{"id":"W2159380553","doi":"10.1093/genetics/165.2.695","title":"Likelihood Models of Somatic Mutation and Codon Substitution in Cancer Genes","year":2003,"lang":"en","type":"article","venue":"Genetics","topic":"Cancer Genomics and Diagnostics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":46,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Alberta","funders":"National Human Genome Research Institute","keywords":"Biology; Genetics; Missense mutation; Mutation rate; Nonsense mutation; Mutation; Germline mutation; Silent mutation; Gene; Transversion; Synonymous substitution; Codon usage bias; Genome","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":[0.00007559552,0.00007790555,0.00009221119,0.00003577364,0.00001930457,0.000007994925,0.00004209567,0.00007716186,0.000004046012],"category_scores_gemma":[0.0000273424,0.00008508845,0.00002036744,0.00005844893,0.00004191089,0.000001957977,0.00002121214,0.00002578455,4.90397e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001446004,"about_ca_system_score_gemma":0.0001044976,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0000520487,"about_ca_topic_score_gemma":0.0006407461,"domain_scores_codex":[0.9994752,0.00002206226,0.0001677039,0.000152658,0.00005910764,0.0001233083],"domain_scores_gemma":[0.9997116,0.000009329784,0.00005858735,0.0001325532,0.00005119137,0.00003676429],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.00004455404,0.0001512524,0.04445424,0.0001511012,0.00004769977,0.000005423806,0.0003310429,0.07800547,0.8545173,0.003207608,0.0001388707,0.0189454],"study_design_scores_gemma":[0.001196943,0.0002316926,0.009774812,0.00003960865,0.00004427897,0.00001745314,0.0001381469,0.007538448,0.9710208,0.006410609,0.003316622,0.0002705842],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9813472,0.01356234,0.004621124,0.00002045325,0.00009203617,0.0001243293,0.00002172823,0.000001996927,0.0002087905],"genre_scores_gemma":[0.9892449,0.008260522,0.002345493,0.00005038703,0.00003538855,0.0000169864,0.00002289184,0.00001021,0.00001317021],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1165035,"threshold_uncertainty_score":0.3469806,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01373980624748314,"score_gpt":0.2507101516144761,"score_spread":0.236970345366993,"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."}}