{"id":"W4385340599","doi":"10.3389/fonc.2023.1221611","title":"Linked-read based analysis of the medulloblastoma genome","year":2023,"lang":"en","type":"article","venue":"Frontiers in Oncology","topic":"Cancer Genomics and Diagnostics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":4,"is_retracted":false,"has_abstract":true,"ca_institutions":"SickKids Foundation; Hospital for Sick Children; Alberta Children's Hospital; McGill University Health Centre; University of Calgary; McGill University","funders":"National Institute of Neurological Disorders and Stroke; Canadian Institutes of Health Research; Canadian Cancer Society Research Institute; National Institutes of Health; Hospital for Sick Children; Cancer Prevention and Research Institute of Texas; Terry Fox Research Institute; National Cancer Institute; University of Toronto; Fondation Charles-Bruneau; Brain Tumour Charity; Stand Up To Cancer; Genome British Columbia; Government of Canada; Genome Canada; McGill University; Government of Ontario; American Association for Cancer Research","keywords":"Chromothripsis; Gene; Gene duplication; Genome; Extrachromosomal DNA; Genetics; Medulloblastoma; Point mutation; Biology; Computational biology; DNA sequencing; Mutation; DNA; Genome instability; DNA damage","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":[0.0002171809,0.00008940274,0.0002595476,0.000249003,0.00003208762,0.000003904596,0.0002952911,0.0001805757,0.00002444681],"category_scores_gemma":[0.0001363659,0.0000764818,0.0001733736,0.0009703884,0.0001298133,8.151247e-7,0.0001020848,0.00007868807,0.000003535955],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00007222516,"about_ca_system_score_gemma":0.0002152446,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00004559509,"about_ca_topic_score_gemma":0.0007737985,"domain_scores_codex":[0.9991874,0.0000722214,0.0002237372,0.0002277254,0.00008010839,0.0002088446],"domain_scores_gemma":[0.9993989,0.00004354479,0.0001028991,0.000371207,0.00004377521,0.00003963815],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0004815724,0.0003505675,0.603374,0.00004116793,0.00181597,0.00003461536,0.0004953518,0.128854,0.1532896,0.0002240332,0.0903165,0.02072266],"study_design_scores_gemma":[0.001292412,0.0004971435,0.5048344,0.000008111952,0.0004793405,0.00000154906,0.0002922193,0.01324826,0.007780417,0.0002722386,0.4710333,0.0002606331],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9927827,0.0005108624,0.003031173,0.000767699,0.001100249,0.000166372,0.000111892,0.000009022499,0.001520012],"genre_scores_gemma":[0.9963177,0.0003950297,0.001767119,0.0007218698,0.000106973,0.00003354874,0.0001858434,0.00001527016,0.0004565882],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.3807168,"threshold_uncertainty_score":0.3118837,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.008626745716016784,"score_gpt":0.2618310009916618,"score_spread":0.253204255275645,"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."}}