{"id":"W4321611576","doi":"10.1128/jcm.01578-22","title":"Genomic Sequencing from Sputum for Tuberculosis Disease Diagnosis, Lineage Determination, and Drug Susceptibility Prediction","year":2023,"lang":"en","type":"article","venue":"Journal of Clinical Microbiology","topic":"Mycobacterium research and diagnosis","field":"Medicine","cited_by":27,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université de Montréal; Centre Hospitalier de l’Université de Montréal","funders":"Fonds de Recherche du Québec - Santé; University of Oxford; Wellcome Trust; Academy of Medical Sciences; National Institute for Health and Care Research; Australian Government; International Seafood Sustainability Foundation","keywords":"Minion; Tuberculosis; Sputum; Mycobacterium tuberculosis; Multiplex; Biology; Drug resistance; Deep sequencing; DNA sequencing; Nanopore sequencing; Virology; Computational biology; Medicine; Genetics; Genome; Gene; Pathology","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":[0.002827612,0.0005417299,0.0004155379,0.00108966,0.0003654952,0.001435194,0.0005126751,0.0006773346,0.03370298],"category_scores_gemma":[0.005034169,0.000335405,0.0003340957,0.0006894141,0.0004361506,0.0004917868,0.0006292099,0.000921118,0.007639567],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003859545,"about_ca_system_score_gemma":0.0008281466,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0007598487,"about_ca_topic_score_gemma":0.002369245,"domain_scores_codex":[0.9976681,0.0007568668,0.0001740759,0.0006020108,0.0005526104,0.000246359],"domain_scores_gemma":[0.9979097,0.0008878296,0.0002402327,0.000337687,0.0003758243,0.0002487759],"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":[0.003756708,0.0007649073,0.1286515,0.001412474,0.0009117963,0.001187643,0.000933621,0.001343721,0.5436261,0.004207367,0.02215681,0.2910473],"study_design_scores_gemma":[0.0004435979,0.003096758,0.3701507,0.0008382076,0.0006239642,0.01125309,0.001257331,0.04620167,0.2697869,0.008023647,0.2882017,0.0001223661],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.6906078,0.009848454,0.1798534,0.002763576,0.001900587,0.00195275,0.02604886,0.005393349,0.08163111],"genre_scores_gemma":[0.8036255,0.001343801,0.1450024,0.001247056,0.0002317359,0.0008584708,0.01521156,0.0007778893,0.03170162],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.03370298,"threshold_uncertainty_score":0.1127477,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.06113864228723981,"score_gpt":0.3852413319730619,"score_spread":0.3241026896858221,"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."}}