{"id":"W4393386186","doi":"10.1016/j.ajhg.2024.03.008","title":"Exome copy number variant detection, analysis, and classification in a large cohort of families with undiagnosed rare genetic disease","year":2024,"lang":"en","type":"article","venue":"The American Journal of Human Genetics","topic":"Genomic variations and chromosomal abnormalities","field":"Biochemistry, Genetics and Molecular Biology","cited_by":21,"is_retracted":false,"has_abstract":false,"ca_institutions":"","funders":"H2020 European Research Council; Eunice Kennedy Shriver National Institute of Child Health and Human Development; National Institute of Neurological Disorders and Stroke; Estonian Research Competency Council; LGMD2D Foundation; National Institute of Mental Health; Sanofi Genzyme; National Institute of Dental and Craniofacial Research; UC Berkeley College of Chemistry; National Health and Medical Research Council; Muscular Dystrophy UK; State Government of Victoria; Kurt+Peter Foundation; University of California, San Diego; Murdoch Children's Research Institute; Fonds de Recherche du Québec - Santé; Limb Girdle Muscular Dystrophy 2I; Massachusetts General Hospital; Children’s Hospital of Wisconsin Research Institute; European Commission; National Institute of Child Health and Human Development; National Institute of Diabetes and Digestive and Kidney Diseases; Sanofi; Research to Prevent Blindness; National Institutes of Health; Türkiye Bilimsel ve Teknolojik Araştırma Kurumu; Foundation Fighting Blindness; Limb Girdle Muscular Dystrophy 2i Research Fund; National Human Genome Research Institute; Ultragenyx Pharmaceutical; National Eye Institute; Eesti Teadusagentuur; Autism Speaks","keywords":"Copy-number variation; Exome sequencing; Exome; Genetics; Genomics; Biology; Genetic testing; Mendelian inheritance; Medical genetics; Computational biology; Phenotype; Genome; Gene","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.000547869,0.0005298137,0.000417901,0.001891981,0.001158312,0.0008541364,0.0005155806,0.0005722364,0.002159244],"category_scores_gemma":[0.003406517,0.0003458892,0.0003388236,0.0009861675,0.0005136695,0.0004661824,0.0006192107,0.0004864262,0.0003176993],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002794783,"about_ca_system_score_gemma":0.0003226004,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.004463835,"about_ca_topic_score_gemma":0.003413233,"domain_scores_codex":[0.999265,0.0001271068,0.00006956772,0.0003048971,0.0001338709,0.00009953662],"domain_scores_gemma":[0.9989501,0.0004263058,0.0002368232,0.0001337202,0.0001040941,0.0001489553],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.00020601,0.00006852448,0.9904428,0.000005359779,0.00004167818,0.003243185,0.0003096475,0.00008828068,0.002674614,0.00007864196,0.000224154,0.002617096],"study_design_scores_gemma":[0.00001854738,0.00008060311,0.9850333,0.000009094645,0.00006062609,0.01245707,0.0003883255,0.0008302756,0.0005220754,0.0001162643,0.0004709519,0.0000127738],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9994555,0.00006717017,0.0001181491,0.00002163342,0.000002847053,0.000003183962,0.0001440273,0.000004281973,0.0001832662],"genre_scores_gemma":[0.9991884,0.00007442124,0.000161803,0.00002593011,0.000009225231,0.000006470588,0.0002852727,0.00000817413,0.0002404974],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.004463835,"threshold_uncertainty_score":0.008875668,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.005428635445040735,"score_gpt":0.2398303321022057,"score_spread":0.234401696657165,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}