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Supplemental Data include 7 figures and 41 tables and can be found with this article online at http://dx.doi.org/10.1016/j.ajhg.2015.05.020. ; The Human Phenotype Ontology (HPO) is widely used in the rare disease community for differential diagnostics, phenotype-driven analysis of next-generation sequence-variation data, and translational research, but a comparable resource has not been available for common disease. Here, we have developed a concept-recognition procedure that analyzes the frequencies of HPO disease annotations as identified in over five million PubMed abstracts by employing an iterative procedure to optimize precision and recall of the identified terms. We derived disease models for 3,145 common human diseases comprising a total of 132,006 HPO annotations. The HPO now comprises over 250,000 phenotypic annotations for over 10,000 rare and common diseases and can be used for examining the phenotypic overlap among common diseases that share risk alleles, as well as between Mendelian diseases and common diseases linked by genomic location. The annotations, as well as the HPO itself, are freely available. ; This work was supported by the Bundesministerium für Bildung und Forschung (project 0313911), the European Commission Seventh Framework Programme (FP7; grant 602300; SYBIL project), the Raine Clinician Research Fellowship (20140101), and the National Health and Medical Research Council of Australia (grant APP1055319, which is partnered with FP7 grant 305444). Oregon Health and Science University acknowledges the support of grant 1R24OD011883-01 from the NIH Office of the Director. T.G. was supported by an Australian Research Council Discovery Early Career Researcher Award (DE120100508). D.V. was supported in part by the BioMedBridges project funded by Research Infrastructures of the FP7 (grant 284209). H.P. was supported by European Molecular Biology Laboratory Core Funds. This work was supported by the director, Basic Energy Sciences, Office of Science, US Department of Energy under contract DE-AC02-05CH11231 and NIH contract 1R24OD011883-01. This document was prepared as an account of work sponsored by the US Government. ; Peer-reviewed ; Publisher Version

National Institutes of Health (NIH) Monarch Initiative [NIH OD #5R24OD011883]; E-RARE 2015 program, Hipbi-RD (harmonizing phenomics information for a better interoperability in the RD field); Director, Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy under [DE-AC02-05CH11231]; Bundesministerium f ¨ur Bildung und Forschung (BMBF) [0313911]; Raine Clinician Research Fellowship (to G.B.); Stanley Institute for Cognitive Genomics at Cold Spring Harbor Laboratory (CSHL to G.J.L.); European Union Seventh Framework Programme [FP7/2007-2013] supported RD-Connect [305444], EURenOmics [2012-305608] and NeurOmics [2012-305121]; Fight for Sight and Retinitis Pigmentosa Fighting Blindness (to N.P.); National Institute for Health Research Biomedical Research Centre at Moorfields Eye Hospital National Health Service Foundation Trust and UCL Institute of Ophthalmology (UK) (to V.C.); University of Kiel, by a grant from the German Research Foundation [HE5415/3-1 to I.H.] within the EuroEPINOMICS framework of the European Science Foundation and grants of the German Research Foundation [DFG, HE5415/5-1, HE5415/6-1], German Ministry for Education and Research [01DH12033, MAR 10/012] and by the German chapter of the International League against Epilepsy (DGfE); International League Against Epilepsy (ILAE to I.H.) within the Epilepsiome initiative of the ILAE Genetics Commission (www.channelopathist. net); National Library of Medicine [R44 LM011585-02 to M.S.]. BBAdV is funded by the Dutch Organisation for Health Research and Development (ZON-MW grants 912-12-109). Funding for open access charge: NIH [R24- OD011883]