{"id":"W4402037460","doi":"10.1016/j.xgen.2024.100639","title":"ONCOLINER: A new solution for monitoring, improving, and harmonizing somatic variant calling across genomic oncology centers","year":2024,"lang":"en","type":"article","venue":"Cell Genomics","topic":"Cancer Genomics and Diagnostics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":2,"is_retracted":false,"has_abstract":true,"ca_institutions":"Ontario Institute for Cancer Research","funders":"Departament d'Empresa i Coneixement, Generalitat de Catalunya; Agencia Estatal de Investigación; Horizon 2020; Instituto de Salud Carlos III; Canadian Institutes of Health Research; Sveučilište Josipa Jurja Strossmayera u Osijeku; Horizon 2020 Framework Programme; Cancéropôle Ile de France; Generalitat de Catalunya; Ministerio de Ciencia e Innovación; Deutsches Krebsforschungszentrum; Federación Española de Enfermedades Raras; Conseil Régional, Île-de-France; Ministerio de Ciencia, Innovación y Universidades; Ministerio de Economía y Competitividad; European Regional Development Fund; European Commission","keywords":"Indel; Personalized medicine; Genome; Computational biology; Precision medicine; Biology; Genomics; Somatic cell; Data science; Genetics; Bioinformatics; Computer science; Gene; Single-nucleotide polymorphism","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":[0.006395658,0.001210994,0.001081,0.002567681,0.0006395299,0.002088916,0.002184127,0.001106087,0.002628122],"category_scores_gemma":[0.01385431,0.00111283,0.001048663,0.002030016,0.0006301939,0.00256049,0.004383995,0.0013115,0.001538795],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0008574704,"about_ca_system_score_gemma":0.00179979,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001944651,"about_ca_topic_score_gemma":0.003275374,"domain_scores_codex":[0.9945639,0.0009431758,0.0003773567,0.002478226,0.001398125,0.000239168],"domain_scores_gemma":[0.993179,0.001974964,0.0008951789,0.002631154,0.000941589,0.0003781214],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.0033796,0.0006154143,0.04918469,0.0005726152,0.00105497,0.0005184774,0.001161473,0.04067149,0.1299697,0.008102227,0.03894598,0.7258234],"study_design_scores_gemma":[0.0006073524,0.001237245,0.02941267,0.0001074602,0.0004064458,0.00154566,0.0003801401,0.6618679,0.1861306,0.02140207,0.09654585,0.0003566148],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.05701748,0.0005793281,0.7974797,0.0007889449,0.0001729441,0.000400712,0.005011418,0.1359262,0.002623216],"genre_scores_gemma":[0.1696463,0.0002080249,0.8142676,0.0005752039,0.00008296942,0.0003961588,0.007742113,0.005139612,0.001941908],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.006395658,"threshold_uncertainty_score":0.03382385,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02465500381274754,"score_gpt":0.2818440400380626,"score_spread":0.257189036225315,"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."}}