Abstracts

Rationale: The Tuberous Sclerosis Complex (TSC) multidisciplinary program at Lurie Children's Hospital of Chicago follows over 100 children. We attempted to molecularly characterize our TSC patients, review variants of uncertain significance (VUS), and identify research opportunities for non-diagnostic patients.

Methods: A single center retrospective study of TSC patients and evaluation of their genetic test results. Patients included met clinical diagnostic criteria for TSC. Molecular test results were reviewed by genetic counselors; patients were categorized as TSC1/2 based on the presence of pathogenic, likely pathogenic (LP), or suspicious VUS in the respective gene. Variant characteristics indicative of a suspicious VUS included segregation in affected relatives, identification in another proband, and the molecular consequence of the variant. Patients without definitive molecular confirmation were classified as non-diagnostic.

Results: Overall, 97 patients were analyzed in our cohort. Most patients (87%) received genetic testing; 81% of patients who received a molecular diagnosis were characterized as TSC1/2, while 19% had non-diagnostic TSC1/2 sequencing and deletion/duplication analysis (Table 1). Of the patients tested, 14% had a VUS in TSC2 and none in TSC1. The majority of TSC2 VUS were indels (7), followed by splicing (2), missense (1), and unspecified (1) variants (Chart 1). 7 VUS were unique variants. We classified 7 of these VUS as suspicious and likely causative of TSC. TSC2 c.1172_1174del was reported in three siblings who inherited the variant from an affected mother. This same variant was reported in two paternal half siblings whose father had a clinical TSC diagnosis but did not undergo genetic testing. TSC2 c.2482_2484del was reported in two siblings who inherited the variant from their likely affected father. The 5 other VUS were not considered suspicious given the lack of additional evidence of pathogenicity. One of these VUS is a splicing variant that can be further evaluated with RNA functional studies and the other 4 did not have parental testing or segregation analysis. Of note, 1 VUS was downgraded to likely benign (LB).

Conclusions: Our data showed that most patients with a clinical diagnosis of TSC receive a molecular diagnosis, which is reflected in the literature. Parental testing, segregation analysis, and functional studies of the VUS in our cohort may upgrade the classification from VUS to LP. Changes in variant classification in our population highlight the importance of reanalysis over time. For patients without a molecular diagnosis, the promise of technologies like whole genome sequencing, long read sequencing, deep sequencing, and tissue testing may identify structural, deep intronic, and low-level mosaic variants that are missed by traditional testing. Because some technologies are currently on a research basis, finding research collaborators interested in identifying novel causes of TSC is crucial. Identifying a molecular diagnosis for families is key for accurate risk assessment and genetic counseling.

Funding: no