Phenotype linkages to NMD common data elements
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1 TREAT-NMD Global Database Oversight Committee and Curators Meeting 19 th -20th September Leuven, Belgium Phenotype linkages to NMD common data elements Prof. C. Béroud & Dr. D. Salgado "Genetics and Bioinformatics" research team Inserm UMR_S910, Marseille, France
2 Background Promote interoperability between registries in general Matchmaker Exchange (mainly genetics) GA4GH HPO, Orphanet, OMIM International Consortium for Human Phenotype Terminologies (ICHPT) Orphanet, HPO, OMIM ICHPT mapping between the core set of terms in HPO, PhenoDB, Orphanet, Elements of Morphology, MeSH, POSSUM, SNOMED and MeDRA
3 Goals ➊ Use data from existing national and international reference registries ➋ Evaluate the possibility to ontologize those existing registries ➌ Select the most relevant ontologies
4 Materials & Methods Materials The International TREAT-NMD DMD registry: The international Dysferlinopathies registry: The French FSHD registry:
5 Materials & Methods Materials The International TREAT-NMD DMD registry: Contains 23 items in English The international Dysferlinopathies registry: Contains 34 items in English The French FSHD registry: Contains 66 items in French
6 Materials & Methods Example of the TREAT-NMD items
7 Materials & Methods Example of the TREAT-NMD items
8 Materials & Methods Methods Translate all items in English Identify true "clinical items", which could be ontologized Search the BioPortal website: Select only a subset of relevant ontologies for genetics diseases
9 TREAT-NMD DMD registry 23 items 16 clinical items Walking Sitting Wheelchair Wheelchair age Steroids Scoliosis surgery Current cardiac medication Cardiac medication Clinical trial Date of birth Follow-up date Zip code Cardiomyopathy Ultrasound (cardiac) Last LVEF LVEF date Non invasive ventilation Invasive ventilation FVC Last FVC Date Muscle biopsy Other registries Other family members
10 TREAT-NMD DMD registry 23 items 16 clinical items The international Dysferlinopathies registry 34 items 29 clinical items Clinical diagnosis Age at diagnosis Birth year First symptom Difference between your right and left sides Age at first symptom How were muscle problems diagnosed? Sport Other family members A single disease-causing mutation Two or more disease-causing mutations Best motor function achieved Run Walking Walking assistive device Does not walk Walking distance Climbing four or more stairs Descending four or more stairs Standing up from a seated position Sitting up from a lying position Stand without any support Heart condition Medication for a heart condition Invasive ventilation device Non-invasive assistive device FVC (Forced Vital Capacity) Steroids Other medication Date of last follow-up Clinical trial Mutational analysis Biological analysis Creatine kinase protein
11 TREAT-NMD DMD registry 23 items 16 clinical items The international Dysferlinopathies registry 34 items 29 clinical items The French FSHD registry 66 items 60 clinical items Diagnosis Zip code Consultation date Physician Walking Clinical trial Height Weight Dominant side Personal situation Work situation School level Other family members Age at first symptom First symptom Facial weakness Dry eyes Inability to fully close eyes during sleep Unable to close eyes Able to whistle Atrophy of tongue Axial muscle weakness Upper extremity Lower extremity Brooke score Bone structure of scapula Detached scapula Scapula surgery Vignos score Difficulty walking on heels Difficulty to get out of bed Difficulty to get out of a chair Asymmetry Muscle and joint pain Pain severity Area of pain Beevor's sign Walking exercise test Clinical severity scale Joint limitation Medicinal treatment Walking assistive device Other genetic test Other blood test EMG (Electromyography) Muscle biopsy MRI of muscle Heart disease ECG (Electrocardiography) ECG Holter (Holter monitoring) Echocardiography Respiratory disorder Skeletal abnormalities Observation of functional respiratory Blood gases Polysomnography Assisted breathing Eye disorder Ophthalmic surgery Hearing disorder Hearing aid Gastrointestinal disease Fiberoptic endoscopic evaluation of swallowing Metabolic disease Lipid-lowering therapy Endocrine disorder Hormone therapy
12 TREAT-NMD DMD registry 23 items 16 clinical items The international Dysferlinopathies registry 34 items 29 clinical items The French FSHD registry 66 items 62 clinical items Diagnosis Zip code Consultation date Physician Walking Clinical trial Height Weight Dominant side Personal situation Work situation School level Other family members Age at first symptom First symptom Facial weakness Dry eyes Inability to fully close eyes during sleep Unable to close eyes Able to whistle Atrophy of tongue Axial muscle weakness Upper extremity Lower extremity Brooke score Bone structure of scapula Detached scapula Scapula surgery Vignos score Difficulty walking on heels Difficulty to get out of bed Difficulty to get out of a chair Asymmetry Muscle and joint pain Pain severity Area of pain Beevor's sign Walking exercise test Clinical severity scale Joint limitation Medicinal treatment Walking assistive device Other genetic test Other blood test EMG (Electromyography) Muscle biopsy MRI of muscle Heart disease ECG (Electrocardiography) ECG Holter (Holter monitoring) Echocardiography Respiratory disorder Skeletal abnormalities Observation of functional respiratory Blood gases Polysomnography Assisted breathing Eye disorder Ophthalmic surgery Hearing disorder Hearing aid Gastrointestinal disease Fiberoptic endoscopic evaluation of swallowing Metabolic disease Lipid-lowering therapy Endocrine disorder Hormone therapy
13 Selected ontologies for first round evaluation: Clinical Trials Ontology (CTO) Read Codes, Clinical Terms Version 3 (CTV3 RCD) Human Phenotype Ontology (HPO) International Classification of External Causes of Injuries (ICECI) International Classification of Functioning, Disability and Health (ICF) Logical Observation Identifier Names and Codes (LOINC) Medical Dictionary for Regulatory Activities (MEDDRA) Medical Subject Headings (MESH) National Cancer Institute Thesaurus (NCIT) NIH NLM Value Sets (NLMVS) Online Mendelian Inheritance in Man (OMIM) PhenX Phenotypic Terms (PHENX) SMASH Ontology (SMASH) Systematized Nomenclature of Medicine - Clinical Terms (SNOMEDCT) Experimental Conditions Ontology (XCO)
14 Ontologies selection using the TREAT-NMD and the FSHD datasets XCO SNOMEDCT SMASH PHENX OMIM NLMVS NCIT MESH MEDDRA LOINC ICF ICECI HPO CTV3 RCD CTO FSHD TREAT-NMD
15 Ontologies selection using the TREAT-NMD and the FSHD datasets XCO SNOMEDCT SMASH PHENX OMIM NLMVS NCIT MESH MEDDRA LOINC ICF ICECI HPO CTV3 RCD CTO FSHD TREAT-NMD 6 ontologies are more efficient
16 Ontologies selection using the TREAT-NMD and the FSHD datasets XCO SNOMEDCT SMASH PHENX OMIM NLMVS NCIT MESH MEDDRA LOINC ICF ICECI HPO CTV3 RCD CTO FSHD TREAT-NMD HPO is not efficient for those datasets
17 Selected ontologies for first round evaluation: Clinical Trials Ontology (CTO) Read Codes, Clinical Terms Version 3 (CTV3 RCD) Human Phenotype Ontology (HPO) International Classification of External Causes of Injuries (ICECI) International Classification of Functioning, Disability and Health (ICF) Logical Observation Identifier Names and Codes (LOINC) Medical Dictionary for Regulatory Activities (MEDDRA) Medical Subject Headings (MESH) National Cancer Institute Thesaurus (NCIT) NIH NLM Value Sets (NLMVS) Online Mendelian Inheritance in Man (OMIM) PhenX Phenotypic Terms (PHENX) SMASH Ontology (SMASH) Systematized Nomenclature of Medicine - Clinical Terms (SNOMEDCT) Experimental Conditions Ontology (XCO)
18 Overlap between ontologies using the 3 datasets SNOMEDCT NCIT MESH MEDDRA LOINC CTV3 RCD IDR FSHD TREAT-NMD
19 Overlap between ontologies using the TREAT-NMD dataset Ontologies Elements
20 Overlap between ontologies using the TREAT-NMD dataset Ontologies Elements Ontologies strongly overlap
21 Remarks Terms are not always clearly labeled: FSHD database: "Concomitant skeletal abnormalities" Unknown in selected ontologies, but present in HPO and the BDO Is it and abnormality of the skeletal physiology or morphology?
22 Conclusions With real data from existing registries, HPO is not the ontology of choice Six ontologies are consistently more efficient than others: CTV3 RCD, LOINC, MEDDRA, MESH, NCIT, SNOMEDCT They strongly overlap 12/17 elements common to 4 or more ontologies for the TREAT-NMD dataset (70.6%) Minimal number of ontologies to capture all elements vary: SNOMEDCT and MEDDRA for the TREAT-NMD dataset SNOMEDCT, MEDDRA and NCIT for the IDR dataset SNOMEDCT, MEDDRA and OMIM for the FSHD dataset SNOMEDCT and MEDDRA are the ontologies of choice for these 3 datasets with occasionally another one To capture all items additional ontologies needs to be combined
23 Conclusions This may be different when creating a database from scratch Use HPO to select symptoms Use SNOMEDCT and MEDDRA for missing terms (or add them to HPO)
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