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Zheng J, Gu M, Xiao S, Li C, Mi H, Xu X. Novel SETBP1 D874V adjacent to the degron causes canonical schinzel-giedion syndrome: a case report and review of the literature. BMC Pediatr 2024; 24:309. [PMID: 38711130 DOI: 10.1186/s12887-024-04779-y] [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: 11/01/2023] [Accepted: 04/22/2024] [Indexed: 05/08/2024] Open
Abstract
Schinzel-Giedion syndrome (SGS) is a severe multisystem disorder characterized by distinctive facial features, profound intellectual disability, refractory epilepsy, cortical visual impairment, hearing loss, and various congenital anomalies. SGS is attributed to gain-of-function (GoF) variants in the SETBP1 gene, with reported variants causing canonical SGS located within a 12 bp hotspot region encoding SETBP1 residues aa868-871 (degron). Here, we describe a case of typical SGS caused by a novel heterozygous missense variant, D874V, adjacent to the degron. The female patient was diagnosed in the neonatal period and presented with characteristic facial phenotype (midface retraction, prominent forehead, and low-set ears), bilateral symmetrical talipes equinovarus, overlapping toes, and severe bilateral hydronephrosis accompanied by congenital heart disease, consistent with canonical SGS. This is the first report of a typical SGS caused by a, SETBP1 non-degron missense variant. This case expands the genetic spectrum of SGS and provides new insights into genotype-phenotype correlations.
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Affiliation(s)
- Jing Zheng
- Department of Pediatrics, The First People's Hospital of Yunnan Province, 157 Jinbi Road, Xishan District, Kunming, 650032, Yunnan Province, China
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
| | - Meiqun Gu
- Department of Pediatrics, The First People's Hospital of Yunnan Province, 157 Jinbi Road, Xishan District, Kunming, 650032, Yunnan Province, China
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
| | - Shasha Xiao
- Department of Pediatrics, The First People's Hospital of Yunnan Province, 157 Jinbi Road, Xishan District, Kunming, 650032, Yunnan Province, China
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
| | - Chongzhen Li
- Department of Pediatrics, The First People's Hospital of Yunnan Province, 157 Jinbi Road, Xishan District, Kunming, 650032, Yunnan Province, China
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
| | - Hongying Mi
- Department of Pediatrics, The First People's Hospital of Yunnan Province, 157 Jinbi Road, Xishan District, Kunming, 650032, Yunnan Province, China
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
| | - Xiaoyan Xu
- Department of Pediatrics, The First People's Hospital of Yunnan Province, 157 Jinbi Road, Xishan District, Kunming, 650032, Yunnan Province, China.
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, China.
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Sullivan JA, Spillmann RC, Schoch K, Walley N, Alkelai A, Stong N, Shea PR, Petrovski S, Jobanputra V, McConkie-Rosell A, Shashi V. The best of both worlds: Blending cutting-edge research with clinical processes for a productive exome clinic. Clin Genet 2024; 105:62-71. [PMID: 37853563 DOI: 10.1111/cge.14437] [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: 08/11/2023] [Revised: 09/29/2023] [Accepted: 10/04/2023] [Indexed: 10/20/2023]
Abstract
Genomic medicine has been transformed by next-generation sequencing (NGS), inclusive of exome sequencing (ES) and genome sequencing (GS). Currently, ES is offered widely in clinical settings, with a less prevalent alternative model consisting of hybrid programs that incorporate research ES along with clinical patient workflows. We were among the earliest to implement a hybrid ES clinic, have provided diagnoses to 45% of probands, and have identified several novel candidate genes. Our program is enabled by a cost-effective investment by the health system and is unique in encompassing all the processes that have been variably included in other hybrid/clinical programs. These include careful patient selection, utilization of a phenotype-agnostic bioinformatics pipeline followed by manual curation of variants and phenotype integration by clinicians, close collaborations between the clinicians and the bioinformatician, pursuit of interesting variants, communication of results to patients in categories that are predicated upon the certainty of a diagnosis, and tracking changes in results over time and the underlying mechanisms for such changes. Due to its effectiveness, scalability to GS and its resource efficiency, specific elements of our paradigm can be incorporated into existing clinical settings, or the entire hybrid model can be implemented within health systems that have genomic medicine programs, to provide NGS in a scientifically rigorous, yet pragmatic setting.
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Affiliation(s)
- Jennifer A Sullivan
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, North Carolina, USA
| | - Rebecca C Spillmann
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, North Carolina, USA
| | - Kelly Schoch
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, North Carolina, USA
| | - Nicole Walley
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, North Carolina, USA
| | - Anna Alkelai
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York, USA
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, New York, USA
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York, USA
- Predictive Sciences, Bristol Myers Squibb, Summit, New Jersey, USA
| | - Patrick R Shea
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York, USA
- Genomics and Bioinformatics Analysis Resource, Columbia University, New York, New York, USA
| | - Slavè Petrovski
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York, USA
- Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, Australia
| | - Vaidehi Jobanputra
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Allyn McConkie-Rosell
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, North Carolina, USA
| | - Vandana Shashi
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, North Carolina, USA
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Wang L, Wang XD, Yang B, Wang XM, Peng YQ, Tan HJ, Xiao HM. Novel SETBP1 mutation in a chinese family with intellectual disability. BMC Med Genomics 2023; 16:233. [PMID: 37798664 PMCID: PMC10552191 DOI: 10.1186/s12920-023-01649-x] [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: 03/01/2023] [Accepted: 08/28/2023] [Indexed: 10/07/2023] Open
Abstract
BACKGROUND Intellectual disability (ID) is characterized by an IQ < 70, which implies below-average intellectual function and a lack of skills necessary for daily living. ID may occur due to multiple causes, such as metabolic, infectious, and chromosomal causes. ID affects approximately 1-3% of the population; however, the cause can be identified in only 25% of clinical patients. METHODS To find the cause of genetic ID in a family, we performed whole-exome sequencing and Sanger sequencing to confirm the presence of a SETBP1 variant and real-time quantitative polymerase chain reaction to detect SETBP1 expression in the proband and normal controls. RESULTS A novel variant, c.942_943insGT (p. Asp316TrpfsTer28), was found in SETBP1. Furthermore, we observed that SETBP1 expression in patients was only 20% that of normal controls (P < 0.05). CONCLUSION A heterozygous variant in SETBP1 associated with ID was found. This report provides further evidence for its genetic basis and support for clinical genetic diagnosis.
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Affiliation(s)
- Le Wang
- School of Basic Medical Science, Hunan University of Medicine, Huaihua, Hunan, China
- Center for System Biology, Data Sciences, and Reproductive Health, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Xu-Dong Wang
- Center for System Biology, Data Sciences, and Reproductive Health, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Bo Yang
- Center for System Biology, Data Sciences, and Reproductive Health, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Xue-Meng Wang
- Center for System Biology, Data Sciences, and Reproductive Health, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Yu-Qian Peng
- Center for System Biology, Data Sciences, and Reproductive Health, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Hang-Jing Tan
- Center for System Biology, Data Sciences, and Reproductive Health, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Hong-Mei Xiao
- Center for System Biology, Data Sciences, and Reproductive Health, School of Basic Medical Science, Central South University, Changsha, Hunan, China.
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Kohyanagi N, Ohama T. The impact of SETBP1 mutations in neurological diseases and cancer. Genes Cells 2023; 28:629-641. [PMID: 37489294 DOI: 10.1111/gtc.13057] [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: 05/30/2023] [Accepted: 07/05/2023] [Indexed: 07/26/2023]
Abstract
SE translocation (SET) is a cancer-promoting factor whose expression is upregulated in many cancers. High SET expression positively correlates with a poor cancer prognosis. SETBP1 (SET-binding protein 1/SEB/MRD29), identified as SET-binding protein, is the causative gene of Schinzel-Giedion syndrome, which is characterized by severe intellectual disability and a distorted facial appearance. Mutations in these genetic regions are also observed in some blood cancers, such as myelodysplastic syndromes, and are associated with a poor prognosis. However, the physiological role of SETBP1 and the molecular mechanisms by which the mutations lead to disease progression have not yet been fully elucidated. In this review, we will describe the current epidemiological data on SETBP1 mutations and shed light on the current knowledge about the SET-dependent and -independent functions of SETBP1.
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Affiliation(s)
- Naoki Kohyanagi
- Laboratory of Veterinary Pharmacology, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Takashi Ohama
- Laboratory of Veterinary Pharmacology, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
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Abstract
Exome sequencing (ES) and genome sequencing (GS) have radically transformed the diagnostic approach to undiagnosed rare/ultrarare Mendelian diseases. Next-generation sequencing (NGS), the technology integral for ES, GS, and most large (100+) gene panels, has enabled previously unimaginable diagnoses, changes in medical management, new treatments, and accurate reproductive risk assessments for patients, as well as new disease gene discoveries. Yet, challenges remain, as most individuals remain undiagnosed with current NGS. Improved NGS technology has resulted in long-read sequencing, which may resolve diagnoses in some patients who do not obtain a diagnosis with current short-read ES and GS, but its effectiveness is unclear, and it is expensive. Other challenges that persist include the resolution of variants of uncertain significance, the urgent need for patients with ultrarare disorders to have access to therapeutics, the need for equity in patient access to NGS-based testing, and the study of ethical concerns. However, the outlook for undiagnosed disease resolution is bright, due to continual advancements in the field.
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Affiliation(s)
- Jennifer A Sullivan
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA;
| | - Kelly Schoch
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA;
| | - Rebecca C Spillmann
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA;
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA;
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Zhou Y, Quan Y, Wu Y, Zhang Y. Prenatal diagnosis and molecular cytogenetic characterization of an inherited microdeletion of 18q12.3 encompassing SETBP1. J Int Med Res 2022; 50:3000605221121955. [PMID: 36113068 PMCID: PMC9478714 DOI: 10.1177/03000605221121955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The 18q12.3 region contains the SET binding protein 1 (SETBP1) gene. SETBP1 mutations or deletions are associated with Schinzel-Giedion syndrome or intellectual developmental disorder, autosomal dominant 29. We report the prenatal diagnosis and genetic counseling of a patient with a maternally inherited 18q12.3 microdeletion. In this family, the mother and son carried the same microdeletion. Chromosomal microdeletions and microduplications are difficult to detect using conventional cytogenetics, whereas the combination of prenatal ultrasound, karyotype analysis, chromosomal microarray analysis, and genetic counseling is helpful for the prenatal diagnosis of chromosomal microdeletions/microduplications.
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Affiliation(s)
- Yaqing Zhou
- Reproductive Center Laboratory, Ninghai County Maternal and Child Health Hospital, Ningbo, Zhejiang, PR China
| | - Yan Quan
- Department of Maternal Health Care, Shiyan Maternal and Child Health Hospital, Shiyan, Hubei, PR China
| | - Yijun Wu
- Department of Obstetrics, Huanggang Central Hospital, Huanggang, Hubei, PR China
| | - Yinxing Zhang
- Department of Obstetrics and Gynecology, Huangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic University, Edong Healthcare Group, Huangshi, Hubei, PR China
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A 9-year-old boy with severe motor and intellectual disabilities and prolonged abdominal distension. J Paediatr Child Health 2022; 58:363-364. [PMID: 35133035 DOI: 10.1111/jpc.2_15459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/03/2021] [Accepted: 03/11/2021] [Indexed: 12/01/2022]
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Yang H, Liu Z, Chen D, Lin W, Wang L, Chen T, Wang R, Yan X. Detection of a novel SETBP1 variant in a Chinese neonate with Schinzel-Giedion syndrome. Front Pediatr 2022; 10:920741. [PMID: 36147799 PMCID: PMC9488805 DOI: 10.3389/fped.2022.920741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 08/12/2022] [Indexed: 11/23/2022] Open
Abstract
Schinzel-Giedion syndrome (SGS) is a multiple malformation syndrome characterized by typical facial features, severe neurodevelopmental delay, and multiple congenital abnormalities. SGS is associated with de novo pathogenic variants in the SETBP1 gene. In specific, SETBP1 variants in over 50 patients with classical or non-classical SGS were clustered within exon 4. A male Chinese neonate with dysmorphic facial features, nervous system disorders, and organ malformations at birth was examined in this study and long-term followed-up. Whole-exome sequencing was performed to identify any underlying pathogenic variants in the proband. Additionally, we reviewed the literature that documents the main clinical features and underlying variants of all patients genetically diagnosed with SGS. The neonate had a characteristic midface retraction, abnormal electroencephalogram waveforms, and genital abnormalities. The patient did not initially develop hydronephrosis or undergo a comprehensive skeletal assessment. Six months after birth, the patient had an epileptic seizure and experienced persistent neurodevelopmental delay with auditory and visual abnormalities. Color Doppler ultrasonography at 18 months revealed hydronephrosis and bilateral widening of the lateral ventricles. The patient died suddenly 20.5 months after birth. Whole-exome sequencing revealed a heterozygous de novo variant (c.2605A > G:p.S869G) in exon 4 degradation sequence in SETBP1. The reported de novo heterozygous variant in SETBP1 (c.2605A > G:p.S869G) broadens the knowledge of the scientific community's on the possible SGS genetic alterations. To the best of our knowledge, this is the first report of SETBP1 variant (c.2605A > G:p.S869G) in SGS. The clinical manifestations of neonatal SGS are atypical, and genetic testing is crucial for diagnosis. Long-term follow-up should be conducted after diagnosis to optimize the therapeutic interventions.
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Affiliation(s)
- Hansong Yang
- Department of Neonatology, Quanzhou Maternity and Children's Hospital, Quanzhou, China
| | - Zhiyong Liu
- Department of Neonatology, Quanzhou Maternity and Children's Hospital, Quanzhou, China
| | - Dongmei Chen
- Department of Neonatology, Quanzhou Maternity and Children's Hospital, Quanzhou, China
| | - Weiru Lin
- Department of Ultrasound, Quanzhou Maternity and Children's Hospital, Quanzhou, China
| | - Lin Wang
- Xiamen Genokon Medical Technology Co., Ltd., Xiamen, China
| | - Tianfeng Chen
- Department of Radiology, Quanzhou Maternity and Children's Hospital, Quanzhou, China
| | - Ruiquan Wang
- Department of Neonatology, Quanzhou Maternity and Children's Hospital, Quanzhou, China
| | - Xialin Yan
- Department of Neonatology, Quanzhou Maternity and Children's Hospital, Quanzhou, China
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Higuchi Y, Namba T, Ebuchi Y, Nakahara Y, Takeuchi A. A 9-year-old boy with severe motor and intellectual disabilities and prolonged abdominal distension. J Paediatr Child Health 2021:jpc.15459. [PMID: 33772930 DOI: 10.1111/jpc.15459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/03/2021] [Accepted: 03/11/2021] [Indexed: 11/28/2022]
Affiliation(s)
- Yousuke Higuchi
- Department of Pediatrics, National Hospital Organization Okayama Medical Center, Okayama, Japan
| | - Takahiro Namba
- Department of Pediatrics, National Hospital Organization Okayama Medical Center, Okayama, Japan
| | - Yuki Ebuchi
- Department of Pediatrics, National Hospital Organization Okayama Medical Center, Okayama, Japan
| | - Yasuo Nakahara
- Department of Pediatric Surgery, National Hospital Organization Okayama Medical Center, Okayama, Japan
| | - Akihito Takeuchi
- Department of Neonatology, National Hospital Organization Okayama Medical Center, Okayama, Japan
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Leonardi E, Bettella E, Pelizza MF, Aspromonte MC, Polli R, Boniver C, Sartori S, Milani D, Murgia A. Identification of SETBP1 Mutations by Gene Panel Sequencing in Individuals With Intellectual Disability or With "Developmental and Epileptic Encephalopathy". Front Neurol 2021; 11:593446. [PMID: 33391157 PMCID: PMC7772201 DOI: 10.3389/fneur.2020.593446] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 11/16/2020] [Indexed: 11/17/2022] Open
Abstract
SETBP1 mutations are associated with the Schinzel-Giedion syndrome (SGS), characterized by profound neurodevelopmental delay, typical facial features, and multiple congenital malformations (OMIM 269150). Refractory epilepsy is a common feature of SGS. Loss of function mutations have been typically associated with a distinct and milder phenotype characterized by intellectual disability and expressive speech impairment. Here we report three variants of SETBP1, two novel de novo truncating mutations, identified by NGS analysis of an Intellectual Disability gene panel in 600 subjects with non-specific neurodevelopmental disorders, and one missense identified by a developmental epilepsy gene panel tested in 56 pediatric epileptic cases. The three individuals carrying the identified SETBP1 variants presented mild to severe developmental delay and lacked the cardinal features of classical SGS. One of these subjects, carrying the c.1765C>T (p.Arg589*) mutation, had mild Intellectual Disability with speech delay; the second one carrying the c.2199_2203del (p.Glu734Alafs19*) mutation had generalized epilepsy, responsive to treatment, and moderate Intellectual Disability; the third patient showed a severe cognitive defects and had a history of drug resistant epilepsy with West syndrome evolved into a Lennox-Gastaut syndrome. This latter subject carries the missense c.2572G>A (p.Glu858Lys) variant, which is absent from the control population, reported as de novo in a subject with ASD, and located close to the SETBP1 hot spot for SGS-associated mutations. Our findings contribute to further characterizing the associated phenotypes and suggest inclusion of SETBP1 in the list of prioritized genes for the genetic diagnosis of overlapping phenotypes ranging from non-specific neurodevelopmental disorders to “developmental and epileptic encephalopathy” (DEE).
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Affiliation(s)
- Emanuela Leonardi
- Molecular Genetics of Neurodevelopment, Department of Woman and Child Health, University of Padova, Padua, Italy.,Fondazione Istituto di Ricerca Pediatrica (IRP), Città Della Speranza, Padua, Italy
| | - Elisa Bettella
- Molecular Genetics of Neurodevelopment, Department of Woman and Child Health, University of Padova, Padua, Italy.,Fondazione Istituto di Ricerca Pediatrica (IRP), Città Della Speranza, Padua, Italy
| | - Maria Federica Pelizza
- Paediatric Neurology and Neurophysiology Unit, Department of Woman and Child Health, University Hospital of Padova, Padua, Italy
| | - Maria Cristina Aspromonte
- Molecular Genetics of Neurodevelopment, Department of Woman and Child Health, University of Padova, Padua, Italy.,Fondazione Istituto di Ricerca Pediatrica (IRP), Città Della Speranza, Padua, Italy
| | - Roberta Polli
- Molecular Genetics of Neurodevelopment, Department of Woman and Child Health, University of Padova, Padua, Italy.,Fondazione Istituto di Ricerca Pediatrica (IRP), Città Della Speranza, Padua, Italy
| | - Clementina Boniver
- Paediatric Neurology and Neurophysiology Unit, Department of Woman and Child Health, University Hospital of Padova, Padua, Italy
| | - Stefano Sartori
- Paediatric Neurology and Neurophysiology Unit, Department of Woman and Child Health, University Hospital of Padova, Padua, Italy
| | - Donatella Milani
- Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Alessandra Murgia
- Molecular Genetics of Neurodevelopment, Department of Woman and Child Health, University of Padova, Padua, Italy.,Fondazione Istituto di Ricerca Pediatrica (IRP), Città Della Speranza, Padua, Italy
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