{"id":"W4362611986","doi":"10.1186/s13073-023-01173-8","title":"Rare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-19","year":2023,"lang":"en","type":"article","venue":"Genome Medicine","topic":"COVID-19 Clinical Research Studies","field":"Medicine","cited_by":77,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"National Center for Advancing Translational Sciences; National Institutes of Health; National Human Genome Research Institute; Mohammed Bin Rashid University of Medicine and Health Sciences; Universiteit Gent; Shahid Beheshti University of Medical Sciences; Necmettin Erbakan Üniversitesi; Universidad de La Sabana; Institute of Genetics; Agence Nationale de la Recherche; Assistance publique-Hôpitaux de Paris; Queen Mary University of London; Sveučilište Josipa Jurja Strossmayera u Osijeku; Mansoura University; Universidad de Córdoba; Tokyo Medical and Dental University; Universitat Autònoma de Barcelona; Hospices Civils de Lyon; Universidade de São Paulo; Università degli Studi di Pavia; Marmara Üniversitesi; Universidad de Antioquia; Université Libanaise; Sahlgrenska Akademin; Gazi Üniversitesi; Fondazione IRCCS Policlinico San Matteo; Universidad Complutense de Madrid; Institut National de la Santé et de la Recherche Médicale; Assistance Publique - Hôpitaux de Paris; Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung; National Center for Research Resources; National and Kapodistrian University of Athens; Karolinska Institutet; Univerzita Karlova v Praze; Karadeniz Teknik Üniversitesi; Istanbul Üniversitesi-Cerrahpasa; Northwell Health; Sorbonne Université; Fundació Institut de Recerca Hospital Universitari Vall d’Hebron; Instituto Tecnológico y de Energías Renovables; Instituto de Salud Carlos III; Universitat de Barcelona; Göteborgs Universitet; Barcelona Institute of Science and Technology; Universitair Ziekenhuis Gent; Howard Hughes Medical Institute; Novo Nordisk Fonden; Sveučilište u Zagrebu; National Institute of Allergy and Infectious Diseases","keywords":"Coronavirus disease 2019 (COVID-19); Gene; Human genetics; 2019-20 coronavirus outbreak; Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); Loss function; Immunity; Biology; Medicine; Genetics; Computational biology; Bioinformatics; Virology; Immune system; Phenotype; Internal medicine; Infectious disease (medical specialty); Disease","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":["metaresearch"],"consensus_categories":[],"category_scores_codex":[0.001957171,0.0002589032,0.001134163,0.0005035774,0.00017604,0.000003960113,0.0002358571,0.0001775269,0.0006150868],"category_scores_gemma":[0.0901248,0.0001778409,0.00009331885,0.00258533,0.000796857,0.00005681102,0.0002440689,0.0004631727,0.0000232679],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002359652,"about_ca_system_score_gemma":0.00103434,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0005420003,"about_ca_topic_score_gemma":0.00005470058,"domain_scores_codex":[0.9969206,0.0002506764,0.0007984692,0.0004141494,0.001124771,0.0004913418],"domain_scores_gemma":[0.9930027,0.004107462,0.0005011826,0.0006420593,0.001150809,0.000595761],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.006481865,0.0004906766,0.9545045,0.003379546,0.002668657,0.0005871488,0.002663975,0.001201765,0.02257449,0.00004577474,0.003397031,0.002004494],"study_design_scores_gemma":[0.006443416,0.004078097,0.9830869,0.0009774092,0.000619979,0.000004393437,0.0009659598,0.0006412817,0.00007878445,0.0001693747,0.002772607,0.0001617832],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9853613,0.001935997,0.000855665,0.009786714,0.000293929,0.000966796,0.0001545893,0.0003235526,0.000321452],"genre_scores_gemma":[0.9950326,0.001827585,0.00004261751,0.001040946,0.0002829405,0.00003105316,0.0004949198,0.00004331748,0.00120404],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.08816762,"threshold_uncertainty_score":0.9175395,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.1118416362418434,"score_gpt":0.3974789806407518,"score_spread":0.2856373443989084,"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."}}