{"id":"W2995766518","doi":"10.1038/s41590-019-0549-0","title":"High-throughput phenotyping reveals expansive genetic and structural underpinnings of immune variation","year":2019,"lang":"en","type":"article","venue":"Nature Immunology","topic":"Single-cell and spatial transcriptomics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":45,"is_retracted":false,"has_abstract":false,"ca_institutions":"University of British Columbia; BC Cancer Agency","funders":"Common Fund; National Institute of Allergy and Infectious Diseases; Medical Research Council; Natural Sciences and Engineering Research Council of Canada; European Commission; National Institutes of Health; Kidney Research UK; Academy of Medical Sciences; Cancer Research UK; King's College London; Genome British Columbia; International Society for Advancement of Cytometry; National Human Genome Research Institute; Wellcome Trust; Genome Canada; Francis Crick Institute; National Institute of General Medical Sciences; National Institute for Health and Care Research; Canadian Institutes of Health Research; Wellcome","keywords":"Biology; Immunophenotyping; Immune system; Genome-wide association study; Genetics; Genetic variation; Gene knockout; Immunocompetence; Gene; Genetic association; Computational biology; Genotype; Single-nucleotide polymorphism","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":[0.00007814953,0.0001584059,0.0002577752,0.00005157585,0.00004988148,0.00001067953,0.0001611964,0.0005873544,0.00002764542],"category_scores_gemma":[0.0000565164,0.0001514912,0.00006253466,0.00007651467,0.0001069216,0.00000653128,0.0000779494,0.0002894571,0.000003757167],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001502938,"about_ca_system_score_gemma":0.00003990685,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001183388,"about_ca_topic_score_gemma":0.000008312611,"domain_scores_codex":[0.9990528,0.00006559489,0.000280258,0.0003206529,0.00007409325,0.0002066005],"domain_scores_gemma":[0.9993622,0.00002432297,0.0001659507,0.0003038008,0.0001232386,0.0000205221],"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":[0.0001667213,0.00001223314,0.003665269,0.00003275281,0.0001267963,7.793878e-7,0.0001959435,0.00005032085,0.9926037,0.001143301,0.00001727733,0.001984946],"study_design_scores_gemma":[0.002539359,0.0006965555,0.4463654,0.00005875855,0.00006382784,0.00006450574,0.0001470163,0.0001611664,0.5451911,0.003277675,0.001022198,0.0004123944],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9870682,0.01054983,0.00113318,0.000132982,0.0008030342,0.0001931727,0.00001130464,0.00001117126,0.00009708561],"genre_scores_gemma":[0.9964498,0.000337549,0.002620186,0.0002330101,0.0001062066,0.000003856235,0.00008087145,0.00002172166,0.0001468246],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.4474125,"threshold_uncertainty_score":0.6177633,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.003289166793730199,"score_gpt":0.2101747388148835,"score_spread":0.2068855720211533,"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."}}