{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.000540753,0.0004450023,0.0004523512,0.0007523581,0.0004077253,0.0005083886,0.0004484904,0.0005558141,0.003951419],"category_scores_gemma":[0.00191861,0.0001821973,0.0007927004,0.000634279,0.0005160725,0.0001999797,0.000456451,0.0006519156,0.0002812924],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001274618,"about_ca_system_score_gemma":0.0001497173,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001285406,"about_ca_topic_score_gemma":0.001237261,"domain_scores_codex":[0.9993014,0.0001871375,0.00006724492,0.0002368884,0.0000980359,0.0001093585],"domain_scores_gemma":[0.9982705,0.0006003679,0.0006713501,0.0001446564,0.00009032427,0.0002228183],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.001190996,0.00003828773,0.9758319,0.00003812362,0.0004058119,0.001476129,0.00006648428,0.0002091411,0.01750237,0.0001122017,0.0001694736,0.002959073],"study_design_scores_gemma":[0.00002714226,0.0002030553,0.9924536,0.0000146651,0.0002478153,0.004222799,0.0001189471,0.0008471762,0.001345607,0.0001743921,0.0003357773,0.0000089966],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9984048,0.0002896732,0.000666173,0.00004679294,0.000009607393,0.000004521652,0.0003154846,0.00001528464,0.0002477172],"genre_scores_gemma":[0.999605,0.00004024427,0.0001432682,0.00001525544,0.000007330131,0.000001694759,0.0001209668,0.000004538163,0.00006172864],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.003951419,"threshold_uncertainty_score":0.01321888,"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). 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