{"id":"W4413955644","doi":"10.1101/2025.09.01.673535","title":"On the analysis of genetic association with long-read sequencing data","year":2025,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Genetic Associations and Epidemiology","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"SickKids Foundation; Hospital for Sick Children; Public Health Ontario; University of Toronto","funders":"Centre for Applied Genomics; Ontario Genomics Institute; Genome Canada","keywords":"Association (psychology); Genetic association; DNA sequencing; Computer science; Computational biology; Genetics; Biology; Psychology; Genotype; Single-nucleotide polymorphism; DNA; Gene","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":[],"consensus_categories":[],"category_scores_codex":[0.01292266,0.000736111,0.0008542813,0.001860059,0.000465114,0.001068218,0.001334483,0.0009272718,0.004177266],"category_scores_gemma":[0.04287948,0.0004623845,0.001350608,0.00197898,0.000863164,0.0009150786,0.001311761,0.00145809,0.0009429816],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0004494572,"about_ca_system_score_gemma":0.001090473,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.003723776,"about_ca_topic_score_gemma":0.003920114,"domain_scores_codex":[0.9938304,0.004031195,0.0002537648,0.001060939,0.0006889154,0.0001348058],"domain_scores_gemma":[0.9544327,0.03989793,0.001795138,0.002326744,0.001168041,0.0003794879],"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":[0.001884499,0.0003897635,0.1536292,0.0008510254,0.002361748,0.001992723,0.0004348217,0.5294895,0.02889838,0.04012507,0.005782347,0.2341609],"study_design_scores_gemma":[0.00008487888,0.0001774344,0.0120917,0.00005102692,0.0001200753,0.0002155634,0.00005548515,0.952706,0.004465424,0.02666576,0.003328075,0.00003858151],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.1266292,0.0006496276,0.865598,0.0006224909,0.0001505898,0.0001341211,0.001631438,0.003220771,0.001363807],"genre_scores_gemma":[0.6145114,0.0004187209,0.3777849,0.000651556,0.0001462236,0.0003641503,0.003334408,0.0006553769,0.00213321],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.01292266,"threshold_uncertainty_score":0.06834239,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02131765624171994,"score_gpt":0.2495374050447443,"score_spread":0.2282197488030244,"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."}}