{"id":"W4306412179","doi":"10.1038/s41588-022-01190-0","title":"Targeted profiling of human extrachromosomal DNA by CRISPR-CATCH","year":2022,"lang":"en","type":"article","venue":"Nature Genetics","topic":"Cancer Genomics and Diagnostics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":123,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Deutsche Forschungsgemeinschaft; Rosetrees Trust; European Commission; National Human Genome Research Institute; Wellcome Trust; Francis Crick Institute; National Institutes of Health; Cancer Research UK; Jonsson Comprehensive Cancer Center; Canadian Institutes of Health Research; National Institute of General Medical Sciences; National Institute for Health and Care Research; National Cancer Institute; Melanoma Research Alliance; National Institute of Allergy and Infectious Diseases; Howard Hughes Medical Institute","keywords":"Biology; CRISPR; Extrachromosomal DNA; Genetics; DNA; Amplicon; Gene; Enhancer; Cas9; Computational biology; Gene expression; Plasmid; Polymerase chain reaction","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001241246,0.0001565436,0.000157995,0.00003654769,0.0001730879,0.00001283381,0.0003415099,0.0002223401,0.00008095651],"category_scores_gemma":[0.00004323892,0.0001813263,0.00009351863,0.000123851,0.00005673279,0.000001085149,0.0003165098,0.0003559138,0.000001169403],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003094823,"about_ca_system_score_gemma":0.0001177184,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000009807765,"about_ca_topic_score_gemma":0.00001100796,"domain_scores_codex":[0.9988757,0.00004299159,0.000249794,0.0003496813,0.0002353642,0.000246454],"domain_scores_gemma":[0.9992735,0.00001230905,0.000132227,0.000410242,0.00009968683,0.0000720702],"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":[0.00003390121,0.0001157035,0.004910001,0.00001884516,0.00003888821,0.000003063926,0.00003521555,0.0002806512,0.9701997,0.00009598598,0.02364906,0.0006189627],"study_design_scores_gemma":[0.0004482767,0.0005030058,0.001264625,0.000002277304,0.00002868276,0.000009005852,0.0000813197,0.00005880531,0.9202177,0.0001392712,0.07703573,0.0002112993],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9819955,0.01587693,0.0001799677,0.0001010419,0.0004353517,0.0002170362,0.0005421742,0.000009894063,0.0006420836],"genre_scores_gemma":[0.9961021,0.000262015,0.001598028,0.0004244672,0.0002894383,0.00003621245,0.00099616,0.00003977328,0.0002518367],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.05338667,"threshold_uncertainty_score":0.739427,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.005729933780264319,"score_gpt":0.2576081929684597,"score_spread":0.2518782591881953,"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."}}