{"id":"W4403381371","doi":"10.1016/j.xgen.2024.100674","title":"Long-read sequencing of an advanced cancer cohort resolves rearrangements, unravels haplotypes, and reveals methylation landscapes","year":2024,"lang":"en","type":"article","venue":"Cell Genomics","topic":"Epigenetics and DNA Methylation","field":"Biochemistry, Genetics and Molecular Biology","cited_by":30,"is_retracted":false,"has_abstract":true,"ca_institutions":"BC Cancer Agency; University of British Columbia; Canada's Michael Smith Genome Sciences Centre","funders":"British Columbia Knowledge Development Fund; National Institutes of Health; BC Cancer Foundation; Terry Fox Foundation; Genome British Columbia; Terry Fox Research Institute; Canada Foundation for Innovation; Canadian Cancer Society Research Institute; Canadian Institutes of Health Research; Genome Canada","keywords":"Haplotype; DNA methylation; Computational biology; Biology; Genetics; Methylation; Cohort; Cancer; Evolutionary biology; DNA sequencing; Gene; Bioinformatics; Medicine; Genotype; Internal medicine","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":[0.0002837633,0.0001137219,0.0001300945,0.00005069594,0.0000420816,0.00003088104,0.00007381681,0.0001075128,0.00001603034],"category_scores_gemma":[0.00001748183,0.0001124947,0.00003537511,0.00006540415,0.00002951156,0.000008330761,0.00004402576,0.0000534798,0.000001541964],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003129729,"about_ca_system_score_gemma":0.00007694114,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00006014707,"about_ca_topic_score_gemma":0.000110868,"domain_scores_codex":[0.999218,0.00004461044,0.0002111376,0.0003125973,0.00008139882,0.000132296],"domain_scores_gemma":[0.9995831,0.00001612688,0.00007320747,0.0002099822,0.00006119489,0.00005639087],"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":[0.00002826737,0.000009138997,0.005341024,0.00009305848,0.00004026468,0.000001461084,0.0001587639,0.001367838,0.9768482,0.00002608315,0.00001839713,0.01606754],"study_design_scores_gemma":[0.0002166228,0.0001560985,0.0115513,0.0000383403,0.00006479177,0.000001159463,0.00006874818,0.001435396,0.9766032,0.0003670665,0.009326403,0.0001709185],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9601128,0.03541201,0.00319863,0.00001974996,0.0001483522,0.0001960574,0.00004203432,0.0000123411,0.0008580178],"genre_scores_gemma":[0.9862369,0.0092034,0.003491765,0.00002144308,0.0001470472,0.00001492091,0.0002056877,0.00003025856,0.0006486336],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.02620861,"threshold_uncertainty_score":0.4587402,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01226342416880211,"score_gpt":0.2708570936523012,"score_spread":0.258593669483499,"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."}}