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1. A common flanking variant is associated with enhanced stability of the FGF14-SCA27B repeat locus

Author

Pellerin, David, Del Gobbo, Giulia F., Couse, Madeline, Dolzhenko, Egor, Nageshwaran, Sathiji K., Cheung, Warren A., Xu, Isaac R. L., Dicaire, Marie-Josée, Spurdens, Guinevere, Matos-Rodrigues, Gabriel, Stevanovski, Igor, Scriba, Carolin K., Rebelo, Adriana, Roth, Virginie, Wandzel, Marion, Bonnet, Céline, Ashton, Catherine, Agarwal, Aman, Peter, Cyril, Hasson, Dan, Tsankova, Nadejda M., Dewar, Ken, Lamont, Phillipa J., Laing, Nigel G., Renaud, Mathilde, Houlden, Henry, Synofzik, Matthis, Usdin, Karen, Nussenzweig, Andre, Napierala, Marek, Chen, Zhao, Jiang, Hong, Deveson, Ira W., Ravenscroft, Gianina, Akbarian, Schahram, Eberle, Michael A., Boycott, Kym M., Pastinen, Tomi, Brais, Bernard, Zuchner, Stephan, and Danzi, Matt C.

Published
2024
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4. Evaluation of the diagnostic accuracy of exome sequencing and its impact on diagnostic thinking for patients with rare disease in a publicly funded health care system: A prospective cohort study

Author

Boycott, Kym, Brudno, Michael, Bernier, Francois, van Karnebeek, Clara, Dyment, David, Kernohan, Kristin, Innes, Micheil, Lamont, Ryan, Parboosingh, Jillian, Marshall, Deborah, Marshall, Christian, Mendoza, Roberto, Dowling, James, Hayeems, Robin, Knoppers, Bartha, Lehman, Anna, Mostafavi, Sara, Hartley, Taila, Acker, Meryl, Fooks, Katharine, Gillespie, Meredith K., Price, E. Magda, Graham, Ian D., White-Brown, Alexandre, MacKay, Layla, Macdonald, Stella K., Brady, Lauren, Hui, Angela Y., Andrews, Joseph D., Chowdhury, Ashfia, Wall, Erika, Soubry, Élisabeth, Ediae, Grace U., Rojas, Samantha, Assamad, Daniel, Tarnopolsky, Mark, Sawyer, Sarah L., Chisholm, Caitlin, Lemire, Gabrielle, Amburgey, Kimberly, Lazier, Joanna, Mendoza-Londono, Roberto, Dowling, James J., Balci, Tugce B., Armour, Christine M., Bhola, Priya T., Costain, Gregory, Dupuis, Lucie, Carter, Melissa, Badalato, Lauren, Richer, Julie, Boswell-Patterson, Christie, Kannu, Peter, Cordeiro, Dawn, Warman-Chardon, Jodi, Graham, Gail, Siu, Victoria Mok, Cytrynbaum, Cheryl, Rusnak, Alison, Aul, Ritu B., Yoon, Grace, Gonorazky, Hernan, McNiven, Vanda, Mercimek-Andrews, Saadet, Guerin, Andrea, Deshwar, Ashish R., Marwaha, Ashish, Weksberg, Rosanna, Karp, Natalya, Campbell, Maggie, Al-Qattan, Sarah, Shuen, Andrew Y., Inbar-Feigenberg, Michal, Cohn, Ronald, Szuto, Anna, Inglese, Cara, Poirier, Myriam, Chad, Lauren, Potter, Beth, and Boycott, Kym M.

Published
2024
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5. Identification of a DNA methylation episignature for recurrent constellations of embryonic malformations

Author

Haghshenas, Sadegheh, Karimi, Karim, Stevenson, Roger E., Levy, Michael A., Relator, Raissa, Kerkhof, Jennifer, Rzasa, Jessica, McConkey, Haley, Lauzon-Young, Carolyn, Balci, Tugce B., White-Brown, Alexandre M., Carter, Melissa T., Richer, Julie, Armour, Christine M., Sawyer, Sarah L., Bhola, Priya T., Tedder, Matthew L., Skinner, Cindy D., van Rooij, Iris A.L.M., van de Putte, Romy, de Blaauw, Ivo, Koeck, Rebekka M., Hoischen, Alexander, Brunner, Han, Esteki, Masoud Zamani, Pelet, Anna, Lyonnet, Stanislas, Amiel, Jeanne, Boycott, Kym M., and Sadikovic, Bekim

Published
2024
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10. Microduplications of ARID1A and ARID1B cause a novel clinical and epigenetic distinct BAFopathy

Author

van der Sluijs, Pleuntje J., Moutton, Sébastien, Dingemans, Alexander J.M., Weis, Denisa, Levy, Michael A., Boycott, Kym M., Arberas, Claudia, Baldassarri, Margherita, Beneteau, Claire, Brusco, Alfredo, Coutton, Charles, Dabir, Tabib, Dentici, Maria L., Devriendt, Koenraad, Faivre, Laurence, van Haelst, Mieke M., Jizi, Khadije, Kempers, Marlies J., Kerkhof, Jennifer, Kharbanda, Mira, Lachlan, Katherine, Marle, Nathalie, McConkey, Haley, Mencarelli, Maria A., Mowat, David., Niceta, Marcello, Nicolas, Claire, Novelli, Antonio, Orlando, Valeria, Pichon, Olivier, Rankin, Julia, Relator, Raissa., Ropers, Fabienne G., Rosenfeld, Jill A., Sachdev, Rani, Sandaradura, Sarah A., Shukarova-Angelovska, Elena, Steenbeek, Duco, Tartaglia, Marco, Tedder, Matthew A., Trajkova, Slavica, Winer, Norbert, Woods, Jeremy, de Vries, Bert B.A., Sadikovic, Bekim, Alders, Marielle, and Santen, Gijs W.E.

Published
2024
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12. The Deep Genome Project

Author

Lloyd, KC Kent, Adams, David J, Baynam, Gareth, Beaudet, Arthur L, Bosch, Fatima, Boycott, Kym M, Braun, Robert E, Caulfield, Mark, Cohn, Ronald, Dickinson, Mary E, Dobbie, Michael S, Flenniken, Ann M, Flicek, Paul, Galande, Sanjeev, Gao, Xiang, Grobler, Anne, Heaney, Jason D, Herault, Yann, de Angelis, Martin Hrabě, Lupski, James R, Lyonnet, Stanislas, Mallon, Ann-Marie, Mammano, Fabio, MacRae, Calum A, McInnes, Roderick, McKerlie, Colin, Meehan, Terrence F, Murray, Stephen A, Nutter, Lauryl MJ, Obata, Yuichi, Parkinson, Helen, Pepper, Michael S, Sedlacek, Radislav, Seong, Je Kyung, Shiroishi, Toshihiko, Smedley, Damian, Tocchini-Valentini, Glauco, Valle, David, Wang, Chi-Kuang Leo, Wells, Sara, White, Jacqueline, Wurst, Wolfgang, Xu, Ying, and Brown, Steve DM

Subjects
Animals, Genes, Genome, Humans, Mice, Mutation, Phenotype, Proteins, Environmental Sciences, Biological Sciences, Information and Computing Sciences, Bioinformatics
Published
2020

13. Identification of rare-disease genes using blood transcriptome sequencing and large control cohorts.

Author

Frésard, Laure, Smail, Craig, Ferraro, Nicole M, Teran, Nicole A, Li, Xin, Smith, Kevin S, Bonner, Devon, Kernohan, Kristin D, Marwaha, Shruti, Zappala, Zachary, Balliu, Brunilda, Davis, Joe R, Liu, Boxiang, Prybol, Cameron J, Kohler, Jennefer N, Zastrow, Diane B, Reuter, Chloe M, Fisk, Dianna G, Grove, Megan E, Davidson, Jean M, Hartley, Taila, Joshi, Ruchi, Strober, Benjamin J, Utiramerur, Sowmithri, Undiagnosed Diseases Network, Care4Rare Canada Consortium, Lind, Lars, Ingelsson, Erik, Battle, Alexis, Bejerano, Gill, Bernstein, Jonathan A, Ashley, Euan A, Boycott, Kym M, Merker, Jason D, Wheeler, Matthew T, and Montgomery, Stephen B

Subjects
Undiagnosed Diseases Network, Care4Rare Canada Consortium, Humans, Rare Diseases, Oxidoreductases Acting on CH-CH Group Donors, Potassium Channels, RNA, Case-Control Studies, Cohort Studies, Sequence Analysis, RNA, RNA Splicing, Mutation, Models, Genetic, Child, Child, Preschool, Female, Male, Genetic Variation, Acid Ceramidase, Whole Exome Sequencing, Human Genome, Clinical Research, Genetics, Biotechnology, 4.1 Discovery and preclinical testing of markers and technologies, 2.1 Biological and endogenous factors, Immunology, Medical and Health Sciences
Abstract

It is estimated that 350 million individuals worldwide suffer from rare diseases, which are predominantly caused by mutation in a single gene1. The current molecular diagnostic rate is estimated at 50%, with whole-exome sequencing (WES) among the most successful approaches2-5. For patients in whom WES is uninformative, RNA sequencing (RNA-seq) has shown diagnostic utility in specific tissues and diseases6-8. This includes muscle biopsies from patients with undiagnosed rare muscle disorders6,9, and cultured fibroblasts from patients with mitochondrial disorders7. However, for many individuals, biopsies are not performed for clinical care, and tissues are difficult to access. We sought to assess the utility of RNA-seq from blood as a diagnostic tool for rare diseases of different pathophysiologies. We generated whole-blood RNA-seq from 94 individuals with undiagnosed rare diseases spanning 16 diverse disease categories. We developed a robust approach to compare data from these individuals with large sets of RNA-seq data for controls (n = 1,594 unrelated controls and n = 49 family members) and demonstrated the impacts of expression, splicing, gene and variant filtering strategies on disease gene identification. Across our cohort, we observed that RNA-seq yields a 7.5% diagnostic rate, and an additional 16.7% with improved candidate gene resolution.

Published
2019

14. A Diagnosis for All Rare Genetic Diseases: The Horizon and the Next Frontiers

Author

Boycott, Kym M, Hartley, Taila, Biesecker, Leslie G, Gibbs, Richard A, Innes, A Micheil, Riess, Olaf, Belmont, John, Dunwoodie, Sally L, Jojic, Nebojsa, Lassmann, Timo, Mackay, Deborah, Temple, I Karen, Visel, Axel, and Baynam, Gareth

Subjects
Biomedical and Clinical Sciences, Biomedical Imaging, Human Genome, Genetics, Good Health and Well Being, Exome, Genetic Testing, Genome, Human, High-Throughput Nucleotide Sequencing, Humans, Rare Diseases, Sequence Analysis, DNA, Translational Research, Biomedical, Exome Sequencing, Biological Sciences, Medical and Health Sciences, Developmental Biology, Biological sciences, Biomedical and clinical sciences
Abstract

The introduction of exome sequencing in the clinic has sparked tremendous optimism for the future of rare disease diagnosis, and there is exciting opportunity to further leverage these advances. To provide diagnostic clarity to all of these patients, however, there is a critical need for the field to develop and implement strategies to understand the mechanisms underlying all rare diseases and translate these to clinical care.

Published
2019

15. PLPHP deficiency: clinical, genetic, biochemical, and mechanistic insights.

Author

Johnstone, Devon L, Al-Shekaili, Hilal H, Tarailo-Graovac, Maja, Wolf, Nicole I, Ivy, Autumn S, Demarest, Scott, Roussel, Yann, Ciapaite, Jolita, van Roermund, Carlo WT, Kernohan, Kristin D, Kosuta, Ceres, Ban, Kevin, Ito, Yoko, McBride, Skye, Al-Thihli, Khalid, Abdelrahim, Rana A, Koul, Roshan, Al Futaisi, Amna, Haaxma, Charlotte A, Olson, Heather, Sigurdardottir, Laufey Yr, Arnold, Georgianne L, Gerkes, Erica H, Boon, M, Heiner-Fokkema, M Rebecca, Noble, Sandra, Bosma, Marjolein, Jans, Judith, Koolen, David A, Kamsteeg, Erik-Jan, Drögemöller, Britt, Ross, Colin J, Majewski, Jacek, Cho, Megan T, Begtrup, Amber, Wasserman, Wyeth W, Bui, Tuan, Brimble, Elise, Violante, Sara, Houten, Sander M, Wevers, Ron A, van Faassen, Martijn, Kema, Ido P, Lepage, Nathalie, Lines, Matthew A, Dyment, David A, Wanders, Ronald JA, Verhoeven-Duif, Nanda, Ekker, Marc, Boycott, Kym M, Friedman, Jan M, Pena, Izabella A, and van Karnebeek, Clara DM

Subjects
Epilepsy, Neurosciences, Brain Disorders, Neurodegenerative, 2.1 Biological and endogenous factors, Aetiology, Neurological, Animals, Disease Models, Animal, Female, HEK293 Cells, Humans, Male, Phenotype, Proteins, Pyridoxal Phosphate, Pyridoxine, Vitamin B 6, Vitamin B 6 Deficiency, Zebrafish, PLPBP, PROSC, epilepsy, pyridoxine, vitamin B6-responsive epilepsy, Care4Rare Canada Consortium, PLPBP, PROSC, Medical and Health Sciences, Psychology and Cognitive Sciences, Neurology & Neurosurgery
Abstract

Biallelic pathogenic variants in PLPBP (formerly called PROSC) have recently been shown to cause a novel form of vitamin B6-dependent epilepsy, the pathophysiological basis of which is poorly understood. When left untreated, the disease can progress to status epilepticus and death in infancy. Here we present 12 previously undescribed patients and six novel pathogenic variants in PLPBP. Suspected clinical diagnoses prior to identification of PLPBP variants included mitochondrial encephalopathy (two patients), folinic acid-responsive epilepsy (one patient) and a movement disorder compatible with AADC deficiency (one patient). The encoded protein, PLPHP is believed to be crucial for B6 homeostasis. We modelled the pathogenicity of the variants and developed a clinical severity scoring system. The most severe phenotypes were associated with variants leading to loss of function of PLPBP or significantly affecting protein stability/PLP-binding. To explore the pathophysiology of this disease further, we developed the first zebrafish model of PLPHP deficiency using CRISPR/Cas9. Our model recapitulates the disease, with plpbp-/- larvae showing behavioural, biochemical, and electrophysiological signs of seizure activity by 10 days post-fertilization and early death by 16 days post-fertilization. Treatment with pyridoxine significantly improved the epileptic phenotype and extended lifespan in plpbp-/- animals. Larvae had disruptions in amino acid metabolism as well as GABA and catecholamine biosynthesis, indicating impairment of PLP-dependent enzymatic activities. Using mass spectrometry, we observed significant B6 vitamer level changes in plpbp-/- zebrafish, patient fibroblasts and PLPHP-deficient HEK293 cells. Additional studies in human cells and yeast provide the first empirical evidence that PLPHP is localized in mitochondria and may play a role in mitochondrial metabolism. These models provide new insights into disease mechanisms and can serve as a platform for drug discovery.

Published
2019

16. Registered access: authorizing data access

Author

Dyke, Stephanie OM, Linden, Mikael, Lappalainen, Ilkka, De Argila, Jordi Rambla, Carey, Knox, Lloyd, David, Spalding, J Dylan, Cabili, Moran N, Kerry, Giselle, Foreman, Julia, Cutts, Tim, Shabani, Mahsa, Rodriguez, Laura L, Haeussler, Maximilian, Walsh, Brian, Jiang, Xiaoqian, Wang, Shuang, Perrett, Daniel, Boughtwood, Tiffany, Matern, Andreas, Brookes, Anthony J, Cupak, Miro, Fiume, Marc, Pandya, Ravi, Tulchinsky, Ilia, Scollen, Serena, Törnroos, Juha, Das, Samir, Evans, Alan C, Malin, Bradley A, Beck, Stephan, Brenner, Steven E, Nyrönen, Tommi, Blomberg, Niklas, Firth, Helen V, Hurles, Matthew, Philippakis, Anthony A, Rätsch, Gunnar, Brudno, Michael, Boycott, Kym M, Rehm, Heidi L, Baudis, Michael, Sherry, Stephen T, Kato, Kazuto, Knoppers, Bartha M, Baker, Dixie, and Flicek, Paul

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Clinical Sciences, Genetics, 8.3 Policy, ethics, and research governance, Health and social care services research, Generic health relevance, Good Health and Well Being, Access to Information, Genetics, Medical, Genomics, Humans, Information Dissemination, Licensure, Practice Guidelines as Topic, Genetics & Heredity, Clinical sciences
Abstract

The Global Alliance for Genomics and Health (GA4GH) proposes a data access policy model-"registered access"-to increase and improve access to data requiring an agreement to basic terms and conditions, such as the use of DNA sequence and health data in research. A registered access policy would enable a range of categories of users to gain access, starting with researchers and clinical care professionals. It would also facilitate general use and reuse of data but within the bounds of consent restrictions and other ethical obligations. In piloting registered access with the Scientific Demonstration data sharing projects of GA4GH, we provide additional ethics, policy and technical guidance to facilitate the implementation of this access model in an international setting.

Published
2018

18. Genetic, structural and clinical analysis of spastic paraplegia 4

Author

Varghaei, Parizad, Estiar, Mehrdad A., Ashtiani, Setareh, Veyron, Simon, Mufti, Kheireddin, Leveille, Etienne, Yu, Eric, Spiegelman, Dan, Rioux, Marie-France, Yoon, Grace, Tarnopolsky, Mark, Boycott, Kym M., Dupre, Nicolas, Suchowersky, Oksana, Trempe, Jean-François, Rouleau, Guy A., and Gan-Or, Ziv

Published
2022
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19. IRF2BPL‐Related Disorder, Causing Neurodevelopmental Disorder with Regression, Abnormal Movements, Loss of Speech and Seizures (NEDAMSS) Is Characterized by Pathology Consistent with DRPLA.

Author

Venkateswaran, Sunita, Michaud, Jean, Ito, Yoko, Geraghty, Michael, Lewis, Evan C., Ellezam, Benjamin, Boycott, Kym M., Dyment, David A., and Kernohan, Kristin D.

Abstract

Background: Childhood neurodegenerative diseases often pose a challenge to clinicians to diagnose because of the degree of genetic heterogeneity and variable presentations. Here, we present a child with progressive neurodegeneration consisting of spasticity, dystonia, and ataxia in which postmortem pathological analysis led to the diagnosis of interferon regulatory factor 2 binding protein like (IRF2BPL)‐related disorder. Methods: Detailed postmortem gross and histological examination was conducted, and findings consistent with dentatorubral‐pallidoluysian atrophy (DRPLA) and included polyglutamine (polyQ) inclusions. Follow up testing for the CAG repeat expansion at ATN1 was non‐diagnostic. Results: Subsequent exome sequencing reanalysis of the research exome identified a pathogenic de novo IRF2BPL variant. The IRF2BPL c.562C>T, p.(Arg188Ter) variant, distal to the polyQ repeat tract, results in variable mRNA levels depending on the cell type examined with decreased mRNA in the brain, as well as destabilization of the protein product and corresponding downstream molecular abnormalities in patient derived cells. Conclusion: We provide the first detailed pathological description for IRF2BPL‐related disorder, termed NEDAMSS (neurodevelopmental disorder with regression, abnormal movements, loss of speech and seizures; Mendelian Inheritance in Man, 618088) and evidence for the inclusion of this condition in the differential diagnosis of spastic‐ataxic neurodegenerative conditions, reminiscent of DRPLA. Although the individuals with NEDAMSS do not carry an expansion, the polyQ repeat tract may play a role in the pathological inclusions that would represent a novel disease mechanism for polyQ repeats. © 2024 International Parkinson and Movement Disorder Society. [ABSTRACT FROM AUTHOR]

Published
2024
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20. GAA-FGF14 Disease: Defining Its Frequency, Molecular Basis, and 4-aminopyridine Response in a Large Cohort of Patients with Downbeat Nystagmus (P6-3.013)

Author

Pellerin, David, primary, Heindl, Felix, additional, Wilke, Carlo, additional, Danzi, Matt, additional, Traschutz, Andreas, additional, Ashton, Catherine, additional, Dicaire, Marie-Josee, additional, Cuillerier, Alexanne, additional, Del Gobbo, Giulia, additional, Boycott, Kym, additional, Claassen, Jens, additional, Rujescu, Dan, additional, Hartmann, Annette, additional, Zuchner, Stephan, additional, Brais, Bernard, additional, Strupp, Michael, additional, and Synofzik, Matthis, additional

Published
2024
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21. Evaluation of the diagnostic accuracy of exome sequencing and its impact on diagnostic thinking for patients with rare disease in a publicly funded health care system: A prospective cohort study

Author

Hartley, Taila, primary, Marshall, Deborah, additional, Acker, Meryl, additional, Fooks, Katharine, additional, Gillespie, Meredith K., additional, Price, E. Magda, additional, Graham, Ian D., additional, White-Brown, Alexandre, additional, MacKay, Layla, additional, Macdonald, Stella K., additional, Brady, Lauren, additional, Hui, Angela Y., additional, Andrews, Joseph D., additional, Chowdhury, Ashfia, additional, Wall, Erika, additional, Soubry, Élisabeth, additional, Ediae, Grace U., additional, Rojas, Samantha, additional, Assamad, Daniel, additional, Dyment, David, additional, Tarnopolsky, Mark, additional, Sawyer, Sarah L., additional, Chisholm, Caitlin, additional, Lemire, Gabrielle, additional, Amburgey, Kimberly, additional, Lazier, Joanna, additional, Mendoza-Londono, Roberto, additional, Dowling, James J., additional, Balci, Tugce B., additional, Armour, Christine M., additional, Bhola, Priya T., additional, Costain, Gregory, additional, Dupuis, Lucie, additional, Carter, Melissa, additional, Badalato, Lauren, additional, Richer, Julie, additional, Boswell-Patterson, Christie, additional, Kannu, Peter, additional, Cordeiro, Dawn, additional, Warman-Chardon, Jodi, additional, Graham, Gail, additional, Siu, Victoria Mok, additional, Cytrynbaum, Cheryl, additional, Rusnak, Alison, additional, Aul, Ritu B., additional, Yoon, Grace, additional, Gonorazky, Hernan, additional, McNiven, Vanda, additional, Mercimek-Andrews, Saadet, additional, Guerin, Andrea, additional, Deshwar, Ashish R., additional, Marwaha, Ashish, additional, Weksberg, Rosanna, additional, Karp, Natalya, additional, Campbell, Maggie, additional, Al-Qattan, Sarah, additional, Shuen, Andrew Y., additional, Inbar-Feigenberg, Michal, additional, Cohn, Ronald, additional, Szuto, Anna, additional, Inglese, Cara, additional, Poirier, Myriam, additional, Chad, Lauren, additional, Potter, Beth, additional, Boycott, Kym M., additional, Hayeems, Robin, additional, Boycott, Kym, additional, Brudno, Michael, additional, Bernier, Francois, additional, van Karnebeek, Clara, additional, Kernohan, Kristin, additional, Innes, Micheil, additional, Lamont, Ryan, additional, Parboosingh, Jillian, additional, Marshall, Christian, additional, Mendoza, Roberto, additional, Dowling, James, additional, Knoppers, Bartha, additional, Lehman, Anna, additional, and Mostafavi, Sara, additional

Published
2024
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22. Model Organisms Facilitate Rare Disease Diagnosis and Therapeutic Research.

Author

Wangler, Michael, Yamamoto, Shinya, Chao, Hsiao-Tuan, Posey, Jennifer, Westerfield, Monte, Postlethwait, John, Hieter, Philip, Boycott, Kym, Campeau, Philippe, and Bellen, Hugo

Subjects
Drosophila, diagnostics, functional genomics, genetic diseases, human, whole-exome sequencing, zebrafish, Animals, Disease Models, Animal, Drosophila, Exome, Genetic Diseases, Inborn, Genetic Testing, Humans, Rare Diseases, Zebrafish
Abstract

Efforts to identify the genetic underpinnings of rare undiagnosed diseases increasingly involve the use of next-generation sequencing and comparative genomic hybridization methods. These efforts are limited by a lack of knowledge regarding gene function, and an inability to predict the impact of genetic variation on the encoded protein function. Diagnostic challenges posed by undiagnosed diseases have solutions in model organism research, which provides a wealth of detailed biological information. Model organism geneticists are by necessity experts in particular genes, gene families, specific organs, and biological functions. Here, we review the current state of research into undiagnosed diseases, highlighting large efforts in North America and internationally, including the Undiagnosed Diseases Network (UDN) (Supplemental Material, File S1) and UDN International (UDNI), the Centers for Mendelian Genomics (CMG), and the Canadian Rare Diseases Models and Mechanisms Network (RDMM). We discuss how merging human genetics with model organism research guides experimental studies to solve these medical mysteries, gain new insights into disease pathogenesis, and uncover new therapeutic strategies.

Published
2017

23. The Human Phenotype Ontology in 2017

Author

Köhler, Sebastian, Vasilevsky, Nicole A, Engelstad, Mark, Foster, Erin, McMurry, Julie, Aymé, Ségolène, Baynam, Gareth, Bello, Susan M, Boerkoel, Cornelius F, Boycott, Kym M, Brudno, Michael, Buske, Orion J, Chinnery, Patrick F, Cipriani, Valentina, Connell, Laureen E, Dawkins, Hugh JS, DeMare, Laura E, Devereau, Andrew D, de Vries, Bert BA, Firth, Helen V, Freson, Kathleen, Greene, Daniel, Hamosh, Ada, Helbig, Ingo, Hum, Courtney, Jähn, Johanna A, James, Roger, Krause, Roland, Laulederkind, Stanley JF, Lochmüller, Hanns, Lyon, Gholson J, Ogishima, Soichi, Olry, Annie, Ouwehand, Willem H, Pontikos, Nikolas, Rath, Ana, Schaefer, Franz, Scott, Richard H, Segal, Michael, Sergouniotis, Panagiotis I, Sever, Richard, Smith, Cynthia L, Straub, Volker, Thompson, Rachel, Turner, Catherine, Turro, Ernest, Veltman, Marijcke WM, Vulliamy, Tom, Yu, Jing, von Ziegenweidt, Julie, Zankl, Andreas, Züchner, Stephan, Zemojtel, Tomasz, Jacobsen, Julius OB, Groza, Tudor, Smedley, Damian, Mungall, Christopher J, Haendel, Melissa, and Robinson, Peter N

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Networking and Information Technology R&D (NITRD), Human Genome, 2.6 Resources and infrastructure (aetiology), 4.5 Resources and infrastructure (detection), Generic health relevance, Good Health and Well Being, Algorithms, Biological Ontologies, Computational Biology, Genetic Association Studies, Genomics, Humans, Phenotype, Precision Medicine, Rare Diseases, Software, Translational Research, Biomedical, Environmental Sciences, Information and Computing Sciences, Developmental Biology, Biological sciences, Chemical sciences, Environmental sciences
Abstract

Deep phenotyping has been defined as the precise and comprehensive analysis of phenotypic abnormalities in which the individual components of the phenotype are observed and described. The three components of the Human Phenotype Ontology (HPO; www.human-phenotype-ontology.org) project are the phenotype vocabulary, disease-phenotype annotations and the algorithms that operate on these. These components are being used for computational deep phenotyping and precision medicine as well as integration of clinical data into translational research. The HPO is being increasingly adopted as a standard for phenotypic abnormalities by diverse groups such as international rare disease organizations, registries, clinical labs, biomedical resources, and clinical software tools and will thereby contribute toward nascent efforts at global data exchange for identifying disease etiologies. This update article reviews the progress of the HPO project since the debut Nucleic Acids Research database article in 2014, including specific areas of expansion such as common (complex) disease, new algorithms for phenotype driven genomic discovery and diagnostics, integration of cross-species mapping efforts with the Mammalian Phenotype Ontology, an improved quality control pipeline, and the addition of patient-friendly terminology.

Published
2017

24. Spliceosome malfunction causes neurodevelopmental disorders with overlapping features

Author

Genetica, Genetica Sectie Research, Cancer, Child Health, Li, Dong, Wang, Qin, Bayat, Allan, Battig, Mark R., Zhou, Yijing, Bosch, Daniëlle G.M., van Haaften, Gijs, Granger, Leslie, Petersen, Andrea K., Pérez-Jurado, Luis A., Aznar-Laín, Gemma, Aneja, Anushree, Hancarova, Miroslava, Bendova, Sarka, Schwarz, Martin, Pourova, Radka Kremlikova, Sedlacek, Zdenek, Keena, Beth A., March, Michael E., Hou, Cuiping, O’Connor, Nora, Bhoj, Elizabeth J., Harr, Margaret H., Lemire, Gabrielle, Boycott, Kym M., Towne, Meghan, Li, Megan, Tarnopolsky, Mark, Brady, Lauren, Parker, Michael J., Faghfoury, Hanna, Parsley, Lea Kristin, Agolini, Emanuele, Dentici, Maria Lisa, Novelli, Antonio, Wright, Meredith, Palmquist, Rachel, Lai, Khanh, Scala, Marcello, Striano, Pasquale, Iacomino, Michele, Zara, Federico, Cooper, Annina, Maarup, Timothy J., Byler, Melissa, Lebel, Robert Roger, Balci, Tugce B., Louie, Raymond, Lyons, Michael, Douglas, Jessica, Nowak, Catherine, Afenjar, Alexandra, Hoyer, Juliane, Keren, Boris, Maas, Saskia M., Motazacker, Mahdi M., Martinez-Agosto, Julian A., Rabani, Ahna M., McCormick, Elizabeth M., Falk, Marni J., Ruggiero, Sarah M., Helbig, Ingo, Møller, Rikke S., Tessarollo, Lino, Ardori, Francesco Tomassoni, Palko, Mary Ellen, Hsieh, Tzung Chien, Krawitz, Peter M., Ganapathi, Mythily, Gelb, Bruce D., Jobanputra, Vaidehi, Wilson, Ashley, Greally, John, Jacquemont, Sébastien, Jizi, Khadijé, Bruel, Ange Line, Quelin, Chloé, Misra, Vinod K., Chick, Erika, Romano, Corrado, Greco, Donatella, Arena, Alessia, Morleo, Manuela, Nigro, Vincenzo, Seyama, Rie, Uchiyama, Yuri, Matsumoto, Naomichi, Taira, Ryoji, Tashiro, Katsuya, Sakai, Yasunari, Yigit, Gökhan, Wollnik, Bernd, Wagner, Michael, Kutsche, Barbara, Hurst, Anna C.E., Thompson, Michelle L., Schmidt, Ryan, Randolph, Linda, Spillmann, Rebecca C., Shashi, Vandana, Higginbotham, Edward J., Cordeiro, Dawn, Carnevale, Amanda, Costain, Gregory, Khan, Tayyaba, Funalot, Benoît, Mau-Them, Frederic Tran, Garcia Moya, Luis Fernandez, García-Miñaúr, Sixto, Osmond, Matthew, Chad, Lauren, Quercia, Nada, Carrasco, Diana, Li, Chumei, Sanchez-Valle, Amarilis, Kelley, Meghan, Nizon, Mathilde, Jensson, Brynjar O., Sulem, Patrick, Stefansson, Kari, Gorokhova, Svetlana, Busa, Tiffany, Rio, Marlène, Habdallah, Hamza Hadj, Lesieur-Sebellin, Marion, Amiel, Jeanne, Pingault, Véronique, Mercier, Sandra, Vincent, Marie, Philippe, Christophe, Fatus-Fauconnier, Clemence, Friend, Kathryn, Halligan, Rebecca K., Biswas, Sunita, Rosser, Jane, Shoubridge, Cheryl, Corbett, Mark, Barnett, Christopher, Gecz, Jozef, Leppig, Kathleen, Slavotinek, Anne, Marcelis, Carlo, Pfundt, Rolph, de Vries, Bert B.A., van Slegtenhorst, Marjon A., Brooks, Alice S., Cogne, Benjamin, Rambaud, Thomas, Tümer, Zeynep, Zackai, Elaine H., Akizu, Naiara, Song, Yuanquan, Hakonarson, Hakon, Genetica, Genetica Sectie Research, Cancer, Child Health, Li, Dong, Wang, Qin, Bayat, Allan, Battig, Mark R., Zhou, Yijing, Bosch, Daniëlle G.M., van Haaften, Gijs, Granger, Leslie, Petersen, Andrea K., Pérez-Jurado, Luis A., Aznar-Laín, Gemma, Aneja, Anushree, Hancarova, Miroslava, Bendova, Sarka, Schwarz, Martin, Pourova, Radka Kremlikova, Sedlacek, Zdenek, Keena, Beth A., March, Michael E., Hou, Cuiping, O’Connor, Nora, Bhoj, Elizabeth J., Harr, Margaret H., Lemire, Gabrielle, Boycott, Kym M., Towne, Meghan, Li, Megan, Tarnopolsky, Mark, Brady, Lauren, Parker, Michael J., Faghfoury, Hanna, Parsley, Lea Kristin, Agolini, Emanuele, Dentici, Maria Lisa, Novelli, Antonio, Wright, Meredith, Palmquist, Rachel, Lai, Khanh, Scala, Marcello, Striano, Pasquale, Iacomino, Michele, Zara, Federico, Cooper, Annina, Maarup, Timothy J., Byler, Melissa, Lebel, Robert Roger, Balci, Tugce B., Louie, Raymond, Lyons, Michael, Douglas, Jessica, Nowak, Catherine, Afenjar, Alexandra, Hoyer, Juliane, Keren, Boris, Maas, Saskia M., Motazacker, Mahdi M., Martinez-Agosto, Julian A., Rabani, Ahna M., McCormick, Elizabeth M., Falk, Marni J., Ruggiero, Sarah M., Helbig, Ingo, Møller, Rikke S., Tessarollo, Lino, Ardori, Francesco Tomassoni, Palko, Mary Ellen, Hsieh, Tzung Chien, Krawitz, Peter M., Ganapathi, Mythily, Gelb, Bruce D., Jobanputra, Vaidehi, Wilson, Ashley, Greally, John, Jacquemont, Sébastien, Jizi, Khadijé, Bruel, Ange Line, Quelin, Chloé, Misra, Vinod K., Chick, Erika, Romano, Corrado, Greco, Donatella, Arena, Alessia, Morleo, Manuela, Nigro, Vincenzo, Seyama, Rie, Uchiyama, Yuri, Matsumoto, Naomichi, Taira, Ryoji, Tashiro, Katsuya, Sakai, Yasunari, Yigit, Gökhan, Wollnik, Bernd, Wagner, Michael, Kutsche, Barbara, Hurst, Anna C.E., Thompson, Michelle L., Schmidt, Ryan, Randolph, Linda, Spillmann, Rebecca C., Shashi, Vandana, Higginbotham, Edward J., Cordeiro, Dawn, Carnevale, Amanda, Costain, Gregory, Khan, Tayyaba, Funalot, Benoît, Mau-Them, Frederic Tran, Garcia Moya, Luis Fernandez, García-Miñaúr, Sixto, Osmond, Matthew, Chad, Lauren, Quercia, Nada, Carrasco, Diana, Li, Chumei, Sanchez-Valle, Amarilis, Kelley, Meghan, Nizon, Mathilde, Jensson, Brynjar O., Sulem, Patrick, Stefansson, Kari, Gorokhova, Svetlana, Busa, Tiffany, Rio, Marlène, Habdallah, Hamza Hadj, Lesieur-Sebellin, Marion, Amiel, Jeanne, Pingault, Véronique, Mercier, Sandra, Vincent, Marie, Philippe, Christophe, Fatus-Fauconnier, Clemence, Friend, Kathryn, Halligan, Rebecca K., Biswas, Sunita, Rosser, Jane, Shoubridge, Cheryl, Corbett, Mark, Barnett, Christopher, Gecz, Jozef, Leppig, Kathleen, Slavotinek, Anne, Marcelis, Carlo, Pfundt, Rolph, de Vries, Bert B.A., van Slegtenhorst, Marjon A., Brooks, Alice S., Cogne, Benjamin, Rambaud, Thomas, Tümer, Zeynep, Zackai, Elaine H., Akizu, Naiara, Song, Yuanquan, and Hakonarson, Hakon

Published
2024

25. Spliceosome malfunction causes neurodevelopmental disorders with overlapping features

Author

Li, Dong, Wang, Qin, Bayat, Allan, Battig, Mark R., Zhou, Yijing, Bosch, Daniëlle G.M., van Haaften, Gijs, Granger, Leslie, Petersen, Andrea K., Pérez-Jurado, Luis A., Aznar-Laín, Gemma, Aneja, Anushree, Hancarova, Miroslava, Bendova, Sarka, Schwarz, Martin, Pourova, Radka Kremlikova, Sedlacek, Zdenek, Keena, Beth A., March, Michael E., Hou, Cuiping, O’Connor, Nora, Bhoj, Elizabeth J., Harr, Margaret H., Lemire, Gabrielle, Boycott, Kym M., Towne, Meghan, Li, Megan, Tarnopolsky, Mark, Brady, Lauren, Parker, Michael J., Faghfoury, Hanna, Parsley, Lea Kristin, Agolini, Emanuele, Dentici, Maria Lisa, Novelli, Antonio, Wright, Meredith, Palmquist, Rachel, Lai, Khanh, Scala, Marcello, Striano, Pasquale, Iacomino, Michele, Zara, Federico, Cooper, Annina, Maarup, Timothy J., Byler, Melissa, Lebel, Robert Roger, Balci, Tugce B., Louie, Raymond, Lyons, Michael, Douglas, Jessica, Nowak, Catherine, Afenjar, Alexandra, Hoyer, Juliane, Keren, Boris, Maas, Saskia M., Motazacker, Mahdi M., Martinez-Agosto, Julian A., Rabani, Ahna M., McCormick, Elizabeth M., Falk, Marni J., Ruggiero, Sarah M., Helbig, Ingo, Møller, Rikke S., Tessarollo, Lino, Ardori, Francesco Tomassoni, Palko, Mary Ellen, Hsieh, Tzung Chien, Krawitz, Peter M., Ganapathi, Mythily, Gelb, Bruce D., Jobanputra, Vaidehi, Wilson, Ashley, Greally, John, Jacquemont, Sébastien, Jizi, Khadijé, Bruel, Ange Line, Quelin, Chloé, Misra, Vinod K., Chick, Erika, Romano, Corrado, Greco, Donatella, Arena, Alessia, Morleo, Manuela, Nigro, Vincenzo, Seyama, Rie, Uchiyama, Yuri, Matsumoto, Naomichi, Taira, Ryoji, Tashiro, Katsuya, Sakai, Yasunari, Yigit, Gökhan, Wollnik, Bernd, Wagner, Michael, Kutsche, Barbara, Hurst, Anna C.E., Thompson, Michelle L., Schmidt, Ryan, Randolph, Linda, Spillmann, Rebecca C., Shashi, Vandana, Higginbotham, Edward J., Cordeiro, Dawn, Carnevale, Amanda, Costain, Gregory, Khan, Tayyaba, Funalot, Benoît, Mau-Them, Frederic Tran, Garcia Moya, Luis Fernandez, García-Miñaúr, Sixto, Osmond, Matthew, Chad, Lauren, Quercia, Nada, Carrasco, Diana, Li, Chumei, Sanchez-Valle, Amarilis, Kelley, Meghan, Nizon, Mathilde, Jensson, Brynjar O., Sulem, Patrick, Stefansson, Kari, Gorokhova, Svetlana, Busa, Tiffany, Rio, Marlène, Habdallah, Hamza Hadj, Lesieur-Sebellin, Marion, Amiel, Jeanne, Pingault, Véronique, Mercier, Sandra, Vincent, Marie, Philippe, Christophe, Fatus-Fauconnier, Clemence, Friend, Kathryn, Halligan, Rebecca K., Biswas, Sunita, Rosser, Jane, Shoubridge, Cheryl, Corbett, Mark, Barnett, Christopher, Gecz, Jozef, Leppig, Kathleen, Slavotinek, Anne, Marcelis, Carlo, Pfundt, Rolph, de Vries, Bert B.A., van Slegtenhorst, Marjon A., Brooks, Alice S., Cogne, Benjamin, Rambaud, Thomas, Tümer, Zeynep, Zackai, Elaine H., Akizu, Naiara, Song, Yuanquan, Hakonarson, Hakon, Li, Dong, Wang, Qin, Bayat, Allan, Battig, Mark R., Zhou, Yijing, Bosch, Daniëlle G.M., van Haaften, Gijs, Granger, Leslie, Petersen, Andrea K., Pérez-Jurado, Luis A., Aznar-Laín, Gemma, Aneja, Anushree, Hancarova, Miroslava, Bendova, Sarka, Schwarz, Martin, Pourova, Radka Kremlikova, Sedlacek, Zdenek, Keena, Beth A., March, Michael E., Hou, Cuiping, O’Connor, Nora, Bhoj, Elizabeth J., Harr, Margaret H., Lemire, Gabrielle, Boycott, Kym M., Towne, Meghan, Li, Megan, Tarnopolsky, Mark, Brady, Lauren, Parker, Michael J., Faghfoury, Hanna, Parsley, Lea Kristin, Agolini, Emanuele, Dentici, Maria Lisa, Novelli, Antonio, Wright, Meredith, Palmquist, Rachel, Lai, Khanh, Scala, Marcello, Striano, Pasquale, Iacomino, Michele, Zara, Federico, Cooper, Annina, Maarup, Timothy J., Byler, Melissa, Lebel, Robert Roger, Balci, Tugce B., Louie, Raymond, Lyons, Michael, Douglas, Jessica, Nowak, Catherine, Afenjar, Alexandra, Hoyer, Juliane, Keren, Boris, Maas, Saskia M., Motazacker, Mahdi M., Martinez-Agosto, Julian A., Rabani, Ahna M., McCormick, Elizabeth M., Falk, Marni J., Ruggiero, Sarah M., Helbig, Ingo, Møller, Rikke S., Tessarollo, Lino, Ardori, Francesco Tomassoni, Palko, Mary Ellen, Hsieh, Tzung Chien, Krawitz, Peter M., Ganapathi, Mythily, Gelb, Bruce D., Jobanputra, Vaidehi, Wilson, Ashley, Greally, John, Jacquemont, Sébastien, Jizi, Khadijé, Bruel, Ange Line, Quelin, Chloé, Misra, Vinod K., Chick, Erika, Romano, Corrado, Greco, Donatella, Arena, Alessia, Morleo, Manuela, Nigro, Vincenzo, Seyama, Rie, Uchiyama, Yuri, Matsumoto, Naomichi, Taira, Ryoji, Tashiro, Katsuya, Sakai, Yasunari, Yigit, Gökhan, Wollnik, Bernd, Wagner, Michael, Kutsche, Barbara, Hurst, Anna C.E., Thompson, Michelle L., Schmidt, Ryan, Randolph, Linda, Spillmann, Rebecca C., Shashi, Vandana, Higginbotham, Edward J., Cordeiro, Dawn, Carnevale, Amanda, Costain, Gregory, Khan, Tayyaba, Funalot, Benoît, Mau-Them, Frederic Tran, Garcia Moya, Luis Fernandez, García-Miñaúr, Sixto, Osmond, Matthew, Chad, Lauren, Quercia, Nada, Carrasco, Diana, Li, Chumei, Sanchez-Valle, Amarilis, Kelley, Meghan, Nizon, Mathilde, Jensson, Brynjar O., Sulem, Patrick, Stefansson, Kari, Gorokhova, Svetlana, Busa, Tiffany, Rio, Marlène, Habdallah, Hamza Hadj, Lesieur-Sebellin, Marion, Amiel, Jeanne, Pingault, Véronique, Mercier, Sandra, Vincent, Marie, Philippe, Christophe, Fatus-Fauconnier, Clemence, Friend, Kathryn, Halligan, Rebecca K., Biswas, Sunita, Rosser, Jane, Shoubridge, Cheryl, Corbett, Mark, Barnett, Christopher, Gecz, Jozef, Leppig, Kathleen, Slavotinek, Anne, Marcelis, Carlo, Pfundt, Rolph, de Vries, Bert B.A., van Slegtenhorst, Marjon A., Brooks, Alice S., Cogne, Benjamin, Rambaud, Thomas, Tümer, Zeynep, Zackai, Elaine H., Akizu, Naiara, Song, Yuanquan, and Hakonarson, Hakon

Abstract

Pre-mRNA splicing is a highly coordinated process. While its dysregulation has been linked to neurological deficits, our understanding of the underlying molecular and cellular mechanisms remains limited. We implicated pathogenic variants in U2AF2 and PRPF19, encoding spliceosome subunits in neurodevelopmental disorders (NDDs), by identifying 46 unrelated individuals with 23 de novo U2AF2 missense variants (including 7 recurrent variants in 30 individuals) and 6 individuals with de novo PRPF19 variants. Eight U2AF2 variants dysregulated splicing of a model substrate. Neuritogenesis was reduced in human neurons differentiated from human pluripotent stem cells carrying two U2AF2 hyper-recurrent variants. Neural loss of function (LoF) of the Drosophila orthologs U2af50 and Prp19 led to lethality, abnormal mushroom body (MB) patterning, and social deficits, which were differentially rescued by wild-type and mutant U2AF2 or PRPF19. Transcriptome profiling revealed splicing substrates or effectors (including Rbfox1, a third splicing factor), which rescued MB defects in U2af50deficient flies. Upon reanalysis of negative clinical exomes followed by data sharing, we further identified 6 patients with NDD who carried RBFOX1 missense variants which, by in vitro testing, showed LoF. Our study implicates 3 splicing factors as NDD-causative genes and establishes a genetic network with hierarchy underlying human brain development and function.

Published
2024

26. Novel variants in TUBA1A cause congenital fibrosis of the extraocular muscles with or without malformations of cortical brain development

Author

Jurgens, Julie A., Barry, Brenda J., Lemire, Gabrielle, Chan, Wai-Man, Whitman, Mary C., Shaaban, Sherin, Robson, Caroline D., MacKinnon, Sarah, England, Eleina M., McMillan, Hugh J., Kelly, Christopher, Pratt, Brandon M., O’Donnell-Luria, Anne, MacArthur, Daniel G., Boycott, Kym M., Hunter, David G., and Engle, Elizabeth C.

Published
2021
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29. Mandibulofacial Dysostosis with Microcephaly: Mutation and Database Update

Author

Huang, Lijia, Vanstone, Megan R, Hartley, Taila, Osmond, Matthew, Barrowman, Nick, Allanson, Judith, Baker, Laura, Dabir, Tabib A, Dipple, Katrina M, Dobyns, William B, Estrella, Jane, Faghfoury, Hanna, Favaro, Francine P, Goel, Himanshu, Gregersen, Pernille A, Gripp, Karen W, Grix, Art, Guion‐Almeida, Maria‐Leine, Harr, Margaret H, Hudson, Cindy, Hunter, Alasdair GW, Johnson, John, Joss, Shelagh K, Kimball, Amy, Kini, Usha, Kline, Antonie D, Lauzon, Julie, Lildballe, Dorte L, López‐González, Vanesa, Martinezmoles, Johanna, Meldrum, Cliff, Mirzaa, Ghayda M, Morel, Chantal F, Morton, Jenny EV, Pyle, Louise C, Quintero‐Rivera, Fabiola, Richer, Julie, Scheuerle, Angela E, Schönewolf‐Greulich, Bitten, Shears, Deborah J, Silver, Josh, Smith, Amanda C, Temple, I Karen, Center, UCLA Clinical Genomics, de Kamp, Jiddeke M, Dijk, Fleur S, Vandersteen, Anthony M, White, Sue M, Zackai, Elaine H, Zou, Ruobing, Consortium, Care4Rare Canada, Bulman, Dennis E, Boycott, Kym M, and Lines, Matthew A

Subjects
Pediatric, Congenital Structural Anomalies, Rare Diseases, Genetics, Prevention, Human Genome, Neurosciences, Clinical Research, Dental/Oral and Craniofacial Disease, 2.1 Biological and endogenous factors, Aetiology, Congenital, Abnormalities, Multiple, Amino Acid Motifs, Databases, Genetic, Gene Expression, Haploinsufficiency, Hearing Loss, Humans, Intellectual Disability, Mandibulofacial Dysostosis, Microcephaly, Models, Molecular, Molecular Sequence Data, Mutation, Penetrance, Peptide Elongation Factors, Phenotype, Protein Structure, Secondary, Protein Structure, Tertiary, RNA Splicing, Ribonucleoprotein, U5 Small Nuclear, Spliceosomes, EFTUD2, mandibulofacial dysostosis with microcephaly, MFDM, mandibulofacial dysostosis Guion-Almeida type, mandibulofacial dysostosis, microcephaly, UCLA Clinical Genomics Center, Care4Rare Canada Consortium, Clinical Sciences, Genetics & Heredity
Abstract

Mandibulofacial dysostosis with microcephaly (MFDM) is a multiple malformation syndrome comprising microcephaly, craniofacial anomalies, hearing loss, dysmorphic features, and, in some cases, esophageal atresia. Haploinsufficiency of a spliceosomal GTPase, U5-116 kDa/EFTUD2, is responsible. Here, we review the molecular basis of MFDM in the 69 individuals described to date, and report mutations in 38 new individuals, bringing the total number of reported individuals to 107 individuals from 94 kindreds. Pathogenic EFTUD2 variants comprise 76 distinct mutations and seven microdeletions. Among point mutations, missense substitutions are infrequent (14 out of 76; 18%) relative to stop-gain (29 out of 76; 38%), and splicing (33 out of 76; 43%) mutations. Where known, mutation origin was de novo in 48 out of 64 individuals (75%), dominantly inherited in 12 out of 64 (19%), and due to proven germline mosaicism in four out of 64 (6%). Highly penetrant clinical features include, microcephaly, first and second arch craniofacial malformations, and hearing loss; esophageal atresia is present in an estimated ∼27%. Microcephaly is virtually universal in childhood, with some adults exhibiting late "catch-up" growth and normocephaly at maturity. Occasionally reported anomalies, include vestibular and ossicular malformations, reduced mouth opening, atrophy of cerebral white matter, structural brain malformations, and epibulbar dermoid. All reported EFTUD2 mutations can be found in the EFTUD2 mutation database (http://databases.lovd.nl/shared/genes/EFTUD2).

Published
2016

31. A deep intronic FGF14 GAA repeat expansion causes late-onset cerebellar ataxia

Author

Pellerin, David, primary, Danzi, Matt, additional, Wilke, Carlo, additional, Renaud, Mathilde, additional, Fazal, Sarah, additional, Dicaire, Marie-Josée, additional, Scriba, Carolin, additional, Ashton, Catherine, additional, Genís, David, additional, Porcel, Laura Molina, additional, Nagy, Sara, additional, Nalini, Atchayaram, additional, Boycott, Kym, additional, Duquette, Antoine, additional, Houlden, Henry, additional, Ravenscroft, Gianina, additional, Laing, Nigel, additional, Lamont, Phillipa, additional, Schöls, Ludger, additional, La Piana, Roberta, additional, Synofzik, Matthis, additional, Zuchner, Stephan, additional, and Brais, Bernard, additional

Published
2023
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32. A call for global action for rare diseases in Africa

Author

Baynam, Gareth S., Groft, Stephen, van der Westhuizen, Francois H., Gassman, Safiyya D., du Plessis, Kelly, Coles, Emily P., Selebatso, Eda, Selebatso, Moses, Gaobinelwe, Boikobo, Selebatso, Tebogo, Joel, Dipesalema, Llera, Virginia A., Vorster, Barend C., Wuebbels, Barbara, Djoudalbaye, Benjamin, Austin, Christopher P., Kumuthini, Judit, Forman, John, Kaufmann, Petra, Chipeta, James, Gavhed, Désirée, Larsson, Annika, Stojiljkovic, Maja, Nordgren, Ann, Roldan, Emilio J. A., Taruscio, Domenica, Wong-Rieger, Durhane, Nowak, Kristen, Bilkey, Gemma A., Easteal, Simon, Bowdin, Sarah, Reichardt, Juergen K. V., Beltran, Sergi, Kosaki, Kenjiro, van Karnebeek, Clara D. M., Gong, Mengchun, Shuyang, Zhang, Mehrian-Shai, Ruty, Adams, David R., Puri, Ratna D., Zhang, Feng, Pachter, Nicholas, Muenke, Maximilian, Nellaker, Christoffer, Gahl, William A., Cederroth, Helene, Broley, Stephanie, Schoonen, Maryke, Boycott, Kym M., and Posada, Manuel

Published
2020
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33. The Matchmaker Exchange: A Platform for Rare Disease Gene Discovery

Author

Philippakis, Anthony A, Azzariti, Danielle R, Beltran, Sergi, Brookes, Anthony J, Brownstein, Catherine A, Brudno, Michael, Brunner, Han G, Buske, Orion J, Carey, Knox, Doll, Cassie, Dumitriu, Sergiu, Dyke, Stephanie OM, den Dunnen, Johan T, Firth, Helen V, Gibbs, Richard A, Girdea, Marta, Gonzalez, Michael, Haendel, Melissa A, Hamosh, Ada, Holm, Ingrid A, Huang, Lijia, Hurles, Matthew E, Hutton, Ben, Krier, Joel B, Misyura, Andriy, Mungall, Christopher J, Paschall, Justin, Paten, Benedict, Robinson, Peter N, Schiettecatte, François, Sobreira, Nara L, Swaminathan, Ganesh J, Taschner, Peter E, Terry, Sharon F, Washington, Nicole L, Züchner, Stephan, Boycott, Kym M, and Rehm, Heidi L

Subjects
Biological Sciences, Genetics, Human Genome, Database Management Systems, Databases, Genetic, Genetic Association Studies, Genetic Predisposition to Disease, Humans, Information Dissemination, Rare Diseases, Software, matchmaking, rare disease, genomic API, gene discovery, Matchmaker Exchange, GA4GH, IRDiRC, Clinical Sciences, Genetics & Heredity, Clinical sciences
Abstract

There are few better examples of the need for data sharing than in the rare disease community, where patients, physicians, and researchers must search for "the needle in a haystack" to uncover rare, novel causes of disease within the genome. Impeding the pace of discovery has been the existence of many small siloed datasets within individual research or clinical laboratory databases and/or disease-specific organizations, hoping for serendipitous occasions when two distant investigators happen to learn they have a rare phenotype in common and can "match" these cases to build evidence for causality. However, serendipity has never proven to be a reliable or scalable approach in science. As such, the Matchmaker Exchange (MME) was launched to provide a robust and systematic approach to rare disease gene discovery through the creation of a federated network connecting databases of genotypes and rare phenotypes using a common application programming interface (API). The core building blocks of the MME have been defined and assembled. Three MME services have now been connected through the API and are available for community use. Additional databases that support internal matching are anticipated to join the MME network as it continues to grow.

Published
2015

36. De novo CCND2 mutations leading to stabilization of cyclin D2 cause megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome

Author

Mirzaa, Ghayda M, Parry, David A, Fry, Andrew E, Giamanco, Kristin A, Schwartzentruber, Jeremy, Vanstone, Megan, Logan, Clare V, Roberts, Nicola, Johnson, Colin A, Singh, Shawn, Kholmanskikh, Stanislav S, Adams, Carissa, Hodge, Rebecca D, Hevner, Robert F, Bonthron, David T, Braun, Kees PJ, Faivre, Laurence, Rivière, Jean-Baptiste, St-Onge, Judith, Gripp, Karen W, Mancini, Grazia MS, Pang, Ki, Sweeney, Elizabeth, van Esch, Hilde, Verbeek, Nienke, Wieczorek, Dagmar, Steinraths, Michelle, Majewski, Jacek, Boycott, Kym M, Pilz, Daniela T, Ross, M Elizabeth, Dobyns, William B, and Sheridan, Eamonn G

Subjects
Pediatric, 2.1 Biological and endogenous factors, Aetiology, Abnormalities, Multiple, Animals, Base Sequence, Blotting, Western, Bromodeoxyuridine, Cyclin D2, Electroporation, Exome, Female, HEK293 Cells, Humans, Hydrocephalus, Immunohistochemistry, Malformations of Cortical Development, Megalencephaly, Mice, Microscopy, Fluorescence, Molecular Sequence Data, Mutagenesis, Site-Directed, Polydactyly, Sequence Analysis, DNA, Syndrome, FORGE Canada Consortium, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract

Activating mutations in genes encoding phosphatidylinositol 3-kinase (PI3K)-AKT pathway components cause megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome (MPPH, OMIM 603387). Here we report that individuals with MPPH lacking upstream PI3K-AKT pathway mutations carry de novo mutations in CCND2 (encoding cyclin D2) that are clustered around a residue that can be phosphorylated by glycogen synthase kinase 3β (GSK-3β). Mutant CCND2 was resistant to proteasomal degradation in vitro compared to wild-type CCND2. The PI3K-AKT pathway modulates GSK-3β activity, and cells from individuals with PIK3CA, PIK3R2 or AKT3 mutations showed similar CCND2 accumulation. CCND2 was expressed at higher levels in brains of mouse embryos expressing activated AKT3. In utero electroporation of mutant CCND2 into embryonic mouse brains produced more proliferating transfected progenitors and a smaller fraction of progenitors exiting the cell cycle compared to cells electroporated with wild-type CCND2. These observations suggest that cyclin D2 stabilization, caused by CCND2 mutation or PI3K-AKT activation, is a unifying mechanism in PI3K-AKT-related megalencephaly syndromes.

Published
2014

37. Long‐read genome sequencing reveals a novel intronic retroelement insertion in NR5A1 associated with 46,XY differences of sexual development.

Author

Del Gobbo, Giulia F., Wang, Xueqi, Couse, Madeline, Mackay, Layla, Goldsmith, Claire, Marshall, Aren E., Liang, Yijing, Lambert, Christine, Zhang, Siyuan, Dhillon, Harsharan, Fanslow, Cairbre, Rowell, William J., Marshall, Christian R., Kernohan, Kristin D., and Boycott, Kym M.

Abstract

Despite significant advancements in rare genetic disease diagnostics, many patients with rare genetic disease remain without a molecular diagnosis. Novel tools and methods are needed to improve the detection of disease‐associated variants and understand the genetic basis of many rare diseases. Long‐read genome sequencing provides improved sequencing in highly repetitive, homologous, and low‐complexity regions, and improved assessment of structural variation and complex genomic rearrangements compared to short‐read genome sequencing. As such, it is a promising method to explore overlooked genetic variants in rare diseases with a high suspicion of a genetic basis. We therefore applied PacBio HiFi sequencing in a large multi‐generational family presenting with autosomal dominant 46,XY differences of sexual development (DSD), for whom extensive molecular testing over multiple decades had failed to identify a molecular diagnosis. This revealed a rare SINE‐VNTR‐Alu retroelement insertion in intron 4 of NR5A1, a gene in which loss‐of‐function variants are an established cause of 46,XY DSD. The insertion segregated among affected family members and was associated with loss‐of‐expression of alleles in cis, demonstrating a functional impact on NR5A1. This case highlights the power of long‐read genome sequencing to detect genomic variants that have previously been intractable to detection by standard short‐read genomic testing. [ABSTRACT FROM AUTHOR]

Published
2024
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39. Phenotypic heterogeneity associated with KIF21A: Two new cases and review of the literature.

Author

Bhola, Priya T., Mishra, Radha, Posey, Jennifer E., Hamilton, Leslie E., Graham, Gail E., Punetha, Jaya, Lupski, James R., Boycott, Kym M., D'Amours, Damien, and Kernohan, Kristin D.

Abstract

Our understanding of genetic and phenotypic heterogeneity associated with the clinical spectrum of rare diseases continues to expand. Thorough phenotypic descriptions and model organism functional studies are valuable tools in dissecting the biology of the disease process. Kinesin genes are well known to be associated with specific disease phenotypes and a subset of kinesin genes, including KIF21A, have been associated with more than one disease. Here we report two patients with KIF21A variants identified by exome sequencing; one with biallelic variants, supporting a novel KIF21A related syndrome with recessive inheritance and the second report of this condition, and another with a heterozygous de novo variant allele representing a phenotypic expansion of the condition described to date. We provide detailed phenotypic information on both families, including a novel neuropathology finding of neuroaxonal dystrophy associated with biallelic variants in KIF21A. Additionally, we studied the dominant variant in Saccharomyces cerevisiae to assess variant pathogenicity and found that this variant appears to impair protein function. KIF21A associated disease has mounting evidence for phenotypic heterogeneity; further patients and study of an allelic series are required to define the phenotypic spectrum and further explore the molecular etiology for each of these conditions. [ABSTRACT FROM AUTHOR]

Published
2024
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40. Spliceosome malfunction causes neurodevelopmental disorders with overlapping features

Author

Li, Dong, primary, Wang, Qin, additional, Bayat, Allan, additional, Battig, Mark R., additional, Zhou, Yijing, additional, Bosch, Daniëlle G.M., additional, van Haaften, Gijs, additional, Granger, Leslie, additional, Petersen, Andrea K., additional, Pérez-Jurado, Luis A., additional, Aznar-Laín, Gemma, additional, Aneja, Anushree, additional, Hancarova, Miroslava, additional, Bendova, Sarka, additional, Schwarz, Martin, additional, Kremlíková Pourová, Radka, additional, Sedlacek, Zdenek, additional, Keena, Beth A., additional, March, Michael E., additional, Hou, Cuiping, additional, O'Connor, Nora, additional, Bhoj, Elizabeth J., additional, Harr, Margaret H., additional, Lemire, Gabrielle, additional, Boycott, Kym M., additional, Towne, Meghan C., additional, Li, Megan, additional, Tarnopolsky, Mark, additional, Brady, Lauren, additional, Parker, Michael J., additional, Faghfoury, Hanna, additional, Parsley, Lea Kristin, additional, Agolini, Emanuele, additional, Dentici, Maria Lisa, additional, Novelli, Antonio, additional, Wright, Meredith S., additional, Palmquist, Rachel, additional, Lai, Khanh, additional, Scala, Marcello, additional, Striano, Pasquale, additional, Iacomino, Michele, additional, Zara, Federico, additional, Cooper, Annina, additional, Maarup, Timothy J., additional, Byler, Melissa, additional, Lebel, Robert Roger, additional, Balci, Tugce B., additional, Louie, Raymond J., additional, Lyons, Michael J., additional, Douglas, Jessica, additional, Nowak, Catherine B., additional, Afenjar, Alexandra, additional, Hoyer, Juliane, additional, Keren, Boris, additional, Maas, Saskia M., additional, Motazacker, Mahdi M., additional, Martinez-Agosto, Julian A., additional, Rabani, Ahna M., additional, McCormick, Elizabeth M., additional, Falk, Marni, additional, Ruggiero, Sarah M., additional, Helbig, Ingo, additional, Møller, Rikke S., additional, Tessarollo, Lino, additional, Tomassoni-Ardori, Francesco, additional, Palko, Mary Ellen, additional, Hsieh, Tzung-Chien, additional, Krawitz, Peter M., additional, Ganapathi, Mythily, additional, Gelb, Bruce D., additional, Jobanputra, Vaidehi, additional, Wilson, Ashley, additional, Greally, John, additional, Jacquemont, Sébastien, additional, Jizi, Khadijé, additional, Ange-Line, Bruel, additional, Quelin, Chloé, additional, Misra, Vinod K., additional, Chick, Erika, additional, Romano, Corrado, additional, Greco, Donatella, additional, Arena, Alessia, additional, Morleo, Manuela, additional, Nigro, Vincenzo, additional, Seyama, Rie, additional, Uchiyama, Yuri, additional, Matsumoto, Naomichi, additional, Taira, Ryoji, additional, Tashiro, Katsuya, additional, Sakai, Yasunari, additional, Yigit, Gökhan, additional, Wollnik, Bernd, additional, Wagner, Michael, additional, Kutsche, Barbara, additional, Hurst, Anna C.E., additional, Thompson, Michelle L., additional, Schmidt, Ryan J., additional, Randolph, Linda M., additional, Spillmann, Rebecca C., additional, Shashi, Vandana, additional, Higginbotham, Edward J., additional, Cordeiro, Dawn, additional, Carnevale, Amanda, additional, Costain, Gregory, additional, Khan, Tayyaba, additional, Funalot, Benoît, additional, Tran Mau-Them, Frederic, additional, Fernandez Garcia Moya, Luis, additional, García-Miñaúr, Sixto, additional, Osmond, Matthew, additional, Chad, Lauren, additional, Quercia, Nada, additional, Carrasco, Diana, additional, Li, Chumei, additional, Sanchez-Valle, Amarilis, additional, Kelley, Meghan, additional, Nizon, Mathilde, additional, Jensson, Brynjar O., additional, Sulem, Patrick, additional, Stefansson, Kari, additional, Gorokhova, Svetlana, additional, Busa, Tiffany, additional, Rio, Marlène, additional, Hadj Abdallah, Hamza, additional, Lesieur-Sebellin, Marion, additional, Amiel, Jeanne, additional, Pingault, Véronique, additional, Mercier, Sandra, additional, Vincent, Marie, additional, Philippe, Christophe, additional, Fatus-Fauconnier, Clemence, additional, Friend, Kathryn, additional, Halligan, Rebecca K., additional, Biswas, Sunita, additional, Rosser, Jane M.R., additional, Shoubridge, Cheryl, additional, Corbett, Mark A., additional, Barnett, Christopher, additional, Gecz, Jozef, additional, Leppig, Kathleen A., additional, Slavotinek, Anne, additional, Marcelis, Carlo, additional, Pfundt, Rolph, additional, de Vries, Bert B.A., additional, van Slegtenhorst, Marjon A., additional, Brooks, Alice S., additional, Cogne, Benjamin, additional, Rambaud, Thomas, additional, Tümer, Zeynep, additional, Zackai, Elaine H., additional, Akizu, Naiara, additional, Song, Yuanquan, additional, and Hakonarson, Hakon, additional

Published
2023
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41. BiallelicSOX8Variants Associated With Novel Syndrome With Myopathy, Skeletal Deformities, Intellectual Disability, and Ovarian Dysfunction

Author

Warman-Chardon, Jodi, primary, Hartley, Taila, additional, Marshall, Aren Elizabeth, additional, McBride, Arran, additional, Couse, Madeline, additional, Macdonald, William, additional, Mann, Mellissa R.W., additional, Bourque, Pierre R., additional, Breiner, Ari, additional, Lochmüller, Hanns, additional, Woulfe, John, additional, Sampaio, Marcos Loreto, additional, Melkus, Gerd, additional, Brais, Bernard, additional, Dyment, David A., additional, Boycott, Kym M., additional, and Kernohan, Kristin, additional

Published
2023
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42. Improved Diagnosis and Care for Rare Diseases through Implementation of Precision Public Health Framework

Author

Baynam, Gareth, Bowman, Faye, Lister, Karla, Walker, Caroline E., Pachter, Nicholas, Goldblatt, Jack, Boycott, Kym M., Gahl, William A., Kosaki, Kenjiro, Adachi, Takeya, Ishii, Ken, Mahede, Trinity, McKenzie, Fiona, Townshend, Sharron, Slee, Jennie, Kiraly-Borri, Cathy, Vasudevan, Anand, Hawkins, Anne, Broley, Stephanie, Schofield, Lyn, Verhoef, Hedwig, Groza, Tudor, Zankl, Andreas, Robinson, Peter N., Haendel, Melissa, Brudno, Michael, Mattick, John S., Dinger, Marcel E., Roscioli, Tony, Cowley, Mark J., Olry, Annie, Hanauer, Marc, Alkuraya, Fowzan S., Taruscio, Domenica, Posada de la Paz, Manuel, Lochmüller, Hanns, Bushby, Kate, Thompson, Rachel, Hedley, Victoria, Lasko, Paul, Mina, Kym, Beilby, John, Tifft, Cynthia, Davis, Mark, Laing, Nigel G., Julkowska, Daria, Le Cam, Yann, Terry, Sharon F., Kaufmann, Petra, Eerola, Iiro, Norstedt, Irene, Rath, Ana, Suematsu, Makoto, Groft, Stephen C., Austin, Christopher P., Draghia-Akli, Ruxandra, Weeramanthri, Tarun S., Molster, Caron, Dawkins, Hugh J. S., COHEN, IRUN R., Series editor, LAJTHA, ABEL, Series editor, LAMBRIS, JOHN D., Series editor, PAOLETTI, RODOLFO, Series editor, REZAEI, NIMA, Series editor, Posada de la Paz, Manuel, editor, Taruscio, Domenica, editor, and Groft, Stephen C., editor

Published
2017
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43. The phenotype of Floating-Harbor syndrome: clinical characterization of 52 individuals with mutations in exon 34 of SRCAP

Author

Nikkel, Sarah M, Dauber, Andrew, de Munnik, Sonja, Connolly, Meghan, Hood, Rebecca L, Caluseriu, Oana, Hurst, Jane, Kini, Usha, Nowaczyk, Malgorzata J M, Afenjar, Alexandra, Albrecht, Beate, Allanson, Judith E, Balestri, Paolo, Ben-Omran, Tawfeg, Brancati, Francesco, Cordeiro, Isabel, da Cunha, Bruna Santos, Delaney, Louisa A, Destrée, Anne, Fitzpatrick, David, Forzano, Francesca, Ghali, Neeti, Gillies, Greta, Harwood, Katerina, Hendriks, Yvonne M C, Héron, Delphine, Hoischen, Alexander, Honey, Engela Magdalena, Hoefsloot, Lies H, Ibrahim, Jennifer, Jacob, Claire M, Kant, Sarina G, Kim, Chong Ae, Kirk, Edwin P, Knoers, Nine V A M, Lacombe, Didier, Lee, Chung, Lo, Ivan F M, Lucas, Luiza S, Mari, Francesca, Mericq, Veronica, Moilanen, Jukka S, Møller, Sanne Traasdahl, Moortgat, Stephanie, Pilz, Daniela T, Pope, Kate, Price, Susan, Renieri, Alessandra, Sá, Joaquim, Schoots, Jeroen, Silveira, Elizabeth L, Simon, Marleen E H, Slavotinek, Anne, Temple, I Karen, van der Burgt, Ineke, de Vries, Bert B A, Weisfeld-Adams, James D, Whiteford, Margo L, Wierczorek, Dagmar, Wit, Jan M, Yee, Connie Fung On, Beaulieu, Chandree L, cpgdsconsortium@cheo.on.ca, White, Sue M, Bulman, Dennis E, Bongers, Ernie, Brunner, Han, Feingold, Murray, and Boycott, Kym M

Abstract

Abstract Background Floating-Harbor syndrome (FHS) is a rare condition characterized by short stature, delays in expressive language, and a distinctive facial appearance. Recently, heterozygous truncating mutations in SRCAP were determined to be disease-causing. With the availability of a DNA based confirmatory test, we set forth to define the clinical features of this syndrome. Methods and results Clinical information on fifty-two individuals with SRCAP mutations was collected using standardized questionnaires. Twenty-four males and twenty-eight females were studied with ages ranging from 2 to 52 years. The facial phenotype and expressive language impairments were defining features within the group. Height measurements were typically between minus two and minus four standard deviations, with occipitofrontal circumferences usually within the average range. Thirty-three of the subjects (63%) had at least one major anomaly requiring medical intervention. We did not observe any specific phenotype-genotype correlations. Conclusions This large cohort of individuals with molecularly confirmed FHS has allowed us to better delineate the clinical features of this rare but classic genetic syndrome, thereby facilitating the development of management protocols.

Published
2013

44. Searching for secondary findings: considering actionability and preserving the right not to know

Author

Isidor, Bertrand, Julia, Sophie, Saugier-Veber, Pascale, Weil-Dubuc, Paul-Loup, Bézieau, Stéphane, Bieth, Eric, Bonnefont, Jean-Paul, Munnich, Arnold, Bourdeaut, Franck, Bourgain, Catherine, Chassaing, Nicolas, Corradini, Nadège, Haye, Damien, Plaisancie, Julie, Dupin-Deguine, Delphine, Calvas, Patrick, Mignot, Cyril, Cogné, Benjamin, Manouvrier, Sylvie, Pasquier, Laurent, Héron, Delphine, Boycott, Kym M, Turrini, Mauro, Vears, Danya F., Nizon, Mathilde, and Vincent, Marie

Published
2019
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47. IntronicFGF14GAA repeat expansions are a common cause of downbeat nystagmus syndromes: frequency, phenotypic profile, and 4-aminopyridine treatment response

Author

Pellerin, David, primary, Heindl, Felix, additional, Wilke, Carlo, additional, Danzi, Matt C., additional, Traschütz, Andreas, additional, Ashton, Catherine, additional, Dicaire, Marie-Josée, additional, Cuillerier, Alexanne, additional, Del Gobbo, Giulia, additional, Boycott, Kym M., additional, Claassen, Jens, additional, Rujescu, Dan, additional, Hartmann, Annette M., additional, Zuchner, Stephan, additional, Brais, Bernard, additional, Strupp, Michael, additional, and Synofzik, Matthis, additional

Published
2023
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48. Protocol for a Prospective, Observational Cost-effectiveness Analysis of Returning Secondary Findings of Genome Sequencing for Unexplained Suspected Genetic Conditions

Author

Ungar, Wendy J., primary, Hayeems, Robin Z., additional, Marshall, Christian R., additional, Gillespie, Meredith K., additional, Szuto, Anna, additional, Chisholm, Caitlin, additional, James Stavropoulos, D., additional, Huang, Lijia, additional, Jarinova, Olga, additional, Wu, Vercancy, additional, Tsiplova, Kate, additional, Lau, Lynnette, additional, Lee, Whiwon, additional, Venkataramanan, Viji, additional, Sawyer, Sarah, additional, Mendoza-Londono, Roberto, additional, Somerville, Martin J., additional, and Boycott, Kym M., additional

Published
2023
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49. Clinical studies in familial VCP myopathy associated with Paget disease of bone and frontotemporal dementia

Author

Kimonis, Virginia E, Mehta, Sarju G, Fulchiero, Erin C, Thomasova, Dana, Pasquali, Marzia, Boycott, Kym, Neilan, Edward G, Kartashov, Alex, Forman, Mark S, Tucker, Stuart, Kimonis, Katerina, Mumm, Steven, Whyte, Michael P, Smith, Charles D, and Watts, Giles DJ

Subjects
Intellectual and Developmental Disabilities (IDD), Neurodegenerative, Muscular Dystrophy, Dementia, Brain Disorders, Neurosciences, Genetics, Rare Diseases, Aging, Acquired Cognitive Impairment, 2.1 Biological and endogenous factors, Aetiology, Neurological, Musculoskeletal, Adenosine Triphosphatases, Adult, Cell Cycle Proteins, Cross-Sectional Studies, Family, Female, Humans, Inclusion Bodies, Male, Middle Aged, Muscle, Skeletal, Muscular Diseases, Osteitis Deformans, Pedigree, Retrospective Studies, Valosin Containing Protein, autosomal dominant, hereditary inclusion body myopathy, limb-girdle muscular dystrophy, Paget disease of bone, frontotemporal dementia, chromosome 9p13.3-12, VCP, Clinical Sciences
Abstract

Inclusion body myopathy with Paget disease of the bone (PDB) and/or frontotemporal dementia (IBMPFD, OMIM 167320), is a progressive autosomal dominant disorder caused by mutations in the Valousin-containing protein (VCP, p97 or CDC48) gene. IBMPFD can be difficult to diagnose. We assembled data on a large set of families to illustrate the number and type of misdiagnoses that occurred. Clinical analysis of 49 affected individuals in nine families indicated that 42 (87%) of individuals had muscle disease. The majority were erroneously diagnosed with limb girdle muscular dystrophy (LGMD), facioscapular muscular dystrophy, peroneal muscular dystrophy, late adult onset distal myopathy, spinal muscular atrophy, scapuloperoneal muscular dystrophy, or amyotrophic lateral sclerosis (ALS) among others. Muscle biopsies showed rimmed vacuoles characteristic of an inclusion body myopathy in 7 of 18 patients (39%), however, inclusion body myopathy was correctly diagnosed among individuals in only families 5 and 15. Frontotemporal dementia (FTD) was diagnosed in 13 individuals (27%) at a mean age of 57 years (range 48.9-60.2 years); however, several individuals had been diagnosed with Alzheimer disease. Histopathological examination of brains of three affected individuals revealed a pattern of ubiquitin positive neuronal intranuclear inclusions and dystrophic neurites. These families expand the clinical phenotype in IBMPFD, a complex disorder caused by mutations in VCP. The presence of PDB in 28 (57%) individuals suggests that measuring serum alkaline phosphatase (ALP) activity may be a useful screen for IBMPFD in patients with myopathy.

Published
2008

50. Germline AGO2 mutations impair RNA interference and human neurological development

Author

Lessel, Davor, Zeitler, Daniela M., Reijnders, Margot R. F., Kazantsev, Andriy, Hassani Nia, Fatemeh, Bartholomäus, Alexander, Martens, Victoria, Bruckmann, Astrid, Graus, Veronika, McConkie-Rosell, Allyn, McDonald, Marie, Lozic, Bernarda, Tan, Ee-Shien, Gerkes, Erica, Johannsen, Jessika, Denecke, Jonas, Telegrafi, Aida, Zonneveld-Huijssoon, Evelien, Lemmink, Henny H., Cham, Breana W. M., Kovacevic, Tanja, Ramsdell, Linda, Foss, Kimberly, Le Duc, Diana, Mitter, Diana, Syrbe, Steffen, Merkenschlager, Andreas, Sinnema, Margje, Panis, Bianca, Lazier, Joanna, Osmond, Matthew, Hartley, Taila, Mortreux, Jeremie, Busa, Tiffany, Missirian, Chantal, Prasun, Pankaj, Lüttgen, Sabine, Mannucci, Ilaria, Lessel, Ivana, Schob, Claudia, Kindler, Stefan, Pappas, John, Rabin, Rachel, Willemsen, Marjolein, Gardeitchik, Thatjana, Löhner, Katharina, Rump, Patrick, Dias, Kerith-Rae, Evans, Carey-Anne, Andrews, Peter Ian, Roscioli, Tony, Brunner, Han G., Chijiwa, Chieko, Lewis, M. E. Suzanne, Jamra, Rami Abou, Dyment, David A., Boycott, Kym M., Stegmann, Alexander P. A., Kubisch, Christian, Tan, Ene-Choo, Mirzaa, Ghayda M., McWalter, Kirsty, Kleefstra, Tjitske, Pfundt, Rolph, Ignatova, Zoya, Meister, Gunter, and Kreienkamp, Hans-Jürgen

Published
2020
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