{"id":"W4386728170","doi":"10.1155/2023/9961341","title":"A Likelihood Ratio Approach for Utilizing Case-Control Data in the Clinical Classification of Rare Sequence Variants: Application to BRCA1 and BRCA2","year":2023,"lang":"en","type":"article","venue":"Human Mutation","topic":"Genomic variations and chromosomal abnormalities","field":"Biochemistry, Genetics and Molecular Biology","cited_by":7,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université Laval; Centre hospitalier universitaire de Québec; University of British Columbia; McGill University; University of Toronto; Royal Victoria Hospital; Queen's University; Lunenfeld-Tanenbaum Research Institute; Mount Sinai Hospital","funders":"Institute of Cancer Research; Servicio Gallego de Salud; Health and Medical Research Fund; Instituto de Salud Carlos III; Cancer Council Western Australia; Cancer Council Victoria; World Cancer Research Fund; Medical Research Council; Manchester Biomedical Research Centre; Seventh Framework Programme; Institut Gustave-Roussy; Imperial Experimental Cancer Medicine Centre; Division of Cancer Prevention, National Cancer Institute; National Institutes of Health; Hellenic Health Foundation; Freistaat Sachsen; National University Health System; Universitätsklinikum Hamburg-Eppendorf; Xunta de Galicia; Mutuelle Générale de l'Education Nationale; Ministero dello Sviluppo Economico; National Institute for Health and Care Research; Centers for Disease Control and Prevention; Memorial Sloan-Kettering Cancer Center; Kreftforeningen; Centre International de Recherche sur le Cancer; Institut National Du Cancer; European Commission; Canadian Institutes of Health Research; Sigrid Juséliuksen Säätiö; Vedecká Grantová Agentúra MŠVVaŠ SR a SAV; Cancer Institute NSW; Medizinischen Hochschule Hannover; Karolinska Institutet; Associazione Italiana per la Ricerca sul Cancro; KWF Kankerbestrijding; Horizon 2020 Framework Programme; Syöpäsäätiö; Vetenskapsrådet; Norges Forskningsråd; Stockholms Läns Landsting; University of Westminster; Ligue Contre le Cancer; Kuopion Yliopistollinen Sairaala; Stichting Tegen Kanker; Deutsche Gesetzliche Unfallversicherung; Public Health Institute; Gentofte Hospital; University of Southern California; Cancerfonden; Itä-Suomen Yliopisto; Eberhard Karls Universität Tübingen; American Cancer Society; Russian Foundation for Basic Research; University of Crete; Institut National de la Santé et de la Recherche Médicale; Canadian Cancer Society; Agence Nationale de la Recherche; Programme Grants for Applied Research; Robert Bosch Stiftung; Cancer Research UK; Fundación Mutua Madrileña; Hamburger Krebsgesellschaft; National University of Singapore; Ministerio de Economía y Competitividad; Research and Innovation Foundation; Ministry of Health -Singapore; National Cancer Institute; European Regional Development Fund; Ministerio de Sanidad, Servicios Sociales e Igualdad; University of Cambridge; Government of Canada; Stavros Niarchos Foundation; Fondation de France; Breast Cancer Campaign; NIHR Biomedical Research Centre, Royal Marsden NHS Foundation Trust/Institute of Cancer Research; National Breast Cancer Foundation; Agence Nationale de Sécurité Sanitaire de l’Alimentation, de l’Environnement et du Travail; National Institute of Environmental Health Sciences; Swedish Cancer Foundation; Ministère du Développement Économique, de l’Innovation et de l’Exportation; Lon V. Smith Foundation; Centre Hospitalier Universitaire de Québec; Genome Canada; Sundhed og Sygdom, Det Frie Forskningsråd; Breast Cancer Research Foundation; McGill University; Uddannelses- og Forskningsministeriet; Against Breast Cancer; University College London; Breast Cancer Now; Université Laval; Ministry of Science and Higher Education of the Russian Federation; California Department of Public Health; McGill University Health Centre; David F. and Margaret T. Grohne Family Foundation; Consellería de Economía, Emprego e Industria, Xunta de Galicia; Fonds Wetenschappelijk Onderzoek; VicHealth; Fondation du cancer du sein du Québec; Rheinische Friedrich-Wilhelms-Universität Bonn; Oak Foundation; Deutsches Krebsforschungszentrum; National Health and Medical Research Council; Deutsche Krebshilfe; National Center for Chronic Disease Prevention and Health Promotion; Ministère de l'Économie, de la Science et de l'Innovation - Québec; Susan G. Komen for the Cure; University of California, San Francisco; U.S. Department of Health and Human Services; Bundesministerium für Bildung und Forschung; Ovarian Cancer Research Fund","keywords":"Biology; Sequence (biology); Computational biology; 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":[],"consensus_categories":[],"category_scores_codex":[0.0009994484,0.00006822513,0.00009216446,0.0000483676,0.0001127202,0.00003055838,0.0001768915,0.0000748899,0.000001195966],"category_scores_gemma":[0.0001335687,0.00006026626,0.00002247317,0.0001274289,0.00003309457,0.00001417634,0.00004501644,0.00004218454,0.000001443892],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000008775934,"about_ca_system_score_gemma":0.00004378758,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00004919416,"about_ca_topic_score_gemma":0.0001290078,"domain_scores_codex":[0.9990913,0.0001161812,0.0003186917,0.0002999546,0.00006767405,0.0001061795],"domain_scores_gemma":[0.9993339,0.0000571562,0.0001157763,0.0003977123,0.00007284088,0.00002264175],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.0003626836,0.0005588682,0.03679073,0.0005519781,0.0002333369,0.00002403321,0.009261543,0.003143818,0.8397096,0.03799596,0.002083661,0.06928375],"study_design_scores_gemma":[0.004681899,0.0009258846,0.7033412,0.00004122995,0.0002193869,0.0003555265,0.02853834,0.2515138,0.003949129,0.004295035,0.00156069,0.0005778376],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8599812,0.00004117688,0.1385325,0.0002065741,0.00002257822,0.0008379864,0.0002571772,0.000009800872,0.0001109622],"genre_scores_gemma":[0.9950524,0.000009929949,0.002148546,0.0001075643,0.0001084673,0.0002342998,0.002313984,0.000008608641,0.00001620604],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.8357605,"threshold_uncertainty_score":0.2457587,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.09327409948535474,"score_gpt":0.3567639310938666,"score_spread":0.2634898316085118,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). 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