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1. Large-scale targeted sequencing identifies risk genes for neurodevelopmental disorders

Author

Wang T., Hoekzema K., Vecchio D., Wu H., Sulovari A., Coe B. P., Gillentine M. A., Wilfert A. B., Perez-Jurado L. A., Kvarnung M., Sleyp Y., Earl R. K., Rosenfeld J. A., Geisheker M. R., Han L., Du B., Barnett C., Thompson E., Shaw M., Carroll R., Friend K., Catford R., Palmer E. E., Zou X., Ou J., Li H., Guo H., Gerdts J., Avola E., Calabrese G., Elia M., Greco D., Lindstrand A., Nordgren A., Anderlid B. -M., Vandeweyer G., Van Dijck A., Van der Aa N., McKenna B., Hancarova M., Bendova S., Havlovicova M., Malerba G., Bernardina B. D., Muglia P., van Haeringen A., Hoffer M. J. V., Franke B., Cappuccio G., Delatycki M., Lockhart P. J., Manning M. A., Liu P., Scheffer I. E., Brunetti Pierri N., Rommelse N., Amaral D. G., Santen G. W. E., Trabetti E., Sedlacek Z., Michaelson J. J., Pierce K., Courchesne E., Kooy R. F., Acampado J., Ace A. J., Amatya A., Astrovskaya I., Bashar A., Brooks E., Butler M. E., Cartner L. A., Chin W., Chung W. K., Daniels A. M., Feliciano P., Fleisch C., Ganesan S., Jensen W., Lash A. E., Marini R., Myers V. J., O'Connor E., Rigby C., Robertson B. E., Shah N., Shah S., Singer E., Snyder L. A. G., Stephens A. N., Tjernagel J., Vernoia B. M., Volfovsky N., White L. C., Hsieh A., Shen Y., Zhou X., Turner T. N., Bahl E., Thomas T. R., Brueggeman L., Koomar T., Michael R. J., O'Roak B. J., Barnard R. A., Gibbs R. A., Muzny D., Sabo A., Ahmed K. L. B., Eichler E. E., Siegel M., Abbeduto L., Hilscher B. A., Li D., Smith K., Thompson S., Albright C., Butter E. M., Eldred S., Hanna N., Jones M., Coury D. L., Scherr J., Pifher T., Roby E., Dennis B., Higgins L., Brown M., Alessandri M., Gutierrez A., Hale M. N., Herbert L. M., Schneider H. L., David G., Annett R. D., Sarver D. E., Arriaga I., Camba A., Gulsrud A. C., Haley M., McCracken J. T., Sandhu S., Tafolla M., Yang W. S., Carpenter L. A., Bradley C. C., Gwynette F., Manning P., Shaffer R., Thomas C., Bernier R. A., Fox E. A., Gerdts J. A., Pepper M., Ho T., Cho D., Piven J., Lechniak H., Soorya L. V., Gordon R., Wainer A., Yeh L., Ochoa-Lubinoff C., Russo N., Berry-Kravis E., Booker S., Erickson C. A., Prock L. M., Pawlowski K. G., Matthews E. T., Brewster S. J., Hojlo M. A., Abada E., Lamarche E., Murali S. C., Harvey W. T., Kaplan H. E., Pierce K. L., DeMarco L., Horner S., Pandey J., Plate S., Sahin M., Riley K. D., Carmody E., Constantini J., Esler A., Fatemi A., Hutter H., Landa R. J., McKenzie A. P., Neely J., Singh V., Van Metre B., Wodka E. L., Fombonne E. J., Huang-Storms L. Y., Pacheco L. D., Mastel S. A., Coppola L. A., Francis S., Jarrett A., Jacob S., Lillie N., Gunderson J., Istephanous D., Simon L., Wasserberg O., Rachubinski A. L., Rosenberg C. R., Kanne S. M., Shocklee A. D., Takahashi N., Bridwell S. L., Klimczac R. L., Mahurin M. A., Cotrell H. E., Grant C. A., Hunter S. G., Martin C. L., Taylor C. M., Walsh L. K., Dent K. A., Mason A., Sziklay A., Smith C. J., Nordenskjold M., Romano C., Peeters H., Gecz J., Xia K., SPARK Consortium, Wang, T., Hoekzema, K., Vecchio, D., Wu, H., Sulovari, A., Coe, B. P., Gillentine, M. A., Wilfert, A. B., Perez-Jurado, L. A., Kvarnung, M., Sleyp, Y., Earl, R. K., Rosenfeld, J. A., Geisheker, M. R., Han, L., Du, B., Barnett, C., Thompson, E., Shaw, M., Carroll, R., Friend, K., Catford, R., Palmer, E. E., Zou, X., Ou, J., Li, H., Guo, H., Gerdts, J., Avola, E., Calabrese, G., Elia, M., Greco, D., Lindstrand, A., Nordgren, A., Anderlid, B. -M., Vandeweyer, G., Van Dijck, A., Van der Aa, N., Mckenna, B., Hancarova, M., Bendova, S., Havlovicova, M., Malerba, G., Bernardina, B. D., Muglia, P., van Haeringen, A., Hoffer, M. J. V., Franke, B., Cappuccio, G., Delatycki, M., Lockhart, P. J., Manning, M. A., Liu, P., Scheffer, I. E., Brunetti Pierri, N., Rommelse, N., Amaral, D. G., Santen, G. W. E., Trabetti, E., Sedlacek, Z., Michaelson, J. J., Pierce, K., Courchesne, E., Kooy, R. F., Acampado, J., Ace, A. J., Amatya, A., Astrovskaya, I., Bashar, A., Brooks, E., Butler, M. E., Cartner, L. A., Chin, W., Chung, W. K., Daniels, A. M., Feliciano, P., Fleisch, C., Ganesan, S., Jensen, W., Lash, A. E., Marini, R., Myers, V. J., O'Connor, E., Rigby, C., Robertson, B. E., Shah, N., Shah, S., Singer, E., Snyder, L. A. G., Stephens, A. N., Tjernagel, J., Vernoia, B. M., Volfovsky, N., White, L. C., Hsieh, A., Shen, Y., Zhou, X., Turner, T. N., Bahl, E., Thomas, T. R., Brueggeman, L., Koomar, T., Michael, R. J., O'Roak, B. J., Barnard, R. A., Gibbs, R. A., Muzny, D., Sabo, A., Ahmed, K. L. B., Eichler, E. E., Siegel, M., Abbeduto, L., Hilscher, B. A., Li, D., Smith, K., Thompson, S., Albright, C., Butter, E. M., Eldred, S., Hanna, N., Jones, M., Coury, D. L., Scherr, J., Pifher, T., Roby, E., Dennis, B., Higgins, L., Brown, M., Alessandri, M., Gutierrez, A., Hale, M. N., Herbert, L. M., Schneider, H. L., David, G., Annett, R. D., Sarver, D. E., Arriaga, I., Camba, A., Gulsrud, A. C., Haley, M., Mccracken, J. T., Sandhu, S., Tafolla, M., Yang, W. S., Carpenter, L. A., Bradley, C. C., Gwynette, F., Manning, P., Shaffer, R., Thomas, C., Bernier, R. A., Fox, E. A., Gerdts, J. A., Pepper, M., Ho, T., Cho, D., Piven, J., Lechniak, H., Soorya, L. V., Gordon, R., Wainer, A., Yeh, L., Ochoa-Lubinoff, C., Russo, N., Berry-Kravis, E., Booker, S., Erickson, C. A., Prock, L. M., Pawlowski, K. G., Matthews, E. T., Brewster, S. J., Hojlo, M. A., Abada, E., Lamarche, E., Murali, S. C., Harvey, W. T., Kaplan, H. E., Pierce, K. L., Demarco, L., Horner, S., Pandey, J., Plate, S., Sahin, M., Riley, K. D., Carmody, E., Constantini, J., Esler, A., Fatemi, A., Hutter, H., Landa, R. J., Mckenzie, A. P., Neely, J., Singh, V., Van Metre, B., Wodka, E. L., Fombonne, E. J., Huang-Storms, L. Y., Pacheco, L. D., Mastel, S. A., Coppola, L. A., Francis, S., Jarrett, A., Jacob, S., Lillie, N., Gunderson, J., Istephanous, D., Simon, L., Wasserberg, O., Rachubinski, A. L., Rosenberg, C. R., Kanne, S. M., Shocklee, A. D., Takahashi, N., Bridwell, S. L., Klimczac, R. L., Mahurin, M. A., Cotrell, H. E., Grant, C. A., Hunter, S. G., Martin, C. L., Taylor, C. M., Walsh, L. K., Dent, K. A., Mason, A., Sziklay, A., Smith, C. J., Nordenskjold, M., Romano, C., Peeters, H., Gecz, J., and Xia, K.

Subjects
0301 basic medicine, Male, CCCTC-Binding Factor, Transcription Factor, Basic Helix-Loop-Helix Transcription Factor, DNA Mutational Analysis, General Physics and Astronomy, RNA-Binding Protein, Heterogeneous-Nuclear Ribonucleoprotein U, VARIANTS, medicine.disease_cause, Cohort Studies, 0302 clinical medicine, Neurodevelopmental Disorder, Basic Helix-Loop-Helix Transcription Factors, SPARK Consortium, 2.1 Biological and endogenous factors, Copy-number variation, Aetiology, lcsh:Science, GABRG2, Genetics, Mutation, Multidisciplinary, biology, Neurodevelopmental disorders, RNA-Binding Proteins, High-Throughput Nucleotide Sequencing, Autism spectrum disorders, Multidisciplinary Sciences, DNA-Binding Proteins, Science & Technology - Other Topics, Female, Case-Control Studie, Engineering sciences. Technology, Human, Science, DNA-Binding Protein, Genetic Association Studie, COPY-NUMBER VARIATION, General Biochemistry, Genetics and Molecular Biology, DNA sequencing, Article, KCNQ3 Potassium Channel, DNA Mutational Analysi, 03 medical and health sciences, medicine, Humans, Genetic Predisposition to Disease, AUTISM, Gene, Genetic Association Studies, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], Science & Technology, DISABILITY, Prevention, Case-control study, General Chemistry, Repressor Protein, medicine.disease, FRAMEWORK, Repressor Proteins, DE-NOVO MUTATION, 030104 developmental biology, CTCF, Neurodevelopmental Disorders, Case-Control Studies, biology.protein, Next-generation sequencing, Autism, lcsh:Q, Cohort Studie, 030217 neurology & neurosurgery, Transcription Factors
Abstract

Most genes associated with neurodevelopmental disorders (NDDs) were identified with an excess of de novo mutations (DNMs) but the significance in case–control mutation burden analysis is unestablished. Here, we sequence 63 genes in 16,294 NDD cases and an additional 62 genes in 6,211 NDD cases. By combining these with published data, we assess a total of 125 genes in over 16,000 NDD cases and compare the mutation burden to nonpsychiatric controls from ExAC. We identify 48 genes (25 newly reported) showing significant burden of ultra-rare (MAF, For many neurodevelopmental disorder (NDD) risk genes, the significance for mutational burden is unestablished. Here, the authors sequence 125 candidate NDD genes in over 16,000 NDD cases; case-control mutational burden analysis identifies 48 genes with a significant burden of severe ultra-rare mutations.

Published
2020

2. The Italian autism network (ITAN): a resource for molecular genetics and biomarker investigations

Author

Muglia, P., Filosi, M., Ros, Da, Kam-Thong, T., Nardocci, F., Trabetti, E., Ratti, E., Rizzini, P., Zuddas, A., Bernardina, B. D., Domenici, Enrico, Alibrio, G., Anchisi, L., Andruccioli, M., Benvenuto, A., Battistella, P. A., Boscaini, F., Bravaccio, C., Ceppi, E., Cosentino, D., Curatolo, P., De Giacomo, A., Di Vita, G., Elia, M., Gitti, F., Grittani, S., Lamanna, A. L., Mani, E., Manzi, B., Margari, L., Masi, G., Molteni, M., Pascotto, A., Parmeggiani, A., Pignatti, P. F., Piroddi, T., Prandini, P., Russo, S., Scifo, R., Tancredi, R., Tiberti, A., Zoccante, L., Pierandrea Muglia, Michele Filosi, Lucio Da Ros, Tony Kam-Thong, Franco Nardocci, Elisabetta Trabetti, Emiliangelo Ratti, Paolo Rizzini, Alessandro Zuddas, Bernardo Dalla Bernardina, Enrico Domenici,..Antonia Parmeggiani, Muglia, Pierandrea, Filosi, Michele, Da Ros, Lucio, Kam-Thong, Tony, Nardocci, Franco, Trabetti, Elisabetta, Ratti, Emiliangelo, Rizzini, Paolo, Zuddas, Alessandro, Bernardina, Bernardo Dalla, Domenici, Enrico, Alibrio, Giovanni, Anchisi, Laura, Andruccioli, Milena, Benvenuto, Arianna, Battistella, Pier Antonio, Boscaini, Flavio, Bravaccio, Carmela, Ceppi, Elisa, Cosentino, Diego, Curatolo, Paolo, De Giacomo, Andrea, Di Vita, Giuseppa, Elia, Massimo, Gitti, Filippo, Grittani, Serenella, Lamanna, Anna Linda, Mani, Elisa, Manzi, Barbara, Margari, Lucia, Masi, Gabriele, Molteni, Massimo, Pascotto, Antonio, Parmeggiani, Antonia, Pignatti, Pier Franco, Piroddi, Tiziana, Prandini, Paola, Russo, Sebastiano, Scifo, Renato, Tancredi, Raffaella, Tiberti, Alessandra, and Zoccante, Leonardo

Subjects
0301 basic medicine, Male, medicine.medical_specialty, Adolescent, lcsh:RC435-571, Autism Spectrum Disorder, Medical Records, Autism Spectrum disorders, 03 medical and health sciences, Study Protocol, 0302 clinical medicine, Genetic, Language assessment, lcsh:Psychiatry, medicine, Pervasive developmental disorder, Child and adolescent psychiatry, Genetics, Humans, Biorepository, Asperger Syndrome, Child, Biomarkers, Wechsler Intelligence Scale for Children, Biological Specimen Banks, business.industry, Leiter International Performance Scale, Medical record, Autism Spectrum disorders, Biomarkers, Biorepository, Genetics, Biomarker, medicine.disease, Settore MED/39 - Neuropsichiatria Infantile, Psychiatry and Mental health, 030104 developmental biology, Databases as Topic, Italy, Psychiatry and Mental Health, Child Development Disorders, Pervasive, Child, Preschool, Autism, Health Resources, Female, business, 030217 neurology & neurosurgery, Clinical psychology
Abstract

BackgroundA substantial genetic component accounts for Autism Spectrum Disorders (ASD) aetiology, with some rare and common genetic risk factors recently identified. Large collections of DNAs from thoroughly characterized ASD families are an essential step to confirm genetic risk factors, identify new variants and investigate genotype-phenotype correlations. The Italian Autism Network aimed at constituting a clinical database and a biorepository of samples derived from ASD subjects and first-degree relatives extensively and consistently characterized by child psychiatry centers in Italy.MethodsThe study was approved by the ethical committee of the University of Verona, the coordinating site, and by the local ethical committees of each recruiting site. Certified staff was specifically trained at each site for the overall study conduct, for clinical protocol administration and handling of biological material. A centralized database was developed to collect clinical assessment and medical records from each recruiting site. Children were eligible for recruitment based on the following inclusion criteria: age 4–18 years, at least one parent or legal guardian giving voluntary written consent, meeting DSM-IV criteria for Autistic Disorder or Asperger’s Disorder or Pervasive Developmental Disorder NOS. Affected individuals were assessed by full psychiatric, neurological and physical examination, evaluation with ADI-R and ADOS scales, cognitive assessment with Wechsler Intelligence Scale for Children or Preschool and Primary, Leiter International Performance Scale or Griffiths Mental Developmental Scale. Additional evaluations included language assessment, the Krug Asperger’s Disorder Index, and instrumental examination such as EEG and structural MRI. DNA, RNA and plasma were collected from eligible individuals and relatives. A central laboratory was established to host the biorepository, perform DNA and RNA extraction and lymphocytes immortalisation. DiscussionThe study has led to an extensive collection of biological samples associated with standardised clinical assessments from a network of expert clinicians and psychologists. Eighteen sites have received ADI/ADOS training, thirteen of which have been actively recruiting. The clinical database currently includes information on 812 individuals from 249 families, and the biorepository has samples for 98% of the subjects. This effort has generated a highly valuable resource for conducting clinical and genetic research of ASD, amenable to further expansion.

Published
2018

3. Brain MRI findings in severe myoclonic epilepsy in infancy and genotype-phenotype correlations

Author

Davide Mei, Carla Marini, Giuseppe Capovilla, Laura Siri, Maria Margherita Mancardi, Francesca Darra, Francesca Ragona, Francesca Longaretti, Maurizio Elia, Roberta Biancheri, Federico Zara, Charlotte Dravet, Fabio Tortora, Nicola Specchio, Giuseppe Gobbi, Antonino Romeo, Lucio Giordano, Elena Gennaro, Tiziana Granata, Renzo Guerrini, Francesca Beccaria, Carlo Minetti, Federico Vigevano, Andrea Rossi, Roberto Gaggero, Salvatore Striano, Bernardo Dalla Bernardina, Pasquale Striano, Roberta Paravidino, Francesca Madia, Striano, P., Mancardi, M. M., Biancheri, R., Madia, F., Gennaro, E., Paravidino, R., Beccaria, F., Capovilla, G., Bernardina, B. D., Darra, F., Elia, M., Giordano, L., Gobbi, G., Granata, T., Ragona, F., Guerrini, R., Marini, C., Mei, D., Longaretti, F., Romeo, A., Siri, L., Specchio, N., Vigevano, F., Striano, Salvatore, Tortora, F., Rossi, A., Minetti, C., Dravet, C., Gaggero, R., Zara, F., Striano, P, Mancardi, Mm, Biancheri, R, Madia, F, Gennaro, E, Paravidino, R, Beccaria, F, Capovilla, G, DALLA BERNARDINA, B, Darra, F, Elia, M, Giordano, L, Gobbi, G, Granata, T, Ragona, F, Guerrini, R, Marini, C, Mei, D, Longaretti, F, Romeo, A, Siri, L, Specchio, N, Vigevano, F, Tortora, F, Rossi, A, Minetti, C, Dravet, C, Gaggero, R, Bernardina, Bd, Striano, S, and Tortora, Fabio

Subjects
Male, Pathology, pathology, Child, Child, pathology, Humans, Infant, Magnetic Resonance Imaging, Epilepsies, Myoclonic, Epilepsies, Hippocampus, Severity of Illness Index, Sodium Channels, Epilepsy, genetics, Child, Chromatography, High Pressure Liquid, Chromatography, Brain, Syndrome, Magnetic Resonance Imaging, statistics /&/ numerical data, Phenotype, Neurology, Child, Preschool, High Pressure Liquid, Cerebellar atrophy, Female, diagnosis/genetics/pathology, Female, Genotype, Hippocampu, genetics, Nerve Tissue Protein, MRI, Adult, genetics, Syndrome, medicine.medical_specialty, Adolescent, Genotype, Nerve Tissue Proteins, Preschool, Chromatography, High Pressure Liquid, Epilepsie, Central nervous system disease, Atrophy, Dravet syndrome, medicine, Humans, Preschool, Adolescent, Adult, Brain, Retrospective Studies, Hippocampal sclerosis, business.industry, statistics /&/ numerical data, Male, Mutation, Infant, Cortical dysplasia, medicine.disease, NAV1.1 Voltage-Gated Sodium Channel, High Pressure Liquid, Epilepsies, Myoclonic, diagnosis/genetics/pathology, Female, Genotype, Hippocampus, genetics, Nerve Tissue Proteins, genetics, Phenotype, Retrospective Studies, Severity of Illness Index, Sodium Channels, Mutation, Myoclonic epilepsy, pathology, Neurology (clinical), business, diagnosis/genetics/pathology, genetics, Phenotype, Retrospective Studies, Severity of Illness Index, Sodium Channel
Abstract

Summary: Introduction: To determine the occurrence of neuroradiological abnormalities and to perform genotype–phenotype correlations in severe myoclonic epilepsy of infancy (SMEI, Dravet syndrome). Patients and Methods: Alpha-subunit type A of voltage-gated sodium channel (SCN1A) mutational screening was performed by denaturing high-performance liquid chromatography (DHPLC) and multiplex ligation probe amplification (MLPA). MRI inclusion criteria were: last examination obtained after the age of 4 years on 1.5-T systems; hippocampal cuts acquired perpendicular to the long axis of the hippocampus; qualitative assessment was performed on T1-weighted, T2-weighted, proton density, and 1–3 mm thick coronal FLAIR images. Results: We collected 58 SMEI patients in whom last MRI was performed at or later than 4 years of age. SCN1A mutations occurred in 35 (60%) cases. Thirteen (22.4%) out of 58 patients showed abnormal MRIs. Eight patients showed cortical brain atrophy of which 3 associated to ventricles abnormalities, 1 to cerebellar atrophy, 1 to white matter hyperintensity; 3 patients had ventricles enlargement only; 1 patient showed hippocampal sclerosis (HS); 1 had focal cortical dysplasia. Genotype–phenotype analysis indicated that abnormal MRIs occurred more frequently in patients without SCN1A mutations (9/23; 39.1%) compared to those carrying SCN1A mutations (4/35; 11.4%) (p = 0.02). Conclusion: Different brain abnormalities may occur in SMEI. Only one case with HS was observed; thus, our study does not support the association between prolonged febrile seizures and HS in SMEI. Abnormal MRIs were significantly more frequent in patients without SCN1A mutations. Prospective MRI studies will assess the etiological role of the changes observed in these patients.

Published
2007

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