{"id":"W3004888802","doi":"10.1038/s41467-019-13885-w","title":"High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations","year":2020,"lang":"en","type":"article","venue":"Nature Communications","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":76,"is_retracted":false,"has_abstract":true,"ca_institutions":"SickKids Foundation; BC Cancer Agency; University of British Columbia; Prostate Cancer Canada; Université de Montréal; Hospital for Sick Children; Lunenfeld-Tanenbaum Research Institute; Mount Sinai Hospital; Princess Margaret Cancer Centre; University of Calgary; Genome Canada; Canada's Michael Smith Genome Sciences Centre; Vector Institute; Simon Fraser University; McGill University; University of Ottawa; McGill University and Génome Québec Innovation Centre; Toronto General Hospital; University Health Network; University of Toronto; Institute of Cancer Research; Ontario Institute for Cancer Research","funders":"National Institute of Environmental Health Sciences; National Institute of General Medical Sciences; U.S. Department of Health and Human Services; National Cancer Institute; National Institutes of Health; Cancer Prevention and Research Institute of Texas","keywords":"Genome; Gene; Biology; Computational biology; Genetics","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":[0.0001188195,0.0001434659,0.0003143584,0.0001012824,0.0001092069,0.00001363483,0.0007700673,0.0002780118,0.00002522302],"category_scores_gemma":[0.00006919875,0.0001583515,0.0001702241,0.0006670777,0.0001414701,0.000005908365,0.0002540332,0.0001985965,0.000001576104],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003930536,"about_ca_system_score_gemma":0.0001065215,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00007365245,"about_ca_topic_score_gemma":0.000519252,"domain_scores_codex":[0.9989196,0.0001115825,0.0004478058,0.0002364684,0.0001455883,0.0001389338],"domain_scores_gemma":[0.9979501,0.00003721522,0.000328014,0.001335858,0.0002637487,0.00008510301],"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":[0.00001883144,0.0000629674,0.001768281,0.00001956637,0.00105064,1.052123e-7,0.0001455586,0.004547619,0.9899085,0.0002882706,0.002025019,0.0001646538],"study_design_scores_gemma":[0.005677409,0.001355587,0.2206849,0.0001166097,0.007104208,0.000004996651,0.001152911,0.05706229,0.4436084,0.0003829362,0.2602922,0.002557469],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9812479,0.0125135,0.001106456,0.001507916,0.00004315464,0.0002406786,0.003116508,0.00001489138,0.0002090137],"genre_scores_gemma":[0.9804795,0.001986985,0.002772575,0.0004275859,0.00002623135,0.00001978843,0.01419648,0.00002106205,0.00006976346],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.5463001,"threshold_uncertainty_score":0.6457387,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.00859776889380641,"score_gpt":0.2445920723105233,"score_spread":0.2359943034167169,"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."}}