{"id":"W3198037870","doi":"10.1038/s41523-021-00320-x","title":"Proteomics-derived basal biomarker DNA-PKcs is associated with intrinsic subtype and long-term clinical outcomes in breast cancer","year":2021,"lang":"en","type":"article","venue":"npj Breast Cancer","topic":"Cancer Genomics and Diagnostics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":9,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of British Columbia Hospital; Centre for Advancing Health Outcomes; University of British Columbia","funders":"Canadian Cancer Society Research Institute; Canadian Institutes of Health Research; Government of Canada","keywords":"Breast cancer; Tissue microarray; DNA-PKcs; Biomarker; Cancer research; Biology; Cancer; Immune system; DNA microarray; Immune checkpoint; Immunohistochemistry; Medicine; DNA damage; DNA; Gene; Gene expression; Immunotherapy; Immunology; Genetics","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":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.0001727918,0.0002984658,0.0004444109,0.00004948025,0.00007002294,0.00007342374,0.0001540599,0.0002988772,0.0002590544],"category_scores_gemma":[0.00006494075,0.0002672094,0.0001146518,0.0001847999,0.0001967596,0.00001075436,0.0002028235,0.0002062158,0.000003737279],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001429604,"about_ca_system_score_gemma":0.0009183306,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0007746003,"about_ca_topic_score_gemma":0.009470846,"domain_scores_codex":[0.9982196,0.00008629238,0.0003983035,0.000699412,0.000170658,0.0004257422],"domain_scores_gemma":[0.9989083,0.00005048173,0.0001902533,0.000374259,0.0002888346,0.0001879109],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0005707978,0.0002139547,0.9634023,0.00002575558,0.0003600773,0.00006386214,0.00003353119,0.000008144405,0.02301682,0.000006220645,0.0008929808,0.01140554],"study_design_scores_gemma":[0.002784876,0.00006303663,0.9883035,0.0001253826,0.0000881757,0.00007767085,0.00001644953,0.00002471698,0.00783002,0.00001700463,0.0002822922,0.0003868386],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9929693,0.001291295,0.00004137484,0.003533538,0.0003819079,0.0002971624,0.001392629,0.00001313882,0.00007969078],"genre_scores_gemma":[0.9922807,0.003770287,0.0001081416,0.002902128,0.000324413,0.0001350808,0.0001566163,0.00005902746,0.0002636311],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.02490122,"threshold_uncertainty_score":0.999978,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01565554726975159,"score_gpt":0.2912315449943927,"score_spread":0.2755759977246411,"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."}}