{"id":"W4414915530","doi":"10.1093/narcan/zcaf036","title":"Reference-free RNA profiling predicts triple negative breast cancer chemoresistance to neoadjuvant treatment","year":2025,"lang":"en","type":"article","venue":"NAR Cancer","topic":"Cancer Genomics and Diagnostics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":2,"is_retracted":false,"has_abstract":true,"ca_institutions":"McGill University; Jewish General Hospital","funders":"H2020 European Research Council; Agence Nationale de la Recherche; Fonds de Recherche du Québec-Société et Culture; Fondation du cancer du sein du Québec; Fondation pour la Recherche Médicale; Fonds de Recherche du Québec - Santé; Fondation ARC pour la Recherche sur le Cancer","keywords":"Triple-negative breast cancer; Breast cancer; Transcriptome; Biomarker; Gene expression profiling; Gene signature; Chemotherapy","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":[0.0007213586,0.000238488,0.0003498162,0.000669651,0.0001666992,0.0005852925,0.0001681853,0.0003200904,0.0007399237],"category_scores_gemma":[0.001769502,0.0001235753,0.0002190919,0.0004258468,0.000300856,0.0001430525,0.0002817205,0.0002331161,0.0002359155],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001804584,"about_ca_system_score_gemma":0.00019386,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0005509859,"about_ca_topic_score_gemma":0.001088435,"domain_scores_codex":[0.999345,0.000137793,0.00005090814,0.0002125449,0.0001813614,0.00007242091],"domain_scores_gemma":[0.9993048,0.000247655,0.0001600009,0.00008890321,0.0001610162,0.00003766805],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.001308036,0.0001580183,0.2444808,0.0002000793,0.0002144933,0.0002405077,0.0003046458,0.002658612,0.7240868,0.0001907261,0.0003526235,0.02580465],"study_design_scores_gemma":[0.00002589359,0.0009134127,0.8240197,0.0000465275,0.0002994321,0.001271941,0.0003056491,0.01218764,0.1576819,0.000406252,0.002799845,0.00004178206],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.992812,0.000623163,0.004550518,0.00004352945,0.00001642008,0.00002824604,0.001409141,0.00003791684,0.0004790691],"genre_scores_gemma":[0.9931544,0.0002512741,0.002648082,0.0000860312,0.0000179599,0.00005277184,0.003236947,0.00001650824,0.0005361066],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.0007399237,"threshold_uncertainty_score":0.003814995,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01321762210894742,"score_gpt":0.2825826608961816,"score_spread":0.2693650387872341,"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."}}