De novo mutations in epileptic encephalopathies
Andrew S. Allen,Samuel F. Berkovic,Patrick Cossette,Norman Delanty,Dennis J. Dlugos,Evan E. Eichler,Michael P. Epstein,Tracy A. Glauser,David Goldstein,Yujun Han,Erin L. Heinzen,Yuki Hitomi,Katherine B. Howell,Marvin Johnson,Ruben Kuzniecky,Daniel H. Lowenstein,Yi-Fan Lu,Maura Madou,Anthony G Marson,Heather C Mefford,Sahar Esmaeeli Nieh,Terence J. O'Brien,Ruth Ottman,Slavé Petrovski,Annapurna Poduri,Elizabeth K. Ruzzo,Ingrid E. Scheffer,Elliott H. Sherr,Christopher J. Yuskaitis,Bassel Abou-Khalil,Brian K. Alldredge,Jocelyn F. Bautista,Alex Boro,Gregory D. Cascino,Damian Consalvo,Patricia K. Crumrine,Orrin Devinsky,Miguel E. Fiol,Nathan B. Fountain,Jacqueline A. French,Daniel Friedman,Eric B. Geller,Simon Glynn,Sheryl R. Haut,Jean Hayward,Sandra L. Helmers,Sucheta M. Joshi,Andres M. Kanner,Heidi E. Kirsch,Robert C. Knowlton,Eric H. Kossoff,Rachel Kuperman,Shannon M. McGuire,Paul V. Motika,Edward J. Novotny,Juliann M. Paolicchi,Juliann M. Paolicchi,Jack M. Parent,Jack M. Parent,Kristen Park,Renée A. Shellhaas,Jerry J. Shih,Rani K. Singh,Joseph I Sirven,Michael C. Smith,Joseph Sullivan,Liu Lin Thio,Anu Venkat,Eileen P.G. Vining,Gretchen Von Allmen,Judith L.Z. Weisenberg,Peter Widdess-Walsh,Melodie R. Winawer +72 more
TLDR
In this paper, a screen for de novo mutations in patients with two classical epileptic encephalopathies: infantile spasms and Lennox-Gastaut syndrome (n = 115) was performed.Abstract:
Epileptic encephalopathies are a devastating group of severe childhood epilepsy disorders for which the cause is often unknown. Here we report a screen for de novo mutations in patients with two classical epileptic encephalopathies: infantile spasms (n = 149) and Lennox-Gastaut syndrome (n = 115). We sequenced the exomes of 264 probands, and their parents, and confirmed 329 de novo mutations. A likelihood analysis showed a significant excess of de novo mutations in the ∼4,000 genes that are the most intolerant to functional genetic variation in the human population (P = 2.9 × 10(-3)). Among these are GABRB3, with de novo mutations in four patients, and ALG13, with the same de novo mutation in two patients; both genes show clear statistical evidence of association with epileptic encephalopathy. Given the relevant site-specific mutation rates, the probabilities of these outcomes occurring by chance are P = 4.1 × 10(-10) and P = 7.8 × 10(-12), respectively. Other genes with de novo mutations in this cohort include CACNA1A, CHD2, FLNA, GABRA1, GRIN1, GRIN2B, HNRNPU, IQSEC2, MTOR and NEDD4L. Finally, we show that the de novo mutations observed are enriched in specific gene sets including genes regulated by the fragile X protein (P < 10(-8)), as has been reported previously for autism spectrum disorders.read more
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References
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Revised Terminology and Concepts for Organization of Seizures and Epilepsies: Report of the ILAE Commission on Classification and Terminology, 2005-2009
Anne T. Berg,Anne T. Berg,Samuel F. Berkovic,Martin J. Brodie,Jeffrey Buchhalter,J. Helen Cross,Walter van Emde Boas,Jerome Engel,Jacqueline A. French,Tracy A. Glauser,Gary W. Mathern,Solomon L. Moshé,Douglas R. Nordli,Perrine Plouin,Ingrid E. Scheffer +14 more
TL;DR: The International League Against Epilepsy (ILAE) Commission on Classification and Terminology has revised concepts, terminology, and approaches for classifying seizures and forms of epilepsy.
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Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations
Brian J. O'Roak,Laura Vives,Santhosh Girirajan,Emre Karakoc,Niklas Krumm,Bradley P. Coe,Roie Levy,Arthur Ko,Choli Lee,Joshua D. Smith,Emily H. Turner,Ian B. Stanaway,Benjamin Vernot,Maika Malig,Carl Baker,Beau Reilly,Joshua M. Akey,Elhanan Borenstein,Elhanan Borenstein,Mark J. Rieder,Deborah A. Nickerson,Raphael Bernier,Jay Shendure,Evan E. Eichler,Evan E. Eichler +24 more
TL;DR: It is shown that de novo point mutations are overwhelmingly paternal in origin (4:1 bias) and positively correlated with paternal age, consistent with the modest increased risk for children of older fathers to develop ASD.
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De novo mutations revealed by whole-exome sequencing are strongly associated with autism
Stephen Sanders,Michael T. Murtha,Abha R. Gupta,John D. Murdoch,Melanie J. Raubeson,A. Jeremy Willsey,A. Gulhan Ercan-Sencicek,Nicholas M. DiLullo,Neelroop N. Parikshak,Jason L. Stein,Michael F. Walker,Gordon T. Ober,Nicole A. Teran,Youeun Song,Paul El-Fishawy,Ryan C. Murtha,Murim Choi,John D. Overton,Robert D. Bjornson,Nicholas Carriero,Kyle A. Meyer,Kaya Bilguvar,Shrikant Mane,Nenad Sestan,Richard P. Lifton,Murat Gunel,Kathryn Roeder,Daniel H. Geschwind,Bernie Devlin,Matthew W. State +29 more
TL;DR: It is shown, using whole-exome sequencing of 928 individuals, including 200 phenotypically discordant sibling pairs, that highly disruptive (nonsense and splice-site) de novo mutations in brain-expressed genes are associated with autism spectrum disorders and carry large effects.
Journal ArticleDOI
Rate of de novo mutations and the importance of father’s age to disease risk
Augustine Kong,Michael L. Frigge,Gisli Masson,Søren Besenbacher,Søren Besenbacher,Patrick Sulem,Gisli Magnusson,Sigurjon A. Gudjonsson,Asgeir Sigurdsson,Aslaug Jonasdottir,Adalbjorg Jonasdottir,Wendy S.W. Wong,Gunnar Th. Sigurdsson,G. Bragi Walters,Stacy Steinberg,Hannes Helgason,Gudmar Thorleifsson,Daniel F. Gudbjartsson,Agnar Helgason,Agnar Helgason,Olafur T. Magnusson,Unnur Thorsteinsdottir,Unnur Thorsteinsdottir,Kari Stefansson,Kari Stefansson +24 more
TL;DR: A study of genome-wide mutation rates by sequencing the entire genomes of 78 Icelandic parent–offspring trios at high coverage shows that the diversity in mutation rate of single nucleotide polymorphisms is dominated by the age of the father at conception of the child.
Journal ArticleDOI
Patterns and rates of exonic de novo mutations in autism spectrum disorders
Benjamin M. Neale,Yan Kou,Li Liu,Avi Ma'ayan,Kaitlin E. Samocha,Kaitlin E. Samocha,Aniko Sabo,Chiao-Feng Lin,Christine Stevens,Li-San Wang,Vladimir Makarov,Paz Polak,Paz Polak,Seungtai Yoon,Jared Maguire,Emily L. Crawford,Nicholas G. Campbell,Evan T. Geller,Otto Valladares,Chad M. Schafer,Han Liu,Tuo Zhao,Guiqing Cai,Jayon Lihm,Ruth Dannenfelser,Omar Jabado,Zuleyma Peralta,Uma Nagaswamy,Donna M. Muzny,Jeffrey G. Reid,Irene Newsham,Yuanqing Wu,Lora Lewis,Yi Han,Benjamin F. Voight,Benjamin F. Voight,Elaine T. Lim,Elaine T. Lim,Elizabeth J. Rossin,Elizabeth J. Rossin,Andrew Kirby,Andrew Kirby,Jason Flannick,Menachem Fromer,Menachem Fromer,Khalid Shakir,Timothy Fennell,Kiran V. Garimella,Eric Banks,Ryan Poplin,Stacey Gabriel,Mark A. DePristo,Jack R. Wimbish,Braden E. Boone,Shawn Levy,Catalina Betancur,Shamil R. Sunyaev,Shamil R. Sunyaev,Eric Boerwinkle,Eric Boerwinkle,Joseph D. Buxbaum,Edwin H. Cook,Bernie Devlin,Richard A. Gibbs,Kathryn Roeder,Gerard D. Schellenberg,James S. Sutcliffe,Mark J. Daly,Mark J. Daly +68 more
TL;DR: Results from de novo events and a large parallel case–control study provide strong evidence in favour of CHD8 and KATNAL2 as genuine autism risk factors and support polygenic models in which spontaneous coding mutations in any of a large number of genes increases risk by 5- to 20-fold.
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