{"id":"W3043344401","doi":"10.3390/genes11070800","title":"De Novo Assembly-Based Analysis of RPGR Exon ORF15 in an Indigenous African Cohort Overcomes Limitations of a Standard Next-Generation Sequencing (NGS) Data Analysis Pipeline","year":2020,"lang":"en","type":"article","venue":"Genes","topic":"Advanced biosensing and bioanalysis techniques","field":"Biochemistry, Genetics and Molecular Biology","cited_by":16,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Rare Disease Foundation","keywords":"Indel; Exome sequencing; Computational biology; Biology; Sequence analysis; DNA sequencing; Genetics; Amplicon; False positive paradox; Exome; Retinitis pigmentosa; Pipeline (software); Amplicon sequencing; Bioinformatics; Gene; Computer science; Mutation; Polymerase chain reaction; Single-nucleotide polymorphism; Genotype; Artificial intelligence","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0009655227,0.0006290043,0.0003879858,0.001145623,0.0007882452,0.0006795317,0.0004172048,0.0004766965,0.001588742],"category_scores_gemma":[0.001998831,0.0002497475,0.0006327825,0.0003553753,0.0003315431,0.0001989576,0.0006515615,0.000521382,0.0005191264],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002935673,"about_ca_system_score_gemma":0.000542835,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002769307,"about_ca_topic_score_gemma":0.006442728,"domain_scores_codex":[0.9995533,0.00006081769,0.00003824722,0.0001912691,0.0001058496,0.00005059463],"domain_scores_gemma":[0.99943,0.0002281186,0.00009951973,0.0001017881,0.00007713441,0.0000634856],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.0011122,0.0003982344,0.3574189,0.0003015485,0.000401265,0.006605063,0.002529589,0.005767222,0.4985236,0.001018819,0.001633671,0.12429],"study_design_scores_gemma":[0.0001878961,0.001254901,0.6192844,0.0001704695,0.0006536266,0.02435219,0.001061669,0.0681614,0.2584057,0.001739494,0.02456898,0.000159388],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9649054,0.0002460454,0.03215203,0.0001407033,0.00002958406,0.0001233604,0.001173079,0.000452162,0.0007775984],"genre_scores_gemma":[0.9472266,0.0001821635,0.04889907,0.00008058058,0.00002312886,0.00008007482,0.002259344,0.0001734241,0.001075562],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.002769307,"threshold_uncertainty_score":0.005506337,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.1217999073504767,"score_gpt":0.33383198363775,"score_spread":0.2120320762872733,"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."}}