A new paradigm emerges from the study of de novo mutations in the context of neurodevelopmental disease

[1]  Fabian Grubert,et al.  Mutations in DNMT1 cause autosomal dominant cerebellar ataxia, deafness and narcolepsy. , 2012, Human molecular genetics.

[2]  A. Singleton,et al.  Exome sequencing reveals an unexpected genetic cause of disease: NOTCH3 mutation in a Turkish family with Alzheimer's disease , 2012, Neurobiology of Aging.

[3]  Michael F. Walker,et al.  De novo mutations revealed by whole-exome sequencing are strongly associated with autism , 2012, Nature.

[4]  Evan T. Geller,et al.  Patterns and rates of exonic de novo mutations in autism spectrum disorders , 2012, Nature.

[5]  S. Cichon,et al.  Genome-wide survey implicates the influence of copy number variants (CNVs) in the development of early-onset bipolar disorder , 2012, Molecular Psychiatry.

[6]  Jay Shendure,et al.  Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations , 2012, Nature Genetics.

[7]  Tadashi Kaname,et al.  New from NPG , 2012, Nature Medicine.

[8]  Christian Gilissen,et al.  Mutations in SWI/SNF chromatin remodeling complex gene ARID1B cause Coffin-Siris syndrome , 2012, Nature Genetics.

[9]  Ruoyu Li,et al.  Exome sequencing reveals mutations in TRPV3 as a cause of Olmsted syndrome. , 2012, American journal of human genetics.

[10]  Bradley P. Coe,et al.  Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations , 2012, Nature.

[11]  J. Shendure,et al.  De novo mutations in the actin genes ACTB and ACTG1 cause Baraitser-Winter syndrome , 2012, Nature Genetics.

[12]  R. Gibbs,et al.  Mutations in KAT6B, encoding a histone acetyltransferase, cause Genitopatellar syndrome. , 2012, American journal of human genetics.

[13]  L. Vissers,et al.  De novo mutations of the gene encoding the histone acetyltransferase KAT6B cause Genitopatellar syndrome. , 2012, American journal of human genetics.

[14]  D. Horn,et al.  Haploinsufficiency of a spliceosomal GTPase encoded by EFTUD2 causes mandibulofacial dysostosis with microcephaly. , 2012, American journal of human genetics.

[15]  Gabriele Gillessen-Kaesbach,et al.  Mutations in SRCAP, encoding SNF2-related CREBBP activator protein, cause Floating-Harbor syndrome. , 2012, American journal of human genetics.

[16]  K. Downes,et al.  A mutation in the thyroid hormone receptor alpha gene. , 2012, The New England journal of medicine.

[17]  Steven J. M. Jones,et al.  Mutations in EZH2 cause Weaver syndrome. , 2012, American journal of human genetics.

[18]  Claudio Carta,et al.  A restricted spectrum of mutations in the SMAD4 tumor-suppressor gene underlies Myhre syndrome. , 2012, American journal of human genetics.

[19]  S Purcell,et al.  De novo CNV analysis implicates specific abnormalities of postsynaptic signalling complexes in the pathogenesis of schizophrenia , 2011, Molecular Psychiatry.

[20]  J. Clayton-Smith,et al.  Whole-exome-sequencing identifies mutations in histone acetyltransferase gene KAT6B in individuals with the Say-Barber-Biesecker variant of Ohdo syndrome. , 2011, American journal of human genetics.

[21]  R. Petersen,et al.  Mutations in the colony stimulating factor 1 receptor (CSF1R) cause hereditary diffuse leukoencephalopathy with spheroids , 2011, Nature Genetics.

[22]  John Quackenbush,et al.  Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV , 2011, Bioinform..

[23]  Hugo Y. K. Lam,et al.  Performance comparison of exome DNA sequencing technologies , 2011, Nature Biotechnology.

[24]  David N Cooper,et al.  On the sequence‐directed nature of human gene mutation: The role of genomic architecture and the local DNA sequence environment in mediating gene mutations underlying human inherited disease , 2011, Human mutation.

[25]  M. Spector,et al.  A comparative analysis of exome capture , 2011, Genome Biology.

[26]  Heikki Joensuu,et al.  Comparison of solution-based exome capture methods for next generation sequencing , 2011, Genome Biology.

[27]  Hui Jiang,et al.  Comprehensive comparison of three commercial human whole-exome capture platforms , 2011, Genome Biology.

[28]  J. Wiszniewska,et al.  Copy number and SNP arrays in clinical diagnostics. , 2011, Annual review of genomics and human genetics.

[29]  S. Levy,et al.  Exome sequencing supports a de novo mutational paradigm for schizophrenia , 2011, Nature Genetics.

[30]  S. Lok,et al.  Increased exonic de novo mutation rate in individuals with schizophrenia , 2011, Nature Genetics.

[31]  Mustafa Tekin,et al.  Mutations in ANKRD11 cause KBG syndrome, characterized by intellectual disability, skeletal malformations, and macrodontia. , 2011, American journal of human genetics.

[32]  Huanming Yang,et al.  Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly , 2011, Nature Biotechnology.

[33]  L. Vissers,et al.  De novo nonsense mutations in ASXL1 cause Bohring-Opitz syndrome , 2011, Nature Genetics.

[34]  J. Shendure,et al.  Spectrum of MLL2 (ALR) mutations in 110 cases of Kabuki syndrome , 2011, American journal of medical genetics. Part A.

[35]  M. DePristo,et al.  Variation in genome-wide mutation rates within and between human families , 2011, Nature Genetics.

[36]  Kathryn Roeder,et al.  Multiple Recurrent De Novo CNVs, Including Duplications of the 7q11.23 Williams Syndrome Region, Are Strongly Associated with Autism , 2011, Neuron.

[37]  Boris Yamrom,et al.  Rare De Novo and Transmitted Copy-Number Variation in Autistic Spectrum Disorders , 2011, Neuron.

[38]  D. Wieczorek,et al.  A mutation screen in patients with Kabuki syndrome , 2011, Human Genetics.

[39]  R. Huganir,et al.  Excess of de novo deleterious mutations in genes associated with glutamatergic systems in nonsyndromic intellectual disability. , 2011, American journal of human genetics.

[40]  Stephan Züchner,et al.  Exome sequencing allows for rapid gene identification in a Charcot‐Marie‐Tooth family , 2011, Annals of neurology.

[41]  David P Bick,et al.  Making a definitive diagnosis: Successful clinical application of whole exome sequencing in a child with intractable inflammatory bowel disease , 2011, Genetics in Medicine.

[42]  H. Smeets,et al.  MLL2 mutation spectrum in 45 patients with Kabuki syndrome , 2011, Human mutation.

[43]  Patrizia Sola,et al.  Exome Sequencing Reveals VCP Mutations as a Cause of Familial ALS , 2011, Neuron.

[44]  Christian Gilissen,et al.  A de novo paradigm for mental retardation , 2010, Nature Genetics.

[45]  E. Fombonne,et al.  De novo mutations in FOXP1 in cases with intellectual disability, autism, and language impairment. , 2010, American journal of human genetics.

[46]  H. Ropers,et al.  Mutations in GRIN2A and GRIN2B encoding regulatory subunits of NMDA receptors cause variable neurodevelopmental phenotypes , 2010, Nature Genetics.

[47]  A. Monaco,et al.  Identification of FOXP1 Deletions in Three Unrelated Patients with Mental Retardation and Significant Speech and Language Deficits , 2010, Human mutation.

[48]  Misko Dzamba,et al.  Detecting copy number variation with mated short reads. , 2010, Genome research.

[49]  Deborah A Nickerson,et al.  De novo rates and selection of large copy number variation. , 2010, Genome research.

[50]  D. Altshuler,et al.  A map of human genome variation from population-scale sequencing , 2010, Nature.

[51]  A. Kasarskis,et al.  A window into third-generation sequencing. , 2010, Human molecular genetics.

[52]  L. DeLisi,et al.  De Novo Truncating Mutation in Kinesin 17 Associated with Schizophrenia , 2010, Biological Psychiatry.

[53]  I. Scheffer,et al.  Clinical spectrum of early-onset epileptic encephalopathies associated with STXBP1 mutations , 2010, Neurology.

[54]  Konrad H. Paszkiewicz,et al.  De novo assembly of short sequence reads , 2010, Briefings Bioinform..

[55]  S. Ellard,et al.  Using SIFT and PolyPhen to predict loss-of-function and gain-of-function mutations. , 2010, Genetic testing and molecular biomarkers.

[56]  Emily H Turner,et al.  Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome , 2010, Nature Genetics.

[57]  R. Hochstenbach,et al.  A three-step workflow procedure for the interpretation of array-based comparative genome hybridization results in patients with idiopathic mental retardation and congenital anomalies , 2010, Genetics in Medicine.

[58]  Gary D Bader,et al.  Functional impact of global rare copy number variation in autism spectrum disorders , 2010, Nature.

[59]  H. Hakonarson,et al.  ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data , 2010, Nucleic acids research.

[60]  P. Stenson,et al.  Genes, mutations, and human inherited disease at the dawn of the age of personalized genomics , 2010, Human mutation.

[61]  Ute Moog,et al.  Mutations in the SHANK2 synaptic scaffolding gene in autism spectrum disorder and mental retardation , 2010, Nature Genetics.

[62]  Christian Gilissen,et al.  De novo mutations of SETBP1 cause Schinzel-Giedion syndrome , 2010, Nature Genetics.

[63]  H. Chugani,et al.  Tourette syndrome is associated with recurrent exonic copy number variants , 2010, Neurology.

[64]  Marie-Pierre Dubé,et al.  De novo mutations in the gene encoding the synaptic scaffolding protein SHANK3 in patients ascertained for schizophrenia , 2010, Proceedings of the National Academy of Sciences.

[65]  Lars Bolund,et al.  State of the art de novo assembly of human genomes from massively parallel sequencing data , 2010, Human Genomics.

[66]  Jake K. Byrnes,et al.  Genome-wide association study of copy number variation in 16,000 cases of eight common diseases and 3,000 shared controls , 2010, Nature.

[67]  Y. Pawitan,et al.  The pursuit of genome-wide association studies: where are we now? , 2010, Journal of Human Genetics.

[68]  J. Gécz,et al.  Mutations in the small GTPase gene RAB39B are responsible for X-linked mental retardation associated with autism, epilepsy, and macrocephaly. , 2010, American journal of human genetics.

[69]  Huanming Yang,et al.  De novo assembly of human genomes with massively parallel short read sequencing. , 2010, Genome research.

[70]  M. Lynch Rate, molecular spectrum, and consequences of human mutation , 2010, Proceedings of the National Academy of Sciences.

[71]  Daniel F. Gudbjartsson,et al.  Parental origin of sequence variants associated with complex diseases , 2009, Nature.

[72]  L. Gallagher,et al.  Copy-number variants in neurodevelopmental disorders: promises and challenges. , 2009, Trends in genetics : TIG.

[73]  Seth G. N. Grant,et al.  The Role of DNA Copy Number Variation in Schizophrenia , 2009, Biological Psychiatry.

[74]  L. Vissers,et al.  Genomic microarrays in mental retardation: from copy number variation to gene, from research to diagnosis , 2009, Journal of Medical Genetics.

[75]  I. Tikhonova,et al.  Genetic diagnosis by whole exome capture and massively parallel DNA sequencing , 2009, Proceedings of the National Academy of Sciences.

[76]  Paul Medvedev,et al.  Computational methods for discovering structural variation with next-generation sequencing , 2009, Nature Methods.

[77]  M. Owen,et al.  Genetic overlap between autism, schizophrenia and bipolar disorder , 2009, Genome Medicine.

[78]  Christian R Marshall,et al.  Phenotypic spectrum associated with de novo and inherited deletions and duplications at 16p11.2 in individuals ascertained for diagnosis of autism spectrum disorder , 2009, Journal of Medical Genetics.

[79]  J. Ragoussis Genotyping technologies for genetic research. , 2009, Annual review of genomics and human genetics.

[80]  Luminita Moruz,et al.  Molecular karyotyping of patients with unexplained mental retardation by SNP arrays: A multicenter study , 2009, Human mutation.

[81]  Joshua M. Korn,et al.  De Novo Copy Number Variants Identify New Genes and Loci in Isolated, Sporadic Tetralogy of Fallot , 2009, Nature Genetics.

[82]  E. Fombonne,et al.  De novo STXBP1 mutations in mental retardation and nonsyndromic epilepsy , 2009, Annals of neurology.

[83]  Robert T. Schultz,et al.  Autism genome-wide copy number variation reveals ubiquitin and neuronal genes , 2009, Nature.

[84]  A. Addington,et al.  Mutations in SYNGAP1 in autosomal nonsyndromic mental retardation. , 2009, The New England journal of medicine.

[85]  K. Hirschhorn,et al.  Clinical Utility of Array CGH for the Detection of Chromosomal Imbalances Associated with Mental Retardation and Multiple Congenital Anomalies , 2009, Annals of the New York Academy of Sciences.

[86]  Dawei Li,et al.  The diploid genome sequence of an Asian individual , 2008, Nature.

[87]  Nancy F. Hansen,et al.  Accurate Whole Human Genome Sequencing using Reversible Terminator Chemistry , 2008, Nature.

[88]  J. Pavelić,et al.  Rett Syndrome: From the Gene to the Disease , 2008, European Neurology.

[89]  Edwin H. Cook,et al.  Copy-number variations associated with neuropsychiatric conditions , 2008, Nature.

[90]  Hanlee P. Ji,et al.  Next-generation DNA sequencing , 2008, Nature Biotechnology.

[91]  Thomas W. Mühleisen,et al.  Large recurrent microdeletions associated with schizophrenia , 2008, Nature.

[92]  H. Kakinuma,et al.  Copy-number variations associated with autism spectrum disorder. , 2008, Pharmacogenomics.

[93]  Joseph A. Gogos,et al.  Strong association of de novo copy number mutations with sporadic schizophrenia , 2008, Nature Genetics.

[94]  A. Singleton,et al.  Rare Structural Variants Disrupt Multiple Genes in Neurodevelopmental Pathways in Schizophrenia , 2008, Science.

[95]  Joseph T. Glessner,et al.  PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. , 2007, Genome research.

[96]  N. Carter Methods and strategies for analyzing copy number variation using DNA microarrays , 2007, Nature Genetics.

[97]  Kenny Q. Ye,et al.  Strong Association of De Novo Copy Number Mutations with Autism , 2007, Science.

[98]  K. Gunderson,et al.  High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping. , 2006, Genome research.

[99]  R. Redon,et al.  Copy number variation: new insights in genome diversity. , 2006, Genome research.

[100]  L. Feuk,et al.  Detection of large-scale variation in the human genome , 2004, Nature Genetics.

[101]  Kenny Q. Ye,et al.  Large-Scale Copy Number Polymorphism in the Human Genome , 2004, Science.

[102]  Steven Henikoff,et al.  SIFT: predicting amino acid changes that affect protein function , 2003, Nucleic Acids Res..

[103]  Warren C. Lathe,et al.  Prediction of deleterious human alleles. , 2001, Human molecular genetics.

[104]  J Dragich,et al.  Rett syndrome: a surprising result of mutation in MECP2. , 2000, Human molecular genetics.

[105]  H. Zoghbi,et al.  Rett syndrome and beyond: recurrent spontaneous and familial MECP2 mutations at CpG hotspots. , 1999, American journal of human genetics.

[106]  H. Zoghbi,et al.  Rett syndrome is caused by mutations in X-linked MECP2, encoding methyl-CpG-binding protein 2 , 1999, Nature Genetics.

[107]  Rodolphe Barrangou,et al.  Human Copy Number Variation and Complex Genetic Disease , 2014 .

[108]  P. Buckley Microdeletions of 3q29 Confer High Risk for Schizophrenia , 2012 .

[109]  M. Metzker Sequencing technologies — the next generation , 2010, Nature Reviews Genetics.

[110]  Jake K. Byrnes,et al.  Genome-wide association study of copy number variation in 16,000 cases of eight common diseases and 3,000 shared controls , 2010 .

[111]  Emily H Turner,et al.  Targeted Capture and Massively Parallel Sequencing of Twelve Human Exomes , 2009, Nature.

[112]  P. Visscher,et al.  Rare chromosomal deletions and duplications increase risk of schizophrenia , 2008, Nature.

[113]  D. Ledbetter,et al.  A de novo X;3 translocation in Rett syndrome. , 1990, American journal of medical genetics.

[114]  P. Shannon,et al.  Supporting Online Material Materials and Methods Som Text Figs. S1 to S9 Tables S1 to S17 References Dataset S1 Analysis of Genetic Inheritance in a Family Quartet by Whole-genome Sequencing , 2022 .