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Functional Analysis of Alleged NOGGIN Mutation G92E Disproves Its Pathogenic Relevance

Julia Zimmer, Sandra C. Doelken, Denise Horn, Jay C. Groppe, Eileen M. Shore, Frederick S. Kaplan, Petra Seemann, Andreas R. Janecke
2012 PLoS ONE  
Photographs of hands (B) and feet (C) were taken after the surgical correction, at the age of 22 months.  ...  Chicken micromass cells were infected with 1*10e07 viral particles/ml containing the gene for BMP2 (A), Bmp4 (B), Bmp7 (C) or GDF5 (D).  ... 
doi:10.1371/journal.pone.0035062 pmid:22529972 pmcid:PMC3329551 fatcat:wa4wvyj3zzfxxcg2jjwr45cfze

MouseFinder: Candidate disease genes from mouse phenotype data

Chao-Kung Chen, Christopher J. Mungall, Georgios V. Gkoutos, Sandra C. Doelken, Sebastian Köhler, Barbara J. Ruef, Cynthia Smith, Monte Westerfield, Peter N. Robinson, Suzanna E. Lewis, Paul N. Schofield, Damian Smedley
2012 Human Mutation  
In addition, PhenomeNET also covers yeast, zebrafish, C. elegans and Drosophila phenotypes, and does not have the overhead of running the pairwise phenotype comparisons and storing the results in a database  ... 
doi:10.1002/humu.22051 pmid:22331800 pmcid:PMC3327758 fatcat:ntsdkmtgbffxhb36zx5tn3pmt4

Clinical interpretation of CNVs with cross-species phenotype data

Sebastian Köhler, Uwe Schoeneberg, Johanna Christina Czeschik, Sandra C Doelken, Jayne Y Hehir-Kwa, Jonas Ibn-Salem, Christopher J Mungall, Damian Smedley, Melissa A Haendel, Peter N Robinson
2014 Journal of Medical Genetics  
Background-Clinical evaluation of CNVs identified via techniques such as array comparative genome hybridisation (aCGH) involves the inspection of lists of known and unknown duplications and deletions with the goal of distinguishing pathogenic from benign CNVs. A key step in this process is the comparison of the individual's phenotypic abnormalities with those associated with Mendelian disorders of the genes affected by the CNV. However, because often there is not much known about these human
more » ... es, an additional source of data that could be used is model organism phenotype data. Currently, almost 6000 genes in mouse and zebrafish are, when knocked out, associated with a phenotype in the model organism, but no disease is known to be caused by mutations in the human ortholog. Yet, searching model organism databases and comparing model organism phenotypes with patient phenotypes for identifying novel disease genes and medical evaluation of CNVs is hindered by the difficulty in integrating phenotype information across species and the lack of appropriate software tools. Methods-Here, we present an integrated ranking scheme based on phenotypic matching, degree of overlap with known benign or pathogenic CNVs and the haploinsufficiency score for the prioritisation of CNVs responsible for a patient's clinical findings. Results-We show that this scheme leads to significant improvements compared with rankings that do not exploit phenotypic information. We provide a software tool called PhenogramViz, which supports phenotype-driven interpretation of aCGH findings based on multiple data sources, including the integrated cross-species phenotype ontology Uberpheno, in order to visualise geneto-phenotype relations.
doi:10.1136/jmedgenet-2014-102633 pmid:25280750 pmcid:PMC4501634 fatcat:dcxpgg3ihbgbjlat2hup77pkhq

A GDF5 Point Mutation Strikes Twice - Causing BDA1 and SYNS2

Elisa Degenkolbe, Jana König, Julia Zimmer, Maria Walther, Carsten Reißner, Joachim Nickel, Frank Plöger, Jelena Raspopovic, James Sharpe, Katarina Dathe, Jacqueline T. Hecht, Stefan Mundlos (+3 others)
2013 PLoS Genetics  
Signaling activities were determined in NIH/3T3 cells using a Smad Binding Element (SBE) luciferase reporter gene assay ( Figure 4A -C).  ...  C: Co-expression of Bmpr1b further increased the signaling activity of wild type GDF5 and GDF5 E491K compared to co-expression with Bmpr1a.  ... 
doi:10.1371/journal.pgen.1003846 pmid:24098149 pmcid:PMC3789827 fatcat:irb64eot6zg35gt2iokjhsdkqy

Construction and accessibility of a cross-species phenotype ontology along with gene annotations for biomedical research

Sebastian Köhler, Sandra C Doelken, Barbara J Ruef, Sebastian Bauer, Nicole Washington, Monte Westerfield, George Gkoutos, Paul Schofield, Damian Smedley, Suzanna E Lewis, Peter N Robinson, Christopher J Mungall
2013 F1000Research  
Construction and accessibility of a cross-species phenotype ontology along with gene annotations for biomedical research. F1000Research, 2, [30].
doi:10.3410/f1000research.2-30.v1 fatcat:v4uquzeugvfr3b6qen4jpswkyy

Construction and accessibility of a cross-species phenotype ontology along with gene annotations for biomedical research

Sebastian Köhler, Sandra C Doelken, Barbara J Ruef, Sebastian Bauer, Nicole Washington, Monte Westerfield, George Gkoutos, Paul Schofield, Damian Smedley, Suzanna E Lewis, Peter N Robinson, Christopher J Mungall
2014 F1000Research  
Construction and accessibility of a cross-species phenotype ontology along with gene annotations for biomedical research. F1000Research, 2, [30].
doi:10.12688/f1000research.2-30.v2 pmid:24358873 pmcid:PMC3799545 fatcat:267pqfzlvjfmxlz6xpel6qwtgu

Construction and accessibility of a cross-species phenotype ontology along with gene annotations for biomedical research

Sebastian Köhler, Sandra C Doelken, Barbara J Ruef, Sebastian Bauer, Nicole Washington, Monte Westerfield, George Gkoutos, Paul Schofield, Damian Smedley, Suzanna E Lewis, Peter N Robinson, Christopher J Mungall
2013 F1000Research  
Köhler S, Doelken SC, Rath A, et al.: Ontological phenotype standards for neurogenetics. Hum Mutat. 2012; 33(9): 1333-1339. PubMed Abstract | Publisher Full Text 15.  ...  F1000Research Sebastian Köhler ( ), Christopher J Mungall ( ) Corresponding authors: sebastian.koehler@charite.de CJMungall@lbl.gov Köhler S, Doelken SC, Ruef BJ How to cite this article: et al.  ... 
doi:10.12688/f1000research.2-30.v1 pmid:24358873 pmcid:PMC3799545 fatcat:wraclszcvrfbddvhdqdflkj7zq

Homozygous missense and nonsense mutations in BMPR1B cause acromesomelic chondrodysplasia-type Grebe

Luitgard M Graul-Neumann, Alexandra Deichsel, Ulrike Wille, Naseebullah Kakar, Randi Koll, Christian Bassir, Jamil Ahmad, Valerie Cormier-Daire, Stefan Mundlos, Christian Kubisch, Guntram Borck, Eva Klopocki (+3 others)
2013 European Journal of Human Genetics  
The nonsense mutation (c.657G4A, p.  ...  Here, we present two consanguineous families with missense (c.157T4C, p.(C53R)) or nonsense (c.657G4A, p.(W219*)) mutations in BMPR1B.  ...  The nonsense mutation c.657G4A, p.  ... 
doi:10.1038/ejhg.2013.222 pmid:24129431 pmcid:PMC4023204 fatcat:lrnfr6pfkvcnnirjhlq7snrboy

Deletions of exons with regulatory activity at the DYNC1I1 locus are associated with split-hand/split-foot malformation: array CGH screening of 134 unrelated families

Naeimeh Tayebi, Aleksander Jamsheer, Ricarda Flöttmann, Anna Sowinska-Seidler, Sandra C Doelken, Barbara Oehl-Jaschkowitz, Wiebke Hülsemann, Rolf Habenicht, Eva Klopocki, Stefan Mundlos, Malte Spielmann
2014 Orphanet Journal of Rare Diseases  
The father of the proband shows central ray deficiency of the hands (c) and right foot (d). The aunt of the proband presents milder phenotype on the left hand (e) and feet (f).  ... 
doi:10.1186/s13023-014-0108-6 pmid:25231166 pmcid:PMC4237947 fatcat:zlqrzbv32zhutn7otovjwwfyne

Getting Ready for the Human Phenome Project: The 2012 Forum of the Human Variome Project

William S. Oetting, Peter N. Robinson, Marc S. Greenblatt, Richard G. Cotton, Tim Beck, John C. Carey, Sandra C. Doelken, Marta Girdea, Tudor Groza, Carol M. Hamilton, Ada Hamosh, Berit Kerner (+11 others)
2013 Human Mutation  
On this, Sandra Doelken, of the Institute of Medical Genetics and Human Genetics at Charité Universitätsmedizin Berlin, spoke on "Phenotypic overlap in the contribution of individual genes to CNV pathogenicity  ...  To do this computationally, one needs ontologies containing logical definitions of phenotypes of the different species along with automated reasoning and integration of data [Doelken et al., 2013] .  ... 
doi:10.1002/humu.22293 pmid:23401191 pmcid:PMC4130157 fatcat:olvqoha4mrcstgbq23cpufuhka

Duplications ofBHLHA9are associated with ectrodactyly and tibia hemimelia inherited in non-Mendelian fashion

Eva Klopocki, Silke Lohan, Sandra C Doelken, Sigmar Stricker, Charlotte W Ockeloen, Renata Soares Thiele de Aguiar, Karina Lezirovitz, Regina Celia Mingroni Netto, Aleksander Jamsheer, Hitesh Shah, Ingo Kurth, Rolf Habenicht (+11 others)
2011 Journal of Medical Genetics  
A scoring system that quantifies the degree of pathology in each limb was applied ( figure 1B,C) .  ...  In addition, sex distribution in healthy carriers (C) is shown. +/+ À/À À /À v + / À e 2 N A N A N A N A + N A 3 +/+ +/+ À/À À /À +/+ e 4 +/+ À/+ À/À À /À À /À e 5 +/+ +/À v À/À +/À e 6 N A N A N A N  ... 
doi:10.1136/jmedgenet-2011-100409 pmid:22147889 fatcat:44kxjcp25jgcrihjnxfdzprd24

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, Isabelle Bailleul-Forestier, Graeme C. M. Black, Danielle L. Brown, Michael Brudno, Jennifer Campbell, David R. FitzPatrick, Janan T. Eppig (+35 others)
2013 Nucleic Acids Research  
The Human Phenotype Ontology (HPO) project, available at http://www.human-phenotype-ontology.org, provides a structured, comprehensive and welldefined set of 10,088 classes (terms) describing human phenotypic abnormalities and 13,326 subclass relations between the HPO classes. In addition we have developed logical definitions for 46% of all HPO classes using terms from ontologies for anatomy, cell types, function, embryology, pathology and other domains. This allows interoperability with
more » ... resources, especially those containing phenotype information on model organisms such as mouse and zebrafish. Here we describe the updated HPO database, which provides annotations of 7,278 human hereditary syndromes listed in OMIM, Orphanet and DECIPHER to classes of the HPO. Various meta-attributes such as frequency, references and negations are associated with each annotation. Several large-scale projects worldwide utilize the HPO for describing phenotype information in their datasets. We have therefore generated equivalence mappings to other phenotype vocabularies such as LDDB, Orphanet, MedDRA, UMLS and phenoDB, allowing integration of existing datasets and interoperability with multiple biomedical resources. We have created various ways to access the HPO database content using flat files, a MySQL database, and Web-based tools. All data and documentation on the HPO project can be found online.
doi:10.1093/nar/gkt1026 pmid:24217912 pmcid:PMC3965098 fatcat:p2ubynvoprbopaeyoboloexzcq

Functional transcriptomics in the post-ENCODE era

J. M. Mudge, A. Frankish, J. Harrow
2013 Genome Research  
Ibrahim, Peter Hansen, Christian Rödelsperger, Asita C. Stiege, Sandra C.  ...  Marinov, Jason Ernst, Manolis Kellis, Ross C. Hardison, Richard M. Myers, and Barbara J.  ... 
doi:10.1101/gr.161315.113 pmid:24172201 pmcid:PMC3847767 fatcat:ahxn3sld2jaqtj7vacuee74m4e

Identity-by-descent filtering of exome sequence data identifies PIGV mutations in hyperphosphatasia mental retardation syndrome

Peter M Krawitz, Michal R Schweiger, Christian Rödelsperger, Carlo Marcelis, Uwe Kölsch, Christian Meisel, Friederike Stephani, Taroh Kinoshita, Yoshiko Murakami, Sebastian Bauer, Melanie Isau, Axel Fischer (+17 others)
2010 Nature Genetics  
[Ala341Glu]+[His385Pro] in family B, c.[766C>A]+[766C>A]; p.[Gln256Lys]+[Gln256Lys] in family C, and c.[1022C>A]+[1022C>T]; p.[Ala341Glu]+[Ala341Val] in family D.  ...  b r i e f c o m m u n i c a t i o n s Hyperphosphatasia mental retardation (HPMR) syndrome is an autosomal recessive form of mental retardation with distinct facial features and elevated serum alkaline  ... 
doi:10.1038/ng.653 pmid:20802478 fatcat:2ezc7jveu5hmbm35xteiaut7q4

Automatic concept recognition using the Human Phenotype Ontology reference and test suite corpora

T. Groza, S. Kohler, S. Doelken, N. Collier, A. Oellrich, D. Smedley, F. M. Couto, G. Baynam, A. Zankl, P. N. Robinson
2015 Database: The Journal of Biological Databases and Curation  
Furthermore, we developed a V C The Author(s)  ...  ., Doelken,S., et al. Automatic concept recognition using the Human Phenotype Ontology reference and test suite corpora.  ...  Sandra Dö lken). The clinical validity of the annotations has been ensured by two of the team members-i.e. Prof. Peter Robinson and Dr.  ... 
doi:10.1093/database/bav005 pmid:25725061 pmcid:PMC4343077 fatcat:6bc3qcxskfbybaevdtjc3u5nra
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