{"id":"W4403924852","doi":"10.1093/bioadv/vbae168","title":"Population-aware permutation-based significance thresholds for genome-wide association studies","year":2024,"lang":"en","type":"article","venue":"Bioinformatics Advances","topic":"Genetic Associations and Epidemiology","field":"Biochemistry, Genetics and Molecular Biology","cited_by":2,"is_retracted":false,"has_abstract":true,"ca_institutions":"Canada's Michael Smith Genome Sciences Centre; University of British Columbia, Okanagan Campus; University of British Columbia","funders":"Bundesministerium für Bildung und Forschung","keywords":"Genome-wide association study; Genetic association; Association (psychology); Population; Genetics; Permutation (music); Biology; Computational biology; Evolutionary biology; Single-nucleotide polymorphism; Medicine; Psychology; Genotype; Gene; Environmental health; Physics","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":[0.01442979,0.0009412487,0.0013465,0.002163425,0.0008183125,0.00186871,0.002359571,0.001225303,0.009591878],"category_scores_gemma":[0.08006688,0.0008890066,0.001658716,0.003346759,0.001352682,0.001417857,0.001822109,0.003140869,0.003427611],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0006013829,"about_ca_system_score_gemma":0.00278984,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001598435,"about_ca_topic_score_gemma":0.002274323,"domain_scores_codex":[0.9908345,0.006020814,0.0005463621,0.001338083,0.001005783,0.0002544718],"domain_scores_gemma":[0.9666415,0.02460841,0.001315907,0.004781404,0.002125634,0.0005271194],"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":[0.002831911,0.0003860384,0.02523682,0.002385924,0.002132587,0.001411941,0.0006555972,0.1103324,0.04522774,0.06416636,0.07274893,0.6724837],"study_design_scores_gemma":[0.001030496,0.0004917483,0.01202714,0.0002530685,0.0004287348,0.001355431,0.0001574803,0.6231638,0.03535448,0.2744403,0.0510455,0.000251944],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.007952648,0.000326561,0.9799532,0.0004304303,0.0001928077,0.0002206308,0.001768377,0.008393181,0.0007621389],"genre_scores_gemma":[0.110365,0.0002064399,0.881385,0.0003560157,0.0001966469,0.001221524,0.003170095,0.002189828,0.0009095255],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.01442979,"threshold_uncertainty_score":0.07631296,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01891542148422085,"score_gpt":0.3156294565846542,"score_spread":0.2967140351004333,"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."}}