{"id":"W3153097092","doi":"10.1136/jmedgenet-2021-107738","title":"Data sharing to improve concordance in variant interpretation across laboratories: results from the Canadian Open Genetics Repository","year":2021,"lang":"en","type":"article","venue":"Journal of Medical Genetics","topic":"Genomics and Rare Diseases","field":"Biochemistry, Genetics and Molecular Biology","cited_by":36,"is_retracted":false,"has_abstract":true,"ca_institutions":"Women's College Hospital; BC Cancer Agency; Calgary Laboratory Services; Hospital for Sick Children; McGill University Health Centre; McGill University; Kingston Health Sciences Centre; Queen's University; Trillium Health Centre; University of Manitoba; Manitoba Health; University of Alberta; Jewish General Hospital; St. Michael's Hospital; Agricultural Research Institute of Ontario; University of Toronto; University of British Columbia; Alberta Hospital Edmonton; University of Calgary; Mount Sinai Hospital; Lunenfeld-Tanenbaum Research Institute","funders":"National Human Genome Research Institute; Canadian Institutes of Health Research; Ontario Genomics Institute","keywords":"Concordance; Genetic variants; Computational biology; Medical genetics; Medicine; Interpretation (philosophy); Genetics; Computer science; Bioinformatics; Biology; Genotype; Gene","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":true,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.001020052,0.0001054234,0.0001726992,0.00001694681,0.00008880641,0.0002562225,0.002132188,0.0001674273,0.000006842913],"category_scores_gemma":[0.001842218,0.00008231326,0.00003628048,0.0001358471,0.00006029208,0.000007147729,0.001295289,0.0002363468,0.000001694654],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00005493683,"about_ca_system_score_gemma":0.002747772,"about_ca_topic_candidate":true,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.005245375,"about_ca_topic_score_gemma":0.1848603,"domain_scores_codex":[0.9983427,0.00009804087,0.0006056174,0.0003519394,0.0003746669,0.000227025],"domain_scores_gemma":[0.9981043,0.00005801151,0.0002136381,0.0008297748,0.000358127,0.0004361882],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"not_applicable","study_design_scores_codex":[0.004064018,0.001087943,0.08422473,0.0001266311,0.001808021,0.01736258,0.01409029,0.009774523,0.548471,0.0002243874,0.1668375,0.1519284],"study_design_scores_gemma":[0.006398777,0.0008546617,0.072684,0.0006830181,0.0001664501,0.0006753835,0.00539783,0.01090265,0.05749563,0.0005318049,0.8434018,0.0008079932],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9858433,0.005970877,0.0008767333,0.00431258,0.001248703,0.0001424108,0.001428558,0.000001036326,0.0001757735],"genre_scores_gemma":[0.9926965,0.001043572,0.002501518,0.002499184,0.000883172,0.000002475263,0.0002735537,0.00001618165,0.00008381905],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.6765643,"threshold_uncertainty_score":0.8300139,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02509979735577414,"score_gpt":0.3322027149691267,"score_spread":0.3071029176133526,"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."}}