Search

Your search keyword '"Michael Talkowski"' showing total 21 results
Start Over Author "Michael Talkowski"
21 results on '"Michael Talkowski"'

1. Genome-wide identification and phenotypic characterization of seizure-associated copy number variations in 741,075 individuals

Author

Ludovica Montanucci, David Lewis-Smith, Ryan L. Collins, Lisa-Marie Niestroj, Shridhar Parthasarathy, Julie Xian, Shiva Ganesan, Marie Macnee, Tobias Brünger, Rhys H. Thomas, Michael Talkowski, Epi25 Collaborative, Ingo Helbig, Costin Leu, and Dennis Lal

Subjects
Science
Abstract

Abstract Copy number variants (CNV) are established risk factors for neurodevelopmental disorders with seizures or epilepsy. With the hypothesis that seizure disorders share genetic risk factors, we pooled CNV data from 10,590 individuals with seizure disorders, 16,109 individuals with clinically validated epilepsy, and 492,324 population controls and identified 25 genome-wide significant loci, 22 of which are novel for seizure disorders, such as deletions at 1p36.33, 1q44, 2p21-p16.3, 3q29, 8p23.3-p23.2, 9p24.3, 10q26.3, 15q11.2, 15q12-q13.1, 16p12.2, 17q21.31, duplications at 2q13, 9q34.3, 16p13.3, 17q12, 19p13.3, 20q13.33, and reciprocal CNVs at 16p11.2, and 22q11.21. Using genetic data from additional 248,751 individuals with 23 neuropsychiatric phenotypes, we explored the pleiotropy of these 25 loci. Finally, in a subset of individuals with epilepsy and detailed clinical data available, we performed phenome-wide association analyses between individual CNVs and clinical annotations categorized through the Human Phenotype Ontology (HPO). For six CNVs, we identified 19 significant associations with specific HPO terms and generated, for all CNVs, phenotype signatures across 17 clinical categories relevant for epileptologists. This is the most comprehensive investigation of CNVs in epilepsy and related seizure disorders, with potential implications for clinical practice.

Published
2023
Full Text
View/download PDF

2. O11: An atlas of 1.2M structural variants across global populations in the Genome Aggregation Database (gnomAD)

Author

Harrison Brand, Xuefang Zhao, Jack Fu, Ryan Collins, Isaac Wong, Cal Liao, Lily Wang, Samantha Baxter, Matthew Solomonson, Philip Darnowsky, Sinéad Chapman, Christine Stevens, Caroline Cusick, Alba Sanchis-Juan, Mark Walker, Nehir Kurtas, Katherine Chao, Stacey Gabriel, Eric Banks, Anne O’Donnell-Luria, Daniel MacArthur, Heidi Rehm, Benjamin Neale, Mark Daly, Kaitlin Samocha, Konrad Karczewski, and Michael Talkowski

Subjects
Genetics, QH426-470, Medicine
Published
2024
Full Text
View/download PDF

3. O43: Analysis of >800,000 diverse sequenced humans in gnomAD improves clinical interpretation and provides insight into gene function

Author

Heidi Rehm, Julia Goodrich, Katherine Chao, Kristen Laricchia, Michael Wilson, Jack Fu, Grace Tiao, Qin He, Daniel Marten, Timothy Poterba, Christopher Vittal, Siwei Chen, Wenhan Lu, Samantha Baxter, Sinéad Chapman, Caroline Cusick, Philip Darnowsky, Laura Gauthier, Leonhard Gruenschloss, Riley Grant, Stephen Jahl, Matthew Solomonson, Christine Stevens, Daniel MacArthur, Michael Talkowski, Benjamin Neale, Anne O'Donnell-Luria, Kaitlin Samocha, Konrad Karczewski, and Mark Daly

Subjects
Genetics, QH426-470, Medicine
Published
2024
Full Text
View/download PDF

4. P575: The Rare Genomes Project: Improving access to genomic sequencing and identifying causes of rare disease

Author

Christina Austin-Tse, Stephanie DiTroia, Melanie O'Leary, Grace VanNoy, Brian Mangilog, Gulalai Shah, Eva Martinez, Jillian Serrano, Lynn Pais, Emily O'Heir, Ikeoluwa Osei-Owusu, Gabrielle Lemire, Vijay Ganesh, Sarah Stenton, Mutaz Amin, Kayla Socarras, Mugdha Singh, Stacey Hall, Katie Larsson, Moriel Singer-Berk, Daniel Marten, Michael Wilson, Hana Snow, Benjamin Blankenmeister, Jialan Ma, Ben Weisburd, Alba Sanchis-Juan, Harrison Brand, Emily Groopman, Alysia Lovgren, Clara Williamson, Marissa Hollyer, Eleina England, Eleanor Seaby, Katherine Chao, Julia Goodrich, Samantha Baxter, Daniel MacArthur, Michael Talkowski, Monica Wojcik, Anne O'Donnell-Luria, and Heidi Rehm

Subjects
Genetics, QH426-470, Medicine
Published
2024
Full Text
View/download PDF

5. P159: Variants in cohesin release factors WAPL, PDS5A, and PDS5B define a new class of cohesinopathies

Author

Philip Boone, Kamli Faour, Kiana Mohajeri, John Lemanski, Bimal Jana, Jack Fu, Jennifer Kerkhof, Haley McConkey, Ryan Collins, Diane Lucente, Celine de Esch, Mariana Moysés-Oliveira, Alexander Nuttle, Aloysius Domingo, Serkan Erdin, Maris Hanley, Amy Watt, Eric Surette, Gloria Lima, Laura Smith, Monica Salani, Rachita Yadav, Ricardo Harripaul, Kathryn O’Keefe, Nicholas Burt, Matthew Larson, Riya Bhavsar, Benjamin Currall, Susan Sell, Roger Ladda, LaDonna Immken, Catherine Buchanan, Bo Yuan, Sally Lynch, Christian Gilissen, Rolph Pfundt, Charlotte Ockeloen, Tjitske Kleefstra, Els Vanhoutte, Margje Sinnema, Sander Stegmann, Servi Stevens, Maria Iascone, Silvia Maitz, Benjamin Cogne, Cedric Le Caignec, Marie Vincent, Mathilde Nizon, Alison Male, Pankaj Agrawal, Michelle Thompson, Pernille Torring, Charlotte Brasch-Andersen, Laurence Faivre, Ange-Line Bruel, Bertrand Isidor, Christophe Philippe, Manuela Morleo, Monica Wojcik, Casie Genetti, Siddharth Srivastava, Sonia Ballal, Sophia Schließke, Rami Abou Jamra, Andree Delahaye, Lydia von Wintzingerode, Viktoria Bothe, Marine Houlier, Timothy Stout, Gaber Bergant, Borut Peterlin, Oana Moldovan, Núria Martínez-Gil, Emanuela Argilli, Elliott Sherr, Tamar Harel, Hallel Rosenberg-Fogler, Jill Rosenfeld, Ingrid Wentzensen, Dominik Westphal, Korbinian Riedhammer, Laura Orec, James Gusella, Bekim Sadikovic, Derek Tai, and Michael Talkowski

Subjects
Genetics, QH426-470, Medicine
Published
2023
Full Text
View/download PDF

6. O34: Application of long-read sequencing and telomere-to-telomere genome assembly unveils complex rearrangements and cryptic breakpoints of Robertsonian translocation and ring chromosomes

Author

Fabiola Quintero-Rivera, Yulia Mostovoy, Philip Boone, Steve Huang, Kiran Garimella, Julian Martinez-Agosto, Bianca Russell, Tera Bowers, Tim De Smet, Stacey Gabriel, James Gusella, Harrison Brand, and Michael Talkowski

Subjects
Genetics, QH426-470, Medicine
Published
2023
Full Text
View/download PDF

8. Functional annotation of rare structural variation in the human brain

Author

Lide Han, Xuefang Zhao, Mary Lauren Benton, Thaneer Perumal, Ryan L. Collins, Gabriel E. Hoffman, Jessica S. Johnson, Laura Sloofman, Harold Z. Wang, Matthew R. Stone, CommonMind Consortium, Kristen J. Brennand, Harrison Brand, Solveig K. Sieberts, Stefano Marenco, Mette A. Peters, Barbara K. Lipska, Panos Roussos, John A. Capra, Michael Talkowski, and Douglas M. Ruderfer

Subjects
Science
Abstract

Structural variants (SVs) contribute to the genetic architecture of many brain-related disorders. Here, the authors integrate SV calls from genome sequencing (n = 755) with RNA-seq data (n = 629) from post-mortem dorsal lateral prefrontal cortex to annotate the gene regulatory effects of SVs in the human brain and their potential to contribute to disease.

Published
2020
Full Text
View/download PDF

9. TSC patient-derived isogenic neural progenitor cells reveal altered early neurodevelopmental phenotypes and rapamycin-induced MNK-eIF4E signaling

Author

Pauline Martin, Vilas Wagh, Surya A. Reis, Serkan Erdin, Roberta L. Beauchamp, Ghalib Shaikh, Michael Talkowski, Elizabeth Thiele, Steven D. Sheridan, Stephen J. Haggarty, and Vijaya Ramesh

Subjects
Tuberous sclerosis complex, TSC1, mTORC1, Induced pluripotent stem cells, Neural progenitor cells, Early neurodevelopment, Neurology. Diseases of the nervous system, RC346-429
Abstract

Abstract Background Tuberous sclerosis complex (TSC) is a neurodevelopmental disorder with frequent occurrence of epilepsy, autism spectrum disorder (ASD), intellectual disability (ID), and tumors in multiple organs. The aberrant activation of mTORC1 in TSC has led to treatment with mTORC1 inhibitor rapamycin as a lifelong therapy for tumors, but TSC-associated neurocognitive manifestations remain unaffected by rapamycin. Methods Here, we generated patient-specific, induced pluripotent stem cells (iPSCs) from a TSC patient with a heterozygous, germline, nonsense mutation in exon 15 of TSC1 and established an isogenic set of heterozygous (Het), null and corrected wildtype (Corr-WT) iPSCs using CRISPR/Cas9-mediated gene editing. We differentiated these iPSCs into neural progenitor cells (NPCs) and examined neurodevelopmental phenotypes, signaling and changes in gene expression by RNA-seq. Results Differentiated NPCs revealed enlarged cell size in TSC1-Het and Null NPCs, consistent with mTORC1 activation. TSC1-Het and Null NPCs also revealed enhanced proliferation and altered neurite outgrowth in a genotype-dependent manner, which was not reversed by rapamycin. Transcriptome analyses of TSC1-NPCs revealed differentially expressed genes that display a genotype-dependent linear response, i.e., genes upregulated/downregulated in Het were further increased/decreased in Null. In particular, genes linked to ASD, epilepsy, and ID were significantly upregulated or downregulated warranting further investigation. In TSC1-Het and Null NPCs, we also observed basal activation of ERK1/2, which was further activated upon rapamycin treatment. Rapamycin also increased MNK1/2-eIF4E signaling in TSC1-deficient NPCs. Conclusion MEK-ERK and MNK-eIF4E pathways regulate protein translation, and our results suggest that aberrant translation distinct in TSC1/2-deficient NPCs could play a role in neurodevelopmental defects. Our data showing upregulation of these signaling pathways by rapamycin support a strategy to combine a MEK or a MNK inhibitor with rapamycin that may be superior for TSC-associated CNS defects. Importantly, our generation of isogenic sets of NPCs from TSC patients provides a valuable platform for translatome and large-scale drug screening studies. Overall, our studies further support the notion that early developmental events such as NPC proliferation and initial process formation, such as neurite number and length that occur prior to neuronal differentiation, represent primary events in neurogenesis critical to disease pathogenesis of neurodevelopmental disorders such as ASD.

Published
2020
Full Text
View/download PDF

10. Lack of association between VNTR polymorphism of dopamine transporter gene (SLC6A3) and schizophrenia in a Brazilian sample Ausência de associação entre o polimorfismo VNTR do gene do transportador de dopamina (SLC6A3) e esquizofrenia em uma população brasileira

Author

Quirino Cordeiro, Michael Talkowski, Joel Wood, Eliza Ikenaga, and Homero Vallada

Subjects
DAT1, SLC6A3, esquizofrenia, polimorfismo genético, associação genética, trios, schizophrenia, genetic polymorphism, genetic association, Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571
Abstract

A role of dopaminergic dysfunction has been postulated in the aetiology of schizophrenia. We hypothesized that variations in the dopamine transporter gene (SLC6A3) may be associated with schizophrenia. We conducted case-control and family based analysis on the polymorphic SLC6A3 variable number tandem repeat (VNTR) in a sample of 220 schizophrenic patients, 226 gender and ethnic matched controls, and 49 additional case-parent trios. No differences were found in allelic or genotypic distributions between cases and controls and no significant transmission distortions from heterozygous parents to schizophrenic offspring were detected. Thus, our results do not support an association of the SLC6A3 VNTR with schizophrenia in our sample.Genes do sistema dopaminérgico são de escolha para a pesquisa de susceptibilidade para a esquizofrenia. Desse modo, possível contribuição do polimorfismo do gene do transportador de dopamina (SLC6A3) no aumento da vulnerabilidade para a esquizofrenia foi investigada no presente estudo. Analisou-se a distribuição do sítio polimórfico do gene do transportador de dopamina (VNTR) em uma população de 220 pacientes com esquizofrenia (critério diagnóstico: DSM-IV) e comparou-se com a distribuição em uma população controle de 226 indivíduos pareados para sexo e etnia. Nenhuma diferença foi observada na distribuição dos alelos entre casos e controles. O mesmo polimorfismo também foi investigado em uma segunda amostra composta por 49 trios (pais e probando). O resultado também foi negativo. Tais dados não dão suporte para a participação do polimorfismo do gene do transportador de dopamina no aumento de susceptibilidade para esquizofrenia na amostra estudada.

Published
2004
Full Text
View/download PDF

11. CNV-ClinViewer: Enhancing the clinical interpretation of large copy-number variants online

Author

Marie Macnee, Eduardo Pérez-Palma, Tobias Brünger, Chiara Klöckner, Konrad Platzer, Arthur Stefanski, Ludovica Montanucci, Allan Bayat, Maximilian Radtke, Ryan L Collins, Michael Talkowski, Daniel Blankenberg, Rikke S Møller, Johannes R Lemke, Michael Nothnagel, Patrick May, Dennis Lal, Fonds National de la Recherche - FnR [sponsor], DFG [sponsor], BMBF [sponsor], Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center], and Fonds National de la Recherche - FnR

Subjects
Statistics and Probability, Copy number variation, CNV, Genomics, Web browser, Biochemistry, eye diseases, Computer Science Applications, Computational Mathematics, Computational Theory and Mathematics, ACMG, Variant classification, Genetics & genetic processes [F10] [Life sciences], Génétique & processus génétiques [F10] [Sciences du vivant], Molecular Biology
Abstract

PurposeLarge copy number variants (CNVs) can cause a heterogeneous spectrum of rare and severe disorders. However, most CNVs are benign and are part of natural variation in human genomes. CNV pathogenicity classification, genotype-phenotype analyses, and therapeutic target identification are challenging and time-consuming tasks that require the integration and analysis of information from multiple scattered sources by experts.MethodsWe developed a web-application combining >250,000 patient and population CNVs together with a large set of biomedical annotations and provide tools for CNV classification based on ACMG/ClinGen guidelines and gene-set enrichment analyses.ResultsHere, we introduce the CNV-ClinViewer (https://cnv-ClinViewer.broadinstitute.org), an open-source web-application for clinical evaluation and visual exploration of CNVs. The application enables real-time interactive exploration of large CNV datasets in a user-friendly designed interface.ConclusionOverall, this resource facilitates semi-automated clinical CNV interpretation and genomic loci exploration and, in combination with clinical judgment, enables clinicians and researchers to formulate novel hypotheses and guide their decision-making process. Subsequently, the CNV-ClinViewer enhances for clinical investigators patient care and for basic scientists translational genomic research.

Published
2023

12. Centers for Mendelian Genomics: A decade of facilitating gene discovery

Author

Samantha M. Baxter, Jennifer E. Posey, Nicole J. Lake, Nara Sobreira, Jessica X. Chong, Steven Buyske, Elizabeth E. Blue, Lisa H. Chadwick, Zeynep H. Coban-Akdemir, Kimberly F. Doheny, Colleen P. Davis, Monkol Lek, Christopher Wellington, Shalini N. Jhangiani, Mark Gerstein, Richard A. Gibbs, Richard P. Lifton, Daniel G. MacArthur, Tara C. Matise, James R. Lupski, David Valle, Michael J. Bamshad, Ada Hamosh, Shrikant Mane, Deborah A. Nickerson, Heidi L. Rehm, Anne O’Donnell-Luria, Marcia Adams, François Aguet, Gulsen Akay, Peter Anderson, Corina Antonescu, Harindra M. Arachchi, Mehmed M. Atik, Christina A. Austin-Tse, Larry Babb, Tamara J. Bacus, Vahid Bahrambeigi, Suganthi Balasubramanian, Yavuz Bayram, Arthur L. Beaudet, Christine R. Beck, John W. Belmont, Jennifer E. Below, Kaya Bilguvar, Corinne D. Boehm, Eric Boerwinkle, Philip M. Boone, Sara J. Bowne, Harrison Brand, Kati J. Buckingham, Alicia B. Byrne, Daniel Calame, Ian M. Campbell, Xiaolong Cao, Claudia Carvalho, Varuna Chander, Jaime Chang, Katherine R. Chao, Ivan K. Chinn, Declan Clarke, Ryan L. Collins, Beryl Cummings, Zain Dardas, Moez Dawood, Kayla Delano, Stephanie P. DiTroia, Harshavardhan Doddapaneni, Haowei Du, Renqian Du, Ruizhi Duan, Mohammad Eldomery, Christine M. Eng, Eleina England, Emily Evangelista, Selin Everett, Jawid Fatih, Adam Felsenfeld, Laurent C. Francioli, Christian D. Frazar, Jack Fu, Emmanuel Gamarra, Tomasz Gambin, Weiniu Gan, Mira Gandhi, Vijay S. Ganesh, Kiran V. Garimella, Laura D. Gauthier, Danielle Giroux, Claudia Gonzaga-Jauregui, Julia K. Goodrich, William W. Gordon, Sean Griffith, Christopher M. Grochowski, Shen Gu, Sanna Gudmundsson, Stacey J. Hall, Adam Hansen, Tamar Harel, Arif O. Harmanci, Isabella Herman, Kurt Hetrick, Hadia Hijazi, Martha Horike-Pyne, Elvin Hsu, Jianhong Hu, Yongqing Huang, Jameson R. Hurless, Steve Jahl, Gail P. Jarvik, Yunyun Jiang, Eric Johanson, Angad Jolly, Ender Karaca, Michael Khayat, James Knight, J. Thomas Kolar, Sushant Kumar, Seema Lalani, Kristen M. Laricchia, Kathryn E. Larkin, Suzanne M. Leal, Gabrielle Lemire, Richard A. Lewis, He Li, Hua Ling, Rachel B. Lipson, Pengfei Liu, Alysia Kern Lovgren, Francesc López-Giráldez, Melissa P. MacMillan, Brian E. Mangilog, Stacy Mano, Dana Marafi, Beth Marosy, Jamie L. Marshall, Renan Martin, Colby T. Marvin, Michelle Mawhinney, Sean McGee, Daniel J. McGoldrick, Michelle Mehaffey, Betselote Mekonnen, Xiaolu Meng, Tadahiro Mitani, Christina Y. Miyake, David Mohr, Shaine Morris, Thomas E. Mullen, David R. Murdock, Mullai Murugan, Donna M. Muzny, Ben Myers, Juanita Neira, Kevin K. Nguyen, Patrick M. Nielsen, Natalie Nudelman, Emily O’Heir, Melanie C. O’Leary, Chrissie Ongaco, Jordan Orange, Ikeoluwa A. Osei-Owusu, Ingrid S. Paine, Lynn S. Pais, Justin Paschall, Karynne Patterson, Davut Pehlivan, Benjamin Pelle, Samantha Penney, Jorge Perez de Acha Chavez, Emma Pierce-Hoffman, Cecilia M. Poli, Jaya Punetha, Aparna Radhakrishnan, Matthew A. Richardson, Eliete Rodrigues, Gwendolin T. Roote, Jill A. Rosenfeld, Erica L. Ryke, Aniko Sabo, Alice Sanchez, Isabelle Schrauwen, Daryl A. Scott, Fritz Sedlazeck, Jillian Serrano, Chad A. Shaw, Tameka Shelford, Kathryn M. Shively, Moriel Singer-Berk, Joshua D. Smith, Hana Snow, Grace Snyder, Matthew Solomonson, Rachel G. Son, Xiaofei Song, Pawel Stankiewicz, Taylorlyn Stephan, V. Reid Sutton, Abigail Sveden, Diana Cornejo Sánchez, Monica Tackett, Michael Talkowski, Machiko S. Threlkeld, Grace Tiao, Miriam S. Udler, Laura Vail, Zaheer Valivullah, Elise Valkanas, Grace E. VanNoy, Qingbo S. Wang, Gao Wang, Lu Wang, Michael F. Wangler, Nicholas A. Watts, Ben Weisburd, Jeffrey M. Weiss, Marsha M. Wheeler, Janson J. White, Clara E. Williamson, Michael W. Wilson, Wojciech Wiszniewski, Marjorie A. Withers, Dane Witmer, Lauren Witzgall, Elizabeth Wohler, Monica H. Wojcik, Isaac Wong, Jordan C. Wood, Nan Wu, Jinchuan Xing, Yaping Yang, Qian Yi, Bo Yuan, Jordan E. Zeiger, Chaofan Zhang, Peng Zhang, Yan Zhang, Xiaohong Zhang, Yeting Zhang, Shifa Zhang, Huda Zoghbi, and Igna van den Veyver

Subjects
Phenotype, Exome Sequencing, Humans, Exome, Genomics, Article, Genetic Association Studies, Genetics (clinical)
Abstract

PURPOSE: Mendelian disease genomic research has undergone a massive transformation over the past decade. With increasing availability of exome and genome sequencing, the role of Mendelian research has expanded beyond data collection, sequencing, and analysis to worldwide data sharing and collaboration. METHODS: Over the past 10 years, the National Institutes of Health–supported Centers for Mendelian Genomics (CMGs) have played a major role in this research and clinical evolution. RESULTS: We highlight the cumulative gene discoveries facilitated by the program, biomedical research leveraged by the approach, and the larger impact on the research community. Beyond generating a list of gene-phenotype relationships and participating in widespread data sharing, the CMGs have created resources, tools, and training for the larger community to foster understanding of genes and genome variation. The CMGs have participated in a wide range of data sharing activities, including deposition of all eligible CMG data into the Analysis, Visualization, and Informatics Lab-space (AnVIL), sharing candidate genes through the Matchmaker Exchange and the CMG website, and sharing variants in Genotypes to Mendelian Phenotypes (Geno2MP) and VariantMatcher. CONCLUSION: The work is far from complete; strengthening communication between research and clinical realms, continued development and sharing of knowledge and tools, and improving access to richly characterized data sets are all required to diagnose the remaining molecularly undiagnosed patients.

Published
2022

13. Genome-wide structural variant analysis identifies risk loci for non-Alzheimer's dementias

Author

Karri Kaivola, Ruth Chia, Jinhui Ding, Memoona Rasheed, Masashi Fujita, Vilas Menon, Ronald L. Walton, Ryan L. Collins, Kimberley Billingsley, Harrison Brand, Michael Talkowski, Xuefang Zhao, Ramita Dewan, Ali Stark, Anindita Ray, Sultana Solaiman, Pilar Alvarez Jerez, Laksh Malik, Ted M. Dawson, Liana S. Rosenthal, Marilyn S. Albert, Olga Pletnikova, Juan C. Troncoso, Mario Masellis, Julia Keith, Sandra E. Black, Luigi Ferrucci, Susan M. Resnick, Toshiko Tanaka, Eric Topol, Ali Torkamani, Pentti Tienari, Tatiana M. Foroud, Bernardino Ghetti, John E. Landers, Mina Ryten, Huw R. Morris, John A. Hardy, Letizia Mazzini, Sandra D'Alfonso, Cristina Moglia, Andrea Calvo, Geidy E. Serrano, Thomas G. Beach, Tanis Ferman, Neill R. Graff-Radford, Bradley F. Boeve, Zbigniew K. Wszolek, Dennis W. Dickson, Adriano Chiò, David A. Bennett, Philip L. De Jager, Owen A. Ross, Clifton L. Dalgard, J. Raphael Gibbs, Bryan J. Traynor, Sonja W. Scholz, Anthony R. Soltis, Coralie Viollet, Gauthaman Sukumar, Camille Alba, Nathaniel Lott, Elisa McGrath Martinez, Meila Tuck, Jatinder Singh, Dagmar Bacikova, Xijun Zhang, Daniel N. Hupalo, Adelani Adeleye, Matthew D. Wilkerson, Harvey B. Pollard, Ziv Gan-Or, Ekaterina Rogaeva, Alexis Brice, Suzanne Lesage, Georgia Xiromerisiou, Antonio Canosa, Adriano Chio, Giancarlo Logroscino, Gabriele Mora, Reijko Krüger, Patrick May, Daniel Alcolea, Jordi Clarimon, Juan Fortea, Isabel Gonzalez-Aramburu, Jon Infante, Carmen Lage, Alberto Lleó, Pau Pastor, Pascual Sanchez-Juan, Francesca Brett, Dag Aarsland, Safa Al-Sarraj, Johannes Attems, Steve Gentleman, Angela K. Hodges, Seth Love, Ian G. McKeith, Christopher M. Morris, Laura Palmer, Stuart Pickering-Brown, Alan J. Thomas, Claire Troakes, Matthew J. Barrett, Lynn M. Bekris, Kelley Faber, Margaret E. Flanagan, Alison Goate, David S. Goldstein, Horacio Kaufmann, Walter A. Kukull, James B. Leverenz, Grisel Lopez, Qinwen Mao, Eliezer Masliah, Edwin Monuki, Kathy L. Newell, Jose-Alberto Palma, Matthew Perkins, Alan E. Renton, Clemens R. Scherzer, Vikram G. Shakkottai, Ellen Sidransky, Nahid Tayebi, Randy Woltjer, Robert H. Baloh, Robert Bowser, James Broach, William Camu, John Cooper-Knock, Carsten Drepper, Vivian E. Drory, Travis L. Dunckley, Eva Feldman, Pietro Fratta, Glenn Gerhard, Summer B. Gibson, Jonathan D. Glass, Matthew B. Harms, Terry D. Heiman-Patterson, Lilja Jansson, Janine Kirby, Justin Kwan, Hannu Laaksovirta, Francesco Landi, Isabelle Le Ber, Serge Lumbroso, Daniel J.L. MacGowan, Nicholas J. Maragakis, Kevin Mouzat, Liisa Myllykangas, Richard W. Orrell, Lyle W. Ostrow, Roger Pamphlett, Erik Pioro, Stefan M. Pulst, John M. Ravits, Wim Robberecht, Jeffrey D. Rothstein, Michael Sendtner, Pamela J. Shaw, Katie C. Sidle, Zachary Simmons, Thor Stein, David J. Stone, Pentti J. Tienari, Miko Valori, Philip Van Damme, Vivianna M. Van Deerlin, Ludo Van Den Bosch, Lorne Zinman, Fonds National de la Recherche - FnR [sponsor], Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center], Luxembourg Centre for Systems Biomedicine (LCSB): Clinical & Experimental Neuroscience (Krüger Group) [research center], and Luxembourg Institute of Health - LIH [research center]

Subjects
amyotrophic lateral sclerosis, Neurologie [D14] [Sciences de la santé humaine], genome-wide association study, Neurology [D14] [Human health sciences], case-control study, Non-Alzheimer dementia, resource, Biochemistry, Genetics and Molecular Biology (miscellaneous), frontotemporal dementia, structural variant, Genetics, non–Alzheimer's dementia, Genetics & genetic processes [F10] [Life sciences], Lewy body dementia, Structural variants, Génétique & processus génétiques [F10] [Sciences du vivant]
Abstract

We characterized the role of structural variants, a largely unexplored type of genetic variation, in two non-Alzheimer’s dementias, namely Lewy body dementia (LBD) and frontotemporal dementia (FTD)/amyotrophic lateral sclerosis (ALS). To do this, we applied an advanced structural variant calling pipeline (GATK-SV) to short-read whole-genome sequence data from 5,213 European-ancestry cases and 4,132 controls. We discovered, replicated, and validated a deletion in TPCN1 as a novel risk locus for LBD and detected the known structural variants at the C9orf72 and MAPT loci as associated with FTD/ALS. We also identified rare pathogenic structural variants in both LBD and FTD/ALS. Finally, we assembled a catalog of structural variants that can be mined for new insights into the pathogenesis of these understudied forms of dementia.

Published
2023

15. ANALYSIS OF RARE CODING AND COMMON VARIANTS IN AUTISM AND COMORBID SUBGROUPS

Author

Jinjie Duan, Jakob Grove, F. Kyle Satterstrom, Jack Fu, Caitlin Carey, Jiebiao Wang, null iPSYCH-BROAD Consortium, Autism Sequencing Consortium, Bernie Devlin, Kathryn Roeder, Joseph Buxbaum, Elise Robinson, Michael Talkowski, Mark Daly, and Anders Børglum

Subjects
Pharmacology, Psychiatry and Mental health, Neurology, Pharmacology (medical), Neurology (clinical), Biological Psychiatry
Published
2022

17. Prevalence and Phenotypic Effects of Copy Number Variants in Isolated Hypogonadotropic Hypogonadism

Author

Maria I Stamou, Harrison Brand, Mei Wang, Isaac Wong, Margaret F Lippincott, Lacey Plummer, William F Crowley, Michael Talkowski, Stephanie Seminara, and Ravikumar Balasubramanian

Subjects
Clinical Research Article, DNA Copy Number Variations, Endocrinology, Diabetes and Metabolism, Hypogonadism, Biochemistry (medical), Clinical Biochemistry, Kallmann Syndrome, Biochemistry, Endocrinology, Klinefelter Syndrome, Phenotype, Mutation, Prevalence, Point Mutation, Humans, Exome
Abstract

Context The genetic architecture of isolated hypogonadotropic hypogonadism (IHH) has not been completely defined. Objective To determine the role of copy number variants (CNVs) in IHH pathogenicity and define their phenotypic spectrum. Methods Exome sequencing (ES) data in IHH probands (n = 1394) (Kallmann syndrome [IHH with anosmia; KS], n = 706; normosmic IHH [nIHH], n = 688) and family members (n = 1092) at the Reproductive Endocrine Unit and the Center for Genomic Medicine of Massachusetts General Hospital were analyzed for CNVs and single nucleotide variants (SNVs)/indels in 62 known IHH genes. IHH subjects without SNVs/indels in known genes were considered “unsolved.” Phenotypes associated with CNVs were evaluated through review of patient medical records. A total of 29 CNVs in 13 genes were detected (overall IHH cohort prevalence: ~2%). Almost all (28/29) CNVs occurred in unsolved IHH cases. While some genes (eg, ANOS1 and FGFR1) frequently harbor both CNVs and SNVs/indels, the mutational spectrum of others (eg, CHD7) was restricted to SNVs/indels. Syndromic phenotypes were seen in 83% and 63% of IHH subjects with multigenic and single gene CNVs, respectively. Conclusion CNVs in known genes contribute to ~2% of IHH pathogenesis. Predictably, multigenic contiguous CNVs resulted in syndromic phenotypes. Syndromic phenotypes resulting from single gene CNVs validate pleiotropy of some IHH genes. Genome sequencing approaches are now needed to identify novel genes and/or other elusive variants (eg, noncoding/complex structural variants) that may explain the remaining missing etiology of IHH.

Published
2022

18. A neurodevelopmental disorder caused by a novel de novo SVA insertion in exon 13 of the SRCAP gene

Author

Boxun Zhao, Jill A. Madden, Jasmine Lin, Gerard T. Berry, Monica H. Wojcik, Xuefang Zhao, Harrison Brand, Michael Talkowski, Eunjung Alice Lee, and Pankaj B. Agrawal

Subjects
Adenosine Triphosphatases, Adult, Craniofacial Abnormalities, Heart Septal Defects, Ventricular, Male, Neurodevelopmental Disorders, Genetics, Humans, Abnormalities, Multiple, Female, Exons, Genetics (clinical)
Abstract

Pathogenic variants in the SRCAP (SNF2-related CREBBP activator protein) gene, which encodes a chromatin-remodeling ATPase, cause neurodevelopmental disorders including Floating Harbor syndrome (FLHS). Here, we report the discovery of a de novo transposon insertion in SRCAP exon 13 from trio genome sequencing in a 28-year-old female with failure to thrive, developmental delay, mood disorder and seizure disorder. The insertion was a full-length (~2.8 kb), antisense-oriented SVA insertion relative to the SRCAP transcript, bearing a 5' transduction and hallmarks of target-primed reverse transcription. The 20-bp 5' transduction allowed us to trace the source SVA element to an intron of a long non-coding RNA on chromosome 12, which is highly expressed in testis. RNA sequencing and qRT-PCR confirmed significant depletion of SRCAP expression and low-level exon skipping in the proband. This case highlights a novel disease-causing structural variant and the importance of transposon analysis in a clinical diagnostic setting.

Published
2022

20. Genome-encoded cytoplasmic double-stranded RNAs, found in

Author

Steven, Rodriguez, Asli, Sahin, Benjamin R, Schrank, Hawra, Al-Lawati, Isabel, Costantino, Eric, Benz, Darian, Fard, Alefiya D, Albers, Luxiang, Cao, Alexis C, Gomez, Kyle, Evans, Elena, Ratti, Merit, Cudkowicz, Matthew P, Frosch, Michael, Talkowski, Peter K, Sorger, Bradley T, Hyman, and Mark W, Albers

Subjects
Mice, DNA Repeat Expansion, C9orf72 Protein, Frontotemporal Dementia, Amyotrophic Lateral Sclerosis, Animals, Brain, Humans, Article, RNA, Double-Stranded
Abstract

Triggers of innate immune signaling in the CNS of amyotrophic lateral sclerosis and frontotemporal degeneration (ALS/FTD) patients remain elusive. We report the presence of cytoplasmic double-stranded RNA (cdsRNA), an established trigger of innate immunity, in ALS-FTD brains carrying C9ORF72 intronic hexanucleotide expansions that included genomically encoded expansions of the G(4)C(2) repeat sequences. Presence of cdsRNA in human brains was coincident with cytoplasmic TAR DNA-binding protein 43 (TDP-43) inclusions, a pathologic hallmark of ALS/FTD. Introducing cdsRNA into cultured human neural cells induced Type I interferon (IFN-I) signaling and death that was rescued by FDA-approved JAK inhibitors. In mice, genomically encoded dsRNAs expressed exclusively in a neuronal class induced IFN-I and death in connected neurons non-cell autonomously. Our findings establish that genomically encoded cdsRNAs trigger sterile, viral-mimetic IFN-I induction, and propagated death within neural circuits and may drive neuroinflammation and neurodegeneration in ALS/FTD patients.

Published
2019

21. Multi-platform discovery of haplotype-resolved structural variation in human genomes

Author

Mark J.P. Chaisson, Ashley D. Sanders, Xuefang Zhao, Ankit Malhotra, David Porubsky, Tobias Rausch, Eugene J. Gardner, Oscar Rodriguez, Li Guo, Ryan L. Collins, Xian Fan, Jia Wen, Robert E. Handsaker, Susan Fairley, Zev N. Kronenberg, Xiangmeng Kong, Fereydoun Hormozdiari, Dillon Lee, Aaron M. Wenger, Alex Hastie, Danny Antaki, Peter Audano, Harrison Brand, Stuart Cantsilieris, Han Cao, Eliza Cerveira, Chong Chen, Xintong Chen, Chen-Shan Chin, Zechen Chong, Nelson T. Chuang, Christine C. Lambert, Deanna M. Church, Laura Clarke, Andrew Farrell, Joey Flores, Timur Galeev, David Gorkin, Madhusudan Gujral, Victor Guryev, William Haynes Heaton, Jonas Korlach, Sushant Kumar, Jee Young Kwon, Jong Eun Lee, Joyce Lee, Wan-Ping Lee, Sau Peng Lee, Shantao Li, Patrick Marks, Karine Viaud-Martinez, Sascha Meiers, Katherine M. Munson, Fabio Navarro, Bradley J. Nelson, Conor Nodzak, Amina Noor, Sofia Kyriazopoulou-Panagiotopoulou, Andy Pang, Yunjiang Qiu, Gabriel Rosanio, Mallory Ryan, Adrian Stütz, Diana C.J. Spierings, Alistair Ward, AnneMarie E. Welch, Ming Xiao, Wei Xu, Chengsheng Zhang, Qihui Zhu, Xiangqun Zheng-Bradley, Ernesto Lowy, Sergei Yakneen, Steven McCarroll, Goo Jun, Li Ding, Chong Lek Koh, Bing Ren, Paul Flicek, Ken Chen, Mark B. Gerstein, Pui-Yan Kwok, Peter M. Lansdorp, Gabor Marth, Jonathan Sebat, Xinghua Shi, Ali Bashir, Kai Ye, Scott E. Devine, Michael Talkowski, Ryan E. Mills, Tobias Marschall, Jan O. Korbel, Evan E. Eichler, and Charles Lee

Subjects
Genetics, 0303 health sciences, Genomics, Human genetic variation, Computational biology, Biology, Genome, DNA sequencing, Structural variation, 03 medical and health sciences, 0302 clinical medicine, Human genome, 1000 Genomes Project, Indel, 030217 neurology & neurosurgery, 030304 developmental biology
Abstract

The incomplete identification of structural variants (SVs) from whole-genome sequencing data limits studies of human genetic diversity and disease association. Here, we apply a suite of long-read, short-read, and strand-specific sequencing technologies, optical mapping, and variant discovery algorithms to comprehensively analyze three human parent–child trios to define the full spectrum of human genetic variation in a haplotype-resolved manner. We identify 818,054 indel variants (

Published
2017
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results