{"id":"W4200619411","doi":"10.1101/2021.12.20.21267194","title":"Rare coding variation illuminates the allelic architecture, risk genes, cellular expression patterns, and phenotypic context of autism","year":2021,"lang":"en","type":"preprint","venue":"medRxiv","topic":"Genomic variations and chromosomal abnormalities","field":"Biochemistry, Genetics and Molecular Biology","cited_by":35,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Weill Institute for Neurosciences, University of California, San Francisco; National Human Genome Research Institute; National Institute of Mental Health; Norwegian Institute of Public Health; Servicio Gallego de Salud; Statens Serum Institut; Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai; Faculty of Medicine and Health, University of Sydney; Department of Internal Medicine, University of Utah; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai; Stanley Center for Psychiatric Research, Broad Institute; Research Institute, Nationwide Children's Hospital; Universidade de Santiago de Compostela; Hospital for Sick Children; H. Lundbeck A/S; Tays; School of Medicine, Emory University; Università degli Studi di Messina; University of Illinois at Urbana-Champaign; Universidade do Minho; University of Pittsburgh; University of Hong Kong; University of California, San Francisco; Simons Foundation Autism Research Initiative; Japan Agency for Medical Research and Development; Children's Hospital of Philadelphia; Universidade de São Paulo; University of Cincinnati; Università degli Studi di Siena; Karolinska Institutet; Harvard T.H. Chan School of Public Health; Ben-Gurion University of the Negev; Helsingin Yliopisto; Nationwide Children's Hospital; University of California, Irvine; Broad Institute; Aarhus Universitet; Leonard M. Miller School of Medicine; University of Toronto; Università degli Studi di Verona; Carnegie Mellon University; Autism Speaks; Emory University; National Science Foundation; Massachusetts General Hospital; Centro de Investigación Biomédica en Red de Salud Mental; Lundbeckfonden; Simons Foundation; University of Miami; Università degli Studi di Trento","keywords":"Copy-number variation; Exome sequencing; Genetics; Missense mutation; Autism; Biology; Exome; Autism spectrum disorder; Gene; Phenotype; Allele; Cohort; Medicine; Genome; Internal medicine; Psychiatry","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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002686068,0.0002298875,0.0002482089,0.00003801186,0.0001471268,0.00005609603,0.0002585569,0.0002707938,0.0000432222],"category_scores_gemma":[0.00005898211,0.0001759256,0.0001176809,0.00003218151,0.00007632798,0.000002955249,0.0006508512,0.0002520062,6.056403e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001124938,"about_ca_system_score_gemma":0.00007874586,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0002822663,"about_ca_topic_score_gemma":0.00009474331,"domain_scores_codex":[0.9986677,0.0002707925,0.0003288701,0.0004252556,0.0001355622,0.000171826],"domain_scores_gemma":[0.9989549,0.00003649367,0.0003387237,0.0005415464,0.00008274228,0.00004558564],"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":[0.00003990483,0.00006499992,0.09078872,0.0004629522,0.000238126,0.00000714441,0.003438749,0.0008015675,0.8987561,0.0003767902,0.00004009372,0.004984811],"study_design_scores_gemma":[0.0004989583,0.00008149508,0.1662171,0.000204815,0.0001646213,0.00001416329,0.00125147,0.0002485057,0.8275947,0.0006049899,0.002702214,0.0004169145],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9778013,0.007309156,0.01394393,0.0001800644,0.0002865999,0.0002400031,0.0001909915,0.000009202207,0.00003873274],"genre_scores_gemma":[0.996013,0.002421749,0.0005363866,0.00005807135,0.0001600953,0.00004646046,0.0006144338,0.00002574084,0.0001240896],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.0754284,"threshold_uncertainty_score":0.7174037,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.00895982263031097,"score_gpt":0.2041280017627236,"score_spread":0.1951681791324126,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). 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