{"id":"W3033597903","doi":"10.1158/1535-7163.mct-20-0094","title":"Endogenous Retrovirus Transcript Levels Are Associated with Immunogenic Signatures in Multiple Metastatic Cancer Types","year":2020,"lang":"en","type":"article","venue":"Molecular Cancer Therapeutics","topic":"Immunotherapy and Immune Responses","field":"Immunology and Microbiology","cited_by":21,"is_retracted":false,"has_abstract":true,"ca_institutions":"Vancouver General Hospital; Terry Fox Research Institute; University Health Network; Ontario Institute for Cancer Research; BC Cancer Agency; Canada's Michael Smith Genome Sciences Centre; University of British Columbia; Pancreas Centre (Canada)","funders":"Canada Research Chairs; Canadian Institutes of Health Research; Genome British Columbia; Canada Foundation for Innovation","keywords":"Biology; Immunogenicity; Pancreatic cancer; Endogenous retrovirus; Cancer; Cancer research; Epigenetics; Colorectal cancer; Epigenomics; Breast cancer; Molecular mimicry; Immunology; Gene; DNA methylation; Gene expression; Genetics; Antibody; 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":[0.0001509856,0.0003896386,0.0005760777,0.0001052376,0.0001713884,0.00003136712,0.0003994641,0.0002493783,0.000649609],"category_scores_gemma":[0.00004450726,0.0003276828,0.0001723564,0.0004897345,0.0002189892,0.0000867466,0.00002420974,0.0006384549,0.00002514435],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001724814,"about_ca_system_score_gemma":0.000282023,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0005628223,"about_ca_topic_score_gemma":0.0003753156,"domain_scores_codex":[0.9979067,0.000578725,0.0003818452,0.0004210398,0.0001085277,0.000603114],"domain_scores_gemma":[0.9991899,0.0001533175,0.0002220002,0.0002953124,0.0001100701,0.00002938758],"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":[0.002323511,0.0001608341,0.001942306,0.00002721327,0.002565404,0.00009178887,0.003096121,0.001163774,0.9832883,0.00001743741,0.00003572533,0.005287605],"study_design_scores_gemma":[0.0054118,0.0005098002,0.007589681,0.0001607765,0.000388334,0.000011443,0.0003597703,0.00006045226,0.966989,0.00002250535,0.01796547,0.0005309347],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.7475632,0.2497649,0.0003732227,0.001092136,0.0002755778,0.0004840489,0.0002854876,0.00009549873,0.00006593292],"genre_scores_gemma":[0.9916024,0.002202824,0.00003218546,0.005561172,0.00001421162,0.0001562896,0.00003768209,0.0000868606,0.0003063273],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.247562,"threshold_uncertainty_score":0.9999175,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.061660860817377,"score_gpt":0.2671429476222009,"score_spread":0.2054820868048239,"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."}}