{"id":"W2753589877","doi":"10.1101/183038","title":"Accuracy of programs for the determination of HLA alleles from NGS data","year":2017,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"T-cell and B-cell Immunology","field":"Immunology and Microbiology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"McGill University and Génome Québec Innovation Centre","funders":"Tekes","keywords":"Human leukocyte antigen; Allele; Exome; Exome sequencing; Genetics; Biology; Genome; DNA sequencing; Computational biology; Gene; Typing; 1000 Genomes Project; Transplantation; Human genome; Antigen; Mutation; Single-nucleotide polymorphism; Genotype; Medicine","routes":{"ca_aff":true,"ca_fund":false,"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":[0.02000448,0.001888126,0.001395362,0.004455904,0.0008210471,0.003256398,0.001849447,0.001990674,0.001953248],"category_scores_gemma":[0.05989502,0.0006033737,0.002125633,0.002541963,0.0008429114,0.001927718,0.001689573,0.002260526,0.001846608],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001271283,"about_ca_system_score_gemma":0.001357859,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.006123439,"about_ca_topic_score_gemma":0.004471111,"domain_scores_codex":[0.9877122,0.005048874,0.001256793,0.003019116,0.002396069,0.000566896],"domain_scores_gemma":[0.9326873,0.05640923,0.002275106,0.003809261,0.00422828,0.0005908604],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"simulation_or_modeling","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.004044314,0.0005664068,0.2014066,0.001621081,0.003337214,0.0003422928,0.0006454425,0.4095049,0.01578484,0.003736374,0.01983094,0.3391796],"study_design_scores_gemma":[0.00005102834,0.00009410572,0.01442757,0.00007541255,0.0001385698,0.0001107384,0.00009214272,0.970019,0.00979361,0.002573394,0.002578793,0.0000456097],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.6469067,0.004552178,0.2932753,0.0009154652,0.0004898586,0.000306498,0.01072793,0.03722462,0.005601432],"genre_scores_gemma":[0.754483,0.0006735749,0.2217633,0.0003961259,0.00009716564,0.0002916637,0.0180284,0.002561338,0.001705337],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.02000448,"threshold_uncertainty_score":0.1057951,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03845842197795333,"score_gpt":0.2624733952645448,"score_spread":0.2240149732865915,"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."}}