{"id":"W4281559669","doi":"10.1101/2022.05.24.493320","title":"Parent-of-origin detection and chromosome-scale haplotyping using long-read DNA methylation sequencing and Strand-seq","year":2022,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Genetic Syndromes and Imprinting","field":"Biochemistry, Genetics and Molecular Biology","cited_by":3,"is_retracted":false,"has_abstract":true,"ca_institutions":"Canada's Michael Smith Genome Sciences Centre; University of British Columbia; BC Cancer Agency","funders":"Canadian Institutes of Health Research; Terry Fox Research Institute; University of British Columbia; Canada Research Chairs","keywords":"Autosome; Genetics; Biology; Haplotype; DNA methylation; DNA sequencing; Indel; Allele; Chromosome; DNA; Gene; Genotype; Single-nucleotide polymorphism","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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0007733621,0.0003566121,0.0003490314,0.0005659466,0.0002713359,0.0004379871,0.0003616032,0.0004808866,0.001527958],"category_scores_gemma":[0.001026707,0.0003093138,0.0003352251,0.0003125473,0.0003121512,0.0002359632,0.0006110723,0.0006302861,0.0006860688],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000306827,"about_ca_system_score_gemma":0.0002944649,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001399808,"about_ca_topic_score_gemma":0.004544247,"domain_scores_codex":[0.9995621,0.00006798891,0.00002928392,0.0001672643,0.0001376355,0.00003575578],"domain_scores_gemma":[0.9993362,0.0002463615,0.0001434287,0.0001256614,0.00008678532,0.00006155908],"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":[0.00008228995,0.00001488294,0.008749702,0.00005776023,0.00004184331,0.00007108296,0.00006903138,0.0009773787,0.980195,0.0003726094,0.0002149723,0.00915352],"study_design_scores_gemma":[0.00001861456,0.00008444052,0.03887379,0.00001851549,0.00004608015,0.0005106482,0.00006629949,0.03027395,0.9229563,0.001232652,0.005874863,0.00004380709],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.6722015,0.0007110957,0.3110279,0.0001957635,0.0001216306,0.0002105887,0.01003452,0.002625539,0.002871474],"genre_scores_gemma":[0.7022691,0.0003025329,0.2889277,0.0001947849,0.00002419274,0.0001818373,0.004551152,0.0004975781,0.003051037],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001527958,"threshold_uncertainty_score":0.005111575,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02300263617016347,"score_gpt":0.2474176973530804,"score_spread":0.2244150611829169,"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."}}