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1. Comprehensive whole-genome sequence analyses provide insights into the genomic architecture of cerebral palsy

Author

Fehlings, Darcy L., Zarrei, Mehdi, Engchuan, Worrawat, Sondheimer, Neal, Thiruvahindrapuram, Bhooma, MacDonald, Jeffrey R., Higginbotham, Edward J., Thapa, Ritesh, Behlim, Tarannum, Aimola, Sabrina, Switzer, Lauren, Ng, Pamela, Wei, John, Danthi, Prakroothi S., Pellecchia, Giovanna, Lamoureux, Sylvia, Ho, Karen, Pereira, Sergio L., de Rijke, Jill, Sung, Wilson W. L., Mowjoodi, Alireza, Howe, Jennifer L., Nalpathamkalam, Thomas, Manshaei, Roozbeh, Ghaffari, Siavash, Whitney, Joseph, Patel, Rohan V., Hamdan, Omar, Shaath, Rulan, Trost, Brett, Knights, Shannon, Samdup, Dawa, McCormick, Anna, Hunt, Carolyn, Kirton, Adam, Kawamura, Anne, Mesterman, Ronit, Gorter, Jan Willem, Dlamini, Nomazulu, Merico, Daniele, Hilali, Murto, Hirschfeld, Kyle, Grover, Kritika, Bautista, Nelson X., Han, Kara, Marshall, Christian R., Yuen, Ryan K. C., Subbarao, Padmaja, Azad, Meghan B., Turvey, Stuart E., Mandhane, Piush, Moraes, Theo J., Simons, Elinor, Maxwell, George, Shevell, Michael, Costain, Gregory, Michaud, Jacques L., Hamdan, Fadi F., Gauthier, Julie, Uguen, Kevin, Stavropoulos, Dimitri J., Wintle, Richard F., Oskoui, Maryam, and Scherer, Stephen W.

Published
2024
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2. Genomic architecture of autism from comprehensive whole-genome sequence annotation.

Author

Trost, Brett, Thiruvahindrapuram, Bhooma, Chan, Ada, Engchuan, Worrawat, Higginbotham, Edward, Howe, Jennifer, Loureiro, Livia, Reuter, Miriam, Roshandel, Delnaz, Whitney, Joe, Zarrei, Mehdi, Bookman, Matthew, Somerville, Cherith, Shaath, Rulan, Abdi, Mona, Aliyev, Elbay, Patel, Rohan, Nalpathamkalam, Thomas, Pellecchia, Giovanna, Hamdan, Omar, Kaur, Gaganjot, Wang, Zhuozhi, MacDonald, Jeffrey, Wei, John, Sung, Wilson, Lamoureux, Sylvia, Hoang, Ny, Selvanayagam, Thanuja, Deflaux, Nicole, Geng, Melissa, Ghaffari, Siavash, Bates, John, Young, Edwin, Ding, Qiliang, Shum, Carole, DAbate, Lia, Bradley, Clarrisa, Rutherford, Annabel, Aguda, Vernie, Apresto, Beverly, Chen, Nan, Desai, Sachin, Du, Xiaoyan, Fong, Matthew, Pullenayegum, Sanjeev, Samler, Kozue, Wang, Ting, Ho, Karen, Paton, Tara, Pereira, Sergio, Herbrick, Jo-Anne, Wintle, Richard, Fuerth, Jonathan, Noppornpitak, Juti, Ward, Heather, Magee, Patrick, Al Baz, Ayman, Kajendirarajah, Usanthan, Kapadia, Sharvari, Vlasblom, Jim, Valluri, Monica, Green, Joseph, Seifer, Vicki, Quirbach, Morgan, Rennie, Olivia, Kelley, Elizabeth, Masjedi, Nina, Lord, Catherine, Szego, Michael, Zawati, Man, Lang, Michael, Strug, Lisa, Marshall, Christian, Costain, Gregory, Calli, Kristina, Iaboni, Alana, Yusuf, Afiqah, Ambrozewicz, Patricia, Gallagher, Louise, Amaral, David, Brian, Jessica, Elsabbagh, Mayada, Georgiades, Stelios, Messinger, Daniel, Ozonoff, Sally, Sebat, Jonathan, Sjaarda, Calvin, Smith, Isabel, Szatmari, Peter, Zwaigenbaum, Lonnie, Kushki, Azadeh, Frazier, Thomas, Vorstman, Jacob, Fakhro, Khalid, Fernandez, Bridget, Lewis, M, Weksberg, Rosanna, Fiume, Marc, Yuen, Ryan, and Anagnostou, Evdokia

Subjects
autism spectrum disorder, copy-number variation, neurodevelopmental disorders, phenotype measures, polygenic risk scores, rare variants, structural variation, whole-genome sequencing, Humans, Autism Spectrum Disorder, Autistic Disorder, Genetic Predisposition to Disease, DNA Copy Number Variations, Genomics
Abstract

Fully understanding autism spectrum disorder (ASD) genetics requires whole-genome sequencing (WGS). We present the latest release of the Autism Speaks MSSNG resource, which includes WGS data from 5,100 individuals with ASD and 6,212 non-ASD parents and siblings (total n = 11,312). Examining a wide variety of genetic variants in MSSNG and the Simons Simplex Collection (SSC; n = 9,205), we identified ASD-associated rare variants in 718/5,100 individuals with ASD from MSSNG (14.1%) and 350/2,419 from SSC (14.5%). Considering genomic architecture, 52% were nuclear sequence-level variants, 46% were nuclear structural variants (including copy-number variants, inversions, large insertions, uniparental isodisomies, and tandem repeat expansions), and 2% were mitochondrial variants. Our study provides a guidebook for exploring genotype-phenotype correlations in families who carry ASD-associated rare variants and serves as an entry point to the expanded studies required to dissect the etiology in the ∼85% of the ASD population that remain idiopathic.

Published
2022

4. Genomic architecture of autism spectrum disorder in Qatar: The BARAKA-Qatar Study

Author

Abdi, Mona, Aliyev, Elbay, Trost, Brett, Kohailan, Muhammad, Aamer, Waleed, Syed, Najeeb, Shaath, Rulan, Gandhi, Geethanjali Devadoss, Engchuan, Worrawat, Howe, Jennifer, Thiruvahindrapuram, Bhooma, Geng, Melissa, Whitney, Joe, Syed, Amira, Lakshmi, Jyothi, Hussein, Sura, Albashir, Najwa, Hussein, Amal, Poggiolini, Ilaria, Elhag, Saba F., Palaniswamy, Sasirekha, Kambouris, Marios, de Fatima Janjua, Maria, Tahir, Mohamed O. El, Nazeer, Ahsan, Shahwar, Durre, Azeem, Muhammad Waqar, Mokrab, Younes, Aati, Nazim Abdel, Akil, Ammira, Scherer, Stephen W., Kamal, Madeeha, and Fakhro, Khalid A.

Published
2023
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6. Impaired OTUD7A-dependent Ankyrin regulation mediates neuronal dysfunction in mouse and human models of the 15q13.3 microdeletion syndrome

Author

Unda, Brianna K., Chalil, Leon, Yoon, Sehyoun, Kilpatrick, Savannah, Irwin, Courtney, Xing, Sansi, Murtaza, Nadeem, Cheng, Anran, Brown, Chad, Afonso, Alexandria, McCready, Elizabeth, Ronen, Gabriel M., Howe, Jennifer, Caye-Eude, Aurélie, Verloes, Alain, Doble, Brad W., Faivre, Laurence, Vitobello, Antonio, Scherer, Stephen W., Lu, Yu, Penzes, Peter, and Singh, Karun K.

Published
2023
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9. Genome-wide rare variant score associates with morphological subtypes of autism spectrum disorder

Author

Chan, Ada J. S., Engchuan, Worrawat, Reuter, Miriam S., Wang, Zhuozhi, Thiruvahindrapuram, Bhooma, Trost, Brett, Nalpathamkalam, Thomas, Negrijn, Carol, Lamoureux, Sylvia, Pellecchia, Giovanna, Patel, Rohan V., Sung, Wilson W. L., MacDonald, Jeffrey R., Howe, Jennifer L., Vorstman, Jacob, Sondheimer, Neal, Takahashi, Nicole, Miles, Judith H., Anagnostou, Evdokia, Tammimies, Kristiina, Zarrei, Mehdi, Merico, Daniele, Stavropoulos, Dimitri J., Yuen, Ryan K. C., Fernandez, Bridget A., and Scherer, Stephen W.

Published
2022
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11. ENPP1 enzyme replacement therapy improves ectopic calcification but does not rescue skeletal phenotype in a mouse model for craniometaphyseal dysplasia.

Author

Reichenberger, Ernst J, O'Brien, Kevin, Hatori, Ayano, Carpenter, Thomas O, van de Wetering, Koen, Flaman, Lisa, Howe, Jennifer, Ortiz, Daniel, Sabbagh, Yves, and Chen, I-Ping

Subjects
ENZYME replacement therapy, FACIAL paralysis, SKELETAL abnormalities, X-ray imaging, GENETIC disorders
Abstract

Craniometaphyseal dysplasia (CMD) is a rare genetic bone disorder, characterized by progressive thickening of craniofacial bones and flared metaphyses of long bones. Craniofacial hyperostosis leads to the obstruction of neural foramina and neurological symptoms such as facial palsy, blindness, deafness, or severe headache. Mutations in ANKH (mouse ortholog ANK), a transporter of small molecules such as citrate and ATP, are responsible for autosomal dominant CMD. Knock-in (KI) mice carrying an ANKF377del mutation (AnkKI/KI) replicate many features of human CMD. Pyrophosphate (PPi) levels in plasma are significantly reduced in AnkKI/KI mice. PPi is a potent inhibitor of mineralization. To examine the extent to which restoration of circulating PPi levels may prevent the development of a CMD-like phenotype, we treated AnkKI/KI mice with the recombinant human ENPP1-Fc protein IMA2a. ENPP1 hydrolyzes ATP into AMP and PPi. Male and female Ank+/+ and AnkKI/KI mice (n ≥ 6/group) were subcutaneously injected with IMA2a or vehicle weekly for 12 wk, starting at the age of 1 wk. Plasma ENPP1 activity significantly increased in AnkKI/KI mice injected with IMA2a (Vehicle/IMA2a: 28.15 ± 1.65/482.7 ± 331.2 mOD/min; p <.01), which resulted in the successful restoration of plasma PPi levels (Ank+/+/AnkKI/KI vehicle treatment/AnkKI/KI IMA2a: 0.94 ± 0.5/0.43 ± 0.2/1.29 ± 0.8 μM; p <.01). We examined the skeletal phenotype by X-Ray imaging and μCT. IMA2a treatment of AnkKI/KI mice did not significantly correct CMD features such as the abnormal shape of femurs, increased bone mass of mandibles, hyperostotic craniofacial bones, or the narrowed foramen magnum. However, μCT imaging showed ectopic calcification near basioccipital bones at the level of the foramen magnum and on joints of AnkKI/KI mice. Interestingly, IMA2a treatment significantly reduced the volume of calcified nodules at both sites. Our data demonstrate that IMA2a is sufficient to restore plasma PPi levels and reduce ectopic calcification but fails to rescue skeletal abnormalities in AnkKI/KI mice under our treatment conditions. Lay Summary: There is limited treatment for craniometaphyseal dysplasia (CMD), a rare genetic bone disorder characterized by progressive thickening of craniofacial bones and flared metaphyses of long bones. Patients with CMD often develop neurological symptoms such as facial palsy, blindness, deafness, or severe headache. Mice (AnkKI/KI mice) carrying an ANKF377del mutation identified in patients with CMD replicate many features of CMD and show significantly reduced plasma pyrophosphate (PPi) levels. We injected AnkKI/KI mice with the recombinant human ENPP1-Fc protein IMA2a, an enzyme capable of converting ATP to AMP and PPi, to restore plasma PPi levels. IMA2a reduces ectopic calcification at multiple sites but does not significantly correct features of CMD in craniofacial and long bones in AnkKI/KI mice under our treatment conditions. [ABSTRACT FROM AUTHOR]

Published
2024
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12. RCL1 copy number variants are associated with a range of neuropsychiatric phenotypes

Author

Brownstein, Catherine A., Smith, Richard S., Rodan, Lance H., Gorman, Mark P., Hojlo, Margaret A., Garvey, Emily A., Li, Jianqiao, Cabral, Kristin, Bowen, Joshua J., Rao, Abhijit S., Genetti, Casie A., Carroll, Devon, Deaso, Emma A., Agrawal, Pankaj B., Rosenfeld, Jill A., Bi, Weimin, Howe, Jennifer, Stavropoulos, Dimitri J., Hansen, Adam W., Hamoda, Hesham M., Pinard, Ferne, Caracansi, Annmarie, Walsh, Christopher A., D’Angelo, Eugene J., Beggs, Alan H., Zarrei, Mehdi, Gibbs, Richard A., Scherer, Stephen W., Glahn, David C., and Gonzalez-Heydrich, Joseph

Published
2021
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13. Inhibition of Vascular Smooth Muscle Cell Proliferation by ENPP1: The Role of CD73 and the Adenosine Signaling Axis.

Author

Tchernychev, Boris, Nitschke, Yvonne, Chu, Di, Sullivan, Caitlin, Flaman, Lisa, O'Brien, Kevin, Howe, Jennifer, Cheng, Zhiliang, Thompson, David, Ortiz, Daniel, Rutsch, Frank, and Sabbagh, Yves

Subjects
VASCULAR smooth muscle, ARTERIAL calcification, ENZYME replacement therapy, CAROTID artery, MUSCLE cells
Abstract

The Ectonucleotide Pyrophosphatase/Phosphodiesterase 1 (ENPP1) ectoenzyme regulates vascular intimal proliferation and mineralization of bone and soft tissues. ENPP1 variants cause Generalized Arterial Calcification of Infancy (GACI), a rare genetic disorder characterized by ectopic calcification, intimal proliferation, and stenosis of large- and medium-sized arteries. ENPP1 hydrolyzes extracellular ATP to pyrophosphate (PPi) and AMP. AMP is the precursor of adenosine, which has been implicated in the control of neointimal formation. Herein, we demonstrate that an ENPP1-Fc recombinant therapeutic inhibits proliferation of vascular smooth muscle cells (VSMCs) in vitro and in vivo. Addition of ENPP1 and ATP to cultured VSMCs generated AMP, which was metabolized to adenosine. It also significantly decreased cell proliferation. AMP or adenosine alone inhibited VSMC growth. Inhibition of ecto-5′-nucleotidase CD73 decreased adenosine accumulation and suppressed the anti-proliferative effects of ENPP1/ATP. Addition of AMP increased cAMP synthesis and phosphorylation of VASP at Ser157. This AMP-mediated cAMP increase was abrogated by CD73 inhibitors or by A2aR and A2bR antagonists. Ligation of the carotid artery promoted neointimal hyperplasia in wild-type mice, which was exacerbated in ENPP1-deficient ttw/ttw mice. Prophylactic or therapeutic treatments with ENPP1 significantly reduced intimal hyperplasia not only in ttw/ttw but also in wild-type mice. These findings provide the first insight into the mechanism of the anti-proliferative effect of ENPP1 and broaden its potential therapeutic applications beyond enzyme replacement therapy. [ABSTRACT FROM AUTHOR]

Published
2024
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15. Genetic variants inDDX53contribute to Autism Spectrum Disorder associated with the Xp22.11 locus

Author

Scala, Marcello, primary, Bradley, Clarrisa A., additional, Howe, Jennifer L., additional, Trost, Brett, additional, Bautista Salazar, Nelson, additional, Shum, Carole, additional, Reuter, Miriam S., additional, MacDonald, Jeffrey R., additional, Ko, Sangyoon Y., additional, Frankland, Paul W., additional, Granger, Leslie, additional, Anadiotis, George, additional, Pullano, Verdiana, additional, Brusco, Alfredo, additional, Keller, Roberto, additional, Parisotto, Sarah, additional, Pedro, Helio F., additional, Lusk, Laina, additional, Pojomovsky McDonnell, Pamela, additional, Helbig, Ingo, additional, Mullegama, Sureni V., additional, Douine, Emilie D., additional, Russell, Bianca E., additional, Nelson, Stanley F., additional, Zara, Federico, additional, and Scherer, Stephen W., additional

Published
2023
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16. A recurrent SHANK3 frameshift variant in Autism Spectrum Disorder

Author

Loureiro, Livia O., Howe, Jennifer L., Reuter, Miriam S., Iaboni, Alana, Calli, Kristina, Roshandel, Delnaz, Pritišanac, Iva, Moses, Alan, Forman-Kay, Julie D., Trost, Brett, Zarrei, Mehdi, Rennie, Olivia, Lau, Lynette Y. S., Marshall, Christian R., Srivastava, Siddharth, Godlewski, Brianna, Buttermore, Elizabeth D., Sahin, Mustafa, Hartley, Dean, Frazier, Thomas, Vorstman, Jacob, Georgiades, Stelios, Lewis, Suzanne M. E., Szatmari, Peter, Bradley, Clarrisa A. (Lisa), Tabet, Anne-Claude, Willems, Marjolaine, Lumbroso, Serge, Piton, Amélie, Lespinasse, James, Delorme, Richard, Bourgeron, Thomas, Anagnostou, Evdokia, and Scherer, Stephen W.

Published
2021
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18. Genome-wide detection of tandem DNA repeats that are expanded in autism

Author

Trost, Brett, Engchuan, Worrawat, Nguyen, Charlotte M., Thiruvahindrapuram, Bhooma, Dolzhenko, Egor, Backstrom, Ian, Mirceta, Mila, Mojarad, Bahareh A., Yin, Yue, Dov, Alona, Chandrakumar, Induja, Prasolava, Tanya, Shum, Natalie, Hamdan, Omar, Pellecchia, Giovanna, Howe, Jennifer L., Whitney, Joseph, Klee, Eric W., Baheti, Saurabh, Amaral, David G., Anagnostou, Evdokia, Elsabbagh, Mayada, Fernandez, Bridget A., Hoang, Ny, Lewis, M. E. Suzanne, Liu, Xudong, Sjaarda, Calvin, Smith, Isabel M., Szatmari, Peter, Zwaigenbaum, Lonnie, Glazer, David, Hartley, Dean, Stewart, A. Keith, Eberle, Michael A., Sato, Nozomu, Pearson, Christopher E., Scherer, Stephen W., and Yuen, Ryan K. C.

Published
2020
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19. A framework for an evidence-based gene list relevant to autism spectrum disorder

Author

Schaaf, Christian P., Betancur, Catalina, Yuen, Ryan K. C., Parr, Jeremy R., Skuse, David H., Gallagher, Louise, Bernier, Raphael A., Buchanan, Janet A., Buxbaum, Joseph D., Chen, Chun-An, Dies, Kira A., Elsabbagh, Mayada, Firth, Helen V., Frazier, Thomas, Hoang, Ny, Howe, Jennifer, Marshall, Christian R., Michaud, Jacques L., Rennie, Olivia, Szatmari, Peter, Chung, Wendy K., Bolton, Patrick F., Cook, Edwin H., Scherer, Stephen W., and Vorstman, Jacob A. S.

Published
2020
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20. Sherman Collection Anchors Civil War and History Auction.

Author

Howe, Jennifer

Abstract

Fleischer's Auctions in Columbus, Ohio recently held an auction featuring over 500 historical items, including a collection of personal effects belonging to Civil War General William Tecumseh Sherman. The collection, which had never been offered for sale before, included Sherman's wartime sword, uniform insignia, family Bible, and a copy of George N. Barnard's Photographic Views of Sherman's Campaign. The auction generated over $2 million in prices realized, with a sell-through rate of over 95%. The auction also included items related to the history of slavery in Charleston, South Carolina, such as rare Charleston free badges and slave badges, as well as photographs of an enslaved drummer boy and a hand-painted Civil War cavalry regimental flag. The auction also featured an archive of General Rufus Ingalls, as well as items related to General Robert E. Lee. [Extracted from the article]

Published
2024

21. Disruption of the ASTN2/TRIM32 locus at 9q33.1 is a risk factor in males for autism spectrum disorders, ADHD and other neurodevelopmental phenotypes

Author

Lionel, Anath C, Tammimies, Kristiina, Vaags, Andrea K, Rosenfeld, Jill A, Ahn, Joo Wook, Merico, Daniele, Noor, Abdul, Runke, Cassandra K, Pillalamarri, Vamsee K, Carter, Melissa T, Gazzellone, Matthew J, Thiruvahindrapuram, Bhooma, Fagerberg, Christina, Laulund, Lone W, Pellecchia, Giovanna, Lamoureux, Sylvia, Deshpande, Charu, Clayton-Smith, Jill, White, Ann C, Leather, Susan, Trounce, John, Bedford, H Melanie, Hatchwell, Eli, Eis, Peggy S, Yuen, Ryan KC, Walker, Susan, Uddin, Mohammed, Geraghty, Michael T, Nikkel, Sarah M, Tomiak, Eva M, Fernandez, Bridget A, Soreni, Noam, Crosbie, Jennifer, Arnold, Paul D, Schachar, Russell J, Roberts, Wendy, Paterson, Andrew D, So, Joyce, Szatmari, Peter, Chrysler, Christina, Woodbury-Smith, Marc, Lowry, R Brian, Zwaigenbaum, Lonnie, Mandyam, Divya, Wei, John, MacDonald, Jeffrey R, Howe, Jennifer L, Nalpathamkalam, Thomas, Wang, Zhuozhi, Tolson, Daniel, Cobb, David S, Wilks, Timothy M, Sorensen, Mark J, Bader, Patricia I, An, Yu, Wu, Bai-Lin, Musumeci, Sebastiano Antonino, Romano, Corrado, Postorivo, Diana, Nardone, Anna M, Della Monica, Matteo, Scarano, Gioacchino, Zoccante, Leonardo, Novara, Francesca, Zuffardi, Orsetta, Ciccone, Roberto, Antona, Vincenzo, Carella, Massimo, Zelante, Leopoldo, Cavalli, Pietro, Poggiani, Carlo, Cavallari, Ugo, Argiropoulos, Bob, Chernos, Judy, Brasch-Andersen, Charlotte, Speevak, Marsha, Fichera, Marco, Ogilvie, Caroline Mackie, Shen, Yiping, Hodge, Jennelle C, Talkowski, Michael E, Stavropoulos, Dimitri J, Marshall, Christian R, and Scherer, Stephen W

Subjects
Pediatric Research Initiative, Pediatric, Intellectual and Developmental Disabilities (IDD), Mental Health, Brain Disorders, Human Genome, Neurosciences, Autism, Clinical Research, Behavioral and Social Science, Genetics, 2.1 Biological and endogenous factors, Aetiology, Mental health, Adolescent, Adult, Attention Deficit Disorder with Hyperactivity, Case-Control Studies, Child, Child Development Disorders, Pervasive, Child, Preschool, Chromosomes, Human, Pair 9, DNA Copy Number Variations, Exons, Female, Gene Expression, Genetic Association Studies, Genetic Predisposition to Disease, Glycoproteins, Humans, Infant, Infant, Newborn, Male, Nerve Tissue Proteins, Organ Specificity, Phenotype, Polymorphism, Single Nucleotide, Protein Isoforms, Receptors, Cell Surface, Risk Factors, Sequence Deletion, Transcription Factors, Transcription Initiation Site, Tripartite Motif Proteins, Ubiquitin-Protein Ligases, Young Adult, Biological Sciences, Medical and Health Sciences, Genetics & Heredity
Abstract

Rare copy number variants (CNVs) disrupting ASTN2 or both ASTN2 and TRIM32 have been reported at 9q33.1 by genome-wide studies in a few individuals with neurodevelopmental disorders (NDDs). The vertebrate-specific astrotactins, ASTN2 and its paralog ASTN1, have key roles in glial-guided neuronal migration during brain development. To determine the prevalence of astrotactin mutations and delineate their associated phenotypic spectrum, we screened ASTN2/TRIM32 and ASTN1 (1q25.2) for exonic CNVs in clinical microarray data from 89 985 individuals across 10 sites, including 64 114 NDD subjects. In this clinical dataset, we identified 46 deletions and 12 duplications affecting ASTN2. Deletions of ASTN1 were much rarer. Deletions near the 3' terminus of ASTN2, which would disrupt all transcript isoforms (a subset of these deletions also included TRIM32), were significantly enriched in the NDD subjects (P = 0.002) compared with 44 085 population-based controls. Frequent phenotypes observed in individuals with such deletions include autism spectrum disorder (ASD), attention deficit hyperactivity disorder (ADHD), speech delay, anxiety and obsessive compulsive disorder (OCD). The 3'-terminal ASTN2 deletions were significantly enriched compared with controls in males with NDDs, but not in females. Upon quantifying ASTN2 human brain RNA, we observed shorter isoforms expressed from an alternative transcription start site of recent evolutionary origin near the 3' end. Spatiotemporal expression profiling in the human brain revealed consistently high ASTN1 expression while ASTN2 expression peaked in the early embryonic neocortex and postnatal cerebellar cortex. Our findings shed new light on the role of the astrotactins in psychopathology and their interplay in human neurodevelopment.

Published
2014

22. Convergence of Genes and Cellular Pathways Dysregulated in Autism Spectrum Disorders

Author

Pinto, Dalila, Delaby, Elsa, Merico, Daniele, Barbosa, Mafalda, Merikangas, Alison, Klei, Lambertus, Thiruvahindrapuram, Bhooma, Xu, Xiao, Ziman, Robert, Wang, Zhuozhi, Vorstman, Jacob AS, Thompson, Ann, Regan, Regina, Pilorge, Marion, Pellecchia, Giovanna, Pagnamenta, Alistair T, Oliveira, Bárbara, Marshall, Christian R, Magalhaes, Tiago R, Lowe, Jennifer K, Howe, Jennifer L, Griswold, Anthony J, Gilbert, John, Duketis, Eftichia, Dombroski, Beth A, De Jonge, Maretha V, Cuccaro, Michael, Crawford, Emily L, Correia, Catarina T, Conroy, Judith, Conceição, Inês C, Chiocchetti, Andreas G, Casey, Jillian P, Cai, Guiqing, Cabrol, Christelle, Bolshakova, Nadia, Bacchelli, Elena, Anney, Richard, Gallinger, Steven, Cotterchio, Michelle, Casey, Graham, Zwaigenbaum, Lonnie, Wittemeyer, Kerstin, Wing, Kirsty, Wallace, Simon, van Engeland, Herman, Tryfon, Ana, Thomson, Susanne, Soorya, Latha, Rogé, Bernadette, Roberts, Wendy, Poustka, Fritz, Mouga, Susana, Minshew, Nancy, McInnes, L Alison, McGrew, Susan G, Lord, Catherine, Leboyer, Marion, Le Couteur, Ann S, Kolevzon, Alexander, González, Patricia Jiménez, Jacob, Suma, Holt, Richard, Guter, Stephen, Green, Jonathan, Green, Andrew, Gillberg, Christopher, Fernandez, Bridget A, Duque, Frederico, Delorme, Richard, Dawson, Geraldine, Chaste, Pauline, Café, Cátia, Brennan, Sean, Bourgeron, Thomas, Bolton, Patrick F, Bölte, Sven, Bernier, Raphael, Baird, Gillian, Bailey, Anthony J, Anagnostou, Evdokia, Almeida, Joana, Wijsman, Ellen M, Vieland, Veronica J, Vicente, Astrid M, Schellenberg, Gerard D, Pericak-Vance, Margaret, Paterson, Andrew D, Parr, Jeremy R, Oliveira, Guiomar, Nurnberger, John I, Monaco, Anthony P, Maestrini, Elena, Klauck, Sabine M, Hakonarson, Hakon, Haines, Jonathan L, Geschwind, Daniel H, Freitag, Christine M, Folstein, Susan E, and Ennis, Sean

Subjects
Genetics, Brain Disorders, Pediatric, Mental Health, Intellectual and Developmental Disabilities (IDD), Neurosciences, Autism, 2.1 Biological and endogenous factors, Aetiology, Child, Child Development Disorders, Pervasive, DNA Copy Number Variations, Female, Gene Regulatory Networks, Humans, Male, Metabolic Networks and Pathways, Multigene Family, Pedigree, Sequence Deletion, Biological Sciences, Medical and Health Sciences, Genetics & Heredity
Abstract

Rare copy-number variation (CNV) is an important source of risk for autism spectrum disorders (ASDs). We analyzed 2,446 ASD-affected families and confirmed an excess of genic deletions and duplications in affected versus control groups (1.41-fold, p = 1.0 × 10(-5)) and an increase in affected subjects carrying exonic pathogenic CNVs overlapping known loci associated with dominant or X-linked ASD and intellectual disability (odds ratio = 12.62, p = 2.7 × 10(-15), ∼3% of ASD subjects). Pathogenic CNVs, often showing variable expressivity, included rare de novo and inherited events at 36 loci, implicating ASD-associated genes (CHD2, HDAC4, and GDI1) previously linked to other neurodevelopmental disorders, as well as other genes such as SETD5, MIR137, and HDAC9. Consistent with hypothesized gender-specific modulators, females with ASD were more likely to have highly penetrant CNVs (p = 0.017) and were also overrepresented among subjects with fragile X syndrome protein targets (p = 0.02). Genes affected by de novo CNVs and/or loss-of-function single-nucleotide variants converged on networks related to neuronal signaling and development, synapse function, and chromatin regulation.

Published
2014

23. Allelic heterogeneity and abnormal vesicle recycling in PLAA-related neurodevelopmental disorders.

Author

Iacomino, Michele, Houerbi, Nadia, Fortuna, Sara, Howe, Jennifer, Shan Li, Scorrano, Giovanna, Riva, Antonella, Kai-Wen Cheng, Steiman, Mandy, Peltekova, Iskra, Yusuf, Afiqah, Baldassari, Simona, Tamburro, Serena, Scudieri, Paolo, Musante, Ilaria, Di Ludovico, Armando, Guerrisi, Sara, Balagura, Ganna, Corsello, Antonio, and Efthymiou, Stephanie

Subjects
CHILDREN with autism spectrum disorders, NEURAL development, AUTISM spectrum disorders, SYNAPTIC vesicles, NEUROLOGICAL disorders, MISSENSE mutation, EXOMES
Abstract

The human PLAA gene encodes Phospholipase-A2-Activating-Protein (PLAA) involved in trafficking of membrane proteins. Through its PUL domain (PLAP, Ufd3p, and Lub1p), PLAA interacts with p97/VCP modulating synaptic vesicles recycling. Although few families carrying biallelic PLAA variants were reported with progressive neurodegeneration, consequences of monoallelic PLAA variants have not been elucidated. Using exome or genome sequencing we identified PLAA de-novo missense variants, affecting conserved residues within the PUL domain, in children affected with neurodevelopmental disorders (NDDs), including psychomotor regression, intellectual disability (ID) and autism spectrum disorders (ASDs). Computational and in-vitro studies of the identified variants revealed abnormal chain arrangements at C-terminal and reduced PLAA-p97/VCP interaction, respectively. These findings expand both allelic and phenotypic heterogeneity associated to PLAA-related neurological disorders, highlighting perturbed vesicle recycling as a potential disease mechanism in NDDs due to genetic defects of PLAA. [ABSTRACT FROM AUTHOR]

Published
2024
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24. Individual common variants exert weak effects on the risk for autism spectrum disorders

Author

Anney, Richard, Klei, Lambertus, Pinto, Dalila, Almeida, Joana, Bacchelli, Elena, Baird, Gillian, Bolshakova, Nadia, Bölte, Sven, Bolton, Patrick F, Bourgeron, Thomas, Brennan, Sean, Brian, Jessica, Casey, Jillian, Conroy, Judith, Correia, Catarina, Corsello, Christina, Crawford, Emily L, de Jonge, Maretha, Delorme, Richard, Duketis, Eftichia, Duque, Frederico, Estes, Annette, Farrar, Penny, Fernandez, Bridget A, Folstein, Susan E, Fombonne, Eric, Gilbert, John, Gillberg, Christopher, Glessner, Joseph T, Green, Andrew, Green, Jonathan, Guter, Stephen J, Heron, Elizabeth A, Holt, Richard, Howe, Jennifer L, Hughes, Gillian, Hus, Vanessa, Igliozzi, Roberta, Jacob, Suma, Kenny, Graham P, Kim, Cecilia, Kolevzon, Alexander, Kustanovich, Vlad, Lajonchere, Clara M, Lamb, Janine A, Law-Smith, Miriam, Leboyer, Marion, Le Couteur, Ann, Leventhal, Bennett L, Liu, Xiao-Qing, Lombard, Frances, Lord, Catherine, Lotspeich, Linda, Lund, Sabata C, Magalhaes, Tiago R, Mantoulan, Carine, McDougle, Christopher J, Melhem, Nadine M, Merikangas, Alison, Minshew, Nancy J, Mirza, Ghazala K, Munson, Jeff, Noakes, Carolyn, Nygren, Gudrun, Papanikolaou, Katerina, Pagnamenta, Alistair T, Parrini, Barbara, Paton, Tara, Pickles, Andrew, Posey, David J, Poustka, Fritz, Ragoussis, Jiannis, Regan, Regina, Roberts, Wendy, Roeder, Kathryn, Roge, Bernadette, Rutter, Michael L, Schlitt, Sabine, Shah, Naisha, Sheffield, Val C, Soorya, Latha, Sousa, Inês, Stoppioni, Vera, Sykes, Nuala, Tancredi, Raffaella, Thompson, Ann P, Thomson, Susanne, Tryfon, Ana, Tsiantis, John, Van Engeland, Herman, Vincent, John B, Volkmar, Fred, Vorstman, JAS, Wallace, Simon, Wing, Kirsty, Wittemeyer, Kerstin, Wood, Shawn, Zurawiecki, Danielle, Zwaigenbaum, Lonnie, and Bailey, Anthony J

Subjects
Behavioral and Social Science, Clinical Research, Human Genome, Mental Health, Genetics, Brain Disorders, Pediatric, Intellectual and Developmental Disabilities (IDD), Autism, Prevention, Aetiology, 2.1 Biological and endogenous factors, Alleles, Child, Child Development Disorders, Pervasive, Female, Gene Frequency, Genetic Predisposition to Disease, Genome-Wide Association Study, Genotype, Humans, Language Development, Male, Membrane Proteins, Nerve Tissue Proteins, Polymorphism, Single Nucleotide, Risk Factors, Biological Sciences, Medical and Health Sciences, Genetics & Heredity
Abstract

While it is apparent that rare variation can play an important role in the genetic architecture of autism spectrum disorders (ASDs), the contribution of common variation to the risk of developing ASD is less clear. To produce a more comprehensive picture, we report Stage 2 of the Autism Genome Project genome-wide association study, adding 1301 ASD families and bringing the total to 2705 families analysed (Stages 1 and 2). In addition to evaluating the association of individual single nucleotide polymorphisms (SNPs), we also sought evidence that common variants, en masse, might affect the risk. Despite genotyping over a million SNPs covering the genome, no single SNP shows significant association with ASD or selected phenotypes at a genome-wide level. The SNP that achieves the smallest P-value from secondary analyses is rs1718101. It falls in CNTNAP2, a gene previously implicated in susceptibility for ASD. This SNP also shows modest association with age of word/phrase acquisition in ASD subjects, of interest because features of language development are also associated with other variation in CNTNAP2. In contrast, allele scores derived from the transmission of common alleles to Stage 1 cases significantly predict case status in the independent Stage 2 sample. Despite being significant, the variance explained by these allele scores was small (Vm< 1%). Based on results from individual SNPs and their en masse effect on risk, as inferred from the allele score results, it is reasonable to conclude that common variants affect the risk for ASD but their individual effects are modest.

Published
2012

25. A genome-wide scan for common alleles affecting risk for autism

Author

Anney, Richard, Klei, Lambertus, Pinto, Dalila, Regan, Regina, Conroy, Judith, Magalhaes, Tiago R, Correia, Catarina, Abrahams, Brett S, Sykes, Nuala, Pagnamenta, Alistair T, Almeida, Joana, Bacchelli, Elena, Bailey, Anthony J, Baird, Gillian, Battaglia, Agatino, Berney, Tom, Bolshakova, Nadia, Bölte, Sven, Bolton, Patrick F, Bourgeron, Thomas, Brennan, Sean, Brian, Jessica, Carson, Andrew R, Casallo, Guillermo, Casey, Jillian, Chu, Su H, Cochrane, Lynne, Corsello, Christina, Crawford, Emily L, Crossett, Andrew, Dawson, Geraldine, de Jonge, Maretha, Delorme, Richard, Drmic, Irene, Duketis, Eftichia, Duque, Frederico, Estes, Annette, Farrar, Penny, Fernandez, Bridget A, Folstein, Susan E, Fombonne, Eric, Freitag, Christine M, Gilbert, John, Gillberg, Christopher, Glessner, Joseph T, Goldberg, Jeremy, Green, Jonathan, Guter, Stephen J, Hakonarson, Hakon, Heron, Elizabeth A, Hill, Matthew, Holt, Richard, Howe, Jennifer L, Hughes, Gillian, Hus, Vanessa, Igliozzi, Roberta, Kim, Cecilia, Klauck, Sabine M, Kolevzon, Alexander, Korvatska, Olena, Kustanovich, Vlad, Lajonchere, Clara M, Lamb, Janine A, Laskawiec, Magdalena, Leboyer, Marion, Le Couteur, Ann, Leventhal, Bennett L, Lionel, Anath C, Liu, Xiao-Qing, Lord, Catherine, Lotspeich, Linda, Lund, Sabata C, Maestrini, Elena, Mahoney, William, Mantoulan, Carine, Marshall, Christian R, McConachie, Helen, McDougle, Christopher J, McGrath, Jane, McMahon, William M, Melhem, Nadine M, Merikangas, Alison, Migita, Ohsuke, Minshew, Nancy J, Mirza, Ghazala K, Munson, Jeff, Nelson, Stanley F, Noakes, Carolyn, Noor, Abdul, Nygren, Gudrun, Oliveira, Guiomar, Papanikolaou, Katerina, Parr, Jeremy R, Parrini, Barbara, Paton, Tara, Pickles, Andrew, Piven, Joseph, Posey, David J, Poustka, Annemarie, and Poustka, Fritz

Subjects
Clinical Research, Human Genome, Mental Health, Genetics, Brain Disorders, Pediatric, Biotechnology, Intellectual and Developmental Disabilities (IDD), Autism, Prevention, Aetiology, 2.1 Biological and endogenous factors, Alleles, Autistic Disorder, DNA Copy Number Variations, Databases, Genetic, Genetic Predisposition to Disease, Genetic Variation, Genome, Human, Genome-Wide Association Study, Genotype, Humans, Polymorphism, Single Nucleotide, Risk Factors, White People, Biological Sciences, Medical and Health Sciences, Genetics & Heredity
Abstract

Although autism spectrum disorders (ASDs) have a substantial genetic basis, most of the known genetic risk has been traced to rare variants, principally copy number variants (CNVs). To identify common risk variation, the Autism Genome Project (AGP) Consortium genotyped 1558 rigorously defined ASD families for 1 million single-nucleotide polymorphisms (SNPs) and analyzed these SNP genotypes for association with ASD. In one of four primary association analyses, the association signal for marker rs4141463, located within MACROD2, crossed the genome-wide association significance threshold of P < 5 × 10(-8). When a smaller replication sample was analyzed, the risk allele at rs4141463 was again over-transmitted; yet, consistent with the winner's curse, its effect size in the replication sample was much smaller; and, for the combined samples, the association signal barely fell below the P < 5 × 10(-8) threshold. Exploratory analyses of phenotypic subtypes yielded no significant associations after correction for multiple testing. They did, however, yield strong signals within several genes, KIAA0564, PLD5, POU6F2, ST8SIA2 and TAF1C.

Published
2010

26. Linkage of whole genome sequencing and administrative health data in autism: A proof of concept study

Author

Baribeau, Danielle A., primary, Arneja, Jasleen, additional, Wang, Xuesong, additional, Howe, Jennifer, additional, McLaughlin, John R., additional, Tu, Karen, additional, Guan, Jun, additional, Iaboni, Alana, additional, Kelley, Elizabeth, additional, Ayub, Muhammad, additional, Nicolson, Robert, additional, Georgiades, Stelios, additional, Scherer, Stephen W., additional, Bronskill, Susan E., additional, Anagnostou, Evdokia, additional, and Brooks, Jennifer D., additional

Published
2023
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27. The clinical and molecular spectrum of the KDM6B-related neurodevelopmental disorder

Author

Rots, Dmitrijs, primary, Jakub, Taryn E., additional, Keung, Crystal, additional, Jackson, Adam, additional, Banka, Siddharth, additional, Pfundt, Rolph, additional, de Vries, Bert B.A., additional, van Jaarsveld, Richard H., additional, Hopman, Saskia M.J., additional, van Binsbergen, Ellen, additional, Valenzuela, Irene, additional, Hempel, Maja, additional, Bierhals, Tatjana, additional, Kortüm, Fanny, additional, Lecoquierre, Francois, additional, Goldenberg, Alice, additional, Hertz, Jens Michael, additional, Andersen, Charlotte Brasch, additional, Kibæk, Maria, additional, Prijoles, Eloise J., additional, Stevenson, Roger E., additional, Everman, David B., additional, Patterson, Wesley G., additional, Meng, Linyan, additional, Gijavanekar, Charul, additional, De Dios, Karl, additional, Lakhani, Shenela, additional, Levy, Tess, additional, Wagner, Matias, additional, Wieczorek, Dagmar, additional, Benke, Paul J., additional, Lopez Garcia, María Soledad, additional, Perrier, Renee, additional, Sousa, Sergio B., additional, Almeida, Pedro M., additional, Simões, Maria José, additional, Isidor, Bertrand, additional, Deb, Wallid, additional, Schmanski, Andrew A., additional, Abdul-Rahman, Omar, additional, Philippe, Christophe, additional, Bruel, Ange-Line, additional, Faivre, Laurence, additional, Vitobello, Antonio, additional, Thauvin, Christel, additional, Smits, Jeroen J., additional, Garavelli, Livia, additional, Caraffi, Stefano G., additional, Peluso, Francesca, additional, Davis-Keppen, Laura, additional, Platt, Dylan, additional, Royer, Erin, additional, Leeuwen, Lisette, additional, Sinnema, Margje, additional, Stegmann, Alexander P.A., additional, Stumpel, Constance T.R.M., additional, Tiller, George E., additional, Bosch, Daniëlle G.M., additional, Potgieter, Stephanus T., additional, Joss, Shelagh, additional, Splitt, Miranda, additional, Holden, Simon, additional, Prapa, Matina, additional, Foulds, Nicola, additional, Douzgou, Sofia, additional, Puura, Kaija, additional, Waltes, Regina, additional, Chiocchetti, Andreas G., additional, Freitag, Christine M., additional, Satterstrom, F. Kyle, additional, De Rubeis, Silvia, additional, Buxbaum, Joseph, additional, Gelb, Bruce D., additional, Branko, Aleksic, additional, Kushima, Itaru, additional, Howe, Jennifer, additional, Scherer, Stephen W., additional, Arado, Alessia, additional, Baldo, Chiara, additional, Patat, Olivier, additional, Bénédicte, Demeer, additional, Lopergolo, Diego, additional, Santorelli, Filippo M., additional, Haack, Tobias B., additional, Dufke, Andreas, additional, Bertrand, Miriam, additional, Falb, Ruth J., additional, Rieß, Angelika, additional, Krieg, Peter, additional, Spranger, Stephanie, additional, Bedeschi, Maria Francesca, additional, Iascone, Maria, additional, Josephi-Taylor, Sarah, additional, Roscioli, Tony, additional, Buckley, Michael F., additional, Liebelt, Jan, additional, Dagli, Aditi I., additional, Aten, Emmelien, additional, Hurst, Anna C.E., additional, Hicks, Alesha, additional, Suri, Mohnish, additional, Aliu, Ermal, additional, Naik, Sunil, additional, Sidlow, Richard, additional, Coursimault, Juliette, additional, Nicolas, Gaël, additional, Küpper, Hanna, additional, Petit, Florence, additional, Ibrahim, Veyan, additional, Top, Deniz, additional, Di Cara, Francesca, additional, Louie, Raymond J., additional, Stolerman, Elliot, additional, Brunner, Han G., additional, Vissers, Lisenka E.L.M., additional, Kramer, Jamie M., additional, and Kleefstra, Tjitske, additional

Published
2023
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28. The Phenotypic variability of 16p11.2 distal BP2–BP3 deletion in a transgenerational family and in neurodevelopmentally ascertained samples.

Author

Woodbury-Smith, Marc, D’Abate, Lia, Stavropoulos, Dimitri J., Howe, Jennifer, Drmic, Irene, Ny Hoang, Zarrei, Mehdi, Trost, Brett, Iaboni, Alana, Anagnostou, Evdokia, and Scherer, Stephen W.

Abstract

Background We present genomic and phenotypic findings of a transgenerational family consisting of three male offspring, each with a maternally inherited distal 220 kb deletion at locus 16p11.2 (BP2–BP3). Genomic analysis of all family members was prompted by a diagnosis of autism spectrum disorder (ASD) in the eldest child, who also presented with a low body mass index. Methods All male offspring underwent extensive neuropsychiatric evaluation. Both parents were also assessed for social functioning and cognition. The family underwent whole-genome sequencing. Further data curation was undertaken from samples ascertained for neurodevelopmental disorders and congenital abnormalities. Results On medical examination, both the second and third-born male offspring presented with obesity. The second-born male offspring met research diagnostic criteria for ASD at 8 years of age and presented with mild attention deficits. The third-born male offspring was only noted as having motor deficits and received a diagnosis of developmental coordination disorder. Other than the 16p11.2 distal deletion, no additional contributing variants of clinical significance were observed. The mother was clinically evaluated and noted as having a broader autism phenotype. Conclusion In this family, the phenotypes observed are most likely caused by the 16p11.2 distal deletion. The lack of other overt pathogenic mutations identified by genomic sequencing reinforces the variable expressivity that should be heeded in a clinical setting. Importantly, distal 16p11.2 deletions can present with a highly variable phenotype even within a single family. Our additional data curation provides further evidence on the variable clinical presentation among those with pathogenetic 16p11.2 (BP2–BP3) mutations. [ABSTRACT FROM AUTHOR]

Published
2023
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29. ANK2 loss-of-function variants are associated with epilepsy, and lead to impaired axon initial segment plasticity and hyperactive network activity in hiPSC-derived neuronal networks

Author

Teunissen, Maria W A, primary, Lewerissa, Elly, additional, van Hugte, Eline J H, additional, Wang, Shan, additional, Ockeloen, Charlotte W, additional, Koolen, David A, additional, Pfundt, Rolph, additional, Marcelis, Carlo L M, additional, Brilstra, Eva, additional, Howe, Jennifer L, additional, Scherer, Stephen W, additional, Le Guillou, Xavier, additional, Bilan, Frédéric, additional, Primiano, Michelle, additional, Roohi, Jasmin, additional, Piton, Amelie, additional, de Saint Martin, Anne, additional, Baer, Sarah, additional, Seiffert, Simone, additional, Platzer, Konrad, additional, Jamra, Rami Abou, additional, Syrbe, Steffen, additional, Doering, Jan H, additional, Lakhani, Shenela, additional, Nangia, Srishti, additional, Gilissen, Christian, additional, Vermeulen, R Jeroen, additional, Rouhl, Rob P W, additional, Brunner, Han G, additional, Willemsen, Marjolein H, additional, and Nadif Kasri, Nael, additional

Published
2023
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30. Gene copy number variation and pediatric mental health/neurodevelopment in a general population

Author

Zarrei, Mehdi, primary, Burton, Christie L, additional, Engchuan, Worrawat, additional, Higginbotham, Edward J, additional, Wei, John, additional, Shaikh, Sabah, additional, Roslin, Nicole M, additional, MacDonald, Jeffrey R, additional, Pellecchia, Giovanna, additional, Nalpathamkalam, Thomas, additional, Lamoureux, Sylvia, additional, Manshaei, Roozbeh, additional, Howe, Jennifer, additional, Trost, Brett, additional, Thiruvahindrapuram, Bhooma, additional, Marshall, Christian R, additional, Yuen, Ryan K C, additional, Wintle, Richard F, additional, Strug, Lisa J, additional, Stavropoulos, Dimitri J, additional, Vorstman, Jacob A S, additional, Arnold, Paul, additional, Merico, Daniele, additional, Woodbury-Smith, Marc, additional, Crosbie, Jennifer, additional, Schachar, Russell, additional, and Scherer, Stephen W, additional

Published
2023
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31. Whole Genome Sequencing to Resolve the Genomic Architecture of Cerebral Palsy in a Canadian Cohort (P13-9.003)

Author

Oskoui, Maryam, primary, Zarrei, Mehdi, additional, Engchuan, Worrawat, additional, Sondheimer, Neal, additional, Thiruv, Bhooma, additional, Higginbotham, Edward, additional, Thapa, Ritesh, additional, Behlim, Tarannum, additional, Aimola, Sabrina, additional, Wei, John, additional, Danthi, Prakroothi, additional, Pellecchia, Giovanna, additional, Ho, Karen, additional, de Rijke, Jill, additional, Howe, Jennifer, additional, Nalpathamkalam, Thomas, additional, Manshaei, Roozbeh, additional, Whitney, Joseph, additional, Patel, Rohan, additional, Hamdan, Omar, additional, Shaath, Rulan, additional, Knights, Shannon, additional, Trost, Brett, additional, Samdup, Dawa, additional, MCCORMICK, ANNA, additional, Hunt, Carolyn, additional, Kirton, Adam, additional, Kawamura, Anne, additional, Mesterman, Ronit, additional, Gorter, Jan Willem, additional, Dlamini, Nomazulu, additional, Merico, Daniele, additional, Yuen, Ryan, additional, Shevell, Michael, additional, Stavropoulos, Dimitri, additional, Wintle, Richard, additional, Fehlings, Darcy, additional, and Scherer, Stephen, additional

Published
2023
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32. ANK2 loss-of-function variants are associated with epilepsy, and lead to impaired axon initial segment plasticity and hyperactive network activity in hiPSC-derived neuronal networks

Author

Genetica Klinische Genetica, Brain, Teunissen, Maria W A, Lewerissa, Elly, van Hugte, Eline J H, Wang, Shan, Ockeloen, Charlotte W, Koolen, David A, Pfundt, Rolph, Marcelis, Carlo L M, Brilstra, Eva, Howe, Jennifer L, Scherer, Stephen W, Le Guillou, Xavier, Bilan, Frédéric, Primiano, Michelle, Roohi, Jasmin, Piton, Amelie, de Saint Martin, Anne, Baer, Sarah, Seiffert, Simone, Platzer, Konrad, Jamra, Rami Abou, Syrbe, Steffen, Doering, Jan Henje, Lakhani, Shenela, Nangia, Srishti, Gilissen, Christian, Vermeulen, R Jeroen, Rouhl, Rob P W, Brunner, Han G, Willemsen, Marjolein H, Kasri, Nael Nadif, Genetica Klinische Genetica, Brain, Teunissen, Maria W A, Lewerissa, Elly, van Hugte, Eline J H, Wang, Shan, Ockeloen, Charlotte W, Koolen, David A, Pfundt, Rolph, Marcelis, Carlo L M, Brilstra, Eva, Howe, Jennifer L, Scherer, Stephen W, Le Guillou, Xavier, Bilan, Frédéric, Primiano, Michelle, Roohi, Jasmin, Piton, Amelie, de Saint Martin, Anne, Baer, Sarah, Seiffert, Simone, Platzer, Konrad, Jamra, Rami Abou, Syrbe, Steffen, Doering, Jan Henje, Lakhani, Shenela, Nangia, Srishti, Gilissen, Christian, Vermeulen, R Jeroen, Rouhl, Rob P W, Brunner, Han G, Willemsen, Marjolein H, and Kasri, Nael Nadif

Published
2023

33. CAPRIN1 haploinsufficiency causes a neurodevelopmental disorder with language impairment, ADHD and ASD

Author

Genetica, Genetica Sectie Genoomdiagnostiek, Pavinato, Lisa, Delle Vedove, Andrea, Carli, Diana, Ferrero, Marta, Carestiato, Silvia, Howe, Jennifer L, Agolini, Emanuele, Coviello, Domenico A, van de Laar, Ingrid, Au, Ping Yee Billie, Di Gregorio, Eleonora, Fabbiani, Alessandra, Croci, Susanna, Mencarelli, Maria Antonietta, Bruno, Lucia P, Renieri, Alessandra, Veltra, Danai, Sofocleous, Christalena, Faivre, Laurence, Mazel, Benoit, Safraou, Hana, Denommé-Pichon, Anne Sophie, van Slegtenhorst, Marjon A, Giesbertz, Noor, van Jaarsveld, Richard H, Childers, Anna, Rogers, R Curtis, Novelli, Antonio, De Rubeis, Silvia, Buxbaum, Joseph D, Scherer, Stephen W, Ferrero, Giovanni Battista, Wirth, Brunhilde, Brusco, Alfredo, Genetica, Genetica Sectie Genoomdiagnostiek, Pavinato, Lisa, Delle Vedove, Andrea, Carli, Diana, Ferrero, Marta, Carestiato, Silvia, Howe, Jennifer L, Agolini, Emanuele, Coviello, Domenico A, van de Laar, Ingrid, Au, Ping Yee Billie, Di Gregorio, Eleonora, Fabbiani, Alessandra, Croci, Susanna, Mencarelli, Maria Antonietta, Bruno, Lucia P, Renieri, Alessandra, Veltra, Danai, Sofocleous, Christalena, Faivre, Laurence, Mazel, Benoit, Safraou, Hana, Denommé-Pichon, Anne Sophie, van Slegtenhorst, Marjon A, Giesbertz, Noor, van Jaarsveld, Richard H, Childers, Anna, Rogers, R Curtis, Novelli, Antonio, De Rubeis, Silvia, Buxbaum, Joseph D, Scherer, Stephen W, Ferrero, Giovanni Battista, Wirth, Brunhilde, and Brusco, Alfredo

Published
2023

34. A large data resource of genomic copy number variation across neurodevelopmental disorders

Author

Zarrei, Mehdi, Burton, Christie L., Engchuan, Worrawat, Young, Edwin J., Higginbotham, Edward J., MacDonald, Jeffrey R., Trost, Brett, Chan, Ada J. S., Walker, Susan, Lamoureux, Sylvia, Heung, Tracy, Mojarad, Bahareh A., Kellam, Barbara, Paton, Tara, Faheem, Muhammad, Miron, Karin, Lu, Chao, Wang, Ting, Samler, Kozue, Wang, Xiaolin, Costain, Gregory, Hoang, Ny, Pellecchia, Giovanna, Wei, John, Patel, Rohan V., Thiruvahindrapuram, Bhooma, Roifman, Maian, Merico, Daniele, Goodale, Tara, Drmic, Irene, Speevak, Marsha, Howe, Jennifer L., Yuen, Ryan K. C., Buchanan, Janet A., Vorstman, Jacob A. S., Marshall, Christian R., Wintle, Richard F., Rosenberg, David R., Hanna, Gregory L., Woodbury-Smith, Marc, Cytrynbaum, Cheryl, Zwaigenbaum, Lonnie, Elsabbagh, Mayada, Flanagan, Janine, Fernandez, Bridget A., Carter, Melissa T., Szatmari, Peter, Roberts, Wendy, Lerch, Jason, Liu, Xudong, Nicolson, Rob, Georgiades, Stelios, Weksberg, Rosanna, Arnold, Paul D., Bassett, Anne S., Crosbie, Jennifer, Schachar, Russell, Stavropoulos, Dimitri J., Anagnostou, Evdokia, and Scherer, Stephen W.

Published
2019
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35. The Personal Genome Project Canada: findings from whole genome sequences of the inaugural 56 participants

Author

Reuter, Miriam S., Walker, Susan, Thiruvahindrapuram, Bhooma, Whitney, Joe, Cohn, Iris, Sondheimer, Neal, Yuen, Ryan K.C., Trost, Brett, Paton, Tara A., Pereira, Sergio L., Herbrick, Jo-Anne, Wintle, Richard F., Merico, Daniele, Howe, Jennifer, MacDonald, Jeffrey R., Lu, Chao, Nalpathamkalam, Thomas, Sung, Wilson W.L., Wang, Zhuozhi, Patel, Rohan V., Pellecchia, Giovanna, Wei, John, Strug, Lisa J., Bell, Sherilyn, Kellam, Barbara, Mahtani, Melanie M., Bassett, Anne S., Bombard, Yvonne, Weksberg, Rosanna, Shuman, Cheryl, Cohn, Ronald D., Stavropoulos, Dimitri J., Bowdin, Sarah, Hildebrandt, Matthew R., Wei, Wei, Romm, Asli, Pasceri, Peter, Ellis, James, Ray, Peter, Meyn, M. Stephen, Monfared, Nasim, Hosseini, S. Mohsen, Joseph-George, Ann M., Keeley, Fred W., Cook, Ryan A., Fiume, Marc, Lee, Hin C., Marshall, Christian R., Davies, Jill, Hazell, Allison, Buchanan, Janet A., Szego, Michael J., and Scherer, Stephen W.

Subjects
Health policy -- Analysis, DNA sequencing -- Analysis, Pharmacogenomics -- Analysis, Health
Abstract

BACKGROUND: The Personal Genome Project Canada is a comprehensive public data resource that integrates whole genome sequencing data and health information. We describe genomic variation identified in the initial recruitment cohort of 56 volunteers. METHODS: Volunteers were screened for eligibility and provided informed consent for open data sharing. Using blood DNA, we performed whole genome sequencing and identified all possible classes of DNA variants. A genetic counsellor explained the implication of the results to each participant. RESULTS: Whole genome sequencing of the first 56 participants identified 207662 805 sequence variants and 27494 copy number variations. We analyzed a prioritized disease-associated data set (n = 1606 variants) according to standardized guidelines, and interpreted 19 variants in 14 participants (25%) as having obvious health implications. Six of these variants (e.g., in BRCA1 or mosaic loss of an X chromosome) were pathogenic or likely pathogenic. Seven were risk factors for cancer, cardiovascular or neurobehavioural conditions. Four other variants--associated with cancer, cardiac or neurodegenerative phenotypes--remained of uncertain significance because of discrepancies among databases. We also identified a large structural chromosome aberration and a likely pathogenic mitochondrial variant. There were 172 recessive disease alleles (e.g., 5 individuals carried mutations for cystic fibrosis). Pharmacogenomics analyses revealed another 3.9 potentially relevant genotypes per individual. INTERPRETATION: Our analyses identified a spectrum of genetic variants with potential health impact in 25% of participants. When also considering recessive alleles and variants with potential pharmacologic relevance, all 56 participants had medically relevant findings. Although access is mostly limited to research, whole genome sequencing can provide specific and novel information with the potential of major impact for health care., Rapid technological advances are enabling a view of human genetic variation in ever-increasing detail and at plummeting costs. (1) Until recently, analysis has been targeted largely to defined genes, but [...]

Published
2018
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36. 3. GENOMIC ARCHITECTURE OF AUTISM SPECTRUM DISORDER FROM COMPREHENSIVE WHOLE-GENOME SEQUENCE ANNOTATION

Author

Trost, Brett, primary, Thiruvahindrapuram, Bhooma, additional, Chan, Ada, additional, Engchuan, Worrawat, additional, Higginbotham, Edward, additional, Howe, Jennifer, additional, Loureiro, Livia, additional, Reuter, Miriam, additional, Roshandel, Delnaz, additional, Whitney, Joe, additional, Zarrei, Mehdi, additional, Vorstman, Jacob, additional, Glazer, David, additional, Hartley, Dean, additional, and Scherer, Stephen, additional

Published
2022
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37. Gene copy number variation in pediatric mental illness in a general population

Author

Zarrei, Mehdi, primary, Burton, Christie L., additional, Engchuan, Worrawat, additional, Higginbotham, Edward J, additional, Wei, John, additional, Shaikh, Sabah, additional, Roslin, Nicole M., additional, MacDonald, Jeffrey R., additional, Pellecchia, Giovanna, additional, Nalpathamkalam, Thomas, additional, Lamoureux, Sylvia, additional, Manshaei, Roozbeh, additional, Howe, Jennifer, additional, Trost, Brett, additional, Thiruvahindrapuram, Bhooma, additional, Marshall, Christian R., additional, Yuen, Ryan K.C., additional, Wintle, Richard F., additional, Strug, Lisa J, additional, Stavropoulos, Dimitri J., additional, Vorstman, Jacob A.S., additional, Arnold, Paul, additional, Merico, Daniele, additional, Woodbury-Smith, Marc, additional, Crosbie, Jennifer, additional, Schachar, Russell, additional, and Scherer, Stephen W., additional

Published
2022
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39. CAPRIN1 haploinsufficiency causes a neurodevelopmental disorder with language impairment, ADHD and ASD

Author

Pavinato, Lisa, primary, Delle Vedove, Andrea, additional, Carli, Diana, additional, Ferrero, Marta, additional, Carestiato, Silvia, additional, Howe, Jennifer L, additional, Agolini, Emanuele, additional, Coviello, Domenico A, additional, van de Laar, Ingrid, additional, Au, Ping Yee Billie, additional, Di Gregorio, Eleonora, additional, Fabbiani, Alessandra, additional, Croci, Susanna, additional, Mencarelli, Maria Antonietta, additional, Bruno, Lucia P, additional, Renieri, Alessandra, additional, Veltra, Danai, additional, Sofocleous, Christalena, additional, Faivre, Laurence, additional, Mazel, Benoit, additional, Safraou, Hana, additional, Denommé-Pichon, Anne-Sophie, additional, van Slegtenhorst, Marjon A, additional, Giesbertz, Noor, additional, van Jaarsveld, Richard H, additional, Childers, Anna, additional, Rogers, R Curtis, additional, Novelli, Antonio, additional, De Rubeis, Silvia, additional, Buxbaum, Joseph D, additional, Scherer, Stephen W, additional, Ferrero, Giovanni Battista, additional, Wirth, Brunhilde, additional, and Brusco, Alfredo, additional

Published
2022
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40. Genotype-phenotype correlations in SCN8A-related disorders reveal prognostic and therapeutic implications

Author

Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center], BMBF, Treat-ION, 01GM1907 [sponsor], Johannesen, Katrine M., Liu, Yuanyuan, Koko, Mahmoud, Gjerulfsen, Cathrine E., Sonnenberg, Lukas, Schubert, Julian, Fenger, Christina D., Eltokhi, Ahmed, Rannap, Maert, Koch, Nils A., Lauxmann, Stephan, Krüger, Johanna, Kegele, Josua, Canafoglia, Laura, Franceschetti, Silvana, Mayer, Thomas, Rebstock, Johannes, Zacher, Pia, Ruf, Susanne, Alber, Michael, Sterbova, Katalin, Lassuthová, Petra, Vlckova, Marketa, Lemke, Johannes R., Platzer, Konrad, Krey, Ilona, Heine, Constanze, Wieczorek, Dagmar, Kroell-Seger, Judith, Lund, Caroline, Klein, Karl Martin, Billie Au, P. Y., Rho, Jong M., Ho, Alice W., Masnada, Silvia, Veggiotti, Pierangelo, Giordano, Lucio, Accorsi, Patrizia, Hoei-Hansen, Christina E., Striano, Pasquale, Zara, Federico, Verhelst, Helene, Verhoeven, Judith S., van der Zwaag, Bert, Harder, Aster V. E., Brilstra, Eva, Pendziwiat, Manuela, Lebon, Sebastian, Vaccarezza, Maria, Minh Le, Ngoc, Christensen, Jakob, Grønborg, Sabine, Scherer, Stephen W., Howe, Jennifer, Fazeli, Walid, Howell, Katherine B., Leventer, Richard, Stutterd, Chloe, Walsh, Sonja, Gerard, Marion, Gerard, Bénédicte, Matricardi, Sara, Bonardi, Claudia M., Sartori, Stefano, Berger, Andrea, Hoffman-Zacharska, Dorota, Mastrangelo, Massimo, Darra, Francesca, Vøllo, Arve, Motazacker, M. Mahdi, Lakeman, Phillis, Nizon, Mathilde, Betzler, Cornelia, Altuzarra, Cecilia, Caume, Roseline, Roubertie, Agathe, Gélisse, Philippe, Marini, Carla, Guerrini, Renzo, Bilan, Frederic, Tibussek, Daniel, Koch-Hogrebe, Margarete, Perry, M. Scott, Ichikawa, Shoji, Dadali, Elena, Sharkov, Artem, Mishina, Irina, Abramov, Mikhail, Kanivets, Ilya, Korostelev, Sergey, Kutsev, Sergey, Wain, Karen E., Eisenhauer, Nancy, Wagner, Monisa, Savatt, Juliann M., Müller-Schlüter, Karen, Bassan, Haim, Borovikov, Artem, Nassogne, Marie-Cecile, Destrée, Anne, Schoonjans, An-Sofie, Meuwissen, Marije, Buzatu, Marga, Jansen, Anna, Scalais, Emmanuel, Srivastava, Siddharth, Tan, Wen-Hann, Olson, Heather E., Loddenkemper, Tobias, Poduri, Annapurna, Helbig, Katherine L., Helbig, Ingo, Fitzgerald, Mark P., Goldberg, Ethan M., Roser, Timo, Borggraefe, Ingo, Brünger, Tobias, May, Patrick, Lal, Dennis, Lederer, Damien, Rubboli, Guido, Heyne, Henrike O., Lesca, Gaetan, Hedrich, Ulrike B. S., Benda, Jan, Gardella, Elena, Lerche, Holger, Møller, Rikke S., Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center], BMBF, Treat-ION, 01GM1907 [sponsor], Johannesen, Katrine M., Liu, Yuanyuan, Koko, Mahmoud, Gjerulfsen, Cathrine E., Sonnenberg, Lukas, Schubert, Julian, Fenger, Christina D., Eltokhi, Ahmed, Rannap, Maert, Koch, Nils A., Lauxmann, Stephan, Krüger, Johanna, Kegele, Josua, Canafoglia, Laura, Franceschetti, Silvana, Mayer, Thomas, Rebstock, Johannes, Zacher, Pia, Ruf, Susanne, Alber, Michael, Sterbova, Katalin, Lassuthová, Petra, Vlckova, Marketa, Lemke, Johannes R., Platzer, Konrad, Krey, Ilona, Heine, Constanze, Wieczorek, Dagmar, Kroell-Seger, Judith, Lund, Caroline, Klein, Karl Martin, Billie Au, P. Y., Rho, Jong M., Ho, Alice W., Masnada, Silvia, Veggiotti, Pierangelo, Giordano, Lucio, Accorsi, Patrizia, Hoei-Hansen, Christina E., Striano, Pasquale, Zara, Federico, Verhelst, Helene, Verhoeven, Judith S., van der Zwaag, Bert, Harder, Aster V. E., Brilstra, Eva, Pendziwiat, Manuela, Lebon, Sebastian, Vaccarezza, Maria, Minh Le, Ngoc, Christensen, Jakob, Grønborg, Sabine, Scherer, Stephen W., Howe, Jennifer, Fazeli, Walid, Howell, Katherine B., Leventer, Richard, Stutterd, Chloe, Walsh, Sonja, Gerard, Marion, Gerard, Bénédicte, Matricardi, Sara, Bonardi, Claudia M., Sartori, Stefano, Berger, Andrea, Hoffman-Zacharska, Dorota, Mastrangelo, Massimo, Darra, Francesca, Vøllo, Arve, Motazacker, M. Mahdi, Lakeman, Phillis, Nizon, Mathilde, Betzler, Cornelia, Altuzarra, Cecilia, Caume, Roseline, Roubertie, Agathe, Gélisse, Philippe, Marini, Carla, Guerrini, Renzo, Bilan, Frederic, Tibussek, Daniel, Koch-Hogrebe, Margarete, Perry, M. Scott, Ichikawa, Shoji, Dadali, Elena, Sharkov, Artem, Mishina, Irina, Abramov, Mikhail, Kanivets, Ilya, Korostelev, Sergey, Kutsev, Sergey, Wain, Karen E., Eisenhauer, Nancy, Wagner, Monisa, Savatt, Juliann M., Müller-Schlüter, Karen, Bassan, Haim, Borovikov, Artem, Nassogne, Marie-Cecile, Destrée, Anne, Schoonjans, An-Sofie, Meuwissen, Marije, Buzatu, Marga, Jansen, Anna, Scalais, Emmanuel, Srivastava, Siddharth, Tan, Wen-Hann, Olson, Heather E., Loddenkemper, Tobias, Poduri, Annapurna, Helbig, Katherine L., Helbig, Ingo, Fitzgerald, Mark P., Goldberg, Ethan M., Roser, Timo, Borggraefe, Ingo, Brünger, Tobias, May, Patrick, Lal, Dennis, Lederer, Damien, Rubboli, Guido, Heyne, Henrike O., Lesca, Gaetan, Hedrich, Ulrike B. S., Benda, Jan, Gardella, Elena, Lerche, Holger, and Møller, Rikke S.

Abstract

We report detailed functional analyses and genotype-phenotype correlations in 392 individuals carrying disease-causing variants in SCN8A, encoding the voltage-gated Na+ channel NaV1.6, with the aim of describing clinical phenotypes related to functional effects. Six different clinical subgroups could be identified: 1) Benign familial infantile epilepsy (BFIE) (n = 15, normal cognition, treatable seizures), 2) intermediate epilepsy (n = 33, mild ID, partially pharmaco-responsive), 3) developmental and epileptic encephalopathy (DEE, n = 177, severe ID, majority pharmaco-resistant), 4) generalized epilepsy (n = 20, mild to moderate ID, frequently with absence seizures), 5) unclassifiable epilepsy (n = 127), and 6) neurodevelopmental disorder without epilepsy (n = 20, mild to moderate ID). Groups 1–3 presented with focal or multifocal seizures (median age of onset: four months) and focal epileptiform discharges, whereas the onset of seizures in group 4 was later (median: 42 months) with generalized epileptiform discharges. We performed functional studies expressing missense variants in ND7/23 neuroblastoma cells and primary neuronal cultures using recombinant tetrodotoxin-insensitive human NaV1.6 channels and whole-cell patch-clamping. Two variants causing DEE showed a strong gain-of-function (GOF, hyperpolarising shift of steady-state activation, strongly increased neuronal firing rate), and one variant causing BFIE or intermediate epilepsy showed a mild GOF (defective fast inactivation, less increased firing). In contrast, all three variants causing generalized epilepsy induced a loss-of-function (LOF, reduced current amplitudes, depolarising shift of steady-state activation, reduced neuronal firing). Including previous studies, functional effects were known for 170 individuals. All 136 individuals carrying a functionally tested GOF variant had either focal (97, groups 1–3), or unclassifiable epilepsy (39), whereas 34 with a LOF variant had either generalized (14), no

Published
2022

41. Genotype-phenotype correlations in SCN8A-related disorders reveal prognostic and therapeutic implications

Author

Johannesen, Katrine M., Liu, Yuanyuan, Koko, Mahmoud, Gjerulfsen, Cathrine E., Sonnenberg, Lukas, Schubert, Julian, Fenger, Christina D., Eltokhi, Ahmed, Rannap, Maert, Koch, Nils A., Lauxmann, Stephan, Krüger, Johanna, Kegele, Josua, Canafoglia, Laura, Franceschetti, Silvana, Mayer, Thomas, Rebstock, Johannes, Zacher, Pia, Ruf, Susanne, Alber, Michael, Sterbova, Katalin, Lassuthová, Petra, Vlckova, Marketa, Lemke, Johannes R., Platzer, Konrad, Krey, Ilona, Heine, Constanze, Wieczorek, Dagmar, Kroell-Seger, Judith, Lund, Caroline, Klein, Karl Martin, Au, P. Y.Billie, Rho, Jong M., Ho, Alice W., Masnada, Silvia, Veggiotti, Pierangelo, Giordano, Lucio, Accorsi, Patrizia, Hoei-Hansen, Christina E., Striano, Pasquale, Zara, Federico, Verhelst, Helene, Verhoeven, Judith S., Braakman, Hilde M.H., van der Zwaag, Bert, Harder, Aster V.E., Brilstra, Eva, Pendziwiat, Manuela, Lebon, Sebastian, Vaccarezza, Maria, Le, Ngoc Minh, Christensen, Jakob, Grønborg, Sabine, Scherer, Stephen W., Howe, Jennifer, Fazeli, Walid, Howell, Katherine B., Leventer, Richard, Stutterd, Chloe, Walsh, Sonja, Gerard, Marion, Gerard, Bénédicte, Matricardi, Sara, Bonardi, Claudia M., Sartori, Stefano, Berger, Andrea, Hoffman-Zacharska, Dorota, Mastrangelo, Massimo, Darra, Francesca, Vøllo, Arve, Motazacker, M. Mahdi, Lakeman, Phillis, Nizon, Mathilde, Betzler, Cornelia, Altuzarra, Cecilia, Caume, Roseline, Roubertie, Agathe, Gélisse, Philippe, Marini, Carla, Guerrini, Renzo, Bilan, Frederic, Tibussek, Daniel, Koch-Hogrebe, Margarete, Perry, M. Scott, Ichikawa, Shoji, Dadali, Elena, Sharkov, Artem, Mishina, Irina, Abramov, Mikhail, Kanivets, Ilya, Korostelev, Sergey, Kutsev, Sergey, Wain, Karen E., Eisenhauer, Nancy, Wagner, Monisa, Savatt, Juliann M., Müller-Schlüter, Karen, Bassan, Haim, Borovikov, Artem, Nassogne, Marie Cecile, Destrée, Anne, Schoonjans, An Sofie, Meuwissen, Marije, Buzatu, Marga, Jansen, Anna, Scalais, Emmanuel, Srivastava, Siddharth, Tan, Wen Hann, Olson, Heather E., Loddenkemper, Tobias, Poduri, Annapurna, Helbig, Katherine L., Helbig, Ingo, Fitzgerald, Mark P., Goldberg, Ethan M., Roser, Timo, Borggraefe, Ingo, Brünger, Tobias, May, Patrick, Lal, Dennis, Lederer, Damien, Rubboli, Guido, Heyne, Henrike O., Lesca, Gaetan, Hedrich, Ulrike B.S., Benda, Jan, Gardella, Elena, Lerche, Holger, Møller, Rikke S., Johannesen, Katrine M., Liu, Yuanyuan, Koko, Mahmoud, Gjerulfsen, Cathrine E., Sonnenberg, Lukas, Schubert, Julian, Fenger, Christina D., Eltokhi, Ahmed, Rannap, Maert, Koch, Nils A., Lauxmann, Stephan, Krüger, Johanna, Kegele, Josua, Canafoglia, Laura, Franceschetti, Silvana, Mayer, Thomas, Rebstock, Johannes, Zacher, Pia, Ruf, Susanne, Alber, Michael, Sterbova, Katalin, Lassuthová, Petra, Vlckova, Marketa, Lemke, Johannes R., Platzer, Konrad, Krey, Ilona, Heine, Constanze, Wieczorek, Dagmar, Kroell-Seger, Judith, Lund, Caroline, Klein, Karl Martin, Au, P. Y.Billie, Rho, Jong M., Ho, Alice W., Masnada, Silvia, Veggiotti, Pierangelo, Giordano, Lucio, Accorsi, Patrizia, Hoei-Hansen, Christina E., Striano, Pasquale, Zara, Federico, Verhelst, Helene, Verhoeven, Judith S., Braakman, Hilde M.H., van der Zwaag, Bert, Harder, Aster V.E., Brilstra, Eva, Pendziwiat, Manuela, Lebon, Sebastian, Vaccarezza, Maria, Le, Ngoc Minh, Christensen, Jakob, Grønborg, Sabine, Scherer, Stephen W., Howe, Jennifer, Fazeli, Walid, Howell, Katherine B., Leventer, Richard, Stutterd, Chloe, Walsh, Sonja, Gerard, Marion, Gerard, Bénédicte, Matricardi, Sara, Bonardi, Claudia M., Sartori, Stefano, Berger, Andrea, Hoffman-Zacharska, Dorota, Mastrangelo, Massimo, Darra, Francesca, Vøllo, Arve, Motazacker, M. Mahdi, Lakeman, Phillis, Nizon, Mathilde, Betzler, Cornelia, Altuzarra, Cecilia, Caume, Roseline, Roubertie, Agathe, Gélisse, Philippe, Marini, Carla, Guerrini, Renzo, Bilan, Frederic, Tibussek, Daniel, Koch-Hogrebe, Margarete, Perry, M. Scott, Ichikawa, Shoji, Dadali, Elena, Sharkov, Artem, Mishina, Irina, Abramov, Mikhail, Kanivets, Ilya, Korostelev, Sergey, Kutsev, Sergey, Wain, Karen E., Eisenhauer, Nancy, Wagner, Monisa, Savatt, Juliann M., Müller-Schlüter, Karen, Bassan, Haim, Borovikov, Artem, Nassogne, Marie Cecile, Destrée, Anne, Schoonjans, An Sofie, Meuwissen, Marije, Buzatu, Marga, Jansen, Anna, Scalais, Emmanuel, Srivastava, Siddharth, Tan, Wen Hann, Olson, Heather E., Loddenkemper, Tobias, Poduri, Annapurna, Helbig, Katherine L., Helbig, Ingo, Fitzgerald, Mark P., Goldberg, Ethan M., Roser, Timo, Borggraefe, Ingo, Brünger, Tobias, May, Patrick, Lal, Dennis, Lederer, Damien, Rubboli, Guido, Heyne, Henrike O., Lesca, Gaetan, Hedrich, Ulrike B.S., Benda, Jan, Gardella, Elena, Lerche, Holger, and Møller, Rikke S.

Abstract

We report detailed functional analyses and genotype-phenotype correlations in 392 individuals carrying disease-causing variants in SCN8A, encoding the voltage-gated Na+ channel Nav1.6, with the aim of describing clinical phenotypes related to functional effects. Six different clinical subgroups were identified: Group 1, benign familial infantile epilepsy (n = 15, normal cognition, treatable seizures); Group 2, intermediate epilepsy (n = 33, mild intellectual disability, partially pharmaco-responsive); Group 3, developmental and epileptic encephalopathy (n = 177, severe intellectual disability, majority pharmaco-resistant); Group 4, generalized epilepsy (n = 20, mild to moderate intellectual disability, frequently with absence seizures); Group 5, unclassifiable epilepsy (n = 127); and Group 6, neurodevelopmental disorder without epilepsy (n = 20, mild to moderate intellectual disability). Those in Groups 1-3 presented with focal or multifocal seizures (median age of onset: 4 months) and focal epileptiform discharges, whereas the onset of seizures in patients with generalized epilepsy was later (median: 42 months) with generalized epileptiform discharges. We performed functional studies expressing missense variants in ND7/23 neuroblastoma cells and primary neuronal cultures using recombinant tetrodotoxin-insensitive human Nav1.6 channels and whole-cell patch-clamping. Two variants causing developmental and epileptic encephalopathy showed a strong gain-of-function (hyperpolarizing shift of steady-state activation, strongly increased neuronal firing rate) and one variant causing benign familial infantile epilepsy or intermediate epilepsy showed a mild gain-of-function (defective fast inactivation, less increased firing). In contrast, all three variants causing generalized epilepsy induced a loss-of-function (reduced current amplitudes, depolarizing shift of steady-state activation, reduced neuronal firing). Functional effects were known for 170 individuals. All 136 i

Published
2022

42. Genotype-phenotype correlations in SCN8A-related disorders reveal prognostic and therapeutic implications

Author

Genetica Sectie Genoomdiagnostiek, Child Health, Genetica Klinische Genetica, Brain, Johannesen, Katrine M, Liu, Yuanyuan, Koko, Mahmoud, Gjerulfsen, Cathrine E, Sonnenberg, Lukas, Schubert, Julian, Fenger, Christina D, Eltokhi, Ahmed, Rannap, Maert, Koch, Nils A, Lauxmann, Stephan, Krüger, Johanna, Kegele, Josua, Canafoglia, Laura, Franceschetti, Silvana, Mayer, Thomas, Rebstock, Johannes, Zacher, Pia, Ruf, Susanne, Alber, Michael, Sterbova, Katalin, Lassuthová, Petra, Vlckova, Marketa, Lemke, Johannes R, Platzer, Konrad, Krey, Ilona, Heine, Constanze, Wieczorek, Dagmar, Kroell-Seger, Judith, Lund, Caroline, Klein, Karl Martin, Billie Au, P Y, Rho, Jong M, Ho, Alice W, Masnada, Silvia, Veggiotti, Pierangelo, Giordano, Lucio, Accorsi, Patrizia, Hoei-Hansen, Christina E, Striano, Pasquale, Zara, Federico, Verhelst, Helene, Verhoeven, Judith S, van der Zwaag, Bert, Harder, Aster V E, Brilstra, Eva, Pendziwiat, Manuela, Lebon, Sebastian, Vaccarezza, Maria, Minh Le, Ngoc, Christensen, Jakob, Grønborg, Sabine, Scherer, Stephen W, Howe, Jennifer, Fazeli, Walid, Howell, Katherine B, Leventer, Richard, Stutterd, Chloe, Walsh, Sonja, Gerard, Marion, Gerard, Bénédicte, Matricardi, Sara, Bonardi, Claudia M, Sartori, Stefano, Berger, Andrea, Hoffman-Zacharska, Dorota, Mastrangelo, Massimo, Darra, Francesca, Vøllo, Arve, Motazacker, M Mahdi, Lakeman, Phillis, Nizon, Mathilde, Betzler, Cornelia, Altuzarra, Cecilia, Caume, Roseline, Roubertie, Agathe, Gélisse, Philippe, Marini, Carla, Guerrini, Renzo, Bilan, Frederic, Tibussek, Daniel, Koch-Hogrebe, Margarete, Perry, M Scott, Ichikawa, Shoji, Dadali, Elena, Sharkov, Artem, Mishina, Irina, Abramov, Mikhail, Kanivets, Ilya, Korostelev, Sergey, Kutsev, Sergey, Wain, Karen E, Eisenhauer, Nancy, Wagner, Monisa, Savatt, Juliann M, Müller-Schlüter, Karen, Bassan, Haim, Borovikov, Artem, Nassogne, Marie-Cecile, Destrée, Anne, Schoonjans, An-Sofie, Meuwissen, Marije, Buzatu, Marga, Jansen, Anna, Scalais, Emmanuel, Srivastava, Siddharth, Tan, Wen-Hann, Olson, Heather E, Loddenkemper, Tobias, Poduri, Annapurna, Helbig, Katherine L, Helbig, Ingo, Fitzgerald, Mark P, Goldberg, Ethan M, Roser, Timo, Borggraefe, Ingo, Brünger, Tobias, May, Patrick, Lal, Dennis, Lederer, Damien, Rubboli, Guido, Heyne, Henrike O, Lesca, Gaetan, Hedrich, Ulrike B S, Benda, Jan, Gardella, Elena, Lerche, Holger, Møller, Rikke S, Genetica Sectie Genoomdiagnostiek, Child Health, Genetica Klinische Genetica, Brain, Johannesen, Katrine M, Liu, Yuanyuan, Koko, Mahmoud, Gjerulfsen, Cathrine E, Sonnenberg, Lukas, Schubert, Julian, Fenger, Christina D, Eltokhi, Ahmed, Rannap, Maert, Koch, Nils A, Lauxmann, Stephan, Krüger, Johanna, Kegele, Josua, Canafoglia, Laura, Franceschetti, Silvana, Mayer, Thomas, Rebstock, Johannes, Zacher, Pia, Ruf, Susanne, Alber, Michael, Sterbova, Katalin, Lassuthová, Petra, Vlckova, Marketa, Lemke, Johannes R, Platzer, Konrad, Krey, Ilona, Heine, Constanze, Wieczorek, Dagmar, Kroell-Seger, Judith, Lund, Caroline, Klein, Karl Martin, Billie Au, P Y, Rho, Jong M, Ho, Alice W, Masnada, Silvia, Veggiotti, Pierangelo, Giordano, Lucio, Accorsi, Patrizia, Hoei-Hansen, Christina E, Striano, Pasquale, Zara, Federico, Verhelst, Helene, Verhoeven, Judith S, van der Zwaag, Bert, Harder, Aster V E, Brilstra, Eva, Pendziwiat, Manuela, Lebon, Sebastian, Vaccarezza, Maria, Minh Le, Ngoc, Christensen, Jakob, Grønborg, Sabine, Scherer, Stephen W, Howe, Jennifer, Fazeli, Walid, Howell, Katherine B, Leventer, Richard, Stutterd, Chloe, Walsh, Sonja, Gerard, Marion, Gerard, Bénédicte, Matricardi, Sara, Bonardi, Claudia M, Sartori, Stefano, Berger, Andrea, Hoffman-Zacharska, Dorota, Mastrangelo, Massimo, Darra, Francesca, Vøllo, Arve, Motazacker, M Mahdi, Lakeman, Phillis, Nizon, Mathilde, Betzler, Cornelia, Altuzarra, Cecilia, Caume, Roseline, Roubertie, Agathe, Gélisse, Philippe, Marini, Carla, Guerrini, Renzo, Bilan, Frederic, Tibussek, Daniel, Koch-Hogrebe, Margarete, Perry, M Scott, Ichikawa, Shoji, Dadali, Elena, Sharkov, Artem, Mishina, Irina, Abramov, Mikhail, Kanivets, Ilya, Korostelev, Sergey, Kutsev, Sergey, Wain, Karen E, Eisenhauer, Nancy, Wagner, Monisa, Savatt, Juliann M, Müller-Schlüter, Karen, Bassan, Haim, Borovikov, Artem, Nassogne, Marie-Cecile, Destrée, Anne, Schoonjans, An-Sofie, Meuwissen, Marije, Buzatu, Marga, Jansen, Anna, Scalais, Emmanuel, Srivastava, Siddharth, Tan, Wen-Hann, Olson, Heather E, Loddenkemper, Tobias, Poduri, Annapurna, Helbig, Katherine L, Helbig, Ingo, Fitzgerald, Mark P, Goldberg, Ethan M, Roser, Timo, Borggraefe, Ingo, Brünger, Tobias, May, Patrick, Lal, Dennis, Lederer, Damien, Rubboli, Guido, Heyne, Henrike O, Lesca, Gaetan, Hedrich, Ulrike B S, Benda, Jan, Gardella, Elena, Lerche, Holger, and Møller, Rikke S

Published
2022

43. Whole-genome sequencing of quartet families with autism spectrum disorder

Author

Yuen, Ryan K.C., Thiruvahindrapuram, Bhooma, Merico, Daniele, Walker, Susan, Tammimies, Kristiina, Hoang, Ny, Chrysler, Christina, Nalpathamkalam, Thomas, Pellecchia, Giovanna, Liu, Yi, Gazzellone, Matthew J., D'Abate, Lia, Deneault, Eric, Howe, Jennifer L., Liu, Richard S.C., Thompson, Ann, Zarrei, Mehdi, Uddin, Mohammed, Marshall, Christian R., Ring, Robert H., Zwaigenbaum, Lonnie, Ray, Peter N., Weksberg, Rosanna, Carter, Melissa T., Fernandez, Bridget A., Roberts, Wendy, Szatmari, Peter, and Scherer, Stephen W.

Subjects
Nucleotide sequencing -- Research, Pervasive developmental disorders -- Genetic aspects, Genetic research, DNA sequencing -- Research, Genomes -- Research, Biological sciences, Health
Abstract

Autism spectrum disorder (ASD) is genetically heterogeneous, with evidence for hundreds of susceptibility loci. Previous microarray and exome-sequencing studies have examined portions of the genome in simplex families (parents and one ASD-affected child) having presumed sporadic forms of the disorder. We used whole-genome sequencing (WGS) of 85 quartet families (parents and two ASD-affected siblings), consisting of 170 individuals with ASD, to generate a comprehensive data resource encompassing all classes of genetic variation (including noncoding variants) and accompanying phenotypes, in apparently familial forms of ASD. By examining de novo and rare inherited single-nucleotide and structural variations in genes previously reported to be associated with ASD or other neurodevelopmental disorders, we found that some (69.4%) of the affected siblings carried different ASD-relevant mutations. These siblings with discordant mutations tended to demonstrate more clinical variability than those who shared a risk variant. Our study emphasizes that substantial genetic heterogeneity exists in ASD, necessitating the use of WGS to delineate all genic and non-genic susceptibility variants in research and in clinical diagnostics., Evidence from twin and family studies suggests substantial heritability in ASD (1). Risk of recurrence in families is high, ranging from 12.9 (ref. 2) to 18.7% (ref. 3), suggesting that [...]

Published
2015
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45. Using extended pedigrees to identify novel autism spectrum disorder (ASD) candidate genes

Author

Woodbury-Smith, Marc, Paterson, Andrew D., Thiruvahindrapduram, Bhooma, Lionel, Anath C., Marshall, Christian R., Merico, Daniele, Fernandez, Bridget A., Duku, Eric, Sutcliffe, James S., O’Conner, Irene, Chrysler, Christina, Thompson, Ann, Kellam, Barbara, Tammimies, Kristiina, Walker, Susan, Yuen, Ryan K. C., Uddin, Mohammed, Howe, Jennifer L., Parlier, Morgan, Whitten, Kathy, Szatmari, Peter, Vieland, Veronica J., Piven, Joseph, and Scherer, Stephen W.

Published
2015
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47. Genomic architecture of Autism Spectrum Disorder from comprehensive whole-genome sequence annotation

Author

Trost, Brett, primary, Thiruvahindrapuram, Bhooma, additional, Chan, Ada J.S., additional, Engchuan, Worrawat, additional, Higginbotham, Edward J., additional, Howe, Jennifer L., additional, Loureiro, Livia O., additional, Reuter, Miriam S., additional, Roshandel, Delnaz, additional, Whitney, Joe, additional, Zarrei, Mehdi, additional, Bookman, Matthew, additional, Somerville, Cherith, additional, Shaath, Rulan, additional, Abdi, Mona, additional, Aliyev, Elbay, additional, Patel, Rohan V., additional, Nalpathamkalam, Thomas, additional, Pellecchia, Giovanna, additional, Hamdan, Omar, additional, Kaur, Gaganjot, additional, Wang, Zhuozhi, additional, MacDonald, Jeffrey R., additional, Wei, John, additional, Sung, Wilson W.L., additional, Lamoureux, Sylvia, additional, Hoang, Ny, additional, Selvanayagam, Thanuja, additional, Deflaux, Nicole, additional, Geng, Melissa, additional, Ghaffari, Siavash, additional, Bates, John, additional, Young, Edwin J., additional, Ding, Qiliang, additional, Shum, Carole, additional, D’abate, Lia, additional, Bradley, Clarissa A., additional, Rutherford, Annabel, additional, Aguda, Vernie, additional, Apresto, Beverly, additional, Chen, Nan, additional, Desai, Sachin, additional, Du, Xiaoyan, additional, Fong, Matthew L.Y., additional, Pullenayegum, Sanjeev, additional, Samler, Kozue, additional, Wang, Ting, additional, Ho, Karen, additional, Paton, Tara, additional, Pereira, Sergio L., additional, Herbrick, Jo-Anne, additional, Wintle, Richard F., additional, Fuerth, Jonathan, additional, Noppornpitak, Juti, additional, Ward, Heather, additional, Magee, Patrick, additional, Baz, Ayman Al, additional, Kajendirarajah, Usanthan, additional, Kapadia, Sharvari, additional, Vlasblom, Jim, additional, Valluri, Monica, additional, Green, Joseph, additional, Seifer, Vicki, additional, Quirbach, Morgan, additional, Rennie, Olivia, additional, Kelley, Elizabeth, additional, Masjedi, Nina, additional, Lord, Catherine, additional, Szego, Michael J., additional, Zawati, Ma’n H., additional, Lang, Michael, additional, Strug, Lisa J., additional, Marshall, Christian R., additional, Costain, Gregory, additional, Calli, Kristina, additional, Iaboni, Alana, additional, Yusuf, Afiqah, additional, Ambrozewicz, Patricia, additional, Gallagher, Louise, additional, Amaral, David G., additional, Brian, Jessica, additional, Elsabbagh, Mayada, additional, Georgiades, Stelios, additional, Messinger, Daniel S., additional, Ozonoff, Sally, additional, Sebat, Jonathan, additional, Sjaarda, Calvin, additional, Smith, Isabel M., additional, Szatmari, Peter, additional, Zwaigenbaum, Lonnie, additional, Kushki, Azadeh, additional, Frazier, Thomas W., additional, Vorstman, Jacob A.S., additional, Fakhro, Khalid A., additional, Fernandez, Bridget A., additional, Lewis, M.E. Suzanne, additional, Weksberg, Rosanna, additional, Fiume, Marc, additional, Yuen, Ryan K.C., additional, Anagnostou, Evdokia, additional, Sondheimer, Neal, additional, Glazer, David, additional, Hartley, Dean M., additional, and Scherer, Stephen W., additional

Published
2022
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48. Regionally defined proteomic profiles of human cerebral tissue and organoids reveal conserved molecular modules of neurodevelopment

Author

Melliou, Sofia, primary, Sangster, Kevin T., additional, Kao, Jennifer, additional, Zarrei, Mehdi, additional, Lam, K.H. Brian, additional, Howe, Jennifer, additional, Papaioannou, Michail-Dimitrios, additional, Tsang, Queenie P.L., additional, Borhani, Okty Abbasi, additional, Sajid, Rifat Shahriar, additional, Bonnet, Céline, additional, Leheup, Bruno, additional, Shannon, Patrick, additional, Scherer, Stephen W., additional, Stavropoulos, Dimitri James, additional, Djuric, Ugljesa, additional, and Diamandis, Phedias, additional

Published
2022
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49. MO751: Calciphylaxis is Characterized by Pyrophosphate Deficiency in Dialysis Patients: A Pilot Study

Author

Nigwekar, Sagar, primary, St Hillien, Shelsea, additional, Seethapathy, Rituvanthikaa, additional, Krinsky, Scott, additional, Torcatti, Jeanfranco, additional, Howe, Jennifer, additional, Kalim, Sahir, additional, Portales-Castillo, Ignacio, additional, Mengesha, Beza, additional, Wen, Wen, additional, Cizman, Borut, additional, and Sabbagh, Yves, additional

Published
2022
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