{"id":"W4408724690","doi":"10.1101/gr.279240.124","title":"Expanded methylome and quantitative trait loci detection by long-read profiling of personal DNA","year":2025,"lang":"en","type":"article","venue":"Genome Research","topic":"Epigenetics and DNA Methylation","field":"Biochemistry, Genetics and Molecular Biology","cited_by":2,"is_retracted":false,"has_abstract":true,"ca_institutions":"McGill University; McGill University and Génome Québec Innovation Centre; McGill Genome Centre; Montreal Heart Institute","funders":"","keywords":"Biology; DNA methylation; Methylation; CpG site; Genetics; Alu element; Quantitative trait locus; Human genome; Genome; Computational biology; DNA; Gene; Gene expression","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":[0.000470498,0.0003483118,0.0002941094,0.001397429,0.0002141551,0.000360507,0.0002797996,0.0002639352,0.003131072],"category_scores_gemma":[0.001228425,0.0001925503,0.000631659,0.001230883,0.0001699797,0.0003048062,0.0004643252,0.0003696078,0.0006342041],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002761353,"about_ca_system_score_gemma":0.0001935777,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002338117,"about_ca_topic_score_gemma":0.00599754,"domain_scores_codex":[0.9996017,0.00005677309,0.000019623,0.0002057655,0.00007732296,0.00003880715],"domain_scores_gemma":[0.9993683,0.0002177049,0.0001704951,0.00009285829,0.00009794853,0.00005281545],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.0009170382,0.00007025238,0.158009,0.0005720917,0.0005960383,0.0002145243,0.0004314289,0.009555343,0.7332313,0.001986473,0.001956875,0.09245969],"study_design_scores_gemma":[0.00004633298,0.0004286957,0.6827593,0.00005607168,0.0005071138,0.0007945955,0.0001974284,0.06586727,0.2239604,0.003466942,0.02182038,0.00009546242],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8767931,0.0008086194,0.09477801,0.00007507415,0.00003150172,0.00006935659,0.02287699,0.001770483,0.002796849],"genre_scores_gemma":[0.8574589,0.0003202649,0.1126419,0.00009072942,0.00001906542,0.0001201697,0.02679262,0.0004656339,0.002090671],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.003131072,"threshold_uncertainty_score":0.01047444,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04577309514510525,"score_gpt":0.3812855995158716,"score_spread":0.3355125043707664,"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."}}