{"id":"W4282591735","doi":"10.1038/s41587-022-01342-x","title":"Estimation of tumor cell total mRNA expression in 15 cancer types predicts disease progression","year":2022,"lang":"en","type":"article","venue":"Nature Biotechnology","topic":"Cancer Genomics and Diagnostics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":76,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Toronto","funders":"Stand Up To Cancer; University of Texas MD Anderson Cancer Center; EMD Serono; National Institutes of Health; CRUK Lung Cancer Centre of Excellence; Kadoorie Charitable Foundation; Novo Nordisk Fonden; Suomen Kulttuurirahasto; Academy of Finland; Syöpäjärjestöt; Genentech; AstraZeneca; European Commission; Vlaamse regering; National Institute for Health and Care Research; Rosetrees Trust; Natera; Mirati Therapeutics; Medical Research Council; American Association for Cancer Research; Servier; Hope Foundation; Les Laboratories Pierre Fabre; Ipsen; Fonds Wetenschappelijk Onderzoek; Array BioPharma; Jazz Pharmaceuticals; Francis Crick Institute; GlaxoSmithKline; Cancer Prevention and Research Institute of Texas; Kreftforeningen; Novo Nordisk; LUNGevity Foundation; Entertainment Industry Foundation; Gilead Sciences; Amgen; Invitae; Ono Pharmaceutical; Cancer Research UK; U.S. Department of Defense; Eli Lilly and Company; Royal Society; Khalifa Bin Zayed Al Nahyan Foundation; Bristol-Myers Squibb; National Cancer Institute; University College London; Wellcome Trust; Johns Hopkins University; Gateway for Cancer Research; Welch Foundation; Daiichi Sankyo Europe; BC Cancer Agency; Innovent Biologics; Pfizer; MEI Pharma; Exelixis; Sanofi; Breast Cancer Research Foundation","keywords":"Biology; Cancer; Transcriptome; Messenger RNA; Phenotype; Tumor progression; Disease; Gene expression; Gene; Cancer research; Genetics; Pathology; Medicine","routes":{"ca_aff":true,"ca_fund":true,"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":[0.00007210629,0.0001006099,0.0001141278,0.0001059517,0.00005352755,0.000003852671,0.0001797049,0.000269308,0.00003527345],"category_scores_gemma":[0.0001084312,0.00009798678,0.00003875579,0.0001575479,0.00006040324,0.000002276692,0.0002687013,0.0003520334,6.984656e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0000459383,"about_ca_system_score_gemma":0.0001522479,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001398442,"about_ca_topic_score_gemma":0.00001686839,"domain_scores_codex":[0.999254,0.00002664268,0.0001549634,0.0002856534,0.0001222275,0.0001565117],"domain_scores_gemma":[0.9995412,0.00001044511,0.000116236,0.000267063,0.00002454888,0.00004051314],"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":[0.0003799416,0.0002114317,0.00349388,0.00005939536,0.000007362637,0.00001799621,0.00002169408,0.008049556,0.9744329,0.0001378518,0.002915633,0.01027232],"study_design_scores_gemma":[0.0006072968,0.0002892208,0.003199093,0.00003215927,0.00001149604,0.000005597239,0.00003050328,0.0012997,0.9822701,0.0001767802,0.01194752,0.000130561],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9840516,0.01433694,0.00008665554,0.0006200261,0.0003624175,0.0002443813,0.0001857743,0.00001845724,0.0000937256],"genre_scores_gemma":[0.9985322,0.0003364297,0.0006202445,0.0001336864,0.00006229388,0.000107125,0.000141285,0.00001481929,0.00005194644],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.01448055,"threshold_uncertainty_score":0.3995785,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.002844783199027403,"score_gpt":0.2430221748249663,"score_spread":0.2401773916259389,"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."}}