{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.07435314,0.001681354,0.002277868,0.008731692,0.0009211677,0.002948758,0.003801941,0.002300192,0.003411081],"category_scores_gemma":[0.2392806,0.001211608,0.002425102,0.003754936,0.002041648,0.002035967,0.002153452,0.002801042,0.0008700503],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0009595429,"about_ca_system_score_gemma":0.00166969,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002691017,"about_ca_topic_score_gemma":0.001865342,"domain_scores_codex":[0.9371505,0.04989739,0.003061543,0.005109611,0.004419007,0.0003619405],"domain_scores_gemma":[0.8334742,0.1492623,0.005546281,0.0070004,0.003990229,0.0007265427],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.00286251,0.0008438469,0.0926754,0.001291248,0.004396776,0.003498272,0.001538331,0.06941743,0.008975524,0.07276166,0.01242073,0.7293182],"study_design_scores_gemma":[0.001002211,0.0009305612,0.01667827,0.0002232373,0.0006756326,0.005673841,0.0002768122,0.8167765,0.0056398,0.1386615,0.01311764,0.0003441647],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.006434444,0.0004161156,0.9911912,0.0002981435,0.00007089548,0.0002532133,0.0002477589,0.0008133632,0.0002748943],"genre_scores_gemma":[0.1333431,0.0003279108,0.8632125,0.0002690613,0.0002231118,0.0008671749,0.0008047021,0.0004068379,0.0005456091],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.07435314,"threshold_uncertainty_score":0.3932217,"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). Scores rank; they never assert a category."}}