{"id":"W4284992560","doi":"10.1101/2022.07.09.499321","title":"A Draft Human Pangenome Reference","year":2022,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Genomics and Rare Diseases","field":"Biochemistry, Genetics and Molecular Biology","cited_by":74,"is_retracted":false,"has_abstract":true,"ca_institutions":"McGill University","funders":"U.S. National Library of Medicine; Agencia Estatal de Investigación; National Institute of Standards and Technology; Novo Nordisk Fonden; National Institute of Food and Agriculture; National Institutes of Health; Bundesministerium für Wirtschaft und Energie; Bundesministerium für Bildung und Forschung; Novo Nordisk; Heinrich-Heine-Universität Düsseldorf; German Network for Bioinformatics Infrastructure; European Commission; Oxford Nanopore Technologies; National Human Genome Research Institute; Wellcome Trust; Ministry of Education, Culture, Sports, Science and Technology; Natural Sciences and Engineering Research Council of Canada; U.S. Department of Agriculture; Howard Hughes Medical Institute; National Science Foundation","keywords":"Haplotype; Biology; Reference genome; Genetics; Computational biology; Human genome; Allele; Gene; Genome","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"],"consensus_categories":[],"category_scores_codex":[0.0002764977,0.0005013109,0.0003783345,0.0001355503,0.0003296835,0.0001416017,0.0008873836,0.0004404186,0.0002769976],"category_scores_gemma":[0.00006225442,0.0005708166,0.0002246408,0.0001540712,0.0001036907,0.00000398846,0.001740442,0.0005102137,0.00003852668],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001109814,"about_ca_system_score_gemma":0.0005962382,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00006260538,"about_ca_topic_score_gemma":0.000005372942,"domain_scores_codex":[0.9975064,0.0001235103,0.000394136,0.001188057,0.0002731072,0.0005148106],"domain_scores_gemma":[0.9975173,0.000007651354,0.0002967154,0.001673319,0.0002251259,0.0002798827],"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":[0.00002704055,0.0001460387,0.002734252,0.0001469527,0.0001692476,0.00006954135,0.000003984002,0.00006514444,0.9951881,0.0003686959,0.001080231,7.269921e-7],"study_design_scores_gemma":[0.001151702,0.0004716319,0.1648155,0.0001481415,0.0003341301,9.840276e-8,0.00002009278,0.0000234323,0.3289519,0.00001209113,0.5011715,0.002899865],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9933665,0.004149189,0.00008953495,0.0000676495,0.0006157357,0.0004668529,0.001034863,0.000102257,0.0001074128],"genre_scores_gemma":[0.9973617,0.0005642754,0.0006131722,0.0003236237,0.0005967612,0.0003178924,0.00001583295,0.0001426884,0.00006407292],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.6662363,"threshold_uncertainty_score":0.9996743,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01595343758177984,"score_gpt":0.2357740780113873,"score_spread":0.2198206404296074,"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."}}