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Ryu SW, Yoon J, Kim D, Han B, Han H, Han J, Lee H, Seo GH, Lee BH. Identification of a complex intrachromosomal inverted insertion in the long arm of chromosome 9 as a cause of tuberous sclerosis complex in a Korean family. Mol Genet Genomic Med 2024; 12:e2330. [PMID: 38265426 PMCID: PMC10958175 DOI: 10.1002/mgg3.2330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 11/13/2023] [Accepted: 11/16/2023] [Indexed: 01/25/2024] Open
Abstract
BACKGROUND Tuberous sclerosis complex (TSC) is an autosomal dominant multisystem disorder, caused by a loss-of-function of either TSC1 or TSC2 gene. However, in 10%-15% TSC patients there is no pathogenic variant identified in either TSC1 or TSC2 genes based on standard clinical testing. METHODS In this study, genome sequencing was performed for families with clinical diagnosis of TSC with negative results from TSC1 and TSC2 single-gene tests. RESULTS Herein, we report a family presenting a classical TSC phenotype with an unusual, complex structural variant involving the TSC1 gene: an intrachromosomal inverted insertion in the long arm of chromosome 9. We speculate that the inverted 9q33.3q34.13 region was inserted into the q31.2 region with the 3'-end of the breakpoint of the inversion being located within the TSC1 gene, resulting in premature termination of TSC1. CONCLUSIONS In this study, we demonstrate the utility of genome sequencing for the identification of complex chromosomal rearrangement. Because the breakpoints are located within the deep intronic/intergenic region, this copy-neutral variant was missed by the TSC1 and TSC2 single-gene tests and contributed to an unknown etiology. Together, this finding suggests that complex structural variants may be underestimated causes for the etiology of TSC.
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Affiliation(s)
| | - Ji‐Hee Yoon
- Department of Pediatrics, Asan Medical Center Children's HospitalUniversity of Ulsan College of MedicineSeoulRepublic of Korea
| | | | | | | | | | | | | | - Beom Hee Lee
- Department of Pediatrics, Asan Medical Center Children's HospitalUniversity of Ulsan College of MedicineSeoulRepublic of Korea
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Ye Z, Lin S, Zhao X, Wallis M, Gao X, Sun L, Wu J, Duan J, Yao Y, Li L, Chen L, Cao D, Hu Z, Zhang VW, Berkovic SF, Scheffer IE, Liao J, Hildebrand MS. Are Germline Mosaic TSC1/2 Variants Present in Controls? Implications for Diagnosis. Pediatr Neurol 2024; 150:37-39. [PMID: 37951160 DOI: 10.1016/j.pediatrneurol.2023.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 09/14/2023] [Accepted: 10/13/2023] [Indexed: 11/13/2023]
Affiliation(s)
- Zimeng Ye
- Department of Medicine, Epilepsy Research Centre, The University of Melbourne, Heidelberg, Victoria, Australia
| | - Sufang Lin
- Department of Neurology, Epilepsy Centre, Shenzhen Children's Hospital, Shenzhen, Guangdong Province, China
| | - Xia Zhao
- Department of Neurology, Epilepsy Centre, Shenzhen Children's Hospital, Shenzhen, Guangdong Province, China
| | - Mathew Wallis
- Tasmania Clinical Genetics Service, Royal Hobart Hospital, Hobart, Tasmania, Australia; School of Medicine, University of Tasmania, Hobart, Tasmania, Australia; Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia; Austin Health, Heidelberg, Victoria, Australia
| | - Xinyi Gao
- AmCare Genomics Laboratory, Guangzhou, Guangdong Province, China
| | - Li Sun
- AmCare Genomics Laboratory, Guangzhou, Guangdong Province, China
| | - Jiarui Wu
- AmCare Genomics Laboratory, Guangzhou, Guangdong Province, China
| | - Jing Duan
- Department of Neurology, Epilepsy Centre, Shenzhen Children's Hospital, Shenzhen, Guangdong Province, China
| | - Yi Yao
- Department of Neurology, Epilepsy Centre, Shenzhen Children's Hospital, Shenzhen, Guangdong Province, China
| | - Lin Li
- Department of Neurology, Epilepsy Centre, Shenzhen Children's Hospital, Shenzhen, Guangdong Province, China
| | - Li Chen
- Department of Neurology, Epilepsy Centre, Shenzhen Children's Hospital, Shenzhen, Guangdong Province, China
| | - Dezhi Cao
- Department of Neurology, Epilepsy Centre, Shenzhen Children's Hospital, Shenzhen, Guangdong Province, China
| | - Zhanqi Hu
- Department of Neurology, Epilepsy Centre, Shenzhen Children's Hospital, Shenzhen, Guangdong Province, China
| | - Victor W Zhang
- AmCare Genomics Laboratory, Guangzhou, Guangdong Province, China
| | - Samuel F Berkovic
- Department of Medicine, Epilepsy Research Centre, The University of Melbourne, Heidelberg, Victoria, Australia; Austin Health, Heidelberg, Victoria, Australia
| | - Ingrid E Scheffer
- Department of Medicine, Epilepsy Research Centre, The University of Melbourne, Heidelberg, Victoria, Australia; Austin Health, Heidelberg, Victoria, Australia; Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia; Department of Paediatrics, The University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia; The Florey Institute, Parkville, Victoria, Australia.
| | - Jianxiang Liao
- Department of Neurology, Epilepsy Centre, Shenzhen Children's Hospital, Shenzhen, Guangdong Province, China.
| | - Michael S Hildebrand
- Department of Medicine, Epilepsy Research Centre, The University of Melbourne, Heidelberg, Victoria, Australia; Austin Health, Heidelberg, Victoria, Australia; Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia.
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Specchio N, Nabbout R, Aronica E, Auvin S, Benvenuto A, de Palma L, Feucht M, Jansen F, Kotulska K, Sarnat H, Lagae L, Jozwiak S, Curatolo P. Updated clinical recommendations for the management of tuberous sclerosis complex associated epilepsy. Eur J Paediatr Neurol 2023; 47:25-34. [PMID: 37669572 DOI: 10.1016/j.ejpn.2023.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 08/27/2023] [Accepted: 08/28/2023] [Indexed: 09/07/2023]
Abstract
Children with tuberous sclerosis complex (TSC), may experience a variety of seizure types in the first year of life, most often focal seizure sand epileptic spasms. Drug resistance is seen early in many patients, and the management of TSC associated epilepsy remain a major challenge for clinicians. In 2018 clinical recommendations for the management of TSC associated epilepsy were published by a panel of European experts. In the last five years considerable progress has been made in understanding the neurobiology of epileptogenesis and three interventional randomized controlled trials have changed the therapeutic approach for the management of TSC associated epilepsy. Pre-symptomatic treatment with vigabatrin may delay seizure onset, may reduce seizure severity and reduce the risk of epileptic encephalopathy. The efficacy of mTOR inhibition with adjunctive everolimus was documented in patients with TSC associated refractory seizures and cannabidiol could be another therapeutic option. Epilepsy surgery has significantly improved seizure outcome in selected patients and should be considered early in all patients with drug resistant epilepsy. There is a need to identify patients who may have a higher risk of developing epilepsy and autism spectrum disorder (ASD). In the recent years significant progress has been made owing to the early identification of risk factors for the development of drug-resistant epilepsy. Better understanding of the mechanism underlying epileptogenesis may improve the management for TSC-related epilepsy. Developmental neurobiology and neuropathology give opportunities for the implementation of concepts related to clinical findings, and an early genetic diagnosis and use of EEG and MRI biomarkers may improve the development of pre-symptomatic and disease-modifying strategies.
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Affiliation(s)
- Nicola Specchio
- Clinical and Experimental Neurology, Bambino Gesu' Children's Hospital IRCCS, Full Member of European Reference Network on Rare and Complex Epilepsies EpiCARE, Rome, Italy.
| | - Rima Nabbout
- Department of Pediatric Neurology, Necker Enfants Malades Hospital, Université Paris Cité, Member of the European Reference Network on Rare and Complex Epilepsies EpiCARE, INSERM U1163, Institut Imagine, Paris, France
| | - Eleonora Aronica
- Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Department of (Neuro)Pathology, Amsterdam, Netherlands; Stichting Epilepsie Instellingen Nederland (SEIN), Heemstede, the Netherlands
| | - Stephane Auvin
- APHP, Service de Neurologie Pédiatrique, Centre Epilepsies Rares, Member of the European Reference Network on Rare and Complex Epilepsies EpiCARE, Hôpital Robert Debré, Paris, France; Université Paris-Cité, INSERM NeuroDiderot, Paris, France; Institut Universitaire de France (IUF), Paris, France
| | | | - Luca de Palma
- Clinical and Experimental Neurology, Bambino Gesu' Children's Hospital IRCCS, Full Member of European Reference Network on Rare and Complex Epilepsies EpiCARE, Rome, Italy
| | - Martha Feucht
- Epilepsy Center, Department of Pediatrics, Medical University Vienna, Austria
| | - Floor Jansen
- Department of Pediatric Neurology, Brain Center UMC Utrecht, the Netherlands
| | - Katarzyna Kotulska
- Department of Neurology and Epileptology, The Children's Memorial Health Institute, Warsaw, Poland
| | - Harvey Sarnat
- Department of Paediatrics (Neurology), Pathology and Laboratory Medicine (Neuropathology) and Clinical Neurosciences, University of Calgary Cumming School of Medicine and Alberta Children's Hospital Research Institute (Owerko Centre), Calgary, AB, Canada
| | - Lieven Lagae
- Department of Paediatric Neurology, University of Leuven, Leuven, Belgium
| | - Sergiusz Jozwiak
- Research Department, The Children's Memorial Health Institute, ERN EPICARE, Warsaw, Poland
| | - Paolo Curatolo
- Child Neurology and Psychiatry Unit, Systems Medicine Department, Tor Vergata University, Rome, Italy
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Curatolo P, Trivisano M, Specchio N. Updated Genotype-Phenotype Correlations in TSC. Semin Pediatr Neurol 2023; 47:101086. [PMID: 37919037 DOI: 10.1016/j.spen.2023.101086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2023]
Abstract
GENOTYPE/PHENOTYPE CORRELATIONS IN TUBEROUS SCLEROSIS COMPLEX Paolo Curatolo MD, Romina Moavero MD, Denis Roberto, Federica Graziola Seminars in Pediatric Neurology Volume 22, Issue 4, December 2015, Pages 259-273 Tuberous sclerosis complex (TSC) is an autosomal dominant disorder characterized by the development of widespread hamartomatous lesions in various organs, including brain, skin, kidneys, heart, and eyes. Central nervous system is almost invariably involved, with up to 85% of patients presenting with epilepsy, and at least half of patients having intellectual disability or other neuropsychiatric disorders including autism spectrum disorder. TSC is caused by the mutation in one of the 2 genes TSC1, at 9q34, and TSC2, at 16p13.3. They respectively encode for hamartin and tuberin, which form an intracellular complex inhibiting the mammalian target of rapamycin. Mammalian target of rapamycin overactivation following the genetic defect determines the cell growth and proliferation responsible for TSC-related lesions, as well as the alterations in neuronal excitability and synaptogenesis leading to epilepsy and neuropsychiatric disorders. A causative mutation for the disorder is identified in about 85% of patients with a clinical diagnosis of TSC. Mosaicism and technology limits likely explain most of the no mutation identified cases. This review confirms that patients with TSC2 mutations considered as a group usually present a more severe phenotype, characterized by higher number of tubers, earlier age at seizure onset and higher prevalence of intellectual disability. However, the clinical phenotype of the disease presents a high variability, thus making the prediction of the phenotype on an individual basis still challenging. The increasing application of new molecular techniques to subjects with TSC has the potential to significantly reduce the rate of patients with no mutation demonstrated and to identify an increasing higher number of mutations. This would hopefully allow a better characterization of higher risk mutations, which might help clinicians to plan individualized surveillance plans. Furthermore, the increasing availability of disease registries to collect clinical and genetics data of patients help to define more valid and clinically oriented genotype or phenotype correlations.
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Affiliation(s)
- Paolo Curatolo
- Child Neurology and Psychiatry Unit, Systems Medicine Department, Tor Vergata University, Rome, Italy
| | - Marina Trivisano
- Child Neurology, Epilepsy and Movement Disorders, Bambino Gesù, IRCCS Children's Hospital, Full Member of European Reference Network EpiCARE, Rome, Italy
| | - Nicola Specchio
- Child Neurology, Epilepsy and Movement Disorders, Bambino Gesù, IRCCS Children's Hospital, Full Member of European Reference Network EpiCARE, Rome, Italy.
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Klonowska K, Giannikou K, Grevelink JM, Boeszoermenyi B, Thorner AR, Herbert ZT, Afrin A, Treichel AM, Hamieh L, Kotulska K, Jozwiak S, Moss J, Darling TN, Kwiatkowski DJ. Comprehensive genetic and phenotype analysis of 95 individuals with mosaic tuberous sclerosis complex. Am J Hum Genet 2023; 110:979-988. [PMID: 37141891 PMCID: PMC10257004 DOI: 10.1016/j.ajhg.2023.04.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 04/12/2023] [Indexed: 05/06/2023] Open
Abstract
Tuberous sclerosis complex (TSC) is a neurogenetic disorder due to loss-of-function TSC1 or TSC2 variants, characterized by tumors affecting multiple organs, including skin, brain, heart, lung, and kidney. Mosaicism for TSC1 or TSC2 variants occurs in 10%-15% of individuals diagnosed with TSC. Here, we report comprehensive characterization of TSC mosaicism by using massively parallel sequencing (MPS) of 330 TSC samples from a variety of tissues and fluids from a cohort of 95 individuals with mosaic TSC. TSC1 variants in individuals with mosaic TSC are much less common (9%) than in germline TSC overall (26%) (p < 0.0001). The mosaic variant allele frequency (VAF) is significantly higher in TSC1 than in TSC2, in both blood and saliva (median VAF: TSC1, 4.91%; TSC2, 1.93%; p = 0.036) and facial angiofibromas (median VAF: TSC1, 7.7%; TSC2 3.7%; p = 0.004), while the number of TSC clinical features in individuals with TSC1 and TSC2 mosaicism was similar. The distribution of mosaic variants across TSC1 and TSC2 is similar to that for pathogenic germline variants in general TSC. The systemic mosaic variant was not present in blood in 14 of 76 (18%) individuals with TSC, highlighting the value of analysis of multiple samples from each individual. A detailed comparison revealed that nearly all TSC clinical features are less common in individuals with mosaic versus germline TSC. A large number of previously unreported TSC1 and TSC2 variants, including intronic and large rearrangements (n = 11), were also identified.
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Affiliation(s)
- Katarzyna Klonowska
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
| | - Krinio Giannikou
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Division of Hematology/Oncology, Cancer and Blood Disease Institute, Children's Hospital Los Angeles, Los Angeles, CA 90027, USA
| | - Joannes M Grevelink
- Boston Dermatology and Laser Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Barbara Boeszoermenyi
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Aaron R Thorner
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Zachary T Herbert
- Molecular Biology Core Facilities, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Antara Afrin
- Department of Dermatology, Uniformed Services University, Bethesda, MA 20814, USA; Pulmonary Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alison M Treichel
- Department of Dermatology, Uniformed Services University, Bethesda, MA 20814, USA; Pulmonary Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; Department of Dermatology, University Hospitals Cleveland Medical Center, Case Western Reserve University Cleveland, Cleveland, OH 44106, USA
| | - Lana Hamieh
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Division of Hospital Medicine, Barnes Jewish Hospital, Washington University in St Louis, St. Louis, MO 63110, USA
| | - Katarzyna Kotulska
- Department of Neurology and Epileptology, Children's Memorial Health Institute, Warsaw 04-736, Poland
| | - Sergiusz Jozwiak
- Department of Neurology and Epileptology, Children's Memorial Health Institute, Warsaw 04-736, Poland; Research Department, Children's Memorial Health Institute, Warsaw 04-736, Poland
| | - Joel Moss
- Pulmonary Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Thomas N Darling
- Department of Dermatology, Uniformed Services University, Bethesda, MA 20814, USA
| | - David J Kwiatkowski
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
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Lü Y, Jiang Y, Zhou X, Hao N, Lü G, Guo X, Guo R, Liu W, Xu C, Chang J, Li M, Zhang H, Zhou J, Zhang W(V, Qi Q. Evaluation and Analysis of Absence of Homozygosity (AOH) Using Chromosome Analysis by Medium Coverage Whole Genome Sequencing (CMA-seq) in Prenatal Diagnosis. Diagnostics (Basel) 2023; 13:diagnostics13030560. [PMID: 36766665 PMCID: PMC9914714 DOI: 10.3390/diagnostics13030560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/29/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
OBJECTIVE Absence of homozygosity (AOH) is a genetic characteristic known to cause human diseases mainly through autosomal recessive or imprinting mechanisms. The importance and necessity of accurate AOH detection has become more clinically significant in recent years. However, it remains a challenging task for sequencing-based methods thus far. METHODS In this study, we developed and optimized a new bioinformatic algorithm based on the assessment of minimum sequencing coverage, optimal bin size, the Z-score threshold of four types of allele count and the frequency for accurate genotyping using 28 AOH negative samples, and redefined the AOH detection cutoff value. We showed the performance of chromosome analysis by five-fold coverage whole genome sequencing (CMA-seq) for AOH identification in 27 typical prenatal/postnatal AOH positive samples, which were previously confirmed by chromosomal microarray analysis with single nucleotide polymorphism array (CMA/SNP array). RESULTS The blinded study indicated that for all three forms of AOH, including whole genomic AOH, single chromosomal AOH and segmental AOH, and all kinds of sample types, including chorionic villus sampling, amniotic fluid, cord blood, peripheral blood and abortive tissue, CMA-seq showed equivalent detection power to that of routine CMA/SNP arrays (750K). The subtle difference between the two methods is that CMA-seq is prone to detect small inconsecutive AOHs, while CMA/SNP array reports it as a whole. CONCLUSION Based on our newly developed bioinformatic algorithm, it is feasible to detect clinically significant AOH using CMA-seq in prenatal diagnosis.
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Affiliation(s)
- Yan Lü
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Yulin Jiang
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Xiya Zhou
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Na Hao
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Guizhen Lü
- AmCare Genomics Lab, Guangzhou 510335, China
| | | | - Ruidong Guo
- AmCare Genomics Lab, Guangzhou 510335, China
| | - Wenjie Liu
- AmCare Genomics Lab, Guangzhou 510335, China
| | - Chenlu Xu
- AmCare Genomics Lab, Guangzhou 510335, China
| | - Jiazhen Chang
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Mengmeng Li
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Hanzhe Zhang
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Jing Zhou
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China
| | | | - Qingwei Qi
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China
- Correspondence: ; Tel.: +86-1851-066-6066
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