{"id":"W2994748066","doi":"10.1038/s41467-020-14351-8","title":"Inferring structural variant cancer cell fraction","year":2020,"lang":"en","type":"article","venue":"Nature Communications","topic":"Cancer Genomics and Diagnostics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":56,"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; University of Ottawa; Simon Fraser University; McGill University; 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; 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 Health and Medical Research Council; Hutchison Whampoa Limited; National Institute of Environmental Health Sciences; Prostate Cancer Foundation of Australia; National Cancer Institute; Prostate Cancer Foundation; University of Cambridge; Cancer Research UK; Cybec Foundation; Francis Crick Institute; Movember Foundation","keywords":"In silico; Genome; Computational biology; Biology; Fraction (chemistry); Breakpoint; Cancer; Structural variation; Genetics; Single-nucleotide polymorphism; Pancreatic cancer; Gene; Genotype","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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.001322583,0.0005417967,0.0008974851,0.001807637,0.0004632763,0.001473025,0.0007758215,0.0009234441,0.001313063],"category_scores_gemma":[0.009372341,0.0004399765,0.0009708692,0.001151616,0.0005461869,0.000655987,0.0008426957,0.0007782466,0.0004016185],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0007590823,"about_ca_system_score_gemma":0.000984203,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.007917622,"about_ca_topic_score_gemma":0.009115704,"domain_scores_codex":[0.9993919,0.0001194538,0.00003250577,0.0002689504,0.0001352579,0.00005195438],"domain_scores_gemma":[0.9964088,0.002564004,0.0002862148,0.0003721065,0.0002651766,0.0001037325],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"simulation_or_modeling","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.001198828,0.0001154208,0.2573243,0.0002739413,0.0005937085,0.0006633361,0.0003744659,0.5618583,0.05274045,0.01192567,0.00391676,0.1090149],"study_design_scores_gemma":[0.00002168098,0.00003004221,0.01094868,0.00001404727,0.00005528655,0.0002755111,0.00003508731,0.9675575,0.01011402,0.009219313,0.001707567,0.00002129822],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.5751947,0.0008671337,0.4148117,0.0002774269,0.00003164347,0.00006168906,0.005508235,0.001794287,0.001453341],"genre_scores_gemma":[0.9090055,0.0002296583,0.08121121,0.0001404006,0.00003453342,0.00007826377,0.008388049,0.0002506711,0.0006616251],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.007917622,"threshold_uncertainty_score":0.01574308,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01601750457986693,"score_gpt":0.298128913925714,"score_spread":0.2821114093458471,"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."}}