{"id":"W3004894219","doi":"10.1016/j.isci.2020.100883","title":"Genotyping and Copy Number Analysis of Immunoglobin Heavy Chain Variable Genes Using Long Reads","year":2020,"lang":"en","type":"article","venue":"iScience","topic":"RNA and protein synthesis mechanisms","field":"Biochemistry, Genetics and Molecular Biology","cited_by":26,"is_retracted":false,"has_abstract":true,"ca_institutions":"Simon Fraser University","funders":"National Institute of General Medical Sciences; University of Louisville; National Science Foundation; Indiana University; National Institutes of Health; Simon Fraser University","keywords":"IGHV@; Genotyping; Copy-number variation; Biology; Computational biology; Genetics; Immunoglobulin heavy chain; Genome; Locus (genetics); Gene; Genotype","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":[0.0002563561,0.00008267872,0.0001589812,0.00002900698,0.00008882572,0.00002483777,0.0001687171,0.0000613827,0.0000441867],"category_scores_gemma":[0.00006107692,0.00007751854,0.00004909721,0.0004578175,0.00008971395,0.000006328105,0.0001169761,0.00002589019,0.000001763817],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000005207953,"about_ca_system_score_gemma":0.00004954878,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00009124921,"about_ca_topic_score_gemma":0.000004886856,"domain_scores_codex":[0.9992534,0.00004575641,0.0001474526,0.0002872642,0.0001102193,0.0001559141],"domain_scores_gemma":[0.9996219,0.00001019306,0.00007791953,0.0001819241,0.00004449742,0.00006362409],"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":[0.00002316941,0.00000673014,0.007202362,0.00001072075,0.0000625119,0.000001009702,0.00007854084,0.0006377539,0.989431,0.0001583516,0.000006411929,0.002381389],"study_design_scores_gemma":[0.00007617592,0.00004971534,0.001193967,0.00001031613,0.00009695092,0.000004965202,0.00005201503,0.00553057,0.9921768,0.00004471884,0.0006484697,0.0001153818],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8967125,0.00190022,0.1009345,0.00006402383,0.000034378,0.00006871815,0.000009231201,0.000004965879,0.0002714811],"genre_scores_gemma":[0.9848003,0.0001463413,0.01475428,0.0001986987,0.00003799934,0.00000264958,0.000005754195,0.000006151808,0.00004782427],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.0880878,"threshold_uncertainty_score":0.3161114,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02021725446479039,"score_gpt":0.2644518953894202,"score_spread":0.2442346409246298,"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."}}