{"id":"W3199647353","doi":"10.1038/s41467-021-25661-w","title":"DNA methylation landscapes of 1538 breast cancers reveal a replication-linked clock, epigenomic instability and cis-regulation","year":2021,"lang":"en","type":"article","venue":"Nature Communications","topic":"Epigenetics and DNA Methylation","field":"Biochemistry, Genetics and Molecular Biology","cited_by":87,"is_retracted":false,"has_abstract":true,"ca_institutions":"Research Institute in Oncology and Hematology","funders":"NIHR Cambridge Biomedical Research Centre; Medical Research Council; National Institute for Health and Care Research; Cancer Research UK; Wellcome Trust","keywords":"Epigenomics; DNA methylation; Epigenetics; Biology; Genome instability; Methylation; CpG site; Breast cancer; Cancer research; Context (archaeology); Genetics; Chromosome instability; Cancer; DNA; Gene; DNA damage; Gene expression","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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001250024,0.0001053681,0.0002366745,0.0005043506,0.0001349551,0.0002179445,0.0001024528,0.0001313643,0.0007945278],"category_scores_gemma":[0.0003696902,0.0001026289,0.0001284008,0.00045927,0.0001162704,0.00006870991,0.0001604444,0.0001070737,0.0002208073],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001939459,"about_ca_system_score_gemma":0.0001194371,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001859537,"about_ca_topic_score_gemma":0.004373989,"domain_scores_codex":[0.999893,0.00001612285,0.00001070685,0.00003653745,0.000024214,0.00001949532],"domain_scores_gemma":[0.9998426,0.00003202736,0.00005827142,0.00002310887,0.00002584304,0.00001803748],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.0007300011,0.00001592938,0.4039851,0.0001143999,0.0002056343,0.0001968152,0.0004220931,0.0005689599,0.5597111,0.000180125,0.0003548866,0.03351495],"study_design_scores_gemma":[0.000006905188,0.0001159545,0.9593533,0.000006051669,0.0001069412,0.001021369,0.0002097721,0.0008338017,0.03579627,0.0001614851,0.002378437,0.00000976086],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.997834,0.0006223035,0.0004901848,0.00002741359,0.000001242619,0.000002724573,0.0007263318,0.00002201822,0.0002738272],"genre_scores_gemma":[0.9979626,0.000237379,0.0004888265,0.00001450329,0.000001849579,0.000005686991,0.0008526368,0.000008860411,0.000427621],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001859537,"threshold_uncertainty_score":0.003697455,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01458176471518675,"score_gpt":0.2947322393566527,"score_spread":0.280150474641466,"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."}}