{"id":"W4200136702","doi":"10.1002/path.5849","title":"Validated biomarker assays confirm that ARID1A loss is confounded with MMR deficiency, CD8 + TIL infiltration, and provides no independent prognostic value in endometriosis‐associated ovarian carcinomas","year":2021,"lang":"en","type":"article","venue":"The Journal of Pathology","topic":"Chromatin Remodeling and Cancer","field":"Biochemistry, Genetics and Molecular Biology","cited_by":42,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Alberta; University of Calgary; Vancouver General Hospital; University of British Columbia; Calgary Laboratory Services; BC Cancer Agency","funders":"H2020 European Research Council; Medical Research and Materiel Command; Cancer Research UK; National Health and Medical Research Council; Swedish Cancer Foundation; Terry Fox Research Institute; Deutsche Forschungsgemeinschaft; National Cancer Institute; BC Cancer Foundation; Canadian Institutes of Health Research; National Center for Research Resources; Cancer Institute NSW; Michael Smith Health Research BC; Breast Cancer Now","keywords":"ARID1A; CD8; Cancer research; Microsatellite instability; Endometriosis; Biology; Immune system; Oncology; Internal medicine; Medicine; Immunology; Mutation; Gene; Genetics","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":true,"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":[0.002469487,0.0005050464,0.0007577555,0.0003015458,0.0002616306,0.000176382,0.0005207908,0.000591182,0.00001248407],"category_scores_gemma":[0.006257656,0.0003814853,0.0001886202,0.000682845,0.0004543448,0.00004573474,0.0002244661,0.0007017781,0.000009421444],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001413647,"about_ca_system_score_gemma":0.001168648,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000121123,"about_ca_topic_score_gemma":0.0001123932,"domain_scores_codex":[0.9957325,0.001191269,0.0009983892,0.0006085377,0.0006687212,0.0008006138],"domain_scores_gemma":[0.9956446,0.001445441,0.001006201,0.0005567883,0.001107958,0.0002390205],"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":[0.0001254263,0.0009571256,0.2195035,0.000224316,0.0008568449,0.001463421,0.006333621,0.004401433,0.7608652,0.0002077708,0.004401966,0.0006594078],"study_design_scores_gemma":[0.02252703,0.006140678,0.2236825,0.000971674,0.002124138,0.02669634,0.01670584,0.01127884,0.6692659,0.00207096,0.01794997,0.000586138],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9904548,0.004649567,0.001964694,0.0001830444,0.0002200058,0.0004902115,0.00008320333,0.00002401813,0.001930467],"genre_scores_gemma":[0.996583,0.001129612,0.0005669976,0.000643933,0.0001479001,0.00002510237,0.0001184199,0.00006635296,0.0007186084],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.09159927,"threshold_uncertainty_score":0.9998637,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01847845810984757,"score_gpt":0.2434947310254057,"score_spread":0.2250162729155581,"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."}}