{"id":"W4221133498","doi":"10.1101/2022.03.28.486092","title":"High Quality Phasing Using Linked-Read Whole Genome Sequencing of Patient Cohorts Informs Genetic Understanding of Complex Traits","year":2022,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Cystic Fibrosis Research Advances","field":"Medicine","cited_by":1,"is_retracted":false,"has_abstract":true,"ca_institutions":"Public Health Ontario; University of Toronto; St. Michael's Hospital; Queen Elizabeth II Health Sciences Centre; Memorial University of Newfoundland; St. Paul's Hospital; Alberta Children's Hospital; Izaak Walton Killam Health Centre; London Health Sciences Centre; Hospital for Sick Children; Université de Montréal; University of Calgary; BC Children's Hospital; Centre Hospitalier de l’Université de Montréal; University of Alberta Hospital; Capital District Health Authority; SickKids Foundation; Kingston Health Sciences Centre","funders":"Common Fund; National Institute of Neurological Disorders and Stroke; National Cancer Institute; NIH Office of the Director; National Human Genome Research Institute; Hospital for Sick Children; National Institute of Mental Health; National Heart, Lung, and Blood Institute; National Institutes of Health; Government of Canada; National Institute on Drug Abuse; Government of Ontario; Natural Sciences and Engineering Research Council of Canada; Cystic Fibrosis Canada; Canadian Institutes of Health Research; Genome Canada","keywords":"Haplotype; Genetics; Biology; Computational biology; Locus (genetics); Structural variation; Exome sequencing; 1000 Genomes Project; Exome; Population; Genome; Viral quasispecies; Phaser; Allele; Genotype; Single-nucleotide polymorphism; Gene; Mutation; Medicine","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":[0.005672629,0.0008650458,0.001021416,0.002246505,0.0008048287,0.001741968,0.0008285069,0.0009462071,0.005302808],"category_scores_gemma":[0.01081121,0.0005539804,0.001553648,0.002142524,0.0005315512,0.0007642304,0.001630621,0.001392785,0.001706409],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0004314651,"about_ca_system_score_gemma":0.000967833,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.003349952,"about_ca_topic_score_gemma":0.007133881,"domain_scores_codex":[0.9978774,0.0008302002,0.0001778038,0.0006390529,0.0003393664,0.0001361669],"domain_scores_gemma":[0.9923697,0.003894656,0.0008223353,0.00160971,0.001029521,0.0002740814],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.002082757,0.0003866198,0.4110917,0.001960437,0.006179814,0.001650964,0.001829403,0.07024658,0.2982703,0.01220309,0.02468956,0.1694089],"study_design_scores_gemma":[0.0005790761,0.000859928,0.5476338,0.0007250513,0.002593395,0.002334751,0.001296412,0.1799824,0.0977999,0.06586383,0.09984798,0.0004835645],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.5729843,0.00313275,0.3668121,0.001061151,0.0003232801,0.000304236,0.04593505,0.003827739,0.005619267],"genre_scores_gemma":[0.7375721,0.0009799489,0.2118262,0.001020173,0.0001891715,0.0003857288,0.04352717,0.002190285,0.002309249],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.005672629,"threshold_uncertainty_score":0.03000009,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.07741671179886701,"score_gpt":0.3107613480825393,"score_spread":0.2333446362836723,"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."}}