{"id":"W4413127728","doi":"10.1101/2025.08.08.668693","title":"Genetic and Epigenetic Reprogramming of Transposable Elements Drives ecDNA-Mediated Metastatic Prostate Cancer","year":2025,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Cancer Genomics and Diagnostics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":3,"is_retracted":false,"has_abstract":true,"ca_institutions":"Ontario Institute for Cancer Research; University of Toronto; Princess Margaret Cancer Centre; University Health Network","funders":"Canadian Institutes of Health Research; Government of Ontario; U.S. Department of Defense","keywords":"Epigenetics; Biology; Chromatin; Extrachromosomal DNA; FOXA1; Prostate cancer; Reprogramming; Histone; Genetics; Androgen receptor; Gene; DNA methylation; Cancer research; Transcription factor; Genome; Cancer; Gene expression","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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001072702,0.0002020618,0.0001048549,0.0002385515,0.00007805876,0.000187906,0.0001578516,0.000168908,0.001446964],"category_scores_gemma":[0.0001344828,0.0001218214,0.0001320696,0.0001311039,0.0001750418,0.00008745395,0.0003305347,0.0003455131,0.0003750515],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002030946,"about_ca_system_score_gemma":0.00009571363,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0006560133,"about_ca_topic_score_gemma":0.001164721,"domain_scores_codex":[0.9998856,0.00001286586,0.000006483086,0.00003496203,0.00003688328,0.00002334488],"domain_scores_gemma":[0.9999243,0.0000165102,0.00002433953,0.00001280047,0.00000508204,0.00001695085],"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":[0.00001834851,0.000007409289,0.0003592179,0.00001103404,0.000002701943,0.00004560782,0.000009449353,0.00007502454,0.99792,0.0001719484,0.00002419443,0.001355142],"study_design_scores_gemma":[0.00001055883,0.0001528315,0.01182152,0.000005425128,0.00001270119,0.0006945909,0.00002954451,0.002982665,0.9803036,0.0001205372,0.003861288,0.000004714529],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9890961,0.0003915421,0.007290543,0.00005389872,0.000020528,0.00002852353,0.0004854973,0.0002403055,0.002393055],"genre_scores_gemma":[0.9925739,0.0001968066,0.003094209,0.00003088351,0.000006549631,0.0000144697,0.0006893412,0.00005002863,0.003343912],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001446964,"threshold_uncertainty_score":0.004840553,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.00838418910619799,"score_gpt":0.2335995438409442,"score_spread":0.2252153547347462,"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."}}