Literature DB >> 24866042

Prioritization of neurodevelopmental disease genes by discovery of new mutations.

Alexander Hoischen1, Niklas Krumm2, Evan E Eichler3.   

Abstract

Advances in genome sequencing technologies have begun to revolutionize neurogenetics, allowing the full spectrum of genetic variation to be better understood in relation to disease. Exome sequencing of hundreds to thousands of samples from patients with autism spectrum disorder, intellectual disability, epilepsy and schizophrenia provides strong evidence of the importance of de novo and gene-disruptive events. There are now several hundred new candidate genes and targeted resequencing technologies that allow screening of dozens of genes in tens of thousands of individuals with high specificity and sensitivity. The decision of which genes to pursue depends on many factors, including recurrence, previous evidence of overlap with pathogenic copy number variants, the position of the mutation in the protein, the mutational burden among healthy individuals and membership of the candidate gene in disease-implicated protein networks. We discuss these emerging criteria for gene prioritization and the potential impact on the field of neuroscience.

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Mesh:

Year:  2014        PMID: 24866042      PMCID: PMC4077789          DOI: 10.1038/nn.3703

Source DB:  PubMed          Journal:  Nat Neurosci        ISSN: 1097-6256            Impact factor:   24.884


  93 in total

1.  Digital RNA sequencing minimizes sequence-dependent bias and amplification noise with optimized single-molecule barcodes.

Authors:  Katsuyuki Shiroguchi; Tony Z Jia; Peter A Sims; X Sunney Xie
Journal:  Proc Natl Acad Sci U S A       Date:  2012-01-09       Impact factor: 11.205

2.  Discovery and statistical genotyping of copy-number variation from whole-exome sequencing depth.

Authors:  Menachem Fromer; Jennifer L Moran; Kimberly Chambert; Eric Banks; Sarah E Bergen; Douglas M Ruderfer; Robert E Handsaker; Steven A McCarroll; Michael C O'Donovan; Michael J Owen; George Kirov; Patrick F Sullivan; Christina M Hultman; Pamela Sklar; Shaun M Purcell
Journal:  Am J Hum Genet       Date:  2012-10-05       Impact factor: 11.025

Review 3.  De novo mutations in human genetic disease.

Authors:  Joris A Veltman; Han G Brunner
Journal:  Nat Rev Genet       Date:  2012-07-18       Impact factor: 53.242

4.  A higher mutational burden in females supports a "female protective model" in neurodevelopmental disorders.

Authors:  Sébastien Jacquemont; Bradley P Coe; Micha Hersch; Michael H Duyzend; Niklas Krumm; Sven Bergmann; Jacques S Beckmann; Jill A Rosenfeld; Evan E Eichler
Journal:  Am J Hum Genet       Date:  2014-02-27       Impact factor: 11.025

5.  Diversity of human copy number variation and multicopy genes.

Authors:  Peter H Sudmant; Jacob O Kitzman; Francesca Antonacci; Can Alkan; Maika Malig; Anya Tsalenko; Nick Sampas; Laurakay Bruhn; Jay Shendure; Evan E Eichler
Journal:  Science       Date:  2010-10-29       Impact factor: 47.728

Review 6.  Hallmarks of cancer: the next generation.

Authors:  Douglas Hanahan; Robert A Weinberg
Journal:  Cell       Date:  2011-03-04       Impact factor: 41.582

7.  Patterns and rates of exonic de novo mutations in autism spectrum disorders.

Authors:  Benjamin M Neale; Yan Kou; Li Liu; Avi Ma'ayan; Kaitlin E Samocha; Aniko Sabo; Chiao-Feng Lin; Christine Stevens; Li-San Wang; Vladimir Makarov; Paz Polak; Seungtai Yoon; Jared Maguire; Emily L Crawford; Nicholas G Campbell; Evan T Geller; Otto Valladares; Chad Schafer; Han Liu; Tuo Zhao; Guiqing Cai; Jayon Lihm; Ruth Dannenfelser; Omar Jabado; Zuleyma Peralta; Uma Nagaswamy; Donna Muzny; Jeffrey G Reid; Irene Newsham; Yuanqing Wu; Lora Lewis; Yi Han; Benjamin F Voight; Elaine Lim; Elizabeth Rossin; Andrew Kirby; Jason Flannick; Menachem Fromer; Khalid Shakir; Tim Fennell; Kiran Garimella; Eric Banks; Ryan Poplin; Stacey Gabriel; Mark DePristo; Jack R Wimbish; Braden E Boone; Shawn E Levy; Catalina Betancur; Shamil Sunyaev; Eric Boerwinkle; Joseph D Buxbaum; Edwin H Cook; Bernie Devlin; Richard A Gibbs; Kathryn Roeder; Gerard D Schellenberg; James S Sutcliffe; Mark J Daly
Journal:  Nature       Date:  2012-04-04       Impact factor: 49.962

8.  Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations.

Authors:  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; Mark J Rieder; Deborah A Nickerson; Raphael Bernier; Jay Shendure; Evan E Eichler
Journal:  Nature       Date:  2012-04-04       Impact factor: 49.962

9.  De novo gene mutations highlight patterns of genetic and neural complexity in schizophrenia.

Authors:  Bin Xu; Iuliana Ionita-Laza; J Louw Roos; Braden Boone; Scarlet Woodrick; Yan Sun; Shawn Levy; Joseph A Gogos; Maria Karayiorgou
Journal:  Nat Genet       Date:  2012-10-03       Impact factor: 38.330

10.  De novo mutations in epileptic encephalopathies.

Authors:  Andrew S Allen; Samuel F Berkovic; Patrick Cossette; Norman Delanty; Dennis Dlugos; Evan E Eichler; Michael P Epstein; Tracy Glauser; David B Goldstein; Yujun Han; Erin L Heinzen; Yuki Hitomi; Katherine B Howell; Michael R Johnson; Ruben Kuzniecky; Daniel H Lowenstein; Yi-Fan Lu; Maura R Z 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; Samuel F Berkovic; Alex Boro; Gregory D Cascino; Damian Consalvo; Patricia Crumrine; Orrin Devinsky; Dennis Dlugos; Michael P Epstein; Miguel Fiol; Nathan B Fountain; Jacqueline French; Daniel Friedman; Eric B Geller; Tracy Glauser; Simon Glynn; Sheryl R Haut; Jean Hayward; Sandra L Helmers; Sucheta Joshi; Andres Kanner; Heidi E Kirsch; Robert C Knowlton; Eric H Kossoff; Rachel Kuperman; Ruben Kuzniecky; Daniel H Lowenstein; Shannon M McGuire; Paul V Motika; Edward J Novotny; Ruth Ottman; Juliann M Paolicchi; Jack M Parent; Kristen Park; Annapurna Poduri; Ingrid E Scheffer; Renée A Shellhaas; Elliott H Sherr; Jerry J Shih; Rani Singh; Joseph Sirven; Michael C Smith; Joseph Sullivan; Liu Lin Thio; Anu Venkat; Eileen P G Vining; Gretchen K Von Allmen; Judith L Weisenberg; Peter Widdess-Walsh; Melodie R Winawer
Journal:  Nature       Date:  2013-08-11       Impact factor: 49.962

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  72 in total

Review 1.  Genetic studies in intellectual disability and related disorders.

Authors:  Lisenka E L M Vissers; Christian Gilissen; Joris A Veltman
Journal:  Nat Rev Genet       Date:  2015-10-27       Impact factor: 53.242

2.  De Novo Variants in TAOK1 Cause Neurodevelopmental Disorders.

Authors:  Marija Dulovic-Mahlow; Joanne Trinh; Krishna Kumar Kandaswamy; Geir Julius Braathen; Nataliya Di Donato; Elisa Rahikkala; Skadi Beblo; Martin Werber; Victor Krajka; Øyvind L Busk; Hauke Baumann; Nouriya Abbas Al-Sannaa; Frauke Hinrichs; Rabea Affan; Nir Navot; Mohammed A Al Balwi; Gabriela Oprea; Øystein L Holla; Maximilian E R Weiss; Rami A Jamra; Anne-Karin Kahlert; Shivendra Kishore; Kristian Tveten; Melissa Vos; Arndt Rolfs; Katja Lohmann
Journal:  Am J Hum Genet       Date:  2019-06-20       Impact factor: 11.025

3.  A Recurrent De Novo PACS2 Heterozygous Missense Variant Causes Neonatal-Onset Developmental Epileptic Encephalopathy, Facial Dysmorphism, and Cerebellar Dysgenesis.

Authors:  Heather E Olson; Nolwenn Jean-Marçais; Edward Yang; Delphine Heron; Katrina Tatton-Brown; Paul A van der Zwaag; Emilia K Bijlsma; Bryan L Krock; E Backer; Erik-Jan Kamsteeg; Margje Sinnema; Margot R F Reijnders; David Bearden; Amber Begtrup; Aida Telegrafi; Roelineke J Lunsing; Lydie Burglen; Gaetan Lesca; Megan T Cho; Lacey A Smith; Beth R Sheidley; Christelle Moufawad El Achkar; Phillip L Pearl; Annapurna Poduri; Cara M Skraban; Jennifer Tarpinian; Addie I Nesbitt; Dietje E Fransen van de Putte; Claudia A L Ruivenkamp; Patrick Rump; Nicolas Chatron; Isabelle Sabatier; Julitta De Bellescize; Laurent Guibaud; David A Sweetser; Jessica L Waxler; Klaas J Wierenga; Jean Donadieu; Vinodh Narayanan; Keri M Ramsey; Caroline Nava; Jean-Baptiste Rivière; Antonio Vitobello; Frédéric Tran Mau-Them; Christophe Philippe; Ange-Line Bruel; Yannis Duffourd; Laurel Thomas; Stefan H Lelieveld; Janneke Schuurs-Hoeijmakers; Han G Brunner; Boris Keren; Julien Thevenon; Laurence Faivre; Gary Thomas; Christel Thauvin-Robinet
Journal:  Am J Hum Genet       Date:  2018-04-12       Impact factor: 11.025

4.  An Incomplete Understanding of Human Genetic Variation.

Authors:  John Huddleston; Evan E Eichler
Journal:  Genetics       Date:  2016-04       Impact factor: 4.562

5.  Genes with de novo mutations are shared by four neuropsychiatric disorders discovered from NPdenovo database.

Authors:  Jinchen Li; Tao Cai; Yi Jiang; Huiqian Chen; Xin He; Chao Chen; Xianfeng Li; Qianzhi Shao; Xia Ran; Zhongshan Li; Kun Xia; Chunyu Liu; Zhong Sheng Sun; Jinyu Wu
Journal:  Mol Psychiatry       Date:  2015-04-07       Impact factor: 15.992

6.  Ultra-sensitive Sequencing Identifies High Prevalence of Clonal Hematopoiesis-Associated Mutations throughout Adult Life.

Authors:  Rocio Acuna-Hidalgo; Hilal Sengul; Marloes Steehouwer; Maartje van de Vorst; Sita H Vermeulen; Lambertus A L M Kiemeney; Joris A Veltman; Christian Gilissen; Alexander Hoischen
Journal:  Am J Hum Genet       Date:  2017-06-29       Impact factor: 11.025

Review 7.  The ageing genome, clonal mosaicism and chronic disease.

Authors:  Mitchell J Machiela; Stephen J Chanock
Journal:  Curr Opin Genet Dev       Date:  2017-01-06       Impact factor: 5.578

Review 8.  Etiology of autism spectrum disorder: a genomics perspective.

Authors:  John J Connolly; Hakon Hakonarson
Journal:  Curr Psychiatry Rep       Date:  2014-11       Impact factor: 5.285

9.  De Novo Variants in SPOP Cause Two Clinically Distinct Neurodevelopmental Disorders.

Authors:  Maria J Nabais Sá; Geniver El Tekle; Arjan P M de Brouwer; Sarah L Sawyer; Daniela Del Gaudio; Michael J Parker; Farah Kanani; Marie-José H van den Boogaard; Koen van Gassen; Margot I Van Allen; Klaas Wierenga; Gabriela Purcarin; Ellen Roy Elias; Amber Begtrup; Jennifer Keller-Ramey; Tiziano Bernasocchi; Laurens van de Wiel; Christian Gilissen; Hanka Venselaar; Rolph Pfundt; Lisenka E L M Vissers; Jean-Philippe P Theurillat; Bert B A de Vries
Journal:  Am J Hum Genet       Date:  2020-02-27       Impact factor: 11.025

Review 10.  Large-scale genomics unveils the genetic architecture of psychiatric disorders.

Authors:  Jacob Gratten; Naomi R Wray; Matthew C Keller; Peter M Visscher
Journal:  Nat Neurosci       Date:  2014-05-27       Impact factor: 24.884

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