{"id":"W3180211998","doi":"10.1186/s13073-021-00929-4","title":"Haplotype-resolved germline and somatic alterations in renal medullary carcinomas","year":2021,"lang":"en","type":"article","venue":"Genome Medicine","topic":"Chromatin Remodeling and Cancer","field":"Biochemistry, Genetics and Molecular Biology","cited_by":12,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"National Institute of General Medical Sciences; National Cancer Institute; Dalhousie University; Children’s Oncology Group; Broad Institute; Nationwide Children's Hospital; Pharmaceutical Research and Manufacturers of America Foundation","keywords":"Germline; Haplotype; Genetics; SMARCB1; Biology; Germline mutation; Locus (genetics); Allele; Loss of heterozygosity; Somatic cell; Mutation; 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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001405787,0.00009988806,0.0001595454,0.00003876995,0.00004481072,0.000007112102,0.00005727179,0.00006454591,0.00009379672],"category_scores_gemma":[0.00008868098,0.00008704254,0.0000232025,0.00009285619,0.00006620852,0.000001825073,0.0000570177,0.00007245476,0.000003475081],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001449038,"about_ca_system_score_gemma":0.00009387055,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00004808543,"about_ca_topic_score_gemma":0.0002235428,"domain_scores_codex":[0.9992422,0.0000406738,0.0002226135,0.0002437849,0.00009967699,0.0001510444],"domain_scores_gemma":[0.9995868,0.00001151703,0.00003543942,0.000237372,0.00005659202,0.00007228566],"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":[0.00001992622,0.00002495939,0.0009725908,0.00004441739,0.0000190148,0.00003339769,0.0003022139,0.0002829435,0.9963425,0.00002941097,0.0003866044,0.001541971],"study_design_scores_gemma":[0.02633398,0.003002995,0.2379058,0.00172572,0.0005897855,0.002151798,0.004167155,0.03945103,0.4624976,0.004262275,0.2149589,0.002953037],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.976823,0.01822615,0.002146272,0.001684779,0.00009570493,0.00008112172,0.000006867976,0.000008838374,0.0009272915],"genre_scores_gemma":[0.9958187,0.0007250356,0.0009912341,0.0006108479,0.0004655009,0.00001268503,0.0002736042,0.00001443992,0.001087889],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.533845,"threshold_uncertainty_score":0.3549491,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01363908117506729,"score_gpt":0.2564216776354201,"score_spread":0.2427825964603528,"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."}}