{"id":"W2122545386","doi":"10.1186/1471-2105-14-s5-s3","title":"Joint genotype inference with germline and somatic mutations","year":2013,"lang":"en","type":"article","venue":"BMC Bioinformatics","topic":"Cancer Genomics and Diagnostics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":4,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université de Montréal; Centre Hospitalier Universitaire Sainte-Justine","funders":"Foreign Affairs and International Trade Canada; Canadian Institutes of Health Research; Terry Fox Research Institute; Government of Canada","keywords":"Genetics; Biology; Genome; 1000 Genomes Project; Germline; Germline mutation; Exome sequencing; Exome; Computational biology; DNA sequencing; Cancer genome sequencing; Genotype; Whole genome sequencing; Mutation; Gene; 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":[0.00004941227,0.0001165719,0.0001052958,0.00003489439,0.00006885616,0.0000784969,0.00007266019,0.00006570068,0.00003750595],"category_scores_gemma":[0.00009248468,0.00009300858,0.00002353852,0.00004887907,0.00008060827,0.00001067131,0.00007836134,0.00004739663,0.0000754267],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000008825159,"about_ca_system_score_gemma":0.0001171908,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00003526785,"about_ca_topic_score_gemma":0.00009202046,"domain_scores_codex":[0.999428,0.000006878422,0.0002271413,0.00009787099,0.00007852973,0.0001615613],"domain_scores_gemma":[0.9994619,0.00002763466,0.00009458471,0.0002352722,0.00008835971,0.00009225986],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.0005170431,0.001492375,0.3344716,0.00674597,0.001187178,0.00002021532,0.01380231,0.05111637,0.2878262,0.02365336,0.056317,0.2228504],"study_design_scores_gemma":[0.00708523,0.003463407,0.2798531,0.0002891163,0.0003429618,0.0003139331,0.00405629,0.6089666,0.05545692,0.005639717,0.03160784,0.002924918],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.841226,0.0003131732,0.1554715,0.0001325759,0.00006813656,0.000438349,0.00003345314,0.00002018252,0.002296651],"genre_scores_gemma":[0.8229252,0.0002436531,0.1757814,0.0005007175,0.00008951758,0.00005514947,0.0001748344,0.00001866386,0.0002109222],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.5578502,"threshold_uncertainty_score":0.379278,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01227374010920817,"score_gpt":0.2259512673781066,"score_spread":0.2136775272688985,"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."}}