{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.03100039,0.0006602716,0.0006895928,0.002355652,0.0009464767,0.002641315,0.001297236,0.001433921,0.0009689143],"category_scores_gemma":[0.1083526,0.0005545396,0.001076746,0.003049476,0.001943779,0.00261037,0.003599845,0.001589768,0.0005348335],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00136211,"about_ca_system_score_gemma":0.001496538,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002135485,"about_ca_topic_score_gemma":0.002314382,"domain_scores_codex":[0.9633474,0.0132061,0.003677678,0.007242797,0.01124387,0.001282147],"domain_scores_gemma":[0.9005687,0.06835039,0.01134256,0.01143993,0.007384383,0.0009140663],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.002528105,0.0001860666,0.6566383,0.001687442,0.001339644,0.001232973,0.003049528,0.03343954,0.05194858,0.008812125,0.008225303,0.2309123],"study_design_scores_gemma":[0.0001803182,0.001531007,0.3312314,0.001349741,0.001276342,0.008152363,0.001751631,0.2469308,0.3023618,0.05919131,0.0456055,0.0004378538],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.7721815,0.005774413,0.2040844,0.002547352,0.0003417375,0.0003222784,0.00481271,0.005165511,0.004770143],"genre_scores_gemma":[0.9274383,0.0006751379,0.06492519,0.001254596,0.00009652093,0.0001556951,0.004276949,0.0006962449,0.0004813664],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.03100039,"threshold_uncertainty_score":0.1639477,"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."}}