RD-Connect: An Integrated Platform Connecting Databases, Registries, Biobanks and Clinical Bioinformatics for Rare Disease Research
Rachel Thompson,Louise Johnston,Domenica Taruscio,Lucia Monaco,Christophe Béroud,Ivo Gut,Mats G. Hansson,Peter-Bram A. ’t Hoen,George P. Patrinos,Hugh Dawkins,Monica Ensini,Kurt Zatloukal,David Koubi,Emma Heslop,Justin Paschall,Manuel Posada,Peter N. Robinson,Kate Bushby,Hanns Lochmüller +18 more
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TLDR
RD-Connect is a global infrastructure project initiated in November 2012 that links genomic data with registries, biobanks, and clinical bioinformatics tools to produce a central research resource for rare diseases.Abstract:
Research into rare diseases is typically fragmented by data type and disease Individual efforts often have poor interoperability and do not systematically connect data across clinical phenotype, genomic data, biomaterial availability, and research/trial data sets Such data must be linked at both an individual-patient and whole-cohort level to enable researchers to gain a complete view of their disease and patient population of interest Data access and authorization procedures are required to allow researchers in multiple institutions to securely compare results and gain new insights Funded by the European Union's Seventh Framework Programme under the International Rare Diseases Research Consortium (IRDiRC), RD-Connect is a global infrastructure project initiated in November 2012 that links genomic data with registries, biobanks, and clinical bioinformatics tools to produce a central research resource for rare diseasesread more
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Journal ArticleDOI
The Human Phenotype Ontology in 2017
Sebastian Köhler,Nicole Vasilevsky,Mark Engelstad,Erin D. Foster,Julie A. McMurry,Ségolène Aymé,Gareth Baynam,Gareth Baynam,Susan M. Bello,Cornelius F. Boerkoel,Kym M. Boycott,Michael Brudno,Orion J. Buske,Patrick F. Chinnery,Valentina Cipriani,Laureen E. Connell,Hugh Dawkins,Laura E. DeMare,Andrew D. Devereau,Bert B.A. de Vries,Helen V. Firth,Kathleen Freson,Daniel Greene,Ada Hamosh,Ingo Helbig,Ingo Helbig,Courtney Hum,Johanna A. Jähn,Roger James,Roland Krause,Stanley J. F. Laulederkind,Hanns Lochmüller,Gholson J. Lyon,Soichi Ogishima,Annie Olry,Willem H. Ouwehand,Nikolas Pontikos,Ana Rath,Franz Schaefer,Richard H. Scott,Michael M. Segal,Panagiotis I. Sergouniotis,Richard Sever,Cynthia L. Smith,Volker Straub,Rachel Thompson,C. Turner,Ernest Turro,Marijcke W. M. Veltman,Tom Vulliamy,Jing Yu,Julie von Ziegenweidt,Andreas Zankl,Stephan Züchner,Tomasz Zemojtel,Julius O.B. Jacobsen,Tudor Groza,Damian Smedley,Christopher J. Mungall,Melissa A. Haendel,Peter N. Robinson +60 more
TL;DR: The progress of the HPO project is reviewed, including specific areas of expansion such as common (complex) disease, new algorithms for phenotype driven genomic discovery and diagnostics, integration of cross-species mapping efforts with the Mammalian Phenotype Ontology, an improved quality control pipeline, and the addition of patient-friendly terminology.
Journal ArticleDOI
Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources
Sebastian Köhler,Leigh C. Carmody,Nicole Vasilevsky,Julius O.B. Jacobsen,Daniel Danis,Jean-Philippe F. Gourdine,Michael A. Gargano,Nomi L. Harris,Nicolas Matentzoglu,Julie A. McMurry,David Osumi-Sutherland,Valentina Cipriani,James P. Balhoff,Tom Conlin,Hannah Blau,Gareth Baynam,Richard Palmer,Dylan Gratian,Hugh Dawkins,Michael M. Segal,Anna Jansen,Ahmed Muaz,Willie H. Chang,Jenna R.E. Bergerson,Stanley J. F. Laulederkind,Zafer Yüksel,Sergi Beltran,Alexandra F. Freeman,Panagiotis I. Sergouniotis,Daniel Durkin,Andrea L. Storm,Marc Hanauer,Michael Brudno,Susan M. Bello,Murat Sincan,Kayli Rageth,Matthew T. Wheeler,Renske Oegema,Halima Lourghi,Maria G. Della Rocca,Rachel Thompson,Francisco Castellanos,James R. Priest,Charlotte Cunningham-Rundles,Ayushi Hegde,Ruth C. Lovering,Catherine Hajek,Annie Olry,Luigi D. Notarangelo,Morgan Similuk,Xingmin Aaron Zhang,David Gómez-Andrés,Hanns Lochmüller,Hélène Dollfus,Sergio Rosenzweig,Shruti Marwaha,Ana Rath,Kathleen E. Sullivan,Cynthia L. Smith,Joshua D. Milner,Dorothée Leroux,Cornelius F. Boerkoel,Amy D. Klion,Melody C. Carter,Tudor Groza,Damian Smedley,Melissa A. Haendel,Melissa A. Haendel,Christopher J. Mungall,Peter N. Robinson +69 more
TL;DR: The HPO’s interoperability with other ontologies has enabled it to be used to improve diagnostic accuracy by incorporating model organism data and plays a key role in the popular Exomiser tool, which identifies potential disease-causing variants from whole-exome or whole-genome sequencing data.
Journal ArticleDOI
Exploiting machine learning for end-to-end drug discovery and development
Sean Ekins,Ana C. Puhl,Kimberley M. Zorn,Thomas J. Lane,Daniel P. Russo,Jennifer J. Klein,Anthony J. Hickey,Anthony J. Hickey,Alex M. Clark +8 more
TL;DR: The application of machine learning models in the design, synthesis and characterisation of molecules at different stages in the drug discovery and development process has considerable implications for developing future therapies and their targeting.
Journal ArticleDOI
International Cooperation to Enable the Diagnosis of All Rare Genetic Diseases.
Kym M. Boycott,Ana Rath,Jessica X. Chong,Taila Hartley,Fowzan S. Alkuraya,Gareth Baynam,Anthony J. Brookes,Michael Brudno,Angel Carracedo,Johan T. den Dunnen,Stephanie O.M. Dyke,Xavier Estivill,Jack Goldblatt,Catherine Gonthier,Stephen C. Groft,Ivo Gut,Ada Hamosh,Philip Hieter,Sophie Höhn,Matthew E. Hurles,Petra Kaufmann,Bartha Maria Knoppers,Jeffrey P. Krischer,Milan Macek,Gert Matthijs,Annie Olry,Samantha Parker,Justin Paschall,Anthony A. Philippakis,Heidi L. Rehm,Peter N. Robinson,Pak C. Sham,Rumen Stefanov,Domenica Taruscio,Divya Unni,Megan R. Vanstone,Feng Zhang,Han G. Brunner,Han G. Brunner,Michael J. Bamshad,Michael J. Bamshad,Hanns Lochmüller +41 more
TL;DR: The current and future bottlenecks to gene discovery are reviewed and strategies for enabling progress are suggested for enabling precision medicine for this patient population.
Journal ArticleDOI
Computational approaches in target identification and drug discovery
TL;DR: It is felt that big data leveraging needs to be cost-effective and focus on personalized medicine and the interplay of information technologies and (chemo)informatic tools on the basis of their synergy is proposed.
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The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data
Sebastian Köhler,Sandra C. Doelken,Christopher J. Mungall,Sebastian Bauer,Helen V. Firth,Helen V. Firth,Isabelle Bailleul-Forestier,Graeme C.M. Black,Danielle L. Brown,Michael Brudno,Jennifer Campbell,Jennifer Campbell,David R. FitzPatrick,Janan T. Eppig,Andrew P. Jackson,Kathleen Freson,Marta Girdea,Ingo Helbig,Jane A. Hurst,Johanna A. Jähn,Laird G. Jackson,Anne M. Kelly,David H. Ledbetter,Sahar Mansour,Christa Lese Martin,Celia Moss,Andrew D Mumford,Willem H. Ouwehand,Willem H. Ouwehand,Soo Mi Park,Erin Rooney Riggs,Richard H. Scott,Sanjay M. Sisodiya,Steven Van Vooren,Ronald J. Wapner,Andrew O.M. Wilkie,Caroline F. Wright,Anneke T. Vulto-van Silfhout,Nicole de Leeuw,Bert B.A. de Vries,Nicole L. Washingthon,Cynthia L. Smith,Monte Westerfield,Paul N. Schofield,Barbara J. Ruef,Georgios V. Gkoutos,Melissa A. Haendel,Damian Smedley,Suzanna E. Lewis,Peter N. Robinson,Peter N. Robinson +50 more
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