{"id":"W4403053527","doi":"10.1101/gr.279273.124","title":"High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation","year":2024,"lang":"en","type":"article","venue":"Genome Research","topic":"Genetic Syndromes and Imprinting","field":"Biochemistry, Genetics and Molecular Biology","cited_by":77,"is_retracted":false,"has_abstract":true,"ca_institutions":"Canadian Bulletin of Medical History","funders":"National Institute of Allergy and Infectious Diseases; National Institute of Neurological Disorders and Stroke; National Institute of General Medical Sciences; National Human Genome Research Institute; National Institute on Drug Abuse; National Institute on Aging; Fonds Wetenschappelijk Onderzoek; National Institute of Standards and Technology; Lustgarten Foundation; National Cancer Institute; National Institutes of Health; National Science Foundation","keywords":"Biology; Indel; 1000 Genomes Project; Structural variation; Genome; Computational biology; Genetics; Concordance; Human genome; Whole genome sequencing; Personal genomics; DNA sequencing; Nanopore sequencing; Copy-number variation; Single-nucleotide polymorphism; Gene; Genotype","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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.000505588,0.0001409048,0.0002143637,0.0001520891,0.0001392222,0.00005816328,0.0004431171,0.0001048792,0.00005680481],"category_scores_gemma":[0.00007873564,0.0001106317,0.00008540128,0.0004583219,0.0001267869,0.000003650378,0.0004734621,0.0001596399,0.0000135076],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0000542886,"about_ca_system_score_gemma":0.0003956972,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.004890588,"about_ca_topic_score_gemma":0.0001230881,"domain_scores_codex":[0.9982191,0.0002050684,0.000356458,0.0004575434,0.0003934383,0.0003684161],"domain_scores_gemma":[0.9988225,0.0001179298,0.00006319318,0.0005798153,0.0003596715,0.00005693571],"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":[0.000009423416,0.00001601619,0.001079885,0.0001180744,0.0001244489,0.000003633789,0.001425671,0.000380909,0.9935765,0.0001537935,0.0001708415,0.002940828],"study_design_scores_gemma":[0.0005319716,0.001535589,0.3484671,0.0002214255,0.00006342671,0.00003535422,0.002180136,0.0001274466,0.6229725,0.001473261,0.02196201,0.0004297192],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9912265,0.006544724,0.001047158,0.0001353548,0.00008134527,0.0005730255,0.0002278268,0.000008301711,0.0001557916],"genre_scores_gemma":[0.9962531,0.0004648512,0.002529386,0.0000288903,0.00023546,0.00004217499,0.0002411149,0.00003168533,0.0001733817],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.3706039,"threshold_uncertainty_score":0.7393138,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.06116980272795516,"score_gpt":0.3402952870025182,"score_spread":0.2791254842745631,"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."}}