{"id":"W3196194192","doi":"10.1038/s41467-021-25432-7","title":"Pan-cancer analysis of longitudinal metastatic tumors reveals genomic alterations and immune landscape dynamics associated with pembrolizumab sensitivity","year":2021,"lang":"en","type":"article","venue":"Nature Communications","topic":"Cancer Genomics and Diagnostics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":128,"is_retracted":false,"has_abstract":true,"ca_institutions":"Vector Institute; Princess Margaret Cancer Centre; University Health Network; Ontario Institute for Cancer Research; University of Toronto","funders":"Merck Canada; Terry Fox Research Institute; Government of Ontario; University of Toronto; Ontario Institute for Cancer Research; Ontario Ministry of Research and Innovation; Princess Margaret Cancer Foundation; Heart and Stroke Foundation of Canada","keywords":"Pembrolizumab; Immune checkpoint; Biology; Microsatellite instability; Transcriptome; Genome instability; Immune system; Immunotherapy; Cancer research; Exome; Tumor microenvironment; Loss of heterozygosity; Cancer; Biomarker; Mutation; Immunology; Exome sequencing; Genetics; Gene; DNA damage; Gene expression; Allele; DNA; Microsatellite","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":[0.000176888,0.000118739,0.0002867359,0.00008622947,0.000158246,0.00003361795,0.0001709286,0.0001096861,0.000009439682],"category_scores_gemma":[0.0002860981,0.0001169594,0.00009987364,0.000486861,0.0001172412,0.000004997835,0.0002450422,0.0002297593,2.67327e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00004326725,"about_ca_system_score_gemma":0.0001998811,"about_ca_topic_candidate":true,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00008045259,"about_ca_topic_score_gemma":0.02307716,"domain_scores_codex":[0.9991816,0.0001531882,0.0002316892,0.0002204431,0.00008630987,0.0001267929],"domain_scores_gemma":[0.998228,0.0002106733,0.0001885557,0.0009401378,0.0003879528,0.00004469131],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0001572886,0.0008104005,0.5394939,0.00004898781,0.009604967,0.0000211872,0.0003172961,0.007651641,0.427383,0.01202415,0.0007199732,0.001767293],"study_design_scores_gemma":[0.0007189775,0.00007664557,0.9744126,0.00004219009,0.002244865,0.00001651116,0.0001624025,0.01649677,0.005150156,0.00008369947,0.000339808,0.0002553421],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9810568,0.01600287,0.0007089977,0.0007255816,0.00002853951,0.0001133519,0.001031796,0.000006294146,0.0003257405],"genre_scores_gemma":[0.9916336,0.00329979,0.001539598,0.0001289173,0.00001595737,0.00002481222,0.003258554,0.00001449521,0.00008429067],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.4349188,"threshold_uncertainty_score":0.9947491,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.011407255293991,"score_gpt":0.2825974151777351,"score_spread":0.2711901598837441,"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."}}