European Journal of Human Genetics (2014) 22, doi:10.1038/ejhg.2013.129 & 2014 Macmillan Publishers Limited All rights reserved 1018-4813/14 www.nature.com/ejhg CLINICAL UTILITY GENE CARD Clinical utility gene card for: Tuberous sclerosis complex (TSC1, TSC2) Karin Mayer*,1, Christa Fonatsch2, Katharina Wimmer3, Ans MW van den Ouweland4 and Anneke JA Maat-Kievit4 European Journal of Human Genetics (2014) 22, doi:10.1038/ejhg.2013.129; published online 12 June 2013 1. DISEASE CHARACTERISTICS For detection of chromosomal rearrangements, oligo and SNP 1.1 Name of the disease (synonyms) array analyses can be performed. An exception is a microdeletion, Tuberous sclerosis complex (TSC), Bourneville-Pringle disease. particularly a TSC2/PKD1 contiguous gene syndrome, which can be detected by FISH (fluorescence in situ hybridisation).2 1.2 OMIM# of the disease Next-generation sequencing approaches can also be used. 191100, 613254. 1.7 Analytical validation Bidirectional sequence analysis or other methods with a comparable 1.3 Name of the analysed genes or DNA/chromosome segments sensitivity as sequence analysis; confirmation of results by a second TSC1, TSC2. DNA extraction or a second method; confirmation of intragenic or larger chromosomal deletions by a second method, for example, 1.4 OMIM# of the gene(s) quantitative PCR, long-range PCR, and FISH. Variants of unknown 605284, 191092. significance should be further investigated at least by in silico analysis and, if possible, by segregation analysis. In some cases (especially for 1.5 Mutational spectrum some missense and splice site variants), it can be still unclear Missense, nonsense, and splice site mutations; insertions, deletions, whether these variants are disease-causing or rare neutral variants. genomic rearrangements, microdeletions, intragenic differences of Functional tests can be used to help resolve whether these variants gene dose/changes of copy number (duplications or deletions of one are likely to be disease-causing.3 Intronic variants, missense, or more exons). and synonymous changes that are suspected to affect RNA splicing Presently, more than 450 different disease-causing mutations are should be verified by investigating an RNA sample, applying known for TSC1 and more than 1300 for TSC2, respectively. The vast RT-PCR for example. majority (80%) of TSC1 mutations are truncating comprising frame- shift, nonsense, and splice mutations. Missense changes represent 1.8 Estimated frequency of the disease (incidence at birth (‘birth 17% and large genomic deletions are rare (3%). Truncating mutations prevalence’) or population prevalence) (65%) are also the most common mutation type in the TSC2 gene. In Birth incidence is estimated to be 1:6000.4 Numbers for prevalence contrast to the TSC1 gene, missense mutations (26%) and large range from 0.7 to 3.8 per 100 000 population in the United Kingdom5 genomic deletions (6%) occur substantially more frequently. Muta- assuming no differences in other ethnical groups. tions that have been published in the literature and mutations submitted without publication are available in the Tuberous sclerosis 1.9 If applicable, prevalence in the ethnic group of investigated 1 database. person Not applicable. 1.6 Analytical methods For detection of point mutations and small insertions/deletions: 1.10 Diagnostic setting complete analysis of all coding regions and neighbouring intron sequences (splice sites) in genomic DNA, by sequence analysis or Yes No. other techniques with a sensitivity comparable to sequence analysis. A. (Differential) diagnostics 2 & For detection of intragenic deletions and duplications with B. Predictive Testing 2 & differences of gene dose: analysis of both genes, for example, by C. Risk assessment in relatives 2 & MLPA (multiplex ligation dependent probe amplification) or quanti- D. Prenatal 2 & tative PCR. 1Center for Human Genetics and Laboratory Diagnostics, Department of Molecular Genetics, Dr. Klein, Dr. Rost and Colleagues, Martinsried, Germany; 2University Council, Medical University of Innsbruck, Innsbruck, Vienna, Austria; 3Division of Human Genetics, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University Innsbruck, Innsbruck, Austria; 4Department Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands *Correspondence: Dr K Mayer, Center for Human Genetics and Laboratory Diagnostics, Department of Molecular Genetics, Dr. Klein, Dr. Rost and Colleagues, Lochhamer Street 29, D-82152 Martinsried, Germany. Tel: +49 89 895578 0; Fax: +49 89 895578 780; E-mail: [email protected] Clinical Utility Gene Card e2 Comment: As there is an almost 100% penetrance, clinical predictive value is Prenatal genetic testing including polar body analysis and pre- 100%. However, there may be highly variable clinical expressivity.16 implantation genetic testing is available for families with a known genetic cause of TSC. Caveat: (germline) mosaicism6 in one of the 2.6 Negative clinical predictive value parents of a patient if they both test negative for the constitutive (probability of not developing the disease if the test is negative) mutation, offer prenatal testing for new pregnancies, and offer to test Assume an increased risk based on family history for a non-affected other siblings of the patient. person. Allelic and locus heterogeneity may need to be considered. Index case in that family had been tested: 2. TEST CHARACTERISTICS If the pathogenic mutation is identified in the index patient and is tested negative in another family member, then the clinical predictive value for the family member is almost 100%. Genotype or disease A: True positives C: False negative Index case in that family had not been tested: B: False positives D: True negative 85%. This question arises in children who have no clinical Present Absent symptoms yet, or in adults with minimal clinical symptoms such that the diagnosis cannot be made by clinical criteria alone. Test Positive A B Sensitivity: A/(A þ C) 3. CLINICAL UTILITY Specificity: D/(D þ B) Negative C D Positive predictive value: A/(A þ B) 3.1 (Differential) diagnostics: The tested person is Negative predictive value: D/(C þ D) clinically affected (To be answered if in 1.10 ‘A’ was marked) 2.1 Analytical sensitivity 3.1.1 Can a diagnosis be made other than through a genetic test? (proportion of positive tests if the genotype is present) Assuming a prevalence of 90% for point mutations and of up to No & (continue with 3.1.4) 2 10% for intragenic deletions/duplications, microdeletions and rear- Yes 2 rangements, germline mutations will be detected in 80–85% of cases7 Clinically Imaging 2 if both genes are analysed by multiple methods, including a deletion/ Endoscopy & duplication screen. Rare splice mutations located deep in introns or Biochemistry & mutations affecting mRNA expression (for example in promoter Electrophysiology & regions) are not detected by current DNA-based diagnostics but can Other (please describe) Through clinical and imaging investigations, a 8 be identified with RNA-based methods. Additional mutations not definite diagnosis of TSC can be made if the detected by routine diagnostic methods like Sanger sequencing and diagnostic criteria are fulfilled. The diagnosis can MLPA may be identified applying next-generation sequencing be ‘probable’ or ‘possible’, owing to the variable 9,10 approaches. expressivity of the clinical signs, young age, or mosaicism. In the latter, a diagnosis may be arrived 2.2 Analytical specificity at if DNA for TSC testing of the tissue in question, (proportion of negative tests if the genotype is not present) in case of segmental or somatic mosaicism, is Nearly 100%. available through surgery or biopsy. Also with weak clinical manifestations (eg, only angiomyolipoma 2.3 Clinical sensitivity (AML) of the kidney or cortical tubers in the brain) (proportion of positive tests if the disease is present) the diagnosis of TSC requires the detection of a The clinical sensitivity can be dependent on variable factors such as causative mutation.17 If the diagnostic criteria for age or family history or incomplete clinical investigations performed. TSC are not definite in a parent or another first In such cases, a general statement should be given, even if a degree relative of an affected person with an quantification can only be made case by case. identified TSC mutation, mutation analysis can Clinical sensitivity reaches 70–85% if the diagnostic criteria of confirm the diagnosis and may guide genetic Roach11 are fulfilled (corresponding to ‘TSC definite’), depending on counselling. the application of one or more analytical methods.12–15 Because of variable clinical expressivity, lower sensitivities are expected in phenotypes corresponding to ‘TSC probable’ and ‘TSC possible’. 3.1.2 Describe the burden of alternative diagnostic methods to the 2.4 Clinical specificity patient (proportion of negative tests if the disease is not present) There is no extra burden of the alternative diagnostic methods to a The clinical specificity can be dependent on variable factors such as patient. When TSC is suspected in a patient, full clinical and imaging age or family history or number of clinical investigations performed. investigations are needed, to get insight into the clinical status of the In such cases, a general statement should be given, even if a patient and to guide further follow-up. Because of the variability of quantification can only be made case by case. TSC, investigation of different organ systems are needed,