{"id":"W2950430797","doi":"10.1371/journal.pcbi.1006596","title":"Whole genomes define concordance of matched primary, xenograft, and organoid models of pancreas cancer","year":2019,"lang":"en","type":"article","venue":"PLoS Computational Biology","topic":"Pancreatic and Hepatic Oncology Research","field":"Medicine","cited_by":61,"is_retracted":false,"has_abstract":true,"ca_institutions":"Vector Institute; Lunenfeld-Tanenbaum Research Institute; Mount Sinai Hospital; Princess Margaret Cancer Centre; University Health Network; University of Toronto; Ontario Institute for Cancer Research; Institute of Cancer Research","funders":"Canadian Institutes of Health Research; Ministero dello Sviluppo Economico; Hebrew University of Jerusalem; Government of Ontario; Ontario Institute for Cancer Research; Natural Sciences and Engineering Research Council of Canada; Princess Margaret Cancer Foundation","keywords":"Concordance; Copy-number variation; Biology; Tumour heterogeneity; Cancer; Computational biology; Organoid; Genome; Pancreatic cancer; Structural variation; Genetic heterogeneity; Metastasis; Cancer research; Gene; Genetics; Phenotype","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":[0.0001327818,0.00009763336,0.0006577533,0.00009663867,0.00001938896,0.000001532278,0.00007017015,0.00009493199,0.0002060318],"category_scores_gemma":[0.00003348829,0.00007911938,0.00003848175,0.0001219605,0.0003006866,0.00003153559,0.00006506244,0.00009886411,0.00001585906],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003881531,"about_ca_system_score_gemma":0.0003761671,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000116684,"about_ca_topic_score_gemma":0.000005776174,"domain_scores_codex":[0.9991071,0.00006471576,0.0003180231,0.0002007727,0.0001433428,0.0001660802],"domain_scores_gemma":[0.9989434,0.0004247383,0.0001468364,0.0001210575,0.0002967019,0.00006727109],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0003586692,0.0002024853,0.8883469,0.0004134273,0.000334637,0.000002324902,0.000233594,0.000453196,0.103326,0.005281065,0.00008338115,0.0009643795],"study_design_scores_gemma":[0.005793508,0.001699129,0.9014891,0.0002360362,0.0002969883,0.00006060722,0.0001273641,0.05582934,0.005110126,0.028764,0.0003698184,0.0002239434],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9930285,0.00291705,0.001122484,0.0007128104,0.00002972468,0.0003723741,0.00009180429,0.00001307855,0.001712174],"genre_scores_gemma":[0.9879889,0.0003852254,0.01084728,0.0002525188,0.00003275741,0.00002307906,0.000147575,0.000010368,0.0003123013],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.09821588,"threshold_uncertainty_score":0.3226395,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03366654101948803,"score_gpt":0.3116270039085722,"score_spread":0.2779604628890842,"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."}}