{"id":"W4408854573","doi":"10.1101/gr.279414.124","title":"Unraveling undiagnosed rare disease cases by HiFi long-read genome sequencing","year":2025,"lang":"en","type":"article","venue":"Genome Research","topic":"Genomics and Rare Diseases","field":"Biochemistry, Genetics and Molecular Biology","cited_by":24,"is_retracted":false,"has_abstract":true,"ca_institutions":"Ottawa Hospital; Children's Hospital of Eastern Ontario; University of Ottawa","funders":"National Institute of Neurological Disorders and Stroke; Canadian Institutes of Health Research; Sigrid Juséliuksen Säätiö; Bundesministerium für Bildung und Forschung; ZonMw; Canada Foundation for Innovation; Deutsche Forschungsgemeinschaft; European Commission; Canada First Research Excellence Fund; Canada Research Chairs; Government of Canada","keywords":"Indel; Biology; Genetics; Genetic testing; Disease; DNA sequencing; Whole genome sequencing; Rare disease; Genome; Computational biology; Gene; Single-nucleotide polymorphism; Genotype; Medicine; Pathology","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":[],"consensus_categories":[],"category_scores_codex":[0.0005799666,0.0002368218,0.000207021,0.0002548057,0.0004434196,0.0001556194,0.0005696782,0.0001507235,0.0001732677],"category_scores_gemma":[0.0004663279,0.000235943,0.0001577232,0.0004196713,0.0002127051,0.000006394827,0.0005133236,0.0002548859,0.00008825135],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001966947,"about_ca_system_score_gemma":0.001068932,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001712257,"about_ca_topic_score_gemma":0.000053162,"domain_scores_codex":[0.997536,0.0002129359,0.000290909,0.0007607742,0.000365854,0.0008335363],"domain_scores_gemma":[0.9983094,0.00009885801,0.00004611786,0.0007727078,0.0003485855,0.0004243302],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"not_applicable","study_design_scores_codex":[0.0004724874,0.0002792691,0.009141427,0.0004051334,0.0002941409,0.001193652,0.0001323901,0.0007171981,0.9779337,0.000328245,0.006274383,0.002827998],"study_design_scores_gemma":[0.004311163,0.001101117,0.1081118,0.0003689587,0.0002587076,0.0001408088,0.003844391,0.0003300058,0.0704525,0.002436694,0.8060212,0.002622679],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9628844,0.0321658,0.0005949964,0.0006551684,0.0001322998,0.0005908181,0.0005820571,0.00002851597,0.002365945],"genre_scores_gemma":[0.9880822,0.002469286,0.00009434323,0.000271692,0.0002685591,0.0001001555,0.00145754,0.00003797068,0.007218277],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.9074812,"threshold_uncertainty_score":0.9621475,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04089740467422606,"score_gpt":0.3496437207074777,"score_spread":0.3087463160332516,"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."}}