Evidence for 28 genetic disorders discovered by combining healthcare and research data

Patrick J. Short | M. Hurles | L. Vissers | R. Pfundt | M. Reijnders | J. Barrett | R. Sandford | P. Danecek | I. Martincorena | D. Baralle | C. Mercer | Alison M. Male | L. Gaunt | J. Clayton-Smith | I. Simonic | Soo-Mi Park | H. Firth | E. Tobias | H. Brunner | K. Prescott | C. Shaw-Smith | I. Temple | J. Hurst | K. Samocha | N. Huang | M. Ryten | E. Gardner | J. Baptista | A. Clarke | J. McRae | D. Goudie | C. Gilissen | M. Porteous | S. Holden | M. Irving | S. Mansour | S. Holder | H. Stewart | A. Fry | D. Pilz | K. Lachlan | R. Newbury-Ecob | D. Fitzpatrick | C. Wright | R. McGowan | N. Canham | B. Kerr | S. McKee | J. Morton | M. Parker | J. Rankin | S. Banka | S. Douzgou | U. Kini | M. Lees | D. Hunt | S. Lelieveld | F. Stewart | L. Wiel | L. Side | M. McEntagart | J. Sampson | S. Mohammed | G. Gallone | T. Homfray | S. Smithson | T. Briggs | C. Tysoe | M. Whiteford | T. Cole | A. Brady | D. Ruddy | Diana S. Johnson | M. Blyth | H. Yntema | J. Carmichael | K. Retterer | M. Tischkowitz | F. Faravelli | A. Barnicoat | N. Foulds | A. Hills | D. Morrogh | E. Hobson | S. Abbs | H. Martin | J. Poulton | C. Dunn | P. Morrison | V. Mcconnell | L. Greenhalgh | J. Juusola | F. Flinter | V. Murday | L. Izatt | R. Armstrong | M. Balasubramanian | J. Berg | B. Bernhard | D. Bourn | C. Brewer | B. Castle | K. Chandler | S. Clasper | N. Cooper | H. Cox | T. Dabir | R. Davidson | C. Deshpande | A. Dixit | D. Donnelly | J. Eason | R. Fisher | C. Gardiner | N. Ghali | S. Hellens | A. Henderson | M. Humphreys | J. Jarvis | L. Jenkins | E. Jones | D. Josifova | S. Joss | E. Kinning | E. Kivuva | A. Kraus | A. Lampe | D. Lim | S. Lynch | A. Magee | K. Marks | E. McCann | K. Metcalfe | T. Montgomery | D. Moore | H. Mugalaasi | J. Paterson | S. Price | N. Ragge | L. Raymond | L. Robert | A. Ross | E. Rosser | A. Saggar | A. Sarkar | N. Shannon | D. Shears | M. Splitt | M. Suri | K. Tatton-Brown | J. Thomson | C. Turner | P. Vasudevan | J. Vogt | E. Wakeling | A. Weber | D. Wellesley | N. Williams | G. Woods | A. Donaldson | C. Longman | O. Quarrell | E. Clement | M. Holder | D. McMullan | D. Donnai | K. Ong | J. Lord | M. Owens | A. Dobbie | L. Wilson | F. Sansbury | N. Lahiri | W. Jones | T. Lester | J. Kaplanis | S. Zwolinski | C. Searle | V. Clowes | A. Stewart | A. Douglas | Claire Langley | I. Scurr | A. Yeung | F. Elmslie | Audrey Smith | R. Eberhardt | D. Osio | Claire Brooks | C. Mcwilliam | C. Clark | I. Ellis | R. Butler | Stefan H. Lelieveld | E. Reid | L. Islam | S. Hewitt | R. Haines | R. Torene | L. Bradley | Andrew M. Jackson | S. Naik | V. Varghese | Denise Williams | E. Burkitt-Wright | S. Loughlin | R. Jewell | Emma Howard | W. Lam | Zhancheng Zhang | S. Yau | D. Cilliers | Mira Kharbanda | S. Tennant | A. Sharif | A. Callaway | E. de Boer | Zoe Allen | Louise Busby | M. O'Driscoll | Elaine M. Cleary | Andrew Swale | A. Norman | K. Low | R. Wright | Emma Baple | A. Beleza | B. Mullaney | A. Procter | Catherine Breen | C. Crosby | J. Willoughby | Kevin J. Arvai | S. McQuaid | A. Kamath | P. Turnpenny | C. Bennett | E. Reavey | Gillian Rea | Z. Miedzybrodzka | Eamonn Sheridan | R. Harrison | V. Stinton | Jennifer Campbell | Rebecca Keelagher | Stacey Mutch | J. Dean | Michael Wright | Volker Straub | C. Pottinger | R. Scott | A. Green | A. Coates | J. Burn | S. McNerlan | E. Roberts | S. Albaba | Madeleine J Tooley | T. Bradley | W. Roworth | Andrew Wilkie | Lisa Cooper-Charles | Stacey Daniels | Edward Blair | Richard J. Gibbons | V. K. A. Kumar | A. Nemeth | Silvia Caroline John Zosia Alison Stephen Tabib Deirdre M Borras Clark Dean Miedzybrodzka Ross Tenna | Silvia Borras | S. Turton | S. Bodek | Joanne Comerford | Eleni Mavrak | Joanne McLean | T. Azam | Aneta Molenda | Eilidh Jackson | Kirsty Bradshaw | Rita Ibitoye | Duncan Baker | Huilin Jin | S. Corrin | Emma-Jane Cassidy | Rosalyn Jewell | D. FitzPatrick | T. Cole | Andrew Jackson | Sarah E Turton | Arveen Kamath | Margot R. F. Reijnders | Andrea Nemeth | Moira Blyth | M. Parker | Andrea M. Nemeth | F. Stewart | R. Y. Eberhardt

[1]  M. Okano,et al.  Cohort Study , 2020, Definitions.

[2]  L. Vissers,et al.  MN1 C-terminal truncation syndrome is a novel neurodevelopmental and craniofacial disorder with partial rhombencephalosynapsis. , 2019, Brain : a journal of neurology.

[3]  Seth I. Berger,et al.  TFE3‐associated neurodevelopmental disorder: A distinct recognizable syndrome , 2019, American journal of medical genetics. Part A.

[4]  M. Swertz,et al.  Improving the diagnostic yield of exome- sequencing by predicting gene–phenotype associations using large-scale gene expression analysis , 2019, Nature Communications.

[5]  Michael B. Stadler,et al.  Lysosomal Signaling Licenses Embryonic Stem Cell Differentiation via Inactivation of Tfe3. , 2019, Cell stem cell.

[6]  Jay F Rowland,et al.  Prenatal exome sequencing analysis in fetal structural anomalies detected by ultrasonography (PAGE): a cohort study , 2019, The Lancet.

[7]  Ryan L. Collins,et al.  The mutational constraint spectrum quantified from variation in 141,456 humans , 2020, Nature.

[8]  David G. Knowles,et al.  Predicting Splicing from Primary Sequence with Deep Learning , 2019, Cell.

[9]  G. Vriend,et al.  MetaDome: Pathogenicity analysis of genetic variants through aggregation of homologous human protein domains , 2019, bioRxiv.

[10]  Matthew W. Mosconi,et al.  Large-Scale Exome Sequencing Study Implicates Both Developmental and Functional Changes in the Neurobiology of Autism , 2019, Cell.

[11]  Damian Szklarczyk,et al.  STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets , 2018, Nucleic Acids Res..

[12]  Trygve E Bakken,et al.  Neurodevelopmental disease genes implicated by de novo mutation and copy number variation morbidity , 2018, Nature Genetics.

[13]  Mark Gerstein,et al.  GENCODE reference annotation for the human and mouse genomes , 2018, Nucleic Acids Res..

[14]  F. McCormick,et al.  SHOC2–MRAS–PP1 complex positively regulates RAF activity and contributes to Noonan syndrome pathogenesis , 2018, Proceedings of the National Academy of Sciences.

[15]  Patrick J. Short,et al.  Pathogenicity and selective constraint on variation near splice sites , 2018, bioRxiv.

[16]  L. A. Lowery,et al.  The Role of the Microtubule Cytoskeleton in Neurodevelopmental Disorders , 2018, Front. Cell. Neurosci..

[17]  G. McVean,et al.  Selfish mutations dysregulating RAS-MAPK signaling are pervasive in aged human testes , 2018, bioRxiv.

[18]  Li Ding,et al.  Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines. , 2018, Cell systems.

[19]  Chuang Tan,et al.  Universal Patterns of Selection in Cancer and Somatic Tissues , 2018, Cell.

[20]  James D Stephenson,et al.  Quantifying the contribution of recessive coding variation to developmental disorders , 2017, Science.

[21]  K. Heimdal,et al.  Heterozygous mutations affecting the protein kinase domain of CDK13 cause a syndromic form of developmental delay and intellectual disability , 2017, Journal of Medical Genetics.

[22]  M. Daly,et al.  Regional missense constraint improves variant deleteriousness prediction , 2017, bioRxiv.

[23]  M. Rivas,et al.  Base-specific mutational intolerance near splice sites clarifies the role of nonessential splice nucleotides , 2017, bioRxiv.

[24]  Deciphering Developmental Disorders Study,et al.  Prevalence and architecture of de novo mutations in developmental disorders , 2017, Nature.

[25]  Joan,et al.  Prevalence and architecture of de novo mutations in developmental disorders , 2017, Nature.

[26]  W. Chung,et al.  Deep Genetic Connection Between Cancer and Developmental Disorders , 2016, Human mutation.

[27]  David P. Nusinow,et al.  Estimating the Selective Effects of Heterozygous Protein Truncating Variants from Human Exome Data , 2017, Nature Genetics.

[28]  Stephan J Sanders,et al.  Refining the role of de novo protein truncating variants in neurodevelopmental disorders using population reference samples , 2016, Nature Genetics.

[29]  F. Cunningham,et al.  The Ensembl Variant Effect Predictor , 2016, bioRxiv.

[30]  E. Giannoulatou,et al.  Visualizing the origins of selfish de novo mutations in individual seminiferous tubules of human testes , 2016, Proceedings of the National Academy of Sciences.

[31]  Robert D. Finn,et al.  The Pfam protein families database: towards a more sustainable future , 2015, Nucleic Acids Res..

[32]  W. Chung,et al.  Clinical application of whole-exome sequencing across clinical indications , 2015, Genetics in Medicine.

[33]  J. Clayton-Smith,et al.  A recurrent synonymous KAT6B mutation causes Say‐Barber‐Biesecker/Young‐Simpson syndrome by inducing aberrant splicing , 2015, American journal of medical genetics. Part A.

[34]  D. Kullmann,et al.  Genetic neurological channelopathies: molecular genetics and clinical phenotypes , 2015, Journal of Neurology, Neurosurgery & Psychiatry.

[35]  James Y. Zou.  Analysis of protein-coding genetic variation in 60,706 humans , 2015, Nature.

[36]  D. Valle,et al.  GeneMatcher: A Matching Tool for Connecting Investigators with an Interest in the Same Gene , 2015, Human mutation.

[37]  Gabor T. Marth,et al.  A global reference for human genetic variation , 2015, Nature.

[38]  N. Matsumoto,et al.  De novo KIF1A mutations cause intellectual deficit, cerebellar atrophy, lower limb spasticity and visual disturbance , 2015, Journal of Human Genetics.

[39]  Alejandro Sifrim,et al.  Genetic diagnosis of developmental disorders in the DDD study: a scalable analysis of genome-wide research data , 2015, The Lancet.

[40]  G. Rouleau,et al.  De Novo Mutations in the Motor Domain of KIF1A Cause Cognitive Impairment, Spastic Paraparesis, Axonal Neuropathy, and Cerebellar Atrophy , 2015, Human mutation.

[41]  M. McCarthy,et al.  Age-related clonal hematopoiesis associated with adverse outcomes. , 2014, The New England journal of medicine.

[42]  Tomas W. Fitzgerald,et al.  Large-scale discovery of novel genetic causes of developmental disorders , 2014, Nature.

[43]  S. Gabriel,et al.  Clonal hematopoiesis and blood-cancer risk inferred from blood DNA sequence. , 2014, The New England journal of medicine.

[44]  Kali T. Witherspoon,et al.  Refining analyses of copy number variation identifies specific genes associated with developmental delay , 2014, Nature Genetics.

[45]  Stephan J Sanders,et al.  A framework for the interpretation of de novo mutation in human disease , 2014, Nature Genetics.

[46]  Allan R. Jones,et al.  Transcriptional Landscape of the Prenatal Human Brain , 2014, Nature.

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

[48]  Christian Gilissen,et al.  A Post‐Hoc Comparison of the Utility of Sanger Sequencing and Exome Sequencing for the Diagnosis of Heterogeneous Diseases , 2013, Human mutation.

[49]  Henning Hermjakob,et al.  The Reactome pathway knowledgebase , 2013, Nucleic Acids Res..

[50]  Deanna M. Church,et al.  ClinVar: public archive of relationships among sequence variation and human phenotype , 2013, Nucleic Acids Res..

[51]  José Luís Oliveira,et al.  A modular framework for biomedical concept recognition , 2013, BMC Bioinformatics.

[52]  Joshua M. Stuart,et al.  The Cancer Genome Atlas Pan-Cancer analysis project , 2013, Nature Genetics.

[53]  Kathryn Roeder,et al.  Integrated Model of De Novo and Inherited Genetic Variants Yields Greater Power to Identify Risk Genes , 2013, PLoS genetics.

[54]  Xiaomei Wu,et al.  Improving the Measurement of Semantic Similarity between Gene Ontology Terms and Gene Products: Insights from an Edge- and IC-Based Hybrid Method , 2013, PloS one.

[55]  Wei Wu,et al.  From neural development to cognition: unexpected roles for chromatin , 2013, Nature Reviews Genetics.

[56]  B. V. van Bon,et al.  Diagnostic exome sequencing in persons with severe intellectual disability. , 2012, The New England journal of medicine.

[57]  A. Wilkie,et al.  Paternal age effect mutations and selfish spermatogonial selection: causes and consequences for human disease. , 2012, American journal of human genetics.

[58]  Gregory M. Cooper,et al.  A Copy Number Variation Morbidity Map of Developmental Delay , 2011, Nature Genetics.

[59]  Ryan E. Mills,et al.  Natural genetic variation caused by small insertions and deletions in the human genome. , 2011, Genome research.

[60]  M. DePristo,et al.  A framework for variation discovery and genotyping using next-generation DNA sequencing data , 2011, Nature Genetics.

[61]  Helga Thorvaldsdóttir,et al.  Integrative Genomics Viewer , 2011, Nature Biotechnology.

[62]  Insuk Lee,et al.  Characterising and Predicting Haploinsufficiency in the Human Genome , 2010, PLoS genetics.

[63]  M. DePristo,et al.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.

[64]  T. Gibson,et al.  Ancient Protostome Origin of Chemosensory Ionotropic Glutamate Receptors and the Evolution of Insect Taste and Olfaction , 2010, PLoS genetics.

[65]  S. Dib-Hajj,et al.  Inherited Neuronal Ion Channelopathies: New Windows on Complex Neurological Diseases , 2008, The Journal of Neuroscience.

[66]  Sandhya Rani,et al.  Human Protein Reference Database—2009 update , 2008, Nucleic Acids Res..

[67]  Naomichi Matsumoto,et al.  De novo mutations in the gene encoding STXBP1 (MUNC18-1) cause early infantile epileptic encephalopathy , 2008, Nature Genetics.

[68]  Stijn van Dongen,et al.  Graph Clustering Via a Discrete Uncoupling Process , 2008, SIAM J. Matrix Anal. Appl..

[69]  T. Hunter,et al.  The Protein Kinase Complement of the Human Genome , 2002, Science.

[70]  Gert Vriend,et al.  Increasing the precision of comparative models with YASARA NOVA—a self‐parameterizing force field , 2002, Proteins.

[71]  W. Weissenhorn,et al.  The X-ray crystal structure of neuronal Sec1 from squid sheds new light on the role of this protein in exocytosis. , 2000, Structure.

[72]  G. Collingridge,et al.  Kainate receptors are involved in synaptic plasticity , 1999, Nature.

[73]  L. Maquat,et al.  A rule for termination-codon position within intron-containing genes: when nonsense affects RNA abundance. , 1998, Trends in biochemical sciences.

[74]  N. Halachmi,et al.  The Sec1 Family: A Novel Family of Proteins Involved in Synaptic Transmission and General Secretion , 1996, Journal of neurochemistry.

[75]  D. Virshup,et al.  Identification of a New Family of Protein Phosphatase 2A Regulatory Subunits (*) , 1995, The Journal of Biological Chemistry.

[76]  Jeffrey H. Miller,et al.  Mutagenic deamination of cytosine residues in DNA , 1980, Nature.

[77]  I. Xenarios,et al.  UniProtKB/Swiss-Prot, the Manually Annotated Section of the UniProt KnowledgeBase: How to Use the Entry View. , 2016, Methods in molecular biology.

[78]  W. Chung,et al.  De novo missense variants in PPP2R5D are associated with intellectual disability, macrocephaly, hypotonia, and autism , 2015, neurogenetics.