{"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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002416553,0.0002167519,0.000206908,0.00004220354,0.0001686773,0.0001781784,0.0001695173,0.0002198339,0.000002584854],"category_scores_gemma":[0.0000443158,0.000240379,0.000120562,0.00004524021,0.00005185656,0.000006487779,0.0002181175,0.0001269084,0.000008193732],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002881579,"about_ca_system_score_gemma":0.0005906904,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0002065989,"about_ca_topic_score_gemma":0.00008544343,"domain_scores_codex":[0.9986311,0.00001695608,0.0003177125,0.0005229473,0.00005423976,0.0004570691],"domain_scores_gemma":[0.99936,0.00006212396,0.000096981,0.0002507909,0.00004261364,0.000187522],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"not_applicable","study_design_scores_codex":[0.00008487326,0.00003424204,0.0002169407,0.0001889426,0.0000598424,0.00001347389,0.0007042937,0.0005789702,0.9524559,0.00005191064,0.00138595,0.04422471],"study_design_scores_gemma":[0.00278478,0.001124535,0.0004053285,0.00009632355,0.0002636796,0.0001598899,0.0006692237,0.05812708,0.2930435,0.0005106564,0.641901,0.0009141043],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8715218,0.016211,0.1094075,0.0002133238,0.001850521,0.000500257,0.0001133877,0.00003400505,0.0001482332],"genre_scores_gemma":[0.9540892,0.00538173,0.03607917,0.0002315867,0.002984072,0.00006672997,0.0001401836,0.000113105,0.0009142155],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.6594124,"threshold_uncertainty_score":0.9802372,"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."}}