{"id":"W2757568770","doi":"10.3389/fmed.2017.00153","title":"TruSeq-Based Gene Expression Analysis of Formalin-Fixed Paraffin-Embedded (FFPE) Cutaneous T-Cell Lymphoma Samples: Subgroup Analysis Results and Elucidation of Biases from FFPE Sample Processing on the TruSeq Platform","year":2017,"lang":"en","type":"article","venue":"Frontiers in Medicine","topic":"Cutaneous lymphoproliferative disorders research","field":"Medicine","cited_by":19,"is_retracted":false,"has_abstract":true,"ca_institutions":"Ottawa Hospital; University of Ottawa; Université Laval; Université de Montréal; McGill University Health Centre","funders":"Department of Medicine, Ottawa Hospital; Fonds de Recherche du Québec - Santé; Canadian Dermatology Foundation; Ottawa Hospital Research Institute; Dermatology Foundation","keywords":"Cutaneous T-cell lymphoma; Gene; Lymphoma; Gene expression; Mycosis fungoides; Stage (stratigraphy); Biology; Medicine; Pathology; Cancer research; 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":[0.001181835,0.000429264,0.002014291,0.001999898,0.0003935067,0.00005363899,0.0005560092,0.0002435597,0.0001234554],"category_scores_gemma":[0.005561507,0.0002879034,0.0003149108,0.001787498,0.0009446991,0.0001788878,0.0001058002,0.0002442304,7.456357e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002379508,"about_ca_system_score_gemma":0.0002921198,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.003157135,"about_ca_topic_score_gemma":0.0008903765,"domain_scores_codex":[0.9957823,0.0002141251,0.00134557,0.0007952548,0.00135631,0.0005063972],"domain_scores_gemma":[0.9948429,0.001679522,0.001246446,0.001588616,0.0004176083,0.0002249297],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.02960652,0.001963347,0.8106146,0.0005597043,0.005840832,0.0002095988,0.01224615,0.006989984,0.08905335,0.00003374771,0.002788533,0.04009367],"study_design_scores_gemma":[0.02491771,0.002355383,0.1740968,0.002031385,0.01267887,0.00002144323,0.009876969,0.4326981,0.3398194,0.0005834178,0.0001836661,0.0007369032],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9707265,0.001210622,0.02546314,0.0008575277,0.0001050746,0.000858154,0.0005276848,0.00003231741,0.0002189019],"genre_scores_gemma":[0.9845358,0.0005317365,0.01279131,0.0002291268,0.0000949169,0.00004798835,0.001671054,0.00004106162,0.00005700473],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.6365178,"threshold_uncertainty_score":0.9999573,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.05909126949065426,"score_gpt":0.3267636422206507,"score_spread":0.2676723727299964,"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."}}