Tuberous Sclerosis Complex (TSC) Deletion/Duplication Testing via MLPA

Tuberous Sclerosis Complex affects multiple organ systems including the skin (hypomelanotic macules, facial angiofibromas, shagreen patches, fibrous facial plaques, ungual fibromas), brain (cortical tubers, astrocytomas, seizures, intellectual disability/developmental delay), kidney (cysts, renal cell carcinomas), heart (rhabdomyomas, arrhythmias), and lungs (lymphangioleiomyomatosis [LAM]) (Northrup et al. 2018. PubMed ID: 20301399). It affects about 1 in 5,800 children in the United States (Osborne et al. 1991. PubMed ID: 2039137). Nearly 100% of individuals with TSC have skin or dental findings detectable via physical examination. Individuals who meet specific clinical findings (major and minor features) and/or have a pathogenic variant in one of the TSC genes have a definite diagnosis of Tuberous Sclerosis (Northrup and Krueger. 2013. PubMed ID: 24053982). For brain abnormalities, such as subependymal giant cell astrocytomas, either surgical resection or mTOR inhibitors can be utilized depending on the presence of singular or multiple lesions. Surveillance of brain, kidney, lung, teeth and other pertinent organs for disease progression have previously been recommended at specific intervals (1-3 years) to include periodic magnetic resonance imaging (MRI), computed tomography (CT), echocardiogram, electroencephalograph (EEG), dermatologic and eye exams (Krueger and Northrup. 2013. PubMed ID: 24053983).

Tuberous Sclerosis Complex (TSC) is caused by pathogenic variants in the TSC1 and TSC2 genes. These genes are tumor suppressors that are involved in cellular proliferation and act through multiple signaling pathways (mTOR/AKT pathways) (Orlova and Crino. 2010. PubMed ID: 20146692). TSC is inherited in an autosomal dominant manner with two-thirds of cases resulting from sporadic germline mutations while one-third of cases are inherited from an affected parent. It presents with near complete penetrance, but has variable expressivity. Phenotypes of TSC types can be similar, but TSC2 pathogenic variants are reported to cause a more severe clinical presentation (Northrup et al. 2018. PubMed ID: 20301399). Causative variants reported to date include nonsense, missense, splice site, small insertions and deletions, and large duplications and deletions (Human Gene Mutation Database). Truncating variants are found in the majority of TSC cases.

This test is only for deletion/duplication testing. For sequencing and deletion/duplication testing see test code 10661.

Individuals with an identifiable TSC pathogenic variant will have either a large deletion or duplication in up to 2% and 0.5% of cases in the TSC2 and TSC1 genes, respectively (Northrup et al. 2018. PubMed ID: 20301399).

Multiplex Ligation-Dependent Probe Amplification (MLPA) enables the detection of deletion and duplications of single and multiple exons within a given gene (Eijk-Van Os and Schouten. 2011). This test involves analysis only of the specific gene(s) of interest for each patient. The MLPA test is designed to have coverage for all exons for each targeted gene. It is a semi-quantitative technique to determine relative copy number using a multiplex PCR-based reaction. Only hybridized and ligated adjacent probe oligonucleotides of approximately 60 nucleotides in length are amplified using PCR and thus are specific for the sequence of interest. A stuffer sequence attached to the probe ensures a particular length for deciphering the probe target. Therefore, MLPA enables the detection of relatively small deletions and duplications within a single exon of a given gene or deletions and duplications encompassing the entire gene. For additional information please see www.mlpa.com.