ArticleAmerican journal of human genetics2020
Semantic Similarity Analysis Reveals Robust Gene-Disease Relationships in Developmental and Epileptic Encephalopathies.
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Article in American journal of human genetics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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24 citing papers in PubMed, 44 citations in OpenAlex.
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- Enriching representation learning using 53 million patient notes through human phenotype ontology embedding.Artificial intelligence in medicine · 2023Article
- Investigating the genetic contribution in febrile infection-related epilepsy syndrome and refractory status epilepticus.Frontiers in neurology · 2023Article
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- Phenotypic homogeneity in childhood epilepsies evolves in gene-specific patterns across 3251 patient-years of clinical data.European journal of human genetics : EJHG · 2021Article
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Authors and funding
22 authors at 6 institutions in 4 countries.
Peter D GalerDivision of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Biomedical and Health Informatics (DBHi), Children's Hospital of Philadelphia, Philadelphia, PA 19146, USA.
Shiva GanesanDivision of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Biomedical and Health Informatics (DBHi), Children's Hospital of Philadelphia, Philadelphia, PA 19146, USA.
David Lewis-SmithTranslational and Clinical Research Institute, Newcastle University, Newcastle-upon-Tyne NE1 7RU, UK; Royal Victoria Infirmary, Newcastle-upon-Tyne NE1 4LP, UK.
Sarah E McKeownDivision of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
Manuela PendziwiatDepartment of Neuropediatrics, Christian-Albrechts-University of Kiel, 24105 Kiel, Germany.
Katherine L HelbigDivision of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Biomedical and Health Informatics (DBHi), Children's Hospital of Philadelphia, Philadelphia, PA 19146, USA.
Colin A EllisThe Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Neurology, University of Pennsylvania, Philadelphia, PA 19104, USA.
Annika RademacherDepartment of Neuropediatrics, Christian-Albrechts-University of Kiel, 24105 Kiel, Germany.
Lacey SmithEpilepsy Genetics Program, Department of Neurology, Boston Children's Hospital, Boston, MA 02115, USA.
Annapurna PoduriEpilepsy Genetics Program, Department of Neurology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Neurology, Harvard Medical School, Boston, MA 02115, USA.
Simone SeiffertDepartment of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, 72076 Tübingen, Germany.
Sarah von SpiczakDepartment of Neuropediatrics, Christian-Albrechts-University of Kiel, 24105 Kiel, Germany; DRK-Northern German Epilepsy Centre for Children and Adolescents, 24223 Schwentinental-Raisdorf, Germany.
Hiltrud MuhleDepartment of Neuropediatrics, Christian-Albrechts-University of Kiel, 24105 Kiel, Germany.
Andreas van BaalenDepartment of Neuropediatrics, Christian-Albrechts-University of Kiel, 24105 Kiel, Germany.
NCEE Study Group
EPGP Investigators
EuroEPINOMICS-RES Consortium
Genomics Research and Innovation Network
Rhys H ThomasTranslational and Clinical Research Institute, Newcastle University, Newcastle-upon-Tyne NE1 7RU, UK; Royal Victoria Infirmary, Newcastle-upon-Tyne NE1 4LP, UK.
Roland KrauseLuxembourg Centre for Systems Biomedicine, University of Luxembourg, 4367 Belvaux, Luxembourg.
Yvonne WeberDepartment of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, 72076 Tübingen, Germany; Department of Epileptology and Neurology, University of Aachen, 52074 Aachen, Germany.
Ingo HelbigDivision of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Biomedical and Health Informatics (DBHi), Children's Hospital of Philadelphia, Philadelphia, PA 19146, USA; Department of Neurology, University of Pennsylvania, Philadelphia, PA 19104, USA. Electronic address: helbigi@email.chop.edu.
Children's Hospital of Philadelphia · USChristian-Albrechts-Universität zu Kiel · DEBoston Children's Hospital · USHertie Institute for Clinical Brain Research · DERoyal Victoria Infirmary · GBUniversity of Luxembourg · LU
Funding
Phenotypic Diversity in COVID-19UL1TR001878 · NCATS · UNIVERSITY OF PENNSYLVANIA · PI FITZGERALD, GARRET A · 2016 to 2025
$102.4MProject 3 - Development and investigation of murine models of channelopathy-associated epilepsyU54NS108874 · NINDS · NORTHWESTERN UNIVERSITY AT CHICAGO · PI KISKINIS, EVANGELOS · 2018 to 2022
$12.1MThe Intellectual and Developmental Disabilities Research Center (IDDRC) at CHOP/PennP50HD105354 · NICHD · CHILDREN'S HOSP OF PHILADELPHIA · PI ERIC D MARSH, ROBERT Thomas SCHULTZ · 2021 to 2026
$9.2MThe Intellectual and Developmental Disabilities Research Center at CHOP/PennU54HD086984 · NICHD · CHILDREN'S HOSP OF PHILADELPHIA · PI YUDKOFF, MARC · 2016 to 2020
$6.3MMouse Neurodevelopmental Behavior CoreU54HD090255 · NICHD · BOSTON CHILDREN'S HOSPITAL · PI SAHIN, MUSTAFA · 2016 to 2020
$5.2MRemapping neurology through translation and innovationT32NS091008 · NINDS · UNIVERSITY OF PENNSYLVANIA · PI AGUIRRE, GEOFFREY KARL, JENSEN, FRANCES E · 2015 to 2024
$3.0MJoint analysis of genomic and electronic medical record data to assess outcomes and drug response in pediatric epilepsiesK02NS112600 · NINDS · CHILDREN'S HOSP OF PHILADELPHIA · PI HELBIG, INGO · 2020 to 2024
$963kNCATS NIH HHS UL1 TR001878NICHD NIH HHS P50 HD105354NICHD NIH HHS U54 HD086984NICHD NIH HHS U54 HD090255NINDS NIH HHS K02 NS112600NINDS NIH HHS T32 NS091008NINDS NIH HHS U54 NS108874Wellcome Trust
Abstract
More than 100 genetic etiologies have been identified in developmental and epileptic encephalopathies (DEEs), but correlating genetic findings with clinical features at scale has remained a hurdle because of a lack of frameworks for analyzing heterogenous clinical data. Here, we analyzed 31,742 Human Phenotype Ontology (HPO) terms in 846 individuals with existing whole-exome trio data and assessed associated clinical features and phenotypic relatedness by using HPO-based semantic similarity analysis for individuals with de novo variants in the same gene. Gene-specific phenotypic signatures included associations of SCN1A with "complex febrile seizures" (HP: 0011172; p = 2.1 × 10
Indexed as
Child, PreschoolCohort StudiesExome SequencingFemaleGABA Plasma Membrane Transport ProteinsGene ExpressionGene OntologyHumansMaleMunc18 ProteinsMutationNAV1.1 Voltage-Gated Sodium ChannelPhenotypeSeizuresSemanticsShab Potassium ChannelsGABA Plasma Membrane Transport ProteinsKCNB1 protein, humanMunc18 ProteinsNAV1.1 Voltage-Gated Sodium ChannelSCN1A protein, humanShab Potassium ChannelsSLC6A1 protein, humanSTXBP1 protein, humanchildhood epilepsiescomputational phenotypesdevelopmental and epileptic encephalopathieselectronic medical recordsHuman Phenotype Ontologyneurogenetic disorderswhole-exome sequencing
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