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Wu R, Li X, Meng Z, Li P, He Z, Liang L. Phenotypic and genetic analysis of children with unexplained neurodevelopmental delay and neurodevelopmental comorbidities in a Chinese cohort using trio-based whole-exome sequencing. Orphanet J Rare Dis 2024; 19:205. [PMID: 38764027 PMCID: PMC11103872 DOI: 10.1186/s13023-024-03214-w] [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: 02/20/2023] [Accepted: 05/10/2024] [Indexed: 05/21/2024] Open
Abstract
BACKGROUND Trio-based whole-exome sequencing (trio-WES) enables identification of pathogenic variants, including copy-number variants (CNVs), in children with unexplained neurodevelopmental delay (NDD) and neurodevelopmental comorbidities (NDCs), including autism spectrum disorder (ASD), epilepsy, and attention deficit hyperactivity disorder. Further phenotypic and genetic analysis on trio-WES-tested NDD-NDCs cases may help to identify key phenotypic factors related to higher diagnostic yield of using trio-WES and novel risk genes associated with NDCs in clinical settings. METHODS In this study, we retrospectively performed phenotypic analysis on 163 trio-WES-tested NDD-NDCs children to determine the phenotypic differences between genetically diagnosed and non-genetically diagnosed groups. Additionally, we conducted genetic analysis of ASD genes with the help of Simons Foundation for Autism Research Institute (SFARI) Gene database to identify novel possible ASD-risk genes underlying genetic NDD conditions. RESULTS Among these 163 patients, pathogenic variants were identified in 82 cases (82/163, 50.3%), including 20 cases with CNVs. By comparing phenotypic variables between genetically diagnosed group (82 cases) and non-genetically diagnosed group (81 cases) with multivariate binary logistic regression analysis, we revealed that NDD-NDCs cases presenting with severe-profound NDD [53/82 vs 17/81, adjusted-OR (95%CI): 4.865 (2.213 - 10.694), adjusted-P < 0.001] or having multiple NDCs [26/82 vs 8/81, adjusted-OR (95%CI): 3.731 (1.399 - 9.950), adjusted-P = 0.009] or accompanying ASD [64/82 vs 35/81, adjusted-OR (95%CI): 3.256 (1.479 - 7.168), adjusted-P = 0.003] and head circumference abnormality [33/82 vs 11/81, adjusted-OR (95%CI): 2.788 (1.148 - 6.774), adjusted-P = 0.024] were more likely to have a genetic diagnosis using trio-WES. Moreover, 37 genes with monogenetic variants were identified in 48 patients genetically diagnosed with NDD-ASD, and 15 dosage-sensitive genes were identified in 16 individuals with NDD-ASD carrying CNVs. Most of those genes had been proven to be ASD-related genes. However, some of them (9 genes) were not proven sufficiently to correlate with ASD. By literature review and constructing protein-protein interaction networks among these 9 candidate ASD-risk genes and 102 established ASD genes obtained from the SFARI Gene database, we identified CUL4B, KCNH1, and PLA2G6 as novel possible ASD-risk genes underlying genetic NDD conditions. CONCLUSIONS Trio-WES testing is recommended for patients with unexplained NDD-NDCs that have severe-profound NDD or multiple NDCs, particularly those with accompanying ASD and head circumference abnormality, as these independent factors may increase the likelihood of genetic diagnosis using trio-WES. Moreover, NDD patients with pathogenic variants in CUL4B, KCNH1 and PLA2G6 should be aware of potential risks of developing ASD during their disease courses.
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Affiliation(s)
- Ruohao Wu
- Department of Children's Neuro-endocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, Guangdong, China
- Children's Medical Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou Guangdong, 510120, China
| | - Xiaojuan Li
- Department of Research and Molecular Diagnostics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, Guangdong, China
| | - Zhe Meng
- Department of Children's Neuro-endocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, Guangdong, China
- Children's Medical Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou Guangdong, 510120, China
| | - Pinggan Li
- Department of Children's Neuro-endocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, Guangdong, China
- Children's Medical Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou Guangdong, 510120, China
| | - Zhanwen He
- Department of Children's Neuro-endocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, Guangdong, China.
- Children's Medical Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou Guangdong, 510120, China.
| | - Liyang Liang
- Department of Children's Neuro-endocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, Guangdong, China.
- Children's Medical Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou Guangdong, 510120, China.
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Kim SH, Seo J, Kwon SS, Teng LY, Won D, Shin S, Lee JS, Lee ST, Choi JR, Kang HC. Common genes and recurrent causative variants in 957 Asian patients with pediatric epilepsy. Epilepsia 2024; 65:766-778. [PMID: 38073125 DOI: 10.1111/epi.17857] [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: 08/14/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 12/23/2023]
Abstract
OBJECTIVE We aimed to identify common genes and recurrent causative variants in a large group of Asian patients with different epilepsy syndromes and subgroups. METHODS Patients with unexplained pediatric-onset epilepsy were identified from the in-house Severance Neurodevelopmental Disorders and Epilepsy Database. All patients underwent either exome sequencing or multigene panels from January 2017 to December 2019, at Severance Children's Hospital in Korea. Clinical data were extracted from the medical records. RESULTS Of the 957 patients studied, 947 (99.0%) were Korean and 570 were male (59.6%). The median age at testing was 4.91 years (interquartile range, 1.53-9.39). The overall diagnostic yield was 32.4% (310/957). Clinical exome sequencing yielded a diagnostic rate of 36.9% (134/363), whereas the epilepsy panel yielded a diagnostic rate of 29.9% (170/569). Diagnostic yield differed across epilepsy syndromes. It was high in Dravet syndrome (87.2%, 41/47) and early infantile developmental epileptic encephalopathy (60.7%, 17/28), but low in West syndrome (21.8%, 34/156) and myoclonic-atonic epilepsy (4.8%, 1/21). The most frequently implicated genes were SCN1A (n = 49), STXBP1 (n = 15), SCN2A (n = 14), KCNQ2 (n = 13), CDKL5 (n = 11), CHD2 (n = 9), SLC2A1 (n = 9), PCDH19 (n = 8), MECP2 (n = 6), SCN8A (n = 6), and PRRT2 (n = 5). The recurrent genetic abnormalities included 15q11.2 deletion/duplication (n = 9), Xq28 duplication (n = 5), PRRT2 deletion (n = 4), MECP2 duplication (n = 3), SCN1A, c.2556+3A>T (n = 3), and 2q24.3 deletion (n = 3). SIGNIFICANCE Here we present the results of a large-scale study conducted in East Asia, where we identified several common genes and recurrent variants that varied depending on specific epilepsy syndromes. The overall genetic landscape of the Asian population aligns with findings from other populations of varying ethnicities.
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Affiliation(s)
- Se Hee Kim
- Division of Pediatric Neurology, Epilepsy Research Institute, Severance Children's Hospital, Yonsei University College of Medicine, Seoul, South Korea
- Department of Pediatrics, Yonsei University College of Medicine, Severance Children's Hospital, Seoul, South Korea
| | - Jieun Seo
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Soon Sung Kwon
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Lip-Yuen Teng
- Pediatric Neurology Unit, Department of Pediatrics, Hospital Tunku Azizah, Kuala Lumpur, Malaysia
| | - DongJu Won
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Saeam Shin
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Joon Soo Lee
- Division of Pediatric Neurology, Epilepsy Research Institute, Severance Children's Hospital, Yonsei University College of Medicine, Seoul, South Korea
- Department of Pediatrics, Yonsei University College of Medicine, Severance Children's Hospital, Seoul, South Korea
| | - Seung-Tae Lee
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Jong Rak Choi
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Hoon-Chul Kang
- Division of Pediatric Neurology, Epilepsy Research Institute, Severance Children's Hospital, Yonsei University College of Medicine, Seoul, South Korea
- Department of Pediatrics, Yonsei University College of Medicine, Severance Children's Hospital, Seoul, South Korea
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Snyder HE, Jain P, RamachandranNair R, Jones KC, Whitney R. Genetic Advancements in Infantile Epileptic Spasms Syndrome and Opportunities for Precision Medicine. Genes (Basel) 2024; 15:266. [PMID: 38540325 PMCID: PMC10970414 DOI: 10.3390/genes15030266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/13/2024] [Accepted: 02/20/2024] [Indexed: 06/15/2024] Open
Abstract
Infantile epileptic spasms syndrome (IESS) is a devastating developmental epileptic encephalopathy (DEE) consisting of epileptic spasms, as well as one or both of developmental regression or stagnation and hypsarrhythmia on EEG. A myriad of aetiologies are associated with the development of IESS; broadly, 60% of cases are thought to be structural, metabolic or infectious in nature, with the remainder genetic or of unknown cause. Epilepsy genetics is a growing field, and over 28 copy number variants and 70 single gene pathogenic variants related to IESS have been discovered to date. While not exhaustive, some of the most commonly reported genetic aetiologies include trisomy 21 and pathogenic variants in genes such as TSC1, TSC2, CDKL5, ARX, KCNQ2, STXBP1 and SCN2A. Understanding the genetic mechanisms of IESS may provide the opportunity to better discern IESS pathophysiology and improve treatments for this condition. This narrative review presents an overview of our current understanding of IESS genetics, with an emphasis on animal models of IESS pathogenesis, the spectrum of genetic aetiologies of IESS (i.e., chromosomal disorders, single-gene disorders, trinucleotide repeat disorders and mitochondrial disorders), as well as available genetic testing methods and their respective diagnostic yields. Future opportunities as they relate to precision medicine and epilepsy genetics in the treatment of IESS are also explored.
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Affiliation(s)
- Hannah E. Snyder
- Division of Neurology, Department of Paediatrics, McMaster University, Hamilton, ON L8N 3Z5, Canada (R.R.)
| | - Puneet Jain
- Division of Neurology, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON M5G 1E8, Canada
| | - Rajesh RamachandranNair
- Division of Neurology, Department of Paediatrics, McMaster University, Hamilton, ON L8N 3Z5, Canada (R.R.)
| | - Kevin C. Jones
- Division of Neurology, Department of Paediatrics, McMaster University, Hamilton, ON L8N 3Z5, Canada (R.R.)
| | - Robyn Whitney
- Division of Neurology, Department of Paediatrics, McMaster University, Hamilton, ON L8N 3Z5, Canada (R.R.)
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Anuar MA, Zainal Abidin M'A, Tan SH, Yeap CF, Yahaya NA. The Clinical Characteristics and Outcomes of Infantile Seizures in the First Year of Life: A Single-Center Study. Pediatr Neurol 2024; 150:10-14. [PMID: 37931500 DOI: 10.1016/j.pediatrneurol.2023.10.004] [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: 08/29/2022] [Revised: 08/29/2023] [Accepted: 10/12/2023] [Indexed: 11/08/2023]
Abstract
BACKGROUND Epilepsy has a high incidence among infants during their first year of life, yet the prognosis can vary significantly. Although considerable research has been conducted on infantile spasms, studies examining infantile-onset epilepsy, excluding infantile spasms, remain limited, particularly concerning the factors influencing outcomes. Therefore, our study aims to elucidate seizure control, developmental outcomes, and prognostic factors in infants with epilepsy during their first year of life, within a single-center study in Malaysia. METHODS We retrieved data from patients who experienced seizures before age 12 months and were followed for over two years, using electronic patient records at Hospital Raja Perempuan Zainab II in Kelantan, a state in Malaysia's east coast. We retrospectively reviewed these records and assessed clinical outcomes based on the last follow-up. RESULTS Of 75 patients, 61 (81.3%) achieved good seizure control or remission. At the last follow-up, 24 (32%) exhibited developmental delay, whereas 19 (25.3%) displayed abnormal neuroimaging. Patients with abnormal background electroencephalographic (EEG) activity, as well as abnormal radiological findings, were more likely to experience poor seizure control and unfavorable developmental outcomes (P < 0.05). CONCLUSIONS Our study underscores that most infants with epilepsy can achieve seizure remission. However, poor seizure control and developmental delay are associated with abnormal EEG background and characteristics, as well as neuroimaging abnormalities. The management of infantile-onset epilepsies may necessitate substantial resources and precise interventions to enhance overall outcomes.
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Affiliation(s)
- Muhamad Azamin Anuar
- Department of Paediatrics, Kulliyyah of Medicine, International Islamic University Malaysia, Kuantan, Pahang, Malaysia; Department of Paediatrics, Hospital Raja Perempuan Zainab II, Kota Bharu, Kelantan, Malaysia.
| | - Muhammad 'Adil Zainal Abidin
- Department of Public Health, Kulliyyah of Medicine, International Islamic University Malaysia, Kuantan, Pahang, Malaysia
| | - Soo Hong Tan
- Department of Paediatrics, Hospital Raja Perempuan Zainab II, Kota Bharu, Kelantan, Malaysia
| | - Cai Fong Yeap
- Department of Paediatrics, Hospital Raja Perempuan Zainab II, Kota Bharu, Kelantan, Malaysia
| | - Nor Azni Yahaya
- Department of Paediatrics, Hospital Raja Perempuan Zainab II, Kota Bharu, Kelantan, Malaysia
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Chourasia N, Yuskaitis CJ, Libenson MH, Bergin AM, Liu S, Zhang B, Poduri A, Harini C. Infantile spasms: assessing the diagnostic yield of an institutional guideline and the impact of etiology on long-term treatment response. Epilepsia 2022; 63:1164-1176. [PMID: 35211955 DOI: 10.1111/epi.17209] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 11/30/2022]
Abstract
OBJECTIVE Neuroimaging and genetic testing have been proposed for diagnostic evaluation of infantile spasms (IS), establishing etiology in ~60% of multicenter IS cohorts. A retrospective analysis of the yield of diagnostic etiology following an institutionally established guideline for investigation/treatment of IS was conducted, and the association between etiological subgroups and sustained response to standard treatment was evaluated. METHODS Etiology of IS, neuroimaging, and genetic results were extracted from clinical records. Etiology was categorized as acquired or non-acquired, the latter including syndromic patients, non-syndromic patients with confirmed etiology, and unknown cases. Regression analyses, using clinical variables including subtypes of etiology, were conducted to determine which factors correlated with favorable (spasms freedom at last follow-up after ≤ 2 standard treatments) versus unfavorable treatment outcome (refractory spasms despite two standard treatments or relapse). RESULTS We included 127 IS patients (60% males) with a follow-up of 2.4 years (range 0.6-5 years). All patients had neuroimaging, and 95% of patients in the non-acquired category (103 of 108 patients) had genetic testing. Etiology was identified in 103/127 (81%, CI-0.73-0.86). At last follow-up, 42 (33%) patients had favorable treatment outcome. No difference in treatment response was observed between acquired and non-acquired etiologies. Among patients with non-acquired etiologies, developmental delay prior to spasms onset increased the odds of unfavorable treatment outcome (p=0.014) while a clearly recognizable dysmorphic/syndromic etiology was associated with a lower risk for treatment failure (p=0.034). In non-acquired etiology without a recognizable dysmorphic/syndrome but with a genetic etiology, unfavorable treatment outcome was more likely (p=0.043). SIGNIFICANCE Rigorous evaluation with neuroimaging and genetic testing yields an etiological diagnosis in most patients with IS. Among patients with a non-acquired etiology, those with recognizable dysmorphic/syndromic diagnosis had a higher likelihood of a favorable treatment outcome, while the absence of such a finding, when associated with an identifiable genetic diagnosis, was associated with unfavorable treatment outcomes.
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Affiliation(s)
- Nitish Chourasia
- Division of Epilepsy and Clinical Neurophysiology, Department of Neurology, Boston Children's Hospital (study performed), Boston, MA, USA.,Le Bonheur Comprehensive Epilepsy Program & Neuroscience Institute, Le Bonheur Children's Hospital (author's current location), Memphis, TN, USA
| | - Christopher J Yuskaitis
- Division of Epilepsy and Clinical Neurophysiology, Department of Neurology, Boston Children's Hospital (study performed), Boston, MA, USA
| | - Mark H Libenson
- Division of Epilepsy and Clinical Neurophysiology, Department of Neurology, Boston Children's Hospital (study performed), Boston, MA, USA
| | - Ann M Bergin
- Division of Epilepsy and Clinical Neurophysiology, Department of Neurology, Boston Children's Hospital (study performed), Boston, MA, USA
| | - Shanshan Liu
- Biostatistics and Research Design Center, Institutional Centers for Clinical and Translational Research, Boston Children's Hospital, Boston, MA, USA
| | - Bo Zhang
- Department of Neurology, Boston Children's Hospital, Biostatistics and Research Design Center, Institutional Centers for Clinical and Translational Research, Boston Children's Hospital, Boston, MA, USA
| | - Annapurna Poduri
- Division of Epilepsy and Clinical Neurophysiology, Department of Neurology, Boston Children's Hospital (study performed), Boston, MA, USA
| | - Chellamani Harini
- Division of Epilepsy and Clinical Neurophysiology, Department of Neurology, Boston Children's Hospital (study performed), Boston, MA, USA
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Cali E, Rocca C, Salpietro V, Houlden H. Epileptic Phenotypes Associated With SNAREs and Related Synaptic Vesicle Exocytosis Machinery. Front Neurol 2022; 12:806506. [PMID: 35095745 PMCID: PMC8792400 DOI: 10.3389/fneur.2021.806506] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 11/16/2021] [Indexed: 01/29/2023] Open
Abstract
SNAREs (soluble N-ethylmaleimide sensitive factor attachment protein receptor) are an heterogeneous family of proteins that, together with their key regulators, are implicated in synaptic vesicle exocytosis and synaptic transmission. SNAREs represent the core component of this protein complex. Although the specific mechanisms of the SNARE machinery is still not completely uncovered, studies in recent years have provided a clearer understanding of the interactions regulating the essential fusion machinery for neurotransmitter release. Mutations in genes encoding SNARE proteins or SNARE complex associated proteins have been associated with a variable spectrum of neurological conditions that have been recently defined as “SNAREopathies.” These include neurodevelopmental disorder, autism spectrum disorder (ASD), movement disorders, seizures and epileptiform abnormalities. The SNARE phenotypic spectrum associated with seizures ranges from simple febrile seizures and infantile spasms, to severe early-onset epileptic encephalopathies. Our study aims to review and delineate the epileptic phenotypes associated with dysregulation of synaptic vesicle exocytosis and transmission, focusing on the main proteins of the SNARE core complex (STX1B, VAMP2, SNAP25), tethering complex (STXBP1), and related downstream regulators.
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Affiliation(s)
- Elisa Cali
- MRC Centre for Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Clarissa Rocca
- MRC Centre for Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Vincenzo Salpietro
- MRC Centre for Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Henry Houlden
- MRC Centre for Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, United Kingdom
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Abstract
Almost 25 years have passed since a mutation of a formin gene, DIAPH1, was identified as being responsible for a human inherited disorder: a form of sensorineural hearing loss. Since then, our knowledge of the links between formins and disease has deepened considerably. Mutations of DIAPH1 and six other formin genes (DAAM2, DIAPH2, DIAPH3, FMN2, INF2 and FHOD3) have been identified as the genetic cause of a variety of inherited human disorders, including intellectual disability, renal disease, peripheral neuropathy, thrombocytopenia, primary ovarian insufficiency, hearing loss and cardiomyopathy. In addition, alterations in formin genes have been associated with a variety of pathological conditions, including developmental defects affecting the heart, nervous system and kidney, aging-related diseases, and cancer. This review summarizes the most recent discoveries about the involvement of formin alterations in monogenic disorders and other human pathological conditions, especially cancer, with which they have been associated. In vitro results and experiments in modified animal models are discussed. Finally, we outline the directions for future research in this field.
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Affiliation(s)
| | - Miguel A. Alonso
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, 28049 Madrid, Spain;
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