Annotating pathogenic non-coding variants in genic regions

[1]  J. Shendure,et al.  Targeted resequencing in epileptic encephalopathies identifies de novo mutations in CHD2 and SYNGAP1 , 2013, Nature Genetics.

[2]  Tom R. Gaunt,et al.  Predicting the Functional, Molecular, and Phenotypic Consequences of Amino Acid Substitutions using Hidden Markov Models , 2012, Human mutation.

[3]  Michael Q. Zhang,et al.  Exonic Splicing Enhancer Motif Recognized by Human SC35 under Splicing Conditions , 2000, Molecular and Cellular Biology.

[4]  P. Bork,et al.  A method and server for predicting damaging missense mutations , 2010, Nature Methods.

[5]  Maja Steinlin,et al.  De novo loss- or gain-of-function mutations in KCNA2 cause epileptic encephalopathy , 2015, Nature Genetics.

[6]  Jinhua Wang,et al.  ESEfinder: a web resource to identify exonic splicing enhancers , 2003, Nucleic Acids Res..

[7]  M. Boguski,et al.  Evolutionary parameters of the transcribed mammalian genome: an analysis of 2,820 orthologous rodent and human sequences. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[8]  Kenny Q. Ye,et al.  De Novo Gene Disruptions in Children on the Autistic Spectrum , 2012, Neuron.

[9]  D. G. MacArthur,et al.  Guidelines for investigating causality of sequence variants in human disease , 2014, Nature.

[10]  A. Goris,et al.  EPHA4 is a disease modifier of amyotrophic lateral sclerosis in animal models and in humans , 2012, Nature Medicine.

[11]  Brittany N. Lasseigne,et al.  Exome sequencing in amyotrophic lateral sclerosis identifies risk genes and pathways , 2015, Science.

[12]  I. Scheffer,et al.  A roadmap for precision medicine in the epilepsies , 2015, The Lancet Neurology.

[13]  Michael D. Wilson,et al.  The Evolutionary Landscape of Alternative Splicing in Vertebrate Species , 2012, Science.

[14]  A. Di Costanzo,et al.  From Genetics to Genomics of Epilepsy , 2012, Neurology research international.

[15]  G. Ast,et al.  DNA-methylation effect on cotranscriptional splicing is dependent on GC architecture of the exon–intron structure , 2013, Genome research.

[16]  D. Burstein,et al.  Changes in exon-intron structure during vertebrate evolution affect the splicing pattern of exons. , 2012, Genome research.

[17]  Epilepsy Phenome,et al.  De novo mutations in synaptic transmission genes including DNM1 cause epileptic encephalopathies. , 2014, American journal of human genetics.

[18]  L. Hurst,et al.  Hearing silence: non-neutral evolution at synonymous sites in mammals , 2006, Nature Reviews Genetics.

[19]  D. Goldstein,et al.  Sequencing studies in human genetics: design and interpretation , 2013, Nature Reviews Genetics.

[20]  Jana Marie Schwarz,et al.  MutationTaster evaluates disease-causing potential of sequence alterations , 2010, Nature Methods.

[21]  Serafim Batzoglou,et al.  Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++ , 2010, PLoS Comput. Biol..

[22]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[23]  Andy Liaw,et al.  Classification and Regression by randomForest , 2007 .

[24]  Cristina Has,et al.  Faculty of 1000 evaluation for Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. , 2018 .

[25]  De novo mutations in epileptic encephalopathies , 2013 .

[26]  Michael D. Wilson,et al.  Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding , 2010, Science.

[27]  Michael Brudno,et al.  Identification of deleterious synonymous variants in human genomes , 2013, Bioinform..

[28]  J. Shendure,et al.  Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data , 2011, Nature Reviews Genetics.

[29]  Christopher J. Lee,et al.  Alternative splicing in the human, mouse and rat genomes is associated with an increased frequency of exon creation and/or loss , 2003, Nature Genetics.

[30]  F. Q. Ribeiro.  The meta-analysis , 2017, Brazilian journal of otorhinolaryngology.

[31]  Michael R. Johnson,et al.  Copy number variant analysis from exome data in 349 patients with epileptic encephalopathy , 2015, Annals of neurology.

[32]  Michael R. Johnson,et al.  De novo mutations in the classic epileptic encephalopathies , 2013, Nature.

[33]  Ricardo Villamarín-Salomón,et al.  ClinVar: public archive of interpretations of clinically relevant variants , 2015, Nucleic Acids Res..

[34]  B. Minassian,et al.  Mutations in CLN7/MFSD8 are a common cause of variant late-infantile neuronal ceroid lipofuscinosis. , 2009, Brain : a journal of neurology.

[35]  E. Budtz-Jørgensen,et al.  NIPA1 mutation in complex hereditary spastic paraplegia with epilepsy , 2011, European journal of neurology.

[36]  Murim Choi,et al.  De novo mutations in histone modifying genes in congenital heart disease , 2013, Nature.

[37]  J. Shendure,et al.  A general framework for estimating the relative pathogenicity of human genetic variants , 2014, Nature Genetics.

[38]  K. M. Steinberg,et al.  Exome sequencing of case-unaffected-parents trios reveals recessive and de novo genetic variants in sporadic ALS , 2015, Scientific Reports.

[39]  Marvin B. Shapiro,et al.  RNA splice junctions of different classes of eukaryotes: sequence statistics and functional implications in gene expression. , 1987, Nucleic acids research.

[40]  L. Chasin,et al.  Computational definition of sequence motifs governing constitutive exon splicing. , 2004, Genes & development.

[41]  E. Wagner,et al.  A Stem Structure in Fibroblast Growth Factor Receptor 2 Transcripts Mediates Cell-Type-Specific Splicing by Approximating Intronic Control Elements , 2003, Molecular and Cellular Biology.

[42]  Raquel E. Gur,et al.  Strong synaptic transmission impact by copy number variations in schizophrenia , 2010, Proceedings of the National Academy of Sciences.

[43]  S. Henikoff,et al.  Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm , 2009, Nature Protocols.

[44]  Michael R. Johnson,et al.  De novo mutations in synaptic transmission genes including DNM1 cause epileptic encephalopathies. , 2014, American journal of human genetics.

[45]  Jared C. Roach,et al.  Kaviar: an accessible system for testing SNV novelty , 2011, Bioinform..

[46]  Alan F. Scott,et al.  Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders , 2002, Nucleic Acids Res..

[47]  A. Xie,et al.  RIT2 rs12456492 polymorphism and the risk of Parkinson’s disease: A meta-analysis , 2015, Neuroscience Letters.

[48]  D. Campion,et al.  De novo deleterious genetic variations target a biological network centered on Aβ peptide in early-onset Alzheimer disease , 2015, Molecular Psychiatry.

[49]  Bale,et al.  Standards and Guidelines for the Interpretation of Sequence Variants: A Joint Consensus Recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology , 2015, Genetics in Medicine.

[50]  G. Kirov,et al.  Pathogenic copy number variants and SCN1A mutations in patients with intellectual disability and childhood-onset epilepsy , 2016, BMC Medical Genetics.