{"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":"codex-gemma-dda1882f352a","candidate_categories":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.0005241292,0.0003837022,0.0004131137,0.0001653313,0.0002246228,0.00009874924,0.0001836334,0.0003647096,0.00002479204],"category_scores_gemma":[0.00008310968,0.0004550672,0.00009905244,0.0001869449,0.000111317,0.00001434445,0.0006113861,0.0003425799,5.213015e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001160605,"about_ca_system_score_gemma":0.0002597625,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001173704,"about_ca_topic_score_gemma":0.00001006705,"domain_scores_codex":[0.9979213,0.000138745,0.0004818561,0.0008742868,0.0002254691,0.0003583416],"domain_scores_gemma":[0.9986743,0.00001888344,0.0004353967,0.0005646947,0.0001593281,0.0001473646],"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":[0.00001203791,0.0000193025,0.03142568,0.0003509082,0.0001049215,0.000003172811,0.00001753153,0.0004514937,0.9675313,0.000005101968,6.935623e-7,0.0000778536],"study_design_scores_gemma":[0.000549693,0.0001544071,0.2163627,0.0002380798,0.000180145,6.138258e-7,0.00003015672,0.002830357,0.778596,0.00000265354,0.0004114088,0.00064378],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9871199,0.003112085,0.008717773,0.0000124773,0.0005000282,0.0004326589,0.00005776107,0.00004300751,0.000004327298],"genre_scores_gemma":[0.9938843,0.0006383073,0.005114778,0.00002010095,0.0002106404,0.00004320296,0.000001597249,0.00008428903,0.000002738582],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1889353,"threshold_uncertainty_score":0.9997901,"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."}}