{"id":"W3094583419","doi":"10.1371/journal.pcbi.1008336","title":"LocusFocus: Web-based colocalization for the annotation and functional follow-up of GWAS","year":2020,"lang":"en","type":"article","venue":"PLoS Computational Biology","topic":"Genetic Associations and Epidemiology","field":"Biochemistry, Genetics and Molecular Biology","cited_by":46,"is_retracted":false,"has_abstract":true,"ca_institutions":"SickKids Foundation; University of Toronto; Hospital for Sick Children","funders":"Hospital for Sick Children; Ontario Genomics Institute; Natural Sciences and Engineering Research Council of Canada; Cystic Fibrosis Canada; Canadian Institutes of Health Research; Genome Canada; Ontario Genomics; Cystic Fibrosis Foundation","keywords":"Genome-wide association study; Expression quantitative trait loci; Biology; Colocalization; Locus (genetics); Genetics; Quantitative trait locus; Computational biology; Genetic association; Linkage disequilibrium; Gene; Single-nucleotide polymorphism; Allele; Haplotype; Genotype; Molecular biology","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":[0.0001618647,0.00009066924,0.0001422838,0.00002510293,0.0001069911,0.000005233991,0.00006812144,0.000124732,0.00001608151],"category_scores_gemma":[0.0005927522,0.00007210974,0.00006161127,0.00008383155,0.0001314668,0.000002100925,0.00003238988,0.00003901236,0.000002410738],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000007032271,"about_ca_system_score_gemma":0.0001220524,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000004169594,"about_ca_topic_score_gemma":0.000007738688,"domain_scores_codex":[0.9992421,0.000103997,0.0002468826,0.0002301336,0.0000597302,0.0001171668],"domain_scores_gemma":[0.9990697,0.0003857755,0.0001560661,0.00006746047,0.0002811092,0.00003989376],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"simulation_or_modeling","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.001476946,0.0002164527,0.2081971,0.0001420783,0.0007917699,2.882868e-7,0.0002792315,0.4835658,0.2597214,0.01504059,0.02285946,0.007708799],"study_design_scores_gemma":[0.004290932,0.001422692,0.08267773,0.000008116404,0.0001270646,0.000003068437,0.0001332604,0.8813236,0.00641152,0.006165955,0.01716971,0.0002663865],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.5010871,0.0004421043,0.4917829,0.006005888,0.0001344225,0.0003468558,0.0001454364,0.00001166882,0.00004369376],"genre_scores_gemma":[0.9911624,0.00002488687,0.005292025,0.002035447,0.0001637275,0.00006368798,0.001231051,0.000009162215,0.00001759893],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.4900753,"threshold_uncertainty_score":0.294055,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02951483153121186,"score_gpt":0.258211786727303,"score_spread":0.2286969551960912,"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."}}