{"id":"W2517179206","doi":"10.1093/bioinformatics/btw536","title":"SiNVICT: ultra-sensitive detection of single nucleotide variants and indels in circulating tumour DNA","year":2016,"lang":"en","type":"article","venue":"Bioinformatics","topic":"Cancer Genomics and Diagnostics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":87,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of British Columbia; Simon Fraser University","funders":"","keywords":"Indel; Computational biology; DNA sequencing; Liquid biopsy; Biology; Deep sequencing; False positive paradox; DNA; Genome; Cancer; Single-nucleotide polymorphism; Genetics; Computer science; Gene; Genotype; Artificial intelligence","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":[0.0001226484,0.00009314324,0.0001171681,0.00005430259,0.00002725268,0.00001364999,0.0000481622,0.00008770946,0.0000013337],"category_scores_gemma":[0.0001936216,0.00007784418,0.00002935747,0.00006220277,0.0000571407,0.00001020176,0.00004257089,0.00002997361,0.000002865754],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002688972,"about_ca_system_score_gemma":0.00003655717,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00002427955,"about_ca_topic_score_gemma":0.00008418576,"domain_scores_codex":[0.9993765,0.0000127606,0.0002920763,0.0001014849,0.00006938161,0.0001477803],"domain_scores_gemma":[0.9995795,0.00004433835,0.0001420511,0.0001310068,0.00005696634,0.0000460776],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.00002259088,0.00002187197,0.001314675,0.00002718188,0.00001072158,0.000001371082,0.0002209252,0.00001693813,0.9828092,0.00003441976,0.00001595425,0.01550408],"study_design_scores_gemma":[0.0007679027,0.0002089065,0.01804798,0.00008187676,0.00001102296,0.00002476681,0.0002690935,0.0006310717,0.9792183,0.0001118261,0.000465546,0.0001617088],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9907643,0.00005594837,0.007858758,0.00003611456,0.00009772383,0.0001142799,0.00004357536,0.000004634797,0.001024724],"genre_scores_gemma":[0.9986861,0.0001357412,0.0009872363,0.00009367174,0.00006351163,0.000002313943,0.000008555131,0.00001007888,0.00001276057],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.01673331,"threshold_uncertainty_score":0.3174393,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.00948069767126719,"score_gpt":0.2085639938520451,"score_spread":0.1990832961807779,"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."}}