{"id":"W3197024050","doi":"10.1186/s12859-021-04337-8","title":"A globally diverse reference alignment and panel for imputation of mitochondrial DNA variants","year":2021,"lang":"en","type":"article","venue":"BMC Bioinformatics","topic":"Mitochondrial Function and Pathology","field":"Biochemistry, Genetics and Molecular Biology","cited_by":15,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"National Institute of Biomedical Imaging and Bioengineering; Canadian Institutes of Health Research; National Institutes of Health; Genentech; IXICO; H. Lundbeck A/S; Servier; Eisai; Northern California Institute for Research and Education; Pfizer; Biogen; BioClinica; JPB Foundation; F. Hoffmann-La Roche; University of Southern California; Eli Lilly and Company; U.S. Department of Defense; Meso Scale Diagnostics; Alzheimer's Disease Neuroimaging Initiative; Novartis Pharmaceuticals Corporation; Bristol-Myers Squibb; National Institute on Aging; Alzheimer's Association; Foundation for the National Institutes of Health","keywords":"Haplogroup; Imputation (statistics); 1000 Genomes Project; Mitochondrial DNA; Biology; Computational biology; Missing data; Genetics; Genome; Genotyping; DNA microarray; Reference genome; Hypervariable region; Single-nucleotide polymorphism; Genotype; Computer science; Haplotype; Gene","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":[0.01499738,0.00185008,0.002200273,0.006332984,0.001925135,0.001993061,0.003292767,0.00216091,0.007320079],"category_scores_gemma":[0.03719002,0.001162387,0.002498499,0.00827485,0.0005615505,0.001150111,0.00305715,0.002781954,0.009003369],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001029342,"about_ca_system_score_gemma":0.003511358,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.005805598,"about_ca_topic_score_gemma":0.01169709,"domain_scores_codex":[0.9891271,0.00345576,0.001093047,0.004073708,0.001785444,0.0004649755],"domain_scores_gemma":[0.9812667,0.004091831,0.001835529,0.005194227,0.007087822,0.0005238587],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"observational","study_design_scores_codex":[0.002695406,0.0006608553,0.1076522,0.001979193,0.002430391,0.00181593,0.002406271,0.0563207,0.1232501,0.01292227,0.1399734,0.5478932],"study_design_scores_gemma":[0.001273426,0.001679211,0.1923203,0.001222135,0.002559094,0.004115927,0.001103856,0.2860104,0.1256726,0.02667587,0.3566978,0.0006692904],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.06599731,0.001391079,0.8635905,0.0005403527,0.000428914,0.0006064536,0.05164074,0.01185563,0.003949051],"genre_scores_gemma":[0.080433,0.0003544337,0.7825933,0.0004013047,0.0001158491,0.001446,0.1300603,0.002287463,0.002308325],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.01499738,"threshold_uncertainty_score":0.07931465,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03677071907624388,"score_gpt":0.2663580795081738,"score_spread":0.2295873604319299,"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."}}