{"id":"W3083661584","doi":"10.1158/1538-7445.am2020-158","title":"Abstract 158: Custom primer design pipeline and analysis workflow for targeted methylation sequencing using NGS Ion AmpliSeq technology","year":2020,"lang":"en","type":"article","venue":"Cancer Research","topic":"Epigenetics and DNA Methylation","field":"Biochemistry, Genetics and Molecular Biology","cited_by":3,"is_retracted":false,"has_abstract":true,"ca_institutions":"Queen's University","funders":"","keywords":"Amplicon; Ion semiconductor sequencing; Computational biology; Bisulfite sequencing; Illumina Methylation Assay; Primer (cosmetics); DNA methylation; Biology; Methylation; Pipeline (software); In silico; Genetics; Computer science; DNA sequencing; Polymerase chain reaction; DNA; Gene; Chemistry; Operating system","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":[0.00334712,0.003011806,0.001924355,0.002006126,0.0008561858,0.001555841,0.002591247,0.001649434,0.03589595],"category_scores_gemma":[0.003628873,0.002485648,0.001875509,0.000915294,0.0008536921,0.001070417,0.001622098,0.003328388,0.02841408],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001028138,"about_ca_system_score_gemma":0.002734791,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001331171,"about_ca_topic_score_gemma":0.001848629,"domain_scores_codex":[0.9965956,0.0004487665,0.0003629031,0.001206036,0.001047721,0.0003389166],"domain_scores_gemma":[0.9986691,0.0004159357,0.0001590934,0.0002508464,0.0003738563,0.0001312137],"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":[0.001225704,0.0002667299,0.001861685,0.001646481,0.0001803422,0.0006206761,0.000436234,0.005530307,0.8464417,0.003261761,0.04268915,0.09583919],"study_design_scores_gemma":[0.0003484495,0.0008056959,0.003203228,0.0002209867,0.0001504217,0.0009951161,0.00007635472,0.03700382,0.7423217,0.003387673,0.2111668,0.0003198785],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.01744785,0.0008984746,0.8931878,0.0003795636,0.0004195068,0.004308491,0.01752714,0.06065473,0.005176408],"genre_scores_gemma":[0.02457238,0.0004479257,0.9104258,0.0008512919,0.00007563373,0.008342112,0.03579066,0.00720036,0.01229386],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.03589595,"threshold_uncertainty_score":0.1200839,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.146895358088155,"score_gpt":0.4072564748593009,"score_spread":0.260361116771146,"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."}}