on the GeneTests website is voluntary, not all laboratories may be listed. To find a specific laboratory doing genetic testing for cystic fibrosis, search for the disease name or for the CFTR gene.

GeneTests can be searched for the location of a laboratory in the country or region of the person to be tested. Not all countries have genetic testing laboratories. Orphanet (http://www.orpha.net/consor/cgi-bin/index.php) is a similar resource for European laboratories. If the patient’s physician or genetic counselor cannot recommend a nearby laboratory, it may be possible to have blood drawn near the patient’s home and shipped to a laboratory in another country for testing. It is important to contact the laboratory first to see if this is possible and to find out the procedure.

Additional Genetics Resources
In addition to the doctor, speaking with a genetic counselor may benefit the patient and his or her family. Genetic Counselors can help with the decision-making process and explain or coordinate testing. Genetic counselors can help interpret the results of the gene sequence test; provide guidance on the best use of the information gained from the test; and answer questions about genetics in general and the types of tests that are available.

Many online resources offer information on genetics and genetic testing:
• Foundation for Genetic Education and Counseling (www.fgec.org) :Educational material for doctors and patients
• National Human Genome Research Institute (www.genome.gov) : Government website with background information as well as research and resources
• National Society of Genetic Counselors (www.nsgc.org/consumer ) : Find a genetic counselor
• U.S. Department of Energy Department of Science (http://www.ornl.gov/sci/techresources/Human_Genome/medicine/genetest.shtml ) :
Basics of genetic testing and FAQ’s about testing
• Your Genes Your Health (www.ygyh.org) : General information about cystic fibrosis
• Your Genome (www.yourgenome.org) : Genetics background information and research
• Gene Test (www.genetests.org): Genetic background and testing information on cystic fibrosis and many other types of diseases
• Cystic Fibrosis Foundation (http://www.cff.org/) : Support for those with CF as well as a registry and listing of clinical trials