Recurrent de novo mutations in neurodevelopmental disorders: properties and clinical implications
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TLDR
The benefit of whole-genome sequencing over whole-exome sequencing (WGS) to understand more complex, multifactorial cases of NDD and how this improved understanding aids diagnosis and management of these disorders are discussed.Abstract:
Next-generation sequencing (NGS) is now more accessible to clinicians and researchers. As a result, our understanding of the genetics of neurodevelopmental disorders (NDDs) has rapidly advanced over the past few years. NGS has led to the discovery of new NDD genes with an excess of recurrent de novo mutations (DNMs) when compared to controls. Development of large-scale databases of normal and disease variation has given rise to metrics exploring the relative tolerance of individual genes to human mutation. Genetic etiology and diagnosis rates have improved, which have led to the discovery of new pathways and tissue types relevant to NDDs. In this review, we highlight several key findings based on the discovery of recurrent DNMs ranging from copy number variants to point mutations. We explore biases and patterns of DNM enrichment and the role of mosaicism and secondary mutations in variable expressivity. We discuss the benefit of whole-genome sequencing (WGS) over whole-exome sequencing (WES) to understand more complex, multifactorial cases of NDD and explain how this improved understanding aids diagnosis and management of these disorders. Comprehensive assessment of the DNM landscape across the genome using WGS and other technologies will lead to the development of novel functional and bioinformatics approaches to interpret DNMs and drive new insights into NDD biology.read more
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Journal ArticleDOI
A Randomized, Controlled Trial of the Analytic and Diagnostic Performance of Singleton and Trio, Rapid Genome and Exome Sequencing in Ill Infants.
Stephen F. Kingsmore,Julie A. Cakici,Julie A. Cakici,Michelle M. Clark,Mary Gaughran,Michele Feddock,Sergey Batalov,Matthew N. Bainbridge,Jeanne Carroll,Jeanne Carroll,Sara A. Caylor,Christina Clarke,Yan Ding,Katarzyna A. Ellsworth,Lauge Farnaes,Lauge Farnaes,Amber Hildreth,Amber Hildreth,Amber Hildreth,Charlotte A. Hobbs,Kiely N. James,Cyrielle Kint,Jerica Lenberg,Shareef Nahas,Lance Prince,Iris Reyes,Lisa Salz,Erica Sanford,Erica Sanford,Peter Schols,Nathaly M. Sweeney,Nathaly M. Sweeney,Mari Tokita,Narayanan Veeraraghavan,Kelly Watkins,Kristen Wigby,Kristen Wigby,Terence C. Wong,Shimul Chowdhury,Meredith S. Wright,David Dimmock,Zaira Bezares,Cinnamon S. Bloss,Joshua J.A. Braun,Carlos Diaz,Dana Mashburn,Dorjee Tamang,Daniken Orendain,Jenni Friedman,Joe Gleeson,Jaime Barea,George Chiang,Casey Cohenmeyer,Nicole G. Coufal,Marva Evans,Jose Honold,Raymond Hovey,Amy S. Kimball,Brian Lane,Crystal Le,Jennie Le,Sandra Leibel,Laurel Moyer,Patrick Mulrooney,Daeheon Oh,Paulina Ordonez,Albert Oriol,Maria Ortiz-Arechiga,Laura Puckett,Mark Speziale,Denise Suttner,Lucitia Van Der Kraan,Gail Knight,Charles Sauer,Richard S. Song,Sarah White,Audra Wise,Catherine Yamada +77 more
TL;DR: In conclusion, rapid genomic sequencing can be performed as a first-tier diagnostic test in inpatient infants and urWGS had the shortest time to result, which was important in unstable infants, and those in whom a genetic diagnosis was likely to impact immediate management.
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Synaptic dysfunction in neurodegenerative and neurodevelopmental diseases: an overview of induced pluripotent stem-cell-based disease models.
TL;DR: This review discusses synaptic dysfunction in prototype neurodevelopmental and neurodegenerative diseases, emphasizing overlapping features of synaptopathy that have been suggested by studies using induced pluripotent stem-cell-based systems.
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Malformations of Cerebral Cortex Development: Molecules and Mechanisms.
TL;DR: This review discusses cortical malformations and focuses on several for which genetic etiologies have elucidated pathogenesis, including those associated with intellectual disability and autism.
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Pathogenic POGZ mutation causes impaired cortical development and reversible autism-like phenotypes
Kensuke Matsumura,Kensuke Matsumura,Kaoru Seiriki,Shota Okada,Masashi Nagase,Shinya Ayabe,Ikuko Yamada,Tamio Furuse,Hirotoshi Shibuya,Yuka Yasuda,Hidenaga Yamamori,Michiko Fujimoto,Kazuki Nagayasu,Kana Yamamoto,Kohei Kitagawa,Hiroki Miura,Nanaka Gotoda-Nishimura,Hisato Igarashi,Misuzu Hayashida,Masayuki Baba,M. Kondo,Shigeru Hasebe,Kosei Ueshima,Atsushi Kasai,Yukio Ago,Atsuko Hayata-Takano,Atsuko Hayata-Takano,Norihito Shintani,Tokuichi Iguchi,Makoto Sato,Makoto Sato,Makoto Sato,Shun Yamaguchi,Masaru Tamura,Shigeharu Wakana,Atsushi Yoshiki,Ayako M. Watabe,Hideyuki Okano,Kazuhiro Takuma,Kazuhiro Takuma,Ryota Hashimoto,Hitoshi Hashimoto,Takanobu Nakazawa +42 more
TL;DR: It is demonstrated that ASD-associated de novo mutations in the POGZ gene, one of a high-confidence ASD gene, lead to ASD-related impaired neuronal development and disrupted mature cortical network function.
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Possible precision medicine implications from genetic testing using combined detection of sequence and intragenic copy number variants in a large cohort with childhood epilepsy
Rebecca Truty,Nila Patil,Raman Sankar,Joseph Sullivan,John Millichap,Gemma L. Carvill,Ali Entezam,Edward D. Esplin,Amy E. Fuller,Michelle Hogue,Britt Johnson,Amirah Khouzam,Yuya Kobayashi,Rachel Lewis,Keith Nykamp,Darlene Riethmaier,Jody Westbrook,Michelle K. Zeman,Robert L. Nussbaum,Swaroop Aradhya +19 more
TL;DR: Detailed studies of the complexities and outcomes of genetic testing for epilepsy can provide useful insights that inform and refine diagnostic approaches and illuminate the potential for precision medicine in epilepsy.
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TL;DR: The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations, and has reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-generation sequencing, deep exome sequencing, and dense microarray genotyping.
Journal ArticleDOI
Analysis of protein-coding genetic variation in 60,706 humans
Monkol Lek,Konrad J. Karczewski,Konrad J. Karczewski,Eric Vallabh Minikel,Eric Vallabh Minikel,Kaitlin E. Samocha,Eric Banks,Timothy Fennell,Anne H. O’Donnell-Luria,Anne H. O’Donnell-Luria,Anne H. O’Donnell-Luria,James S. Ware,Andrew J. Hill,Andrew J. Hill,Andrew J. Hill,Beryl B. Cummings,Beryl B. Cummings,Taru Tukiainen,Taru Tukiainen,Daniel P. Birnbaum,Jack A. Kosmicki,Laramie E. Duncan,Laramie E. Duncan,Karol Estrada,Karol Estrada,Fengmei Zhao,Fengmei Zhao,James Zou,Emma Pierce-Hoffman,Emma Pierce-Hoffman,Joanne Berghout,David Neil Cooper,Nicole A. Deflaux,Mark A. DePristo,Ron Do,Jason Flannick,Jason Flannick,Menachem Fromer,Laura D. Gauthier,Jackie Goldstein,Jackie Goldstein,Namrata Gupta,Daniel P. Howrigan,Daniel P. Howrigan,Adam Kiezun,Mitja I. Kurki,Mitja I. Kurki,Ami Levy Moonshine,Pradeep Natarajan,Lorena Orozco,Gina M. Peloso,Gina M. Peloso,Ryan Poplin,Manuel A. Rivas,Valentin Ruano-Rubio,Samuel A. Rose,Douglas M. Ruderfer,Khalid Shakir,Peter D. Stenson,Christine Stevens,Brett Thomas,Brett Thomas,Grace Tiao,María Teresa Tusié-Luna,Ben Weisburd,Hong-Hee Won,Dongmei Yu,David Altshuler,David Altshuler,Diego Ardissino,Michael Boehnke,John Danesh,Stacey Donnelly,Roberto Elosua,Jose C. Florez,Jose C. Florez,Stacey Gabriel,Gad Getz,Gad Getz,Stephen J. Glatt,Christina M. Hultman,Sekar Kathiresan,Markku Laakso,Steven A. McCarroll,Steven A. McCarroll,Mark I. McCarthy,Mark I. McCarthy,Dermot P.B. McGovern,Ruth McPherson,Benjamin M. Neale,Benjamin M. Neale,Aarno Palotie,Shaun Purcell,Danish Saleheen,Jeremiah M. Scharf,Pamela Sklar,Patrick F. Sullivan,Patrick F. Sullivan,Jaakko Tuomilehto,Ming T. Tsuang,Hugh Watkins,Hugh Watkins,James G. Wilson,Mark J. Daly,Mark J. Daly,Daniel G. MacArthur,Daniel G. MacArthur +106 more
TL;DR: The aggregation and analysis of high-quality exome (protein-coding region) DNA sequence data for 60,706 individuals of diverse ancestries generated as part of the Exome Aggregation Consortium (ExAC) provides direct evidence for the presence of widespread mutational recurrence.
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A general framework for estimating the relative pathogenicity of human genetic variants
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Strong Association of De Novo Copy Number Mutations with Autism
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An Expanded View of Complex Traits: From Polygenic to Omnigenic
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