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"rna_he_after": 19, "rna_he_met_after": 17, "in_active_scope": true, "withheld": [], "context": { "target_project_donor": 19 }, "context_met": { "target_project_donor": 17 } } }, "BRCA": { "label": "BRCA", "role": "discovery", "projects": [ "BRCA" ], "selected_analysis": { "total": 1062, "rna": 1060, "met": 764, "paired": 762, "rna_only": 298, "met_only": 2 }, "contributions": { "BRCA": { "total": 1062, "rna": 1060, "met": 764, "paired": 762, "rna_only": 298, "met_only": 2 } }, "normal": { "rna_he_before": 98, "rna_he_after": 98, "rna_he_met_after": 73, "in_active_scope": true, "withheld": [], "context": { "target_project_donor": 98 }, "context_met": { "target_project_donor": 73 } } }, "CRC": { "label": "Colorectal adenocarcinoma (COAD + READ)", "role": "discovery", "projects": [ "COAD", "READ" ], "selected_analysis": { "total": 581, "rna": 579, "met": 373, "paired": 371, "rna_only": 208, "met_only": 2 }, "contributions": { "COAD": { "total": 427, "rna": 425, "met": 281, "paired": 279, "rna_only": 146, "met_only": 2 }, "READ": { "total": 154, "rna": 154, "met": 92, "paired": 92, "rna_only": 62, "met_only": 0 } }, "normal": { "rna_he_before": 47, "rna_he_after": 47, "rna_he_met_after": 19, "in_active_scope": true, "withheld": [], "context": { "target_project_donor": 46, "non_target_or_uncertain_or_recurrent_donor": 1 }, "context_met": { "target_project_donor": 19 } }, "reported_sites": { "Sigmoid colon": { "COAD": 103 }, "Ascending colon": { "COAD": 97 }, "Colon, NOS": { "COAD": 89, "READ": 6 }, "Rectum, NOS": { "READ": 81 }, "Cecum": { "COAD": 79 }, "Rectosigmoid junction": { "COAD": 7, "READ": 64 }, "Transverse colon": { "COAD": 20 }, "Descending colon": { "COAD": 17 }, "Hepatic flexure of colon": { "COAD": 10 }, "Splenic flexure of colon": { "COAD": 5 }, "Connective, subcutaneous and other soft tissues of abdomen": { "READ": 2 }, "Unknown primary site": { "READ": 1 } }, "site_overrides": [ { "patient": "TCGA-AF-2692", "project": "READ", "site_reported": "Rectum, NOS", "resection_site_reported": "Not Reported", "override": "colon_unspecified", "selected": true, "layers": "rna-only" }, { "patient": "TCGA-AF-2693", "project": "READ", "site_reported": "Rectosigmoid junction", "resection_site_reported": "Sigmoid colon", "override": "colon_unspecified", "selected": true, "layers": "both" }, { "patient": "TCGA-AY-4071", "project": "COAD", "site_reported": "Sigmoid colon", "resection_site_reported": "Colon, NOS", "override": "rectum", "selected": true, "layers": "rna-only" }, { "patient": "TCGA-CM-4750", "project": "COAD", "site_reported": "Rectosigmoid junction", "resection_site_reported": "Colon, NOS", "override": "rectum", "selected": true, "layers": "both" } ], "withheld": [ { "patient": "TCGA-5M-AAT5", "project": "COAD", "disposition": "diagnosis_identity_or_episode_exclusion_hold" }, { "patient": "TCGA-5M-AATA", "project": "COAD", "disposition": "diagnosis_identity_or_episode_exclusion_hold" }, { "patient": "TCGA-AA-3521", "project": "COAD", "disposition": "known_treatment_exclusion" }, { "patient": "TCGA-AA-3524", "project": "COAD", "disposition": "known_treatment_exclusion" }, { "patient": "TCGA-AA-3525", "project": "COAD", "disposition": "diagnosis_identity_or_episode_exclusion_hold" }, { "patient": "TCGA-AA-3543", "project": "COAD", "disposition": "known_treatment_exclusion" }, { "patient": "TCGA-AA-3552", "project": "COAD", "disposition": "known_treatment_exclusion" }, { "patient": "TCGA-AA-3675", "project": "COAD", "disposition": "treatment_unknown_hold" }, { "patient": "TCGA-AA-3715", "project": "COAD", "disposition": "diagnosis_identity_or_episode_exclusion_hold" }, { "patient": "TCGA-AA-3811", "project": "COAD", "disposition": "diagnosis_identity_or_episode_exclusion_hold" }, { "patient": "TCGA-AA-3814", "project": "COAD", "disposition": "diagnosis_identity_or_episode_exclusion_hold" }, { "patient": "TCGA-AA-A00Z", "project": "COAD", "disposition": "treatment_unknown_hold" }, { "patient": "TCGA-CI-6620", "project": "READ", "disposition": "known_treatment_exclusion" }, { "patient": "TCGA-CM-5863", "project": "COAD", "disposition": "diagnosis_identity_or_episode_exclusion_hold" }, { "patient": "TCGA-F5-6810", "project": "READ", "disposition": "diagnosis_identity_or_episode_exclusion_hold" }, { "patient": "TCGA-G4-6294", "project": "COAD", "disposition": "treatment_unknown_hold" }, { "patient": "TCGA-G4-6298", "project": "COAD", "disposition": "treatment_unknown_hold" }, { "patient": "TCGA-G4-6321", "project": "COAD", "disposition": "known_treatment_exclusion" } ] }, "CSCC": { "label": "Cervical squamous cell carcinoma", "role": "discovery", "projects": [ "CESC" ], "selected_analysis": { "total": 249, "rna": 248, "met": 249, "paired": 248, "rna_only": 0, "met_only": 1 }, "contributions": { "CESC": { "total": 249, "rna": 248, "met": 249, "paired": 248, "rna_only": 0, "met_only": 1 } }, "normal": { "rna_he_before": 2, "rna_he_after": 2, "rna_he_met_after": 2, "in_active_scope": true, "withheld": [], "context": { "target_project_donor": 2 }, "context_met": { "target_project_donor": 2 } }, "strata": [ { "stratum": "Squamous", "project": "CESC", "total": 249, "rna": 248, "met": 249, "paired": 248, "rna_only": 0, "met_only": 1, "publication_members": 142, "selected": 249 }, { "stratum": "Adenocarcinoma", "project": "CESC", "total": 46, "rna": 46, "met": 46, "paired": 46, "rna_only": 0, "met_only": 0, "publication_members": 30, "selected": 0 }, { "stratum": "Adenosquamous", "project": "CESC", "total": 6, "rna": 5, "met": 6, "paired": 5, "rna_only": 0, "met_only": 1, "publication_members": 3, "selected": 0 } ], "annotations": { "histology_evidence": [ [ "TCGA cervical publication table CLIN:Dx_merged", 142, 142 ], [ "GDC morphology fallback", 107, 106 ] ], "hpv_status_publication": [ [ "positive", 138, 138 ], [ null, 107, 106 ], [ "negative", 4, 4 ] ], "endometrial_like_publication": [ [ "No", 140, 140 ], [ null, 107, 106 ], [ "Yes", 2, 2 ] ] } }, "ESCC": { "label": "Confirmed oesophageal squamous cell carcinoma", "role": "discovery", "projects": [ "ESCA" ], "selected_analysis": { "total": 90, "rna": 90, "met": 90, "paired": 90, "rna_only": 0, "met_only": 0 }, "contributions": { "ESCA": { "total": 90, "rna": 90, "met": 90, "paired": 90, "rna_only": 0, "met_only": 0 } }, "normal": { "rna_he_before": 2, "rna_he_after": 2, "rna_he_met_after": 2, "in_active_scope": true, "withheld": [], "context": { "target_project_donor": 2 }, "context_met": { "target_project_donor": 2 } } }, "GLIOMA": { "label": "Diffuse glioma classification benchmark (LGG + GBM)", "role": "classification-benchmark", "projects": [ "LGG", "GBM" ], "selected_analysis": { "total": 727, "rna": 643, "met": 632, "paired": 548, "rna_only": 95, "met_only": 84 }, "contributions": { "LGG": { "total": 502, "rna": 502, "met": 502, "paired": 502, "rna_only": 0, "met_only": 0 }, "GBM": { "total": 225, "rna": 141, "met": 130, "paired": 46, "rna_only": 95, "met_only": 84 } }, "normal": { "rna_he_before": 5, "rna_he_after": 5, "rna_he_met_after": 1, "in_active_scope": true, "withheld": [], "context": { "normal_only_donor_primary_diagnosis_unreported": 5 }, "context_met": { "normal_only_donor_primary_diagnosis_unreported": 1 } }, "subsets": [ { "id": "GLIOMA-LGG-only", "label": "TCGA-LGG patients only", "total": 502, "rna": 502, "met": 502, "paired": 502, "rna_only": 0, "met_only": 0, "patients": [ "TCGA-CS-4938", "TCGA-CS-4941", "TCGA-CS-4942", "TCGA-CS-4943", "TCGA-CS-4944", "TCGA-CS-5390", "TCGA-CS-5394", "TCGA-CS-5395", "TCGA-CS-5396", "TCGA-CS-5397", "TCGA-CS-6186", "TCGA-CS-6188", "TCGA-CS-6290", "TCGA-CS-6665", "TCGA-CS-6666", "TCGA-CS-6667", "TCGA-CS-6668", "TCGA-CS-6669", "TCGA-DB-5273", "TCGA-DB-5274", "TCGA-DB-5275", "TCGA-DB-5276", "TCGA-DB-5277", "TCGA-DB-5278", "TCGA-DB-5279", "TCGA-DB-5280", "TCGA-DB-5281", "TCGA-DB-A4X9", "TCGA-DB-A4XA", "TCGA-DB-A4XB", "TCGA-DB-A4XC", "TCGA-DB-A4XD", "TCGA-DB-A4XE", "TCGA-DB-A4XF", "TCGA-DB-A4XG", "TCGA-DB-A4XH", 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"TCGA-DU-7010", "TCGA-DU-7012", "TCGA-DU-7013", "TCGA-DU-7014", "TCGA-DU-7015", "TCGA-DU-7018", "TCGA-DU-7019", "TCGA-DU-7290", "TCGA-DU-7292", "TCGA-DU-7294", "TCGA-DU-7298", "TCGA-DU-7299", "TCGA-DU-7300", "TCGA-DU-7301", "TCGA-DU-7302", "TCGA-DU-7304", "TCGA-DU-7306", "TCGA-DU-7309", "TCGA-DU-8158", "TCGA-DU-8161", "TCGA-DU-8162", "TCGA-DU-8163", "TCGA-DU-8164", "TCGA-DU-8165", "TCGA-DU-8166", "TCGA-DU-8167", "TCGA-DU-8168", "TCGA-DU-A5TR", "TCGA-DU-A5TS", "TCGA-DU-A5TT", "TCGA-DU-A5TU", "TCGA-DU-A5TW", "TCGA-DU-A5TY", "TCGA-DU-A6S2", "TCGA-DU-A6S3", "TCGA-DU-A6S6", "TCGA-DU-A6S7", "TCGA-DU-A6S8", "TCGA-DU-A76K", "TCGA-DU-A76L", "TCGA-DU-A76O", "TCGA-DU-A76R", "TCGA-DU-A7T6", "TCGA-DU-A7T8", "TCGA-DU-A7TA", "TCGA-DU-A7TB", "TCGA-DU-A7TC", "TCGA-DU-A7TD", "TCGA-DU-A7TG", "TCGA-DU-A7TI", "TCGA-DU-A7TJ", "TCGA-E1-5302", "TCGA-E1-5303", "TCGA-E1-5304", "TCGA-E1-5305", "TCGA-E1-5307", "TCGA-E1-5311", "TCGA-E1-5318", "TCGA-E1-5319", "TCGA-E1-5322", "TCGA-E1-A7YD", "TCGA-E1-A7YE", 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"TCGA-HT-8011", "TCGA-HT-8012", "TCGA-HT-8013", "TCGA-HT-8015", "TCGA-HT-8018", "TCGA-HT-8019", "TCGA-HT-8104", "TCGA-HT-8105", "TCGA-HT-8106", "TCGA-HT-8107", "TCGA-HT-8108", "TCGA-HT-8109", "TCGA-HT-8110", "TCGA-HT-8111", "TCGA-HT-8113", "TCGA-HT-8114", "TCGA-HT-8558", "TCGA-HT-8563", "TCGA-HT-8564", "TCGA-HT-A4DS", "TCGA-HT-A4DV", "TCGA-HT-A5R5", "TCGA-HT-A5R7", "TCGA-HT-A5R9", "TCGA-HT-A5RA", "TCGA-HT-A5RB", "TCGA-HT-A5RC", "TCGA-HT-A614", "TCGA-HT-A615", "TCGA-HT-A616", "TCGA-HT-A617", "TCGA-HT-A618", "TCGA-HT-A61A", "TCGA-HT-A61B", "TCGA-HT-A61C", "TCGA-HT-A74H", "TCGA-HT-A74J", "TCGA-HT-A74K", "TCGA-HT-A74L", "TCGA-HT-A74O", "TCGA-HW-7486", "TCGA-HW-7487", "TCGA-HW-7489", "TCGA-HW-7490", "TCGA-HW-7491", "TCGA-HW-7493", "TCGA-HW-7495", "TCGA-HW-8319", "TCGA-HW-8320", "TCGA-HW-8321", "TCGA-HW-8322", "TCGA-HW-A5KJ", "TCGA-HW-A5KK", "TCGA-HW-A5KL", "TCGA-HW-A5KM", "TCGA-IK-7675", "TCGA-IK-8125", "TCGA-KT-A74X", "TCGA-KT-A7W1", "TCGA-P5-A5ET", "TCGA-P5-A5EU", "TCGA-P5-A5EV", 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"TCGA-XD-AAUG", "TCGA-XD-AAUH", "TCGA-XD-AAUI", "TCGA-XD-AAUL", "TCGA-XN-A8T3", "TCGA-XN-A8T5", "TCGA-YB-A89D", "TCGA-YH-A8SY", "TCGA-YY-A8LH", "TCGA-Z5-AAPL" ] } ] }, "PRAD": { "label": "PRAD", "role": "discovery", "projects": [ "PRAD" ], "selected_analysis": { "total": 402, "rna": 401, "met": 402, "paired": 401, "rna_only": 0, "met_only": 1 }, "contributions": { "PRAD": { "total": 402, "rna": 401, "met": 402, "paired": 401, "rna_only": 0, "met_only": 1 } }, "normal": { "rna_he_before": 48, "rna_he_after": 48, "rna_he_met_after": 32, "in_active_scope": true, "withheld": [], "context": { "target_project_donor": 48 }, "context_met": { "target_project_donor": 32 } } }, "STAD": { "label": "STAD", "role": "discovery", "projects": [ "STAD" ], "selected_analysis": { "total": 414, "rna": 385, "met": 377, "paired": 348, "rna_only": 37, "met_only": 29 }, "contributions": { "STAD": { "total": 414, "rna": 385, "met": 377, "paired": 348, "rna_only": 37, "met_only": 29 } }, "normal": { 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"TCGA-EO-A3AY", "TCGA-EO-A3B0", "TCGA-EO-A3KX", "TCGA-EO-A3L0", "TCGA-EY-A1GC", "TCGA-EY-A1GD", "TCGA-EY-A1GE", "TCGA-EY-A1GF", "TCGA-EY-A1GH", "TCGA-EY-A1GI", "TCGA-EY-A1GJ", "TCGA-EY-A1GK", "TCGA-EY-A1GL", "TCGA-EY-A1GO", "TCGA-EY-A1GP", "TCGA-EY-A1GQ", "TCGA-EY-A1GR", "TCGA-EY-A1GT", "TCGA-EY-A1GU", "TCGA-EY-A1GW", "TCGA-EY-A1GX", "TCGA-EY-A1H0", "TCGA-EY-A214", "TCGA-EY-A215", "TCGA-EY-A2OM", "TCGA-EY-A2OP", "TCGA-EY-A2OQ", "TCGA-EY-A3L3", "TCGA-EY-A547", "TCGA-EY-A548", "TCGA-EY-A549", "TCGA-EY-A54A", "TCGA-EY-A5W2", "TCGA-EY-A72D", "TCGA-FI-A2CX", "TCGA-FI-A2D0", "TCGA-FI-A2D4", "TCGA-FI-A2D5", "TCGA-FI-A2D6", "TCGA-FI-A2F4", "TCGA-FI-A2F9", "TCGA-H5-A2HR", "TCGA-PG-A916", "TCGA-PG-A917", "TCGA-QF-A5YS", "TCGA-QF-A5YT", "TCGA-QS-A5YQ", "TCGA-QS-A5YR", "TCGA-QS-A744", "TCGA-SJ-A6ZI", "TCGA-SJ-A6ZJ", "TCGA-SL-A6J9", "TCGA-SL-A6JA" ] } ], "strata": [ { "stratum": "Endometrioid", "project": "UCEC", "total": 398, "rna": 396, "met": 305, "paired": 303, "rna_only": 93, "met_only": 2, "publication_members": 293, "selected": 398 }, { "stratum": "Serous", "project": "UCEC", "total": 112, "rna": 112, "met": 98, "paired": 98, "rna_only": 14, "met_only": 0, "publication_members": 49, "selected": 112 }, { "stratum": "Mixed", "project": "UCEC", "total": 12, "rna": 12, "met": 11, "paired": 11, "rna_only": 1, "met_only": 0, "publication_members": 12, "selected": 12 }, { "stratum": "Other", "project": "UCEC", "total": 1, "rna": 1, "met": 1, "paired": 1, "rna_only": 0, "met_only": 0, "publication_members": 0, "selected": 1 } ], "annotations": { "histology_stratum": [ [ "Endometrioid", 398, 303 ], [ "Serous", 112, 98 ], [ "Mixed", 12, 11 ], [ "Other", 1, 1 ] ], "histology_evidence": [ [ "TCGA endometrial publication table histology", 354, 244 ], [ "GDC morphology fallback", 169, 169 ] ], "grade_publication": [ [ null, 169, 169 ], [ "Grade 3", 165, 120 ], [ "Grade 2", 102, 72 ], [ "Grade 1", 87, 52 ] ], "published_subtype": [ [ null, 169, 169 ], [ "Notassigned", 131, 120 ], [ "CN low", 88, 51 ], [ "MSI", 63, 28 ], [ "CN high", 55, 36 ], [ "POLE", 17, 9 ] ] } } }, "panel": { "assay_qc": { "total": 8139, "rna": 7977, "met": 6970, "paired": 6808, "rna_only": 1169, "met_only": 162 }, "after_patient_screen": { "total": 7970, "rna": 7813, "met": 6860, "paired": 6703, "rna_only": 1110, "met_only": 157 }, "selected_analysis": { "total": 7826, "rna": 7671, "met": 6716, "paired": 6561, "rna_only": 1110, "met_only": 155 }, "discovery": { "total": 7099, "rna": 7028, "met": 6084, "paired": 6013, "rna_only": 1015, "met_only": 71 }, "benchmark": { "total": 727, "rna": 643, "met": 632, "paired": 548, "rna_only": 95, "met_only": 84 }, "dispositions": { "pass_annotation_screen": 7970, "known_treatment_exclusion": 67, "diagnosis_identity_or_episode_exclusion_hold": 62, "treatment_unknown_hold": 40 }, "reason_dimensions": { "treatment_exclusion": 74, "treatment_hold": 47, "diagnosis_identity_episode": 62 }, "normal": { "rna_he_before": 663, "rna_he_after": 656, "rna_he_met_after": 377, "in_active_scope": true, "withheld": [ "TCGA-56-8623", "TCGA-73-4676", "TCGA-90-6837", "TCGA-CV-7406", "TCGA-CV-7416", "TCGA-CV-7437", "TCGA-CV-7440" ], "context": { "normal_only_donor_primary_diagnosis_unreported": 5, "target_project_donor": 634, "non_target_or_uncertain_or_recurrent_donor": 5, "organ_specific_control": 12 }, "context_met": { "normal_only_donor_primary_diagnosis_unreported": 1, "target_project_donor": 362, "non_target_or_uncertain_or_recurrent_donor": 2, "organ_specific_control": 12 } } } }