{"id":"W2766787629","doi":"10.1186/s12859-018-2046-0","title":"Germline contamination and leakage in whole genome somatic single nucleotide variant detection","year":2018,"lang":"en","type":"article","venue":"BMC Bioinformatics","topic":"Genomics and Rare Diseases","field":"Biochemistry, Genetics and Molecular Biology","cited_by":14,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Toronto; Ontario Institute for Cancer Research","funders":"National Cancer Institute; Ontario Institute for Cancer Research; National Human Genome Research Institute; Natural Sciences and Engineering Research Council of Canada; Prostate Cancer Canada; Government of Ontario; Google; Canadian Institutes of Health Research; Genome Canada; National Institutes of Health; Terry Fox Research Institute; Movember Foundation","keywords":"Germline; Somatic cell; Biology; Germline mutation; Genetics; Computational biology; Genome; Gene; Mutation","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":[0.0001328935,0.0001048277,0.00009838533,0.00006956974,0.00007085049,0.00004577865,0.00007228152,0.00008687544,0.000006504033],"category_scores_gemma":[0.00005721482,0.00009891015,0.00003142412,0.00006881142,0.00007025115,0.00001258256,0.00006875932,0.00003665867,0.00002899031],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0000200162,"about_ca_system_score_gemma":0.00003379435,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000009386784,"about_ca_topic_score_gemma":0.0002861879,"domain_scores_codex":[0.9993765,0.00001857665,0.0002645274,0.0001142337,0.0000666423,0.0001594867],"domain_scores_gemma":[0.9996051,0.000008451044,0.00009827468,0.0001741096,0.00005653386,0.00005754768],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.000155451,0.0003033024,0.004464137,0.0004474207,0.00005218504,0.00001054511,0.001845462,0.0001776685,0.9724623,0.0001195183,0.0001748455,0.01978719],"study_design_scores_gemma":[0.007757988,0.003903173,0.3623385,0.000215932,0.0001834242,0.0004924259,0.004684673,0.3883663,0.1493695,0.001356039,0.07926197,0.002070085],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9647853,0.000151596,0.03399422,0.00002509429,0.00011464,0.0001879505,0.00002883128,0.00001171238,0.0007007007],"genre_scores_gemma":[0.992855,0.00002821597,0.006544557,0.0001350573,0.0001525054,0.000007155551,0.000125587,0.00001218162,0.0001397762],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.8230928,"threshold_uncertainty_score":0.4033439,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.009098428916075674,"score_gpt":0.2141057889500732,"score_spread":0.2050073600339975,"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."}}