{"id":"W4389914448","doi":"10.1371/journal.pgen.1011074","title":"cLD: Rare-variant linkage disequilibrium between genomic regions identifies novel genomic interactions","year":2023,"lang":"en","type":"article","venue":"PLoS Genetics","topic":"Genetic Associations and Epidemiology","field":"Biochemistry, Genetics and Molecular Biology","cited_by":4,"is_retracted":false,"has_abstract":true,"ca_institutions":"Alberta Children's Hospital; University of Calgary","funders":"Natural Sciences and Engineering Research Council of Canada; Alberta Innovates; China Scholarship Council; Canada Foundation for Innovation; National Institutes of Health; National Institute of General Medical Sciences; American Diabetes Association","keywords":"Linkage disequilibrium; Biology; Genetics; Genetic association; Computational biology; Gene; Disequilibrium; Evolutionary biology; Haplotype; Allele; Single-nucleotide polymorphism; Genotype","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":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.0002793039,0.0002701391,0.0003322703,0.0001598071,0.0002583607,0.00005938377,0.0004414252,0.0002695615,0.00004589066],"category_scores_gemma":[0.0002443015,0.0002897211,0.000209346,0.0002665287,0.000124964,0.000005465242,0.0005005741,0.0002072836,0.0003928559],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00005359379,"about_ca_system_score_gemma":0.0001394938,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001461284,"about_ca_topic_score_gemma":0.00007234842,"domain_scores_codex":[0.9979795,0.000122024,0.0005594955,0.0006045994,0.0001487001,0.0005856584],"domain_scores_gemma":[0.9986158,0.0001095962,0.0002208433,0.000749012,0.0001238578,0.0001808666],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.00001321645,0.00009343827,0.0548587,0.00002711195,0.0003848035,0.00000709187,0.0001821363,0.001315307,0.9305422,0.00006773771,0.01218686,0.0003213828],"study_design_scores_gemma":[0.001643723,0.0004130093,0.7620783,0.00005612659,0.0005964789,0.00006516105,0.0005986683,0.009742077,0.06717832,0.002124236,0.1541028,0.001401023],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9934252,0.000506731,0.002898367,0.001167604,0.0005560791,0.0003160116,0.0003176412,0.00008754365,0.0007248041],"genre_scores_gemma":[0.9906602,0.0006344801,0.001608408,0.0002580963,0.001197414,0.00007408875,0.001260877,0.00007714402,0.004229324],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.8633639,"threshold_uncertainty_score":0.9999555,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04382298841673176,"score_gpt":0.28981788648437,"score_spread":0.2459948980676382,"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."}}