{"id":"W4307838508","doi":"10.1038/s41592-022-01640-x","title":"A framework for detecting noncoding rare-variant associations of large-scale whole-genome sequencing studies","year":2022,"lang":"en","type":"article","venue":"Nature Methods","topic":"Genetic Associations and Epidemiology","field":"Biochemistry, Genetics and Molecular Biology","cited_by":109,"is_retracted":false,"has_abstract":false,"ca_institutions":"University of Saskatchewan; Université Laval; University of Ottawa; McGill University; University of Calgary; Providence Health Care","funders":"National Institute on Minority Health and Health Disparities; National Center for Advancing Translational Sciences; National Institute of Environmental Health Sciences; National Institute of Neurological Disorders and Stroke; National Institute of General Medical Sciences; National Cancer Institute; National Human Genome Research Institute; National Institute of Mental Health; National Heart, Lung, and Blood Institute; National Institute of Diabetes and Digestive and Kidney Diseases; National Institute of Arthritis and Musculoskeletal and Skin Diseases; National Center for Research Resources; National Institute of Allergy and Infectious Diseases; Universität des Saarlandes; National Institutes of Health; Regeneron Pharmaceuticals; National Institute on Aging; Quest Diagnostics; National Institute on Drug Abuse; University of Pennsylvania; Boston Scientific Corporation; Yale University; Eli Lilly and Company; AstraZeneca; Amgen","keywords":"Computational biology; Genome; Biology; Annotation; Gene; Whole genome sequencing; DNA sequencing; Genetics; Genome project; Genetic association; Gene Annotation; Human genome; Single-nucleotide polymorphism; Genotype","routes":{"ca_aff":true,"ca_fund":false,"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":[0.04732138,0.002163979,0.003501009,0.008613593,0.002143345,0.008113661,0.005519849,0.00363982,0.002690367],"category_scores_gemma":[0.1091095,0.001695801,0.004291276,0.00511032,0.004307555,0.004378758,0.008282173,0.005474823,0.001158181],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001715191,"about_ca_system_score_gemma":0.005547315,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.006616788,"about_ca_topic_score_gemma":0.007954203,"domain_scores_codex":[0.9715442,0.0161152,0.002520833,0.004843479,0.004199757,0.0007764262],"domain_scores_gemma":[0.9086413,0.07126081,0.005285875,0.007899385,0.005089777,0.001822961],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"theoretical_or_conceptual","study_design_gemma":"theoretical_or_conceptual","study_design_scores_codex":[0.0006023844,0.0003102788,0.02837306,0.002121925,0.002520958,0.001792833,0.001255176,0.07022827,0.01352892,0.4918449,0.01223876,0.3751825],"study_design_scores_gemma":[0.0002010753,0.0001828069,0.00468115,0.0004003038,0.0007020698,0.00122721,0.0002247133,0.3039325,0.003296429,0.6625799,0.02238131,0.000190647],"study_design_candidate":"theoretical_or_conceptual","study_design_consensus":"theoretical_or_conceptual","genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.0009501996,0.0003687081,0.9969221,0.0004998681,0.00005141414,0.0001124835,0.0002123674,0.0005472706,0.0003355548],"genre_scores_gemma":[0.03637831,0.0003966173,0.96091,0.0005169968,0.0001588498,0.000532306,0.0004629108,0.000137229,0.0005067849],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.04732138,"threshold_uncertainty_score":0.2502624,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.05853989703365103,"score_gpt":0.4277764677260754,"score_spread":0.3692365706924243,"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."}}