{"id":"W2140658698","doi":"10.1186/s13058-015-0567-2","title":"An original phylogenetic approach identified mitochondrial haplogroup T1a1 as inversely associated with breast cancer risk in BRCA2 mutation carriers","year":2015,"lang":"en","type":"article","venue":"Breast Cancer Research","topic":"Mitochondrial Function and Pathology","field":"Biochemistry, Genetics and Molecular Biology","cited_by":35,"is_retracted":false,"has_abstract":true,"ca_institutions":"St. Michael's Hospital; Cancer Care Ontario; University of Toronto; McGill University; Université Laval; Lunenfeld-Tanenbaum Research Institute; Mount Sinai Hospital; Centre hospitalier de l'Université Laval; Canada Research Chairs; Centre hospitalier universitaire de Québec","funders":"Jonsson Comprehensive Cancer Center; Medical Research Council; National Institutes of Health; Centre Léon Bérard; National Cancer Institute; Liga Portuguesa Contra o Cancro; Ministero dello Sviluppo Economico; Radboud Universitair Medisch Centrum; Deutsche Krebshilfe; Universitair Medisch Centrum Groningen; Leids Universitair Medisch Centrum; Hospices Civils de Lyon; Ministerio de Ciencia e Innovación; European Regional Development Fund; Centre National de la Recherche Scientifique; National Health and Medical Research Council; Jewish General Hospital; State Education Development Agency Republic of Latvia; Lietuvos Mokslo Taryba; University of California, Los Angeles; Università degli Studi di Firenze; KWF Kankerbestrijding; Universitair Ziekenhuis Gent; Nederlandse Organisatie voor Wetenschappelijk Onderzoek; Ministero della Salute; Generalitat de Catalunya; Erasmus Medisch Centrum; Pomorski Uniwersytet Medyczny W Szczecinie; Vrije Universiteit Amsterdam; NIH Office of the Director; Institut Claudius Regaud; Universiteit Leiden; Cancer Australia; National Breast Cancer Foundation; Ministerstvo Zdravotnictví Ceské Republiky; Centre Hospitalier Universitaire de Nantes; European Commission; National Institute for Health and Care Research; Canadian Breast Cancer Research Alliance; Génome Québec; David F. and Margaret T. Grohne Family Foundation; Breast Cancer Research Foundation; McGill University; Univerzita Karlova v Praze; Unicancer; Clalit Health Services; Deutsches Krebsforschungszentrum; U.S. Department of Defense; Cancer Research UK; Associazione Italiana per la Ricerca sul Cancro; Beckman Research Institute, City of Hope; Cancer Center, University of Kansas; Cancerfonden; Radboud Universiteit; Ministère du Développement Économique, de l’Innovation et de l’Exportation; Fundación Mutua Madrileña; Israel Cancer Association; Institut Català de la Salut; Institut Gustave-Roussy; University of Pennsylvania; Susan G. Komen; Hungarian Scientific Research Fund; Cedars-Sinai Medical Center; Fundación Ramón Areces; Helsingin ja Uudenmaan Sairaanhoitopiiri; Landspítali Háskólasjúkrahús; University of Kansas; University of California, San Francisco; Masarykova Univerzita; Universiteit Gent; Mayo Clinic; Creighton University; Istituto Oncologico Veneto; Royal Marsden NHS Foundation Trust; European Social Fund; University of Chicago; Memorial Sloan-Kettering Cancer Center; Canadian Institutes of Health Research; General Secretariat for Research and Technology; Dr. Ralph and Marian Falk Medical Research Trust; Kansas Bioscience Authority; Istituto Toscano Tumori; Cancer Association of South Africa; Instituto de Salud Carlos III; Ohio State University; Institut Bergonié; American Cancer Society","keywords":"Breast cancer; Surgical oncology; Haplogroup; Mitochondrial DNA; Human mitochondrial DNA haplogroup; Genetics; Phylogenetic tree; Mutation; Medicine; Biology; Bioinformatics; Oncology; Internal medicine; Cancer; Gene; Haplotype; Genotype","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":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.00095717,0.0002736103,0.0002910201,0.0002827789,0.0001986306,0.0001111436,0.0003981755,0.0003805103,0.0002305965],"category_scores_gemma":[0.0001570348,0.0002474861,0.00007013015,0.0007564891,0.0003799549,0.00002910669,0.0000885007,0.0005671863,0.00003262961],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000376178,"about_ca_system_score_gemma":0.001702803,"about_ca_topic_candidate":true,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.01579488,"about_ca_topic_score_gemma":0.01415787,"domain_scores_codex":[0.9960281,0.001152735,0.0003055551,0.0009283246,0.0007733114,0.0008120058],"domain_scores_gemma":[0.997987,0.00002782402,0.0001469707,0.0004986961,0.0008375585,0.0005019403],"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":[0.01942957,0.001085287,0.4281539,0.0000761775,0.0006088435,0.0002043665,0.002196049,0.01006404,0.5084775,0.0001897344,0.01560527,0.01390918],"study_design_scores_gemma":[0.0479821,0.005866861,0.8464738,0.0004244189,0.0004843941,0.002725055,0.009463049,0.006863538,0.05370214,0.001030939,0.02125868,0.003725065],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.996214,0.0002927635,0.0003919088,0.0002568986,0.0007196411,0.0006892271,0.0006501757,0.0000297131,0.0007556209],"genre_scores_gemma":[0.9961524,0.000150628,0.000239148,0.0001326733,0.001225177,0.0005673324,0.0004978902,0.00006263343,0.0009721033],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.4547754,"threshold_uncertainty_score":0.9999977,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04020520409984338,"score_gpt":0.3404477698499055,"score_spread":0.3002425657500621,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). 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