{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0003769258,0.0004111434,0.0002352349,0.001694676,0.0002265951,0.0005378597,0.0003133233,0.0004702597,0.003159725],"category_scores_gemma":[0.001561677,0.0001440614,0.0005765299,0.000837779,0.000183336,0.0002331997,0.0004956434,0.0003812258,0.0008733869],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003469941,"about_ca_system_score_gemma":0.0002472857,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001444324,"about_ca_topic_score_gemma":0.002454034,"domain_scores_codex":[0.9995639,0.00006504986,0.00002517814,0.0001882684,0.0001204289,0.0000372417],"domain_scores_gemma":[0.9993561,0.0002494831,0.0001489344,0.00007324076,0.0001162345,0.00005598036],"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":[0.0005409478,0.00009929348,0.03166781,0.0004842691,0.000379555,0.0008549422,0.0003700871,0.004007082,0.9042811,0.00154165,0.0009266259,0.05484668],"study_design_scores_gemma":[0.00005672238,0.0006933807,0.2713006,0.000120071,0.0005251536,0.003219491,0.0004349496,0.05835158,0.6273724,0.00475756,0.0330625,0.0001054461],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8306636,0.002771773,0.1273277,0.0001911967,0.00009154934,0.000227944,0.0295211,0.003429272,0.005775851],"genre_scores_gemma":[0.8500091,0.0005218469,0.1246163,0.0002978236,0.00004319549,0.0001395048,0.02096987,0.0003934429,0.003008966],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.003159725,"threshold_uncertainty_score":0.01057035,"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."}}