{"id":"W4386251031","doi":"10.1038/s41467-023-40909-3","title":"Diagnostic implications of pitfalls in causal variant identification based on 4577 molecularly characterized families","year":2023,"lang":"en","type":"article","venue":"Nature Communications","topic":"Genomics and Rare Diseases","field":"Biochemistry, Genetics and Molecular Biology","cited_by":41,"is_retracted":false,"has_abstract":true,"ca_institutions":"North York General Hospital; University of Toronto","funders":"Bill and Melinda Gates Foundation","keywords":"Exome sequencing; Mendelian inheritance; Identification (biology); Genetics; Disease; Computational biology; Exome; Biology; Bioinformatics; Phenotype; Medicine; Gene","routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001963059,0.0001088038,0.0001192341,0.0001908758,0.0001043024,0.00002206308,0.0006646296,0.0001942188,0.000004234497],"category_scores_gemma":[0.0006661204,0.0001124494,0.00008160037,0.0004310059,0.00008447189,0.000004544753,0.0001646757,0.0002030803,0.00001751974],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001777135,"about_ca_system_score_gemma":0.0001162504,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00002526109,"about_ca_topic_score_gemma":0.0001535855,"domain_scores_codex":[0.9991339,0.000119965,0.0002812634,0.0002271131,0.00009501649,0.0001427371],"domain_scores_gemma":[0.9978476,0.0001950043,0.0001237228,0.001639131,0.000147354,0.00004717148],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.0000545541,0.0005171069,0.01832918,0.00003003434,0.00005276928,0.000005342592,0.0001063418,0.0005751768,0.96884,0.008110279,0.002263995,0.00111521],"study_design_scores_gemma":[0.0005473134,0.00007139383,0.9790791,0.00003677058,0.00003292149,0.000003093464,0.00007317139,0.001844557,0.0105777,0.0003434205,0.007189406,0.0002011173],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9909341,0.001236453,0.0005470281,0.004920012,0.0001463163,0.0005884421,0.0006047258,0.00005708288,0.0009658579],"genre_scores_gemma":[0.9944461,0.001296141,0.0005192961,0.0003768637,0.00002359653,0.0001967217,0.00306843,0.00001925595,0.00005360365],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.9607499,"threshold_uncertainty_score":0.4585554,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01208196404947506,"score_gpt":0.2831291964305033,"score_spread":0.2710472323810282,"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."}}