{"id":"W4406313043","doi":"10.1038/s41525-024-00453-5","title":"Pre-T cell receptor-α immunodeficiency detected exclusively using whole genome sequencing","year":2025,"lang":"en","type":"article","venue":"npj Genomic Medicine","topic":"Immunodeficiency and Autoimmune Disorders","field":"Immunology and Microbiology","cited_by":1,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Toronto; SickKids Foundation; Hospital for Sick Children","funders":"Immunodeficiency Canada","keywords":"T-cell receptor; Exome sequencing; Whole genome sequencing; Biology; T cell; Immunodeficiency; Genome; Genetics; DNA sequencing; Computational biology; Gene; Cell; Mutation; Immune system","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","insufficient_payload"],"consensus_categories":[],"category_scores_codex":[0.0007357881,0.0004439406,0.0006685434,0.0004801203,0.0008350092,0.00002053788,0.0007932525,0.0003777335,0.001496539],"category_scores_gemma":[0.0001762152,0.0003944986,0.0001483322,0.000713026,0.000683487,0.0001225466,0.0002829816,0.0006594178,0.0005958259],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0004670127,"about_ca_system_score_gemma":0.0005218462,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0008746593,"about_ca_topic_score_gemma":0.000003581181,"domain_scores_codex":[0.9971923,0.0002618953,0.0009005956,0.0006730681,0.00009262581,0.0008795141],"domain_scores_gemma":[0.998583,0.0001587954,0.000313134,0.0007690596,0.0001591483,0.00001688437],"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":[0.00012118,0.00008060625,0.0001239647,0.00007227698,0.00009524965,0.000003767001,0.002819568,0.0004157058,0.9918598,0.0001800255,0.0002199846,0.004007905],"study_design_scores_gemma":[0.01862632,0.001259438,0.03754316,0.00129925,0.0009325947,0.0002215087,0.02208009,0.001257538,0.4552186,0.001300987,0.4576387,0.002621823],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8762051,0.1062389,0.003538341,0.0003331344,0.002224603,0.0005416634,0.00003123505,0.0001874353,0.01069955],"genre_scores_gemma":[0.9855426,0.0003055766,0.0001529658,0.0005829965,0.00002099651,0.00002321122,0.0002299721,0.00003915843,0.01310255],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.5366412,"threshold_uncertainty_score":0.9998507,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01413077086776922,"score_gpt":0.2473054916816813,"score_spread":0.2331747208139121,"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."}}