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Vulpius SA, Werge S, Jørgensen IF, Siggaard T, Hernansanz Biel J, Knudsen GM, Brunak S, Pinborg LH. Text mining of electronic health records can validate a register-based diagnosis of epilepsy and subgroup into focal and generalized epilepsy. Epilepsia 2023; 64:2750-2760. [PMID: 37548470 DOI: 10.1111/epi.17734] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 08/01/2023] [Accepted: 08/01/2023] [Indexed: 08/08/2023]
Abstract
OBJECTIVE Combining population-based health registries and electronic health records offers the opportunity to create large, phenotypically detailed patient cohorts of high quality. In this study, we used text mining of clinical notes to confirm International Classification of Diseases, 10th Revision (ICD-10)-registered epilepsy diagnoses and classify patients according to focal and generalized epilepsy types. METHODS Using the Danish National Patient Registry, we identified patients who between 2006 and 2016 received an ICD-10 diagnosis of epilepsy. To validate the epilepsy diagnosis and stratify patients into focal and generalized epilepsy types, we constructed dictionaries for text mining-based extraction of clinical notes. Two physicians manually reviewed the clinical notes for a total of 527 patients and assigned epilepsy diagnoses, which were compared with the text-mined diagnoses. RESULTS We identified 23 632 patients with an ICD-10 diagnosis of epilepsy, of whom 50% were registered with an unspecified epilepsy diagnosis. In total, 11 211 patients were considered likely to have epilepsy by text mining, with an F1 measure ranging from 82% to 90%. Manual review of the electronic health records for 310 patients revealed a false discovery rate of 29%. This rate was decreased to 4% by the text mining algorithm. The weighted average F1 measure for text mining-assigned epilepsy types was 79% (82% for focal and 76% for generalized epilepsy). Text mining successfully assigned a focal or generalized epilepsy type to 92% of the text mining-eligible patients registered with unspecified epilepsy. SIGNIFICANCE Text mining of electronic health records can be used to establish a patient cohort with much higher likelihood of having a diagnosis of epilepsy and a focal or generalized epilepsy type compared to the cohort created from ICD-10 epilepsy codes alone. We believe the concept will be essential for future genome-wide and phenome-wide association studies and subsequently the development of precision medicine for epilepsy patients.
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Affiliation(s)
- Siri A Vulpius
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Sebastian Werge
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Isabella Friis Jørgensen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Troels Siggaard
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Jorge Hernansanz Biel
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Gitte M Knudsen
- Epilepsy Clinic and Neurobiology Research Unit, University Hospital Rigshospitalet, Copenhagen, Denmark
- Institute for Clinical Medicine, Faculty of Health and Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Lars H Pinborg
- Epilepsy Clinic and Neurobiology Research Unit, University Hospital Rigshospitalet, Copenhagen, Denmark
- Institute for Clinical Medicine, Faculty of Health and Medicine, University of Copenhagen, Copenhagen, Denmark
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Oja KT, Ilisson M, Reinson K, Muru K, Reimand T, Peterson H, Fishman D, Esko T, Haller T, Kronberg J, Wojcik MH, Kennedy A, Michelotti G, O’Donnell-Luria A, Õiglane-Šlik E, Pajusalu S, Õunap K. Untargeted metabolomics profiling in pediatric patients and adult populations indicates a connection between lipid imbalance and epilepsy. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.29.23287640. [PMID: 37034709 PMCID: PMC10081398 DOI: 10.1101/2023.03.29.23287640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
Introduction Epilepsy is a common central nervous system disorder characterized by abnormal brain electrical activity. We aimed to compare the metabolic profiles of plasma from patients with epilepsy across different etiologies, seizure frequency, seizure type, and patient age to try to identify common disrupted pathways. Material and methods We used data from three separate cohorts. The first cohort (PED-C) consisted of 31 pediatric patients with suspicion of a genetic disorder with unclear etiology; the second cohort (AD-C) consisted of 250 adults from the Estonian Biobank (EstBB), and the third cohort consisted of 583 adults ≥ 69 years of age from the EstBB (ELD-C). We compared untargeted metabolomics and lipidomics data between individuals with and without epilepsy in each cohort. Results In the PED-C, significant alterations (p-value <0.05) were detected in sixteen different glycerophosphatidylcholines (GPC), dimethylglycine and eicosanedioate (C20-DC). In the AD-C, nine significantly altered metabolites were found, mainly triacylglycerides (TAG), which are also precursors in the GPC synthesis pathway. In the ELD-C, significant changes in twenty metabolites including multiple TAGs were observed in the metabolic profile of participants with previously diagnosed epilepsy. Pathway analysis revealed that among the metabolites that differ significantly between epilepsy-positive and epilepsy-negative patients in the PED-C, the lipid superpathway (p = 3.2*10-4) and phosphatidylcholine (p = 9.3*10-8) and lysophospholipid (p = 5.9*10-3) subpathways are statistically overrepresented. Analogously, in the AD-C, the triacylglyceride subclass turned out to be statistically overrepresented (p = 8.5*10-5) with the lipid superpathway (p = 1.4*10-2). The presented p-values are FDR-corrected. Conclusion Our results suggest that cell membrane fluidity may have a significant role in the mechanism of epilepsy, and changes in lipid balance may indicate epilepsy. However, further studies are needed to evaluate whether untargeted metabolomics analysis could prove helpful in diagnosing epilepsy earlier.
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Affiliation(s)
- Kaisa Teele Oja
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
- Department of Clinical Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia
| | - Mihkel Ilisson
- Department of Clinical Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia
| | - Karit Reinson
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
- Department of Clinical Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia
| | - Kai Muru
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
- Department of Clinical Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia
| | - Tiia Reimand
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
- Department of Clinical Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia
| | - Hedi Peterson
- Institute of Computer Science, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Dmytro Fishman
- Institute of Computer Science, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Tõnu Esko
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Toomas Haller
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Jaanika Kronberg
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Monica H. Wojcik
- Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, Boston, MA, USA
- Division of Newborn Medicine, Department of Pediatrics, Boston Children’s Hospital, Boston, MA, USA
| | - Adam Kennedy
- Metabolon, 615 Davis Drive, Suite 100, Morrisville, NC, USA
| | | | - Anne O’Donnell-Luria
- Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, Boston, MA, USA
| | - Eve Õiglane-Šlik
- Department of Pediatrics, Institute of Clinical Medicine, Faculty of Medicine, University of Tartu
- Children’s Clinic of Tartu University Hospital, Tartu University Hospital
| | - Sander Pajusalu
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
- Department of Clinical Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia
| | - Katrin Õunap
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
- Department of Clinical Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia
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Ayele BA, Belay HD, Oda DM, Gelan YD, Negash HA, Kifelew S, Gebrewold MA, Hagos T, Zewde YZ, Yifru YM, Tsehayneh F, Amare A, Moges A, Gugssa SA, Mengesha AT. Electroencephalographic Findings, Antiepileptic Drugs and Risk Factors of 433 Individuals Referred to a Tertiary Care Hospital in Ethiopia. Ethiop J Health Sci 2022; 32:905-912. [PMID: 36262703 PMCID: PMC9554775 DOI: 10.4314/ejhs.v32i5.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 05/15/2022] [Indexed: 11/17/2022] Open
Abstract
Background Little is known about the characteristics of electroencephalogram (EEG) findings in epileptic patients in Ethiopia. The objective of this study was to characterize the EEG patterns, indications, antiepileptic drugs (AEDs), and epilepsy risk factors. Methods A retrospective observational review of EEG test records of 433 patients referred to our electrophysiology unit between July 01, 2020 and December 31, 2021. Results The age distribution in the study participants was right skewed unipolar age distribution for both sexes and the mean age of 33.8 (SD=15.7) years. Male accounted for 51.7%. Generalized tonic clonic seizure was the most common seizure type. The commonest indication for EEG was abnormal body movement with loss of consciousness (35.2%). Abnormal EEG findings were observed in 55.2%; more than half of them were Interictal epileptiform discharges, followed by focal/or generalized slowing. Phenobarbitone was the commonest AEDs. A quarter (20.1%) of the patients were getting a combination of two AEDs and 5.2% were on 3 different AEDs. Individuals taking the older AEDs and those on 2 or more AEDs tended to have abnormal EEG findings. A cerebrovascular disorder (27.4%) is the prevalent risk factor identified followed by brain tumor, HIV infection, and traumatic head injury respectively. Conclusions High burden of abnormal EEG findings among epileptic patients referred to our unit. The proportion of abnormal EEG patterns was higher in patients taking older generation AEDs and in those on 2 or more AEDs. Stroke, brain tumor, HIV infection and traumatic head injury were the commonest identified epilepsy risk factors.
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Affiliation(s)
- Biniyam A Ayele
- Department of Neurology, College of Health Science, Addis Ababa University
| | | | - Dereje Melka Oda
- Department of Neurology, College of Health Science, Addis Ababa University
| | - Yohannes D Gelan
- Department of Neurology, College of Health Science, Addis Ababa University
| | | | - Selam Kifelew
- Department of Neurology, College of Health Science, Addis Ababa University
| | | | - Teklil Hagos
- Department of Neurology, College of Health Science, Addis Ababa University
| | - Yared Z Zewde
- Department of Neurology, College of Health Science, Addis Ababa University
| | | | - Fikru Tsehayneh
- Department of Neurology, College of Health Science, Addis Ababa University
| | - Amanuel Amare
- Department of Neurology, College of Health Science, Addis Ababa University
| | - Ayalew Moges
- Department of Paediatrics and Child Health, College of Health Science, Addis Ababa University
| | - Seid Ali Gugssa
- Department of Neurology, College of Health Science, Addis Ababa University
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Yang C, Shi Y, Li X, Guan L, Li H, Lin J. Cadherins and the pathogenesis of epilepsy. Cell Biochem Funct 2022; 40:336-348. [PMID: 35393670 DOI: 10.1002/cbf.3699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 02/22/2022] [Accepted: 03/12/2022] [Indexed: 12/13/2022]
Abstract
Epilepsy is a nervous system disease caused by abnormal discharge of brain neurons, which is characterized by recurrent seizures. The factors that induce epilepsy include genetic and environmental factors. Genetic factors are important pathogenic factors of epilepsy, such as epilepsy caused by protocadherin-19 (PCDH-19) mutation, which is an X-linked genetic disease. It is more common in female heterozygotes, which are caused by mutations in the PCDH-19 gene. Epilepsy caused by environmental factors is mainly caused by brain injury, which is commonly caused by brain tumors, brain surgery, or trauma to the brain. In addition, the pathogenesis of epilepsy is closely related to abnormalities in some signaling pathways. The Wnt/β-catenin signaling pathway is considered a new target for the treatment of epilepsy. This review summarizes these factors inducing epilepsy and the research hypotheses regarding the pathogenesis of epilepsy. The focus of this review centers on cadherins and the pathogenesis of epilepsy. We analyzed the pathogenesis of epilepsy induced by N-cadherin and PCDH-19 in the cadherin family members. Finally, we expect that in the future, new breakthroughs will be made in the study of the pathogenesis and mechanism of epilepsy at the cellular and molecular levels.
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Affiliation(s)
- Ciqing Yang
- Stem Cells & Biotherapy Engineering Research Center of Henan, College of Life Science and Technology, Xinxiang Medical University, Xinxiang, China.,Henan Key Laboratory of Medical Tissue Regeneration, Xinxiang, China
| | - Yaping Shi
- Stem Cells & Biotherapy Engineering Research Center of Henan, College of Life Science and Technology, Xinxiang Medical University, Xinxiang, China
| | - Xiaoying Li
- Stem Cells & Biotherapy Engineering Research Center of Henan, College of Life Science and Technology, Xinxiang Medical University, Xinxiang, China
| | - Lihong Guan
- Stem Cells & Biotherapy Engineering Research Center of Henan, College of Life Science and Technology, Xinxiang Medical University, Xinxiang, China
| | - Han Li
- Stem Cells & Biotherapy Engineering Research Center of Henan, College of Life Science and Technology, Xinxiang Medical University, Xinxiang, China
| | - Juntang Lin
- Stem Cells & Biotherapy Engineering Research Center of Henan, College of Life Science and Technology, Xinxiang Medical University, Xinxiang, China.,Henan Key Laboratory of Medical Tissue Regeneration, Xinxiang, China
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