{"id":"W2910384493","doi":"10.1101/517565","title":"Tumor mutational landscape is a record of the pre-malignant state","year":2019,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Cancer Genomics and Diagnostics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":28,"is_retracted":false,"has_abstract":true,"ca_institutions":"McGill University; McGill University Health Centre; Canada's Michael Smith Genome Sciences Centre; University of Toronto; BC Cancer Agency; Ontario Institute for Cancer Research","funders":"Congressionally Directed Medical Research Programs; Vlaamse regering; Massachusetts General Hospital; Hrvatska Zaklada za Znanost; National Research Foundation of Korea; Fonds Wetenschappelijk Onderzoek; European Commission; Prostate Cancer Foundation; Cancer Research UK; National Research Foundation; Ovarian Cancer Action; National Institutes of Health; Ministry of Science, ICT and Future Planning; Howard Hughes Medical Institute","keywords":"Chromatin; Somatic cell; Biology; Cancer; Ovarian cancer; Genome; Genetics; DNA; Cell of origin; Cell type; Cancer cell; Cell; Evolutionary biology; Computational biology; 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":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.0002265438,0.0003227144,0.0003260305,0.00006138616,0.00006284076,0.00006262498,0.0005594632,0.0002364617,0.00003680476],"category_scores_gemma":[0.0001625703,0.0002825834,0.0002186138,0.0001356946,0.00008931711,0.000003480306,0.0007219287,0.0002604852,0.00001559881],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00004807103,"about_ca_system_score_gemma":0.001145684,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0000758921,"about_ca_topic_score_gemma":0.00001085306,"domain_scores_codex":[0.9983132,0.00005970181,0.0004243552,0.0006570971,0.0002446498,0.0003009511],"domain_scores_gemma":[0.9977471,0.00003181115,0.0004952548,0.001233,0.0003937835,0.00009900562],"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":[0.000127392,0.0001267668,0.04141669,0.0003665783,0.0002664116,0.000008820652,0.00001815514,0.001335529,0.9506158,0.0001105148,0.005602244,0.000005096795],"study_design_scores_gemma":[0.0005712454,0.0001159911,0.1406952,0.0002208013,0.00009132727,4.049685e-8,0.000002335215,0.0003888188,0.8331149,0.00000973472,0.02426919,0.0005204609],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9944477,0.001359943,0.0006010483,0.0001546688,0.00126701,0.0005808557,0.001551667,0.00001683239,0.00002028],"genre_scores_gemma":[0.9975514,0.0004452391,0.0009337996,0.0005497152,0.0003272131,0.00008154671,0.000001900034,0.00007449704,0.0000347236],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1175009,"threshold_uncertainty_score":0.9999626,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.006979390903237208,"score_gpt":0.2087466413751627,"score_spread":0.2017672504719255,"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."}}