Literature DB >> 27479843

Meta-analysis of 2,104 trios provides support for 10 new genes for intellectual disability.

Stefan H Lelieveld1, Margot R F Reijnders2, Rolph Pfundt2, Helger G Yntema2, Erik-Jan Kamsteeg2, Petra de Vries2, Bert B A de Vries2, Marjolein H Willemsen2, Tjitske Kleefstra2, Katharina Löhner3, Maaike Vreeburg4, Servi J C Stevens4, Ineke van der Burgt2, Ernie M H F Bongers2, Alexander P A Stegmann4, Patrick Rump3, Tuula Rinne2, Marcel R Nelen2, Joris A Veltman2,4, Lisenka E L M Vissers2, Han G Brunner2,4, Christian Gilissen2.   

Abstract

To identify candidate genes for intellectual disability, we performed a meta-analysis on 2,637 de novo mutations, identified from the exomes of 2,104 patient-parent trios. Statistical analyses identified 10 new candidate ID genes: DLG4, PPM1D, RAC1, SMAD6, SON, SOX5, SYNCRIP, TCF20, TLK2 and TRIP12. In addition, we show that these genes are intolerant to nonsynonymous variation and that mutations in these genes are associated with specific clinical ID phenotypes.

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Year:  2016        PMID: 27479843     DOI: 10.1038/nn.4352

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


  17 in total

1.  A post-hoc comparison of the utility of sanger sequencing and exome sequencing for the diagnosis of heterogeneous diseases.

Authors:  Kornelia Neveling; Ilse Feenstra; Christian Gilissen; Lies H Hoefsloot; Erik-Jan Kamsteeg; Arjen R Mensenkamp; Richard J T Rodenburg; Helger G Yntema; Liesbeth Spruijt; Sascha Vermeer; Tuula Rinne; Koen L van Gassen; Danielle Bodmer; Dorien Lugtenberg; Rick de Reuver; Wendy Buijsman; Ronny C Derks; Nienke Wieskamp; Bert van den Heuvel; Marjolijn J L Ligtenberg; Hannie Kremer; David A Koolen; Bart P C van de Warrenburg; Frans P M Cremers; Carlo L M Marcelis; Jan A M Smeitink; Saskia B Wortmann; Wendy A G van Zelst-Stams; Joris A Veltman; Han G Brunner; Hans Scheffer; Marcel R Nelen
Journal:  Hum Mutat       Date:  2013-10-18       Impact factor: 4.878

2.  Genome sequencing identifies major causes of severe intellectual disability.

Authors:  Christian Gilissen; Jayne Y Hehir-Kwa; Djie Tjwan Thung; Maartje van de Vorst; Bregje W M van Bon; Marjolein H Willemsen; Michael Kwint; Irene M Janssen; Alexander Hoischen; Annette Schenck; Richard Leach; Robert Klein; Rick Tearle; Tan Bo; Rolph Pfundt; Helger G Yntema; Bert B A de Vries; Tjitske Kleefstra; Han G Brunner; Lisenka E L M Vissers; Joris A Veltman
Journal:  Nature       Date:  2014-06-04       Impact factor: 49.962

3.  Brief Report: SETD2 Mutation in a Child with Autism, Intellectual Disabilities and Epilepsy.

Authors:  Heidi S Lumish; Julia Wynn; Orrin Devinsky; Wendy K Chung
Journal:  J Autism Dev Disord       Date:  2015-11

4.  Diagnostic exome sequencing in persons with severe intellectual disability.

Authors:  Joep de Ligt; Marjolein H Willemsen; Bregje W M van Bon; Tjitske Kleefstra; Helger G Yntema; Thessa Kroes; Anneke T Vulto-van Silfhout; David A Koolen; Petra de Vries; Christian Gilissen; Marisol del Rosario; Alexander Hoischen; Hans Scheffer; Bert B A de Vries; Han G Brunner; Joris A Veltman; Lisenka E L M Vissers
Journal:  N Engl J Med       Date:  2012-10-03       Impact factor: 91.245

5.  A systematic survey of loss-of-function variants in human protein-coding genes.

Authors:  Daniel G MacArthur; Suganthi Balasubramanian; Adam Frankish; Ni Huang; James Morris; Klaudia Walter; Luke Jostins; Lukas Habegger; Joseph K Pickrell; Stephen B Montgomery; Cornelis A Albers; Zhengdong D Zhang; Donald F Conrad; Gerton Lunter; Hancheng Zheng; Qasim Ayub; Mark A DePristo; Eric Banks; Min Hu; Robert E Handsaker; Jeffrey A Rosenfeld; Menachem Fromer; Mike Jin; Xinmeng Jasmine Mu; Ekta Khurana; Kai Ye; Mike Kay; Gary Ian Saunders; Marie-Marthe Suner; Toby Hunt; If H A Barnes; Clara Amid; Denise R Carvalho-Silva; Alexandra H Bignell; Catherine Snow; Bryndis Yngvadottir; Suzannah Bumpstead; David N Cooper; Yali Xue; Irene Gallego Romero; Jun Wang; Yingrui Li; Richard A Gibbs; Steven A McCarroll; Emmanouil T Dermitzakis; Jonathan K Pritchard; Jeffrey C Barrett; Jennifer Harrow; Matthew E Hurles; Mark B Gerstein; Chris Tyler-Smith
Journal:  Science       Date:  2012-02-17       Impact factor: 47.728

6.  The contribution of de novo coding mutations to autism spectrum disorder.

Authors:  Ivan Iossifov; Brian J O'Roak; Stephan J Sanders; Michael Ronemus; Niklas Krumm; Dan Levy; Holly A Stessman; Kali T Witherspoon; Laura Vives; Karynne E Patterson; Joshua D Smith; Bryan Paeper; Deborah A Nickerson; Jeanselle Dea; Shan Dong; Luis E Gonzalez; Jeffrey D Mandell; Shrikant M Mane; Michael T Murtha; Catherine A Sullivan; Michael F Walker; Zainulabedin Waqar; Liping Wei; A Jeremy Willsey; Boris Yamrom; Yoon-ha Lee; Ewa Grabowska; Ertugrul Dalkic; Zihua Wang; Steven Marks; Peter Andrews; Anthony Leotta; Jude Kendall; Inessa Hakker; Julie Rosenbaum; Beicong Ma; Linda Rodgers; Jennifer Troge; Giuseppe Narzisi; Seungtai Yoon; Michael C Schatz; Kenny Ye; W Richard McCombie; Jay Shendure; Evan E Eichler; Matthew W State; Michael Wigler
Journal:  Nature       Date:  2014-10-29       Impact factor: 69.504

7.  Genic intolerance to functional variation and the interpretation of personal genomes.

Authors:  Slavé Petrovski; Quanli Wang; Erin L Heinzen; Andrew S Allen; David B Goldstein
Journal:  PLoS Genet       Date:  2013-08-22       Impact factor: 5.917

8.  Rate of de novo mutations and the importance of father's age to disease risk.

Authors:  Augustine Kong; Michael L Frigge; Gisli Masson; Soren Besenbacher; Patrick Sulem; Gisli Magnusson; Sigurjon A Gudjonsson; Asgeir Sigurdsson; Aslaug Jonasdottir; Adalbjorg Jonasdottir; Wendy S W Wong; Gunnar Sigurdsson; G Bragi Walters; Stacy Steinberg; Hannes Helgason; Gudmar Thorleifsson; Daniel F Gudbjartsson; Agnar Helgason; Olafur Th Magnusson; Unnur Thorsteinsdottir; Kari Stefansson
Journal:  Nature       Date:  2012-08-23       Impact factor: 49.962

9.  Assessing the necessity of confirmatory testing for exome-sequencing results in a clinical molecular diagnostic laboratory.

Authors:  Samuel P Strom; Hane Lee; Kingshuk Das; Eric Vilain; Stanley F Nelson; Wayne W Grody; Joshua L Deignan
Journal:  Genet Med       Date:  2014-01-09       Impact factor: 8.822

10.  A framework for the interpretation of de novo mutation in human disease.

Authors:  Kaitlin E Samocha; Elise B Robinson; Stephan J Sanders; Christine Stevens; Aniko Sabo; Lauren M McGrath; Jack A Kosmicki; Karola Rehnström; Swapan Mallick; Andrew Kirby; Dennis P Wall; Daniel G MacArthur; Stacey B Gabriel; Mark DePristo; Shaun M Purcell; Aarno Palotie; Eric Boerwinkle; Joseph D Buxbaum; Edwin H Cook; Richard A Gibbs; Gerard D Schellenberg; James S Sutcliffe; Bernie Devlin; Kathryn Roeder; Benjamin M Neale; Mark J Daly
Journal:  Nat Genet       Date:  2014-08-03       Impact factor: 38.330

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  166 in total

1.  A genome-wide case-only test for the detection of digenic inheritance in human exomes.

Authors:  Gaspard Kerner; Matthieu Bouaziz; Aurélie Cobat; Benedetta Bigio; Andrew T Timberlake; Jacinta Bustamante; Richard P Lifton; Jean-Laurent Casanova; Laurent Abel
Journal:  Proc Natl Acad Sci U S A       Date:  2020-07-27       Impact factor: 11.205

2.  De novo FBXO11 mutations are associated with intellectual disability and behavioural anomalies.

Authors:  Daniel Fritzen; Alma Kuechler; Mona Grimmel; Jessica Becker; Sophia Peters; Marc Sturm; Hela Hundertmark; Axel Schmidt; Martina Kreiß; Tim M Strom; Dagmar Wieczorek; Tobias B Haack; Stefanie Beck-Wödl; Kirsten Cremer; Hartmut Engels
Journal:  Hum Genet       Date:  2018-05-23       Impact factor: 4.132

Review 3.  Measuring intolerance to mutation in human genetics.

Authors:  Zachary L Fuller; Jeremy J Berg; Hakhamanesh Mostafavi; Guy Sella; Molly Przeworski
Journal:  Nat Genet       Date:  2019-04-08       Impact factor: 38.330

4.  Progressive myoclonus epilepsies-Residual unsolved cases have marked genetic heterogeneity including dolichol-dependent protein glycosylation pathway genes.

Authors:  Carolina Courage; Karen L Oliver; Eon Joo Park; Jillian M Cameron; Kariona A Grabińska; Mikko Muona; Laura Canafoglia; Antonio Gambardella; Edith Said; Zaid Afawi; Betul Baykan; Christian Brandt; Carlo di Bonaventura; Hui Bein Chew; Chiara Criscuolo; Leanne M Dibbens; Barbara Castellotti; Patrizia Riguzzi; Angelo Labate; Alessandro Filla; Anna T Giallonardo; Geza Berecki; Christopher B Jackson; Tarja Joensuu; John A Damiano; Sara Kivity; Amos Korczyn; Aarno Palotie; Pasquale Striano; Davide Uccellini; Loretta Giuliano; Eva Andermann; Ingrid E Scheffer; Roberto Michelucci; Melanie Bahlo; Silvana Franceschetti; William C Sessa; Samuel F Berkovic; Anna-Elina Lehesjoki
Journal:  Am J Hum Genet       Date:  2021-04-01       Impact factor: 11.025

5.  Mutation-specific pathophysiological mechanisms define different neurodevelopmental disorders associated with SATB1 dysfunction.

Authors:  Joery den Hoed; Elke de Boer; Norine Voisin; Alexander J M Dingemans; Nicolas Guex; Laurens Wiel; Christoffer Nellaker; Shivarajan M Amudhavalli; Siddharth Banka; Frederique S Bena; Bruria Ben-Zeev; Vincent R Bonagura; Ange-Line Bruel; Theresa Brunet; Han G Brunner; Hui B Chew; Jacqueline Chrast; Loreta Cimbalistienė; Hilary Coon; Emmanuèlle C Délot; Florence Démurger; Anne-Sophie Denommé-Pichon; Christel Depienne; Dian Donnai; David A Dyment; Orly Elpeleg; Laurence Faivre; Christian Gilissen; Leslie Granger; Benjamin Haber; Yasuo Hachiya; Yasmin Hamzavi Abedi; Jennifer Hanebeck; Jayne Y Hehir-Kwa; Brooke Horist; Toshiyuki Itai; Adam Jackson; Rosalyn Jewell; Kelly L Jones; Shelagh Joss; Hirofumi Kashii; Mitsuhiro Kato; Anja A Kattentidt-Mouravieva; Fernando Kok; Urania Kotzaeridou; Vidya Krishnamurthy; Vaidutis Kučinskas; Alma Kuechler; Alinoë Lavillaureix; Pengfei Liu; Linda Manwaring; Naomichi Matsumoto; Benoît Mazel; Kirsty McWalter; Vardiella Meiner; Mohamad A Mikati; Satoko Miyatake; Takeshi Mizuguchi; Lip H Moey; Shehla Mohammed; Hagar Mor-Shaked; Hayley Mountford; Ruth Newbury-Ecob; Sylvie Odent; Laura Orec; Matthew Osmond; Timothy B Palculict; Michael Parker; Andrea K Petersen; Rolph Pfundt; Eglė Preikšaitienė; Kelly Radtke; Emmanuelle Ranza; Jill A Rosenfeld; Teresa Santiago-Sim; Caitlin Schwager; Margje Sinnema; Lot Snijders Blok; Rebecca C Spillmann; Alexander P A Stegmann; Isabelle Thiffault; Linh Tran; Adi Vaknin-Dembinsky; Juliana H Vedovato-Dos-Santos; Samantha A Schrier Vergano; Eric Vilain; Antonio Vitobello; Matias Wagner; Androu Waheeb; Marcia Willing; Britton Zuccarelli; Usha Kini; Dianne F Newbury; Tjitske Kleefstra; Alexandre Reymond; Simon E Fisher; Lisenka E L M Vissers
Journal:  Am J Hum Genet       Date:  2021-01-28       Impact factor: 11.025

6.  Spatial Clustering of de Novo Missense Mutations Identifies Candidate Neurodevelopmental Disorder-Associated Genes.

Authors:  Stefan H Lelieveld; Laurens Wiel; Hanka Venselaar; Rolph Pfundt; Gerrit Vriend; Joris A Veltman; Han G Brunner; Lisenka E L M Vissers; Christian Gilissen
Journal:  Am J Hum Genet       Date:  2017-08-31       Impact factor: 11.025

7.  A Statistical Framework for Mapping Risk Genes from De Novo Mutations in Whole-Genome-Sequencing Studies.

Authors:  Yuwen Liu; Yanyu Liang; A Ercument Cicek; Zhongshan Li; Jinchen Li; Rebecca A Muhle; Martina Krenzer; Yue Mei; Yan Wang; Nicholas Knoblauch; Jean Morrison; Siming Zhao; Yi Jiang; Evan Geller; Iuliana Ionita-Laza; Jinyu Wu; Kun Xia; James P Noonan; Zhong Sheng Sun; Xin He
Journal:  Am J Hum Genet       Date:  2018-05-10       Impact factor: 11.025

8.  De Novo Mutations and Rare Variants Occurring in NMDA Receptors.

Authors:  Wenshu XiangWei; Yuwu Jiang; Hongjie Yuan
Journal:  Curr Opin Physiol       Date:  2017-12-27

9.  De Novo Truncating Variants in ASXL2 Are Associated with a Unique and Recognizable Clinical Phenotype.

Authors:  Vandana Shashi; Loren D M Pena; Katherine Kim; Barbara Burton; Maja Hempel; Kelly Schoch; Magdalena Walkiewicz; Heather M McLaughlin; Megan Cho; Nicholas Stong; Scott E Hickey; Christine M Shuss; Michael S Freemark; Jane S Bellet; Martha Ann Keels; Melanie J Bonner; Maysantoine El-Dairi; Megan Butler; Peter G Kranz; Constance T R M Stumpel; Sylvia Klinkenberg; Karin Oberndorff; Malik Alawi; Rene Santer; Slavé Petrovski; Outi Kuismin; Satu Korpi-Heikkilä; Olli Pietilainen; Palotie Aarno; Mitja I Kurki; Alexander Hoischen; Anna C Need; David B Goldstein; Fanny Kortüm
Journal:  Am J Hum Genet       Date:  2016-09-29       Impact factor: 11.025

10.  Monocytic Infiltrates Contribute to Autistic-like Behaviors in a Two-Hit Model of Neurodevelopmental Defects.

Authors:  Hong-Ru Chen; Ching-Wen Chen; Nandita Mandhani; Jonah C Short-Miller; Marchelle R Smucker; Yu-Yo Sun; Chia-Yi Kuan
Journal:  J Neurosci       Date:  2020-10-30       Impact factor: 6.167

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