The UAB Medical Genomics Laboratory serves an integral role in supporting patient care and advancing neurofibromatosis research. Viewed in the medical and scientific communities as the gold standard for NF genetic testing, the laboratory offers clinical genetic testing for all forms of neurofibromatosis, including NF1, NF2, Schwannomatosis, as well as Legius syndrome and other Rasopathies. Based on more than 15 years of experience, the Medical Genomics Laboratory has identified mutations in more than 8,000 unrelated patients and has identified more than 3,000 NF1 mutations, representing the world’s largest database repository of NF mutations. This month’s blog features insights from the Director of the UAB Medical Genomics Laboratory Yulong Fu, PhD, FACMG, and Laboratory Genetic Counselor Bryce Brown, MS, LGC. Dr. Fu and Mrs. Brown discuss how the laboratory’s unique testing capabilities, advanced technologies, and distinctive expertise support patients, physicians, and research scientists by providing information about NF variants that may be otherwise unavailable.
What is the role of NF genetic testing in establishing an NF diagnosis, and why is it important?
Dr. Fu: The original diagnostic criteria for NF1 established in 1987 did not include genetic testing because the technology was not available. For years after this, some in the NF scientific community did not believe genetic testing was needed because a diagnosis can be made based on clinical presentation, or phenotype, in most patients. However, because of advances in genetic testing for NF, largely due to the efforts of Dr. Ludwine Messiaen who established the UAB Medical Genomics Laboratory, genetic testing has now been incorporated into the diagnostic criteria for NF1. Genetic testing is particularly helpful in cases where a clinical diagnosis may be inconclusive or needs to be confirmed.
For example, some patients may have only one clinical feature of NF, whereas the clinical criteria require two features. Genetic testing can provide that second criterion, especially in young children who are not yet old enough to manifest any sign other than café-au-lait spots. Some patients also have an unusual presentation of clinical features, such as those with mosaic NF1. Genetic testing can be especially helpful in distinguishing NF1 from Legius syndrome in the child with multiple café-au-lait spots. This is important, because Legius syndrome can be indistinguishable from NF1 in a young child, yet, unlike NF1, does not predispose to tumors. It therefore has very different implications regarding surveillance and management. Regarding NF2, many people present with just one vestibular schwannoma (hearing nerve tumor) and may not develop a second feature for many years. Genetic testing can help to establish a diagnosis for such individuals.
In other cases, patients have the phenotype, or clinical features, of NF and want to confirm the diagnosis with genetic testing to better understand the risk of having an affected offspring. Identification of a genomic variant can also make it possible to offer prenatal testing to determine if the mutation has been passed to a fetus who is at risk based on the mother or father being affected.
Bryce: Providing patients with a conclusive diagnosis in cases where NF is suspected based on clinical features, or phenotype, is very helpful. Although many of the variants do not predict the severity or specific complications, there are instances where specific variants are associated with either a more severe or mild course of NF. Receiving a conclusive diagnosis based on genetic testing is valuable for many patients in helping them to understand more about the expected course of their condition. Also, patients with an unusual presentation of NF features can benefit from genetic testing to determine if an NF mutation is involved at all.
How does the Medical Genomics Laboratory advise patients and physicians in the types of genetic testing that should be done to confirm a suspected diagnosis of NF?
Dr. Fu: We maintain an active dialog both with referring clinicians and also with NF experts at UAB. This enables us to work together with referring clinicians to help advise them on the best testing strategy and in interpretation of test results.
Bryce: My primary role is to serve as a bridge between clinicians and the laboratory. I have a thorough understanding of the various patient phenotypes and can communicate this information to the laboratory so that the most appropriate type of testing can be determined. I also have an in-depth knowledge of the testing we perform which allows me to develop the best testing approach alongside the clinician based on the patient’s presentation.
In complex cases, we often roundtable with clinicians to discuss what future testing would be beneficial. Dr. Korf provides us with invaluable insight in these meetings, based on his extensive clinical expertise. We also have a weekly meeting with Dr. Korf to discuss cases and collaborate about recommendations for testing. These meetings are especially important in cases of unusual presentation of clinical features or unexpected results.
While my role is less patient-facing, I may sometimes speak to patients on the phone to discuss test results, most often in cases of prenatal counseling or preconception counseling.
What advanced technologies and capabilities does the Medical Genomics Laboratory offer that distinguish it from other similar laboratories?
Dr. Fu: Our laboratory offers unique testing capabilities that no other laboratories in the U.S. provide. Specifically, we offer RNA-based testing that provides more information than next-generation sequencing (NGS). RNA-based testing is a highly specialized, intensive process that involves cell culturing and requires well-trained technicians with specialized expertise.
The reason we do RNA-based testing is that the NF gene is very large, and there are thousands of variants. Next-generation sequencing often cannot identify all of these variants. However, because RNA-based testing is a functional level test, many patients who received an inconclusive result with NGS are able to receive a definitive diagnosis with RNA-based testing.
We are also the only laboratory in the U.S. to perform biopsy testing of tumor tissue, which can be critical in achieving a diagnosis in patients with mosaic NF1 in which only some of the cells contain the NF1 variant. Because tumors from NF1 patients are cellularly heterogenous, and only a small portion of cells bear the variant, directly sequencing the biopsied tissue may not be able to identity the variant due to low tumor cellularity. To overcome this, we have established a cell culture system in which only tumor cells will grow. This allows us to extract DNA and sequence only those cells to achieve a conclusive result.
Bryce: While there are many labs in the U.S. and internationally that perform NF testing, our testing is a “deep dive” that provides extensive interpretation of the Rasopathies. We also have highly skilled technicians who have been here since the laboratory was started. By offering in-depth expertise in both the testing and interpretation, our patients and clinicians can have confidence in the results we provide. We do everything possible to find answers for our patients.
How does the laboratory’s database of NF variants, the world’s largest, assist in the diagnostic process and help to advance NF research?
Dr. Fu: Our database includes more than 3,000 NF1 variants, and these can be helpful in determining whether a specific variant that has been identified in a patient is pathogenic. Testing in some patients will reveal variants of unknown significance, which can provoke anxiety in both patients and clinicians. Because of our very large database, we can often verify whether a specific variant has been seen before in a person with NF, helping to resolve whether the variant is in fact a cause of NF. I receive emails from all over the world inquiring about specific variants. We are considering making the database public, although this will take some time given its vast size. The database of NF variants is also instrumental in advancing NF research at UAB. For example, genetic scientists can use the database to identify the most prevalent variants to guide their development of animal models and personalized gene therapies.
