New in Genetic Testing:
NextGen Sequencing

 

By Kristina Kocsis, MS, CGC
Genetic Counselor, Children’s Hospital Colorado

testingKristina with oldest son, Ethan (7)

There are several causes of hearing loss. There are environmental causes like prematurity, low birth weight, severe jaundice and maternal infections. However, there are also genetic causes.  In fact, it is estimated that 50% or half of all congenital hearing loss, or hearing loss present at birth, is caused by genetic factors.  Most of the time there is no family history of hearing loss.  This is because parents can “carry” hearing loss genes but they themselves are hearing. Only when two people who “carry” the same gene have children do we even know they “carry” a hearing loss gene. To date, there have been more than 100 genes identified that cause hearing loss, and more are discovered every day. In the past, genetic testing was limited to just Connexin 26 gene testing, which is the most common gene associated with hearing loss. While it is the most common gene, Connexin 26 related hearing loss still only accounts for 20-25% of genetically caused hearing loss or 10% of all congenital hearing loss.

Over the past few years, the technology known as NextGen sequencing has revolutionized the field of genetics. NextGen sequencing simultaneously tests several genes in a single test.  This means instead of only being able to test one gene at a time, like Connexin 26, we can now test several genes at the same time. This is not only more efficient timewise; it is cheaper than analyzing each gene individually. Currently, there are a few NextGen hearing loss panels available in the United States - Cincinnati Children’s, Harvard and University of Iowa to name a few. These panels differ primarily in which genes are included and pricing.

The major limitation with these panels is the time it takes to get results. Results can take 4-6 months for families to receive. The reason for this long wait is the large amount of data generated that requires interpretation and the limited number of specialists who can interpret the data.

There are several parts to any given gene. Some parts of a gene are not important and mutations or changes do not change how a person might function, while other parts are important and mutations or changes can impact function. It is knowing the difference between the two that can be challenging. Similarly, mutations in many of the genes in a given panel may not be known or been reported before in the medical literature. So it is not uncommon to get results with unclear meaning. There are three possible results when genetic testing is pursued and a gene change is identified:  1) the gene change is pathogenic or known to cause hearing loss 2) the gene change is considered benign and not likely to cause hearing loss or 3) the gene change has unknown clinical significance meaning it is not known whether the change can cause hearing loss or not. It is this last scenario that can be most difficult for families to understand and doctors or genetic counselors to explain. While the data are still new, it is now estimated that with these panels, approximately 70% of all genetically caused hearing loss can be identified. When a parent has a hearing loss similar to their child’s hearing loss, just over 50% of time a specific gene is identified.

In general, insurance carriers have covered this testing.  Sometimes testing is covered at 100% and sometimes families are obligated to pay a portion (or percentage) of the testing.  Occasionally, a letter of medical necessity is required but given the strong stand by leading health organizations (e.g. American College of Medical Genetics and Early Hearing Detection and Intervention) supporting genetic testing, testing is usually approved after the letter is submitted.  In some cases, a family’s insurance policy may have a genetic testing exclusion clause in which case testing is not covered. Given the wide variability with insurance providers, it is advised families check with their insurance providers before testing is pursued.

There are multiple reasons why a family decides to pursue or decline genetic testing. It is a very personal decision and a family must weigh the benefits and limitations of testing.  Genetic counseling by someone familiar with hearing loss is key to helping families decide about genetic testing.  Importantly, genetic counseling does not mean genetic testing. Genetic counseling just allows families to make informed decisions about the option of genetic testing. For example, some families do not care why their child has a hearing loss and would prefer to focus on how to best manage their child’s educational and social needs. Other families want to know the cause as that may provide information about whether their child’s hearing loss may worsen over time or if their child may develop other health and/or developmental concerns, or they may want to know what the chances are to have another child with hearing loss. Genetic testing is a complicated process and being informed is the first step. To learn more about genetic testing options and genetic counseling for hearing loss, families may call me personally at 303-724-2345 or email at kristina.kocsis@childrenscolorado.org

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