{"id":"W2951328010","doi":"10.1101/204370","title":"Germline Contamination and Leakage in Whole Genome Somatic Single Nucleotide Variant Detection","year":2017,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Cancer Genomics and Diagnostics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Toronto; Ontario Institute for Cancer Research","funders":"Natural Sciences and Engineering Research Council of Canada; Prostate Cancer Canada; Government of Ontario; Canadian Institutes of Health Research; Genome Canada; National Institutes of Health; Ontario Institute for Cancer Research; Movember Foundation; Google","keywords":"Germline; Somatic cell; Germline mutation; Biology; Genetics; Genome; Computational biology; 1000 Genomes Project; Single-nucleotide polymorphism; Gene; Mutation; Genotype","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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.03175979,0.0005808006,0.0007083484,0.002352237,0.0008959579,0.002753116,0.001367436,0.001278069,0.001127828],"category_scores_gemma":[0.1025256,0.0005264219,0.0009880136,0.003084211,0.001736977,0.002457174,0.003732593,0.001577079,0.0005904192],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001384975,"about_ca_system_score_gemma":0.001504638,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002397056,"about_ca_topic_score_gemma":0.002373649,"domain_scores_codex":[0.9615421,0.01389993,0.004101462,0.007319495,0.01170904,0.001427957],"domain_scores_gemma":[0.8899912,0.07237455,0.0119372,0.01381086,0.01075177,0.001134352],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.002592081,0.0001883997,0.6681068,0.001630643,0.001388653,0.001044357,0.002525479,0.02822199,0.05000939,0.007627549,0.01028731,0.2263774],"study_design_scores_gemma":[0.0001864804,0.001456476,0.3294429,0.001329607,0.001259966,0.006902616,0.001840853,0.2486443,0.3032476,0.05220468,0.0530333,0.0004513042],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8128825,0.005044672,0.1618111,0.002748331,0.0003303457,0.000280848,0.006192869,0.005929079,0.00478028],"genre_scores_gemma":[0.9420857,0.0005490785,0.04967014,0.001221902,0.00009419705,0.0001319047,0.00503503,0.0007137797,0.000498166],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.03175979,"threshold_uncertainty_score":0.1679638,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.00954588878102096,"score_gpt":0.2105814158159247,"score_spread":0.2010355270349038,"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."}}