{"id":"W4411753936","doi":"10.1101/2025.06.26.25330270","title":"A flexible pipeline for reproducible exome-wide rare variant gene-trait associations","year":2025,"lang":"en","type":"preprint","venue":"medRxiv","topic":"Genomics and Rare Diseases","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"McGill University Health Centre; McGill University; HEC Montréal; Jewish General Hospital","funders":"Fonds de Recherche du Québec - Santé; Canadian Institutes of Health Research; Jewish General Hospital; Public Health Agency; Compute Canada; National Institutes of Health; Public Health Agency of Canada; Cancer Research UK; McGill University","keywords":"Exome sequencing; Pipeline (software); Trait; Exome; Computational biology; Gene; Genetics; Biology; Computer science; Phenotype","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":["metaresearch"],"consensus_categories":[],"category_scores_codex":[0.01166818,0.00193247,0.001638774,0.002778667,0.002116916,0.004452174,0.003060072,0.001214965,0.03800492],"category_scores_gemma":[0.01790205,0.002031042,0.003599079,0.00203187,0.001237542,0.002497973,0.007926373,0.003773422,0.02231267],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001336696,"about_ca_system_score_gemma":0.006431209,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.004293733,"about_ca_topic_score_gemma":0.005576381,"domain_scores_codex":[0.9956697,0.0007945065,0.0004573271,0.001604347,0.001049697,0.0004243717],"domain_scores_gemma":[0.9930154,0.003102257,0.0004272207,0.001950982,0.0008962226,0.0006078783],"domain_codex":null,"domain_gemma":"reproducibility","domain_candidate":"reproducibility","domain_consensus":null,"study_design_codex":"not_applicable","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.003283867,0.0002504717,0.01612535,0.003104005,0.001564306,0.001608248,0.001301593,0.01673753,0.07184417,0.03029311,0.6412131,0.2126742],"study_design_scores_gemma":[0.001664333,0.0002236893,0.02704636,0.0006522746,0.0005507557,0.001634737,0.0003614406,0.1148717,0.1015679,0.1412328,0.6094378,0.0007561792],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.008116417,0.00055164,0.5936688,0.00154001,0.0005674221,0.0006820952,0.09679716,0.2928143,0.005262198],"genre_scores_gemma":[0.06600616,0.0007096859,0.6783798,0.002269249,0.0002992294,0.003337069,0.1672248,0.07262554,0.009148572],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.9883318,"threshold_uncertainty_score":0.1271391,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02263775004457648,"score_gpt":0.2864636300978439,"score_spread":0.2638258800532675,"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."}}