{"id":"W4313214635","doi":"10.1016/j.xgen.2022.100233","title":"Parent-of-origin detection and chromosome-scale haplotyping using long-read DNA methylation sequencing and Strand-seq","year":2022,"lang":"en","type":"article","venue":"Cell Genomics","topic":"Genetic Syndromes and Imprinting","field":"Biochemistry, Genetics and Molecular Biology","cited_by":33,"is_retracted":false,"has_abstract":true,"ca_institutions":"Terry Fox Research Institute; Canada's Michael Smith Genome Sciences Centre; University of British Columbia","funders":"","keywords":"Autosome; Biology; Genetics; Haplotype; DNA methylation; Indel; DNA sequencing; Human genome; Allele; Chromosome; Genome; DNA; Gene; Genotype; Single-nucleotide polymorphism","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":[0.0001866177,0.000102997,0.0001190318,0.00004346182,0.0001797237,0.00001992587,0.00005849249,0.0000553787,0.00001496834],"category_scores_gemma":[0.000007099889,0.000122062,0.00003468964,0.00005778993,0.00003785893,0.000004027853,0.0001551592,0.0000729895,2.427543e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00004726816,"about_ca_system_score_gemma":0.00005175663,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0000447199,"about_ca_topic_score_gemma":0.0000140614,"domain_scores_codex":[0.9992916,0.00004359941,0.0001866051,0.0002583171,0.00006666383,0.0001531939],"domain_scores_gemma":[0.9996686,0.000008054795,0.0001162949,0.0001373106,0.00002271261,0.00004700061],"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":[0.000008061656,0.000008137835,0.006900043,0.00003925791,0.0000139389,5.017517e-7,0.0002064602,0.002486737,0.9799573,0.000001078095,5.266529e-7,0.01037799],"study_design_scores_gemma":[0.0007786574,0.0003092062,0.01874079,0.00001299065,0.00007299919,0.0001696541,0.001202915,0.01494758,0.9617788,0.00006950698,0.001598135,0.0003188265],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9890325,0.001561348,0.009013537,0.000004777066,0.0001420065,0.0001353785,0.000008156979,0.000005814566,0.00009650263],"genre_scores_gemma":[0.996984,0.0002276242,0.00262382,0.00001592014,0.00006155982,0.000005324461,0.00001977147,0.00002042699,0.00004153468],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.01817853,"threshold_uncertainty_score":0.4977544,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.0227371679962748,"score_gpt":0.2406285228433502,"score_spread":0.2178913548470754,"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."}}