{"id":"W2338589459","doi":"10.1038/srep24607","title":"A somatic reference standard for cancer genome sequencing","year":2016,"lang":"en","type":"article","venue":"Scientific Reports","topic":"Cancer Genomics and Diagnostics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":91,"is_retracted":false,"has_abstract":true,"ca_institutions":"Canada's Michael Smith Genome Sciences Centre","funders":"Stand Up To Cancer; European Bioinformatics Institute; Entertainment Industry Foundation; Melanoma Research Alliance; National Institute of Standards and Technology; American Association for Cancer Research","keywords":"Biology; Computational biology; Cancer genome sequencing; Genetics; Genome; Somatic cell; DNA sequencing; Point mutation; Whole genome sequencing; Mutation; Germline mutation; Gene","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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0004529385,0.0001000054,0.000113779,0.00003776024,0.0001539253,0.00008600059,0.0001054308,0.00006174264,0.00007514008],"category_scores_gemma":[0.0002557679,0.00007226718,0.0000652116,0.00006609987,0.0001130746,0.000004454637,0.00007214389,0.00001974796,0.000004902955],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00009682095,"about_ca_system_score_gemma":0.0005756996,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00002344981,"about_ca_topic_score_gemma":0.0001979053,"domain_scores_codex":[0.998786,0.00000920625,0.0002575441,0.0005401452,0.0001487931,0.0002582806],"domain_scores_gemma":[0.9989498,0.00001829513,0.0001555378,0.0005745875,0.0002118399,0.00008993893],"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":[0.00001901486,0.000005949613,0.0008701066,0.00001811874,0.0000154531,0.00001012539,0.00002945045,0.00003370767,0.990605,0.00006309344,0.003890448,0.004439552],"study_design_scores_gemma":[0.0002260074,0.00008728406,0.0003199123,0.00004024822,0.00001753428,0.00003571113,0.00002391879,0.00000910419,0.4810538,0.004942157,0.5130605,0.0001837967],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9844894,0.0009522497,0.01030684,0.0002498996,0.002710453,0.0003606341,0.0001272818,0.00001526986,0.0007879569],"genre_scores_gemma":[0.9941338,0.0001211192,0.001354914,0.00006640726,0.0002112464,0.0001205276,0.0000688278,0.00001786828,0.003905261],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.5095512,"threshold_uncertainty_score":0.294697,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02273334925674964,"score_gpt":0.2765527834884001,"score_spread":0.2538194342316504,"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."}}