{"id":"W4392242077","doi":"10.26508/lsa.202302181","title":"A comparative study of structural variant calling in WGS from Alzheimer’s disease families","year":2024,"lang":"en","type":"article","venue":"Life Science Alliance","topic":"Genomics and Rare Diseases","field":"Biochemistry, Genetics and Molecular Biology","cited_by":6,"is_retracted":false,"has_abstract":true,"ca_institutions":"Institute of Aging","funders":"U.S. National Library of Medicine; National Institute of Neurological Disorders and Stroke; National Institute on Deafness and Other Communication Disorders; National Heart, Lung, and Blood Institute; Uniformed Services University of the Health Sciences; National Institutes of Health; Österreichische Forschungsförderungsgesellschaft; National Institute on Aging; Medizinische Universität Graz; Broad Institute; Oesterreichische Nationalbank; Nederlandse Organisatie voor Wetenschappelijk Onderzoek; National Alzheimer's Coordinating Center; Erasmus Medisch Centrum; Austrian Science Fund; ZonMw; Vanderbilt University; EU Joint Programme – Neurodegenerative Disease Research; European Commission; University of Pennsylvania; National Human Genome Research Institute; Russian Foundation for Basic Research; University of Miami; University of Toronto; Case Western Reserve University; Karl-Franzens-Universität Graz; U.S. Department of Health and Human Services","keywords":"Sanger sequencing; Indel; Genotyping; Biology; Genetics; Computational biology; Genome; Whole genome sequencing; Breakpoint; DNA sequencing; Single-nucleotide polymorphism; Gene; Genotype; Chromosome","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":[0.000108229,0.0001089468,0.0001366554,0.00004245722,0.00007427737,0.00005924792,0.0003210081,0.00002260485,0.000008549964],"category_scores_gemma":[0.00005086834,0.00009129094,0.00003777974,0.0002809106,0.0002262679,0.00001296728,0.0001170963,0.00006370559,0.000004668797],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000009487202,"about_ca_system_score_gemma":0.0003399797,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0002585652,"about_ca_topic_score_gemma":0.0001659292,"domain_scores_codex":[0.9989478,0.00003006669,0.0001860016,0.0004567997,0.0001897909,0.0001895524],"domain_scores_gemma":[0.9995285,0.00001604304,0.00003824514,0.0002228051,0.00005394679,0.0001405014],"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":[0.0008627077,0.00109728,0.2535817,0.0001132341,0.0005038048,0.0005909036,0.01716445,0.05084985,0.6695053,0.00183453,0.0005366071,0.00335961],"study_design_scores_gemma":[0.001122245,0.0006639969,0.9088944,0.0001887477,0.000150956,0.000003864216,0.01183893,0.04797662,0.02568449,0.001168262,0.001560954,0.0007465641],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.991095,0.008248194,0.00004308642,0.00004752776,0.0002241056,0.0002015636,0.00006020636,0.000007758626,0.00007253589],"genre_scores_gemma":[0.9994889,0.000128627,0.0001859679,0.00005929903,0.00007579123,0.00001555169,0.00002012943,0.000005877577,0.00001987364],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.6553127,"threshold_uncertainty_score":0.3722736,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03162028866889537,"score_gpt":0.3200239697807732,"score_spread":0.2884036811118778,"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."}}