TCGA.RNASeqV2: Integrated genomic analyses of ovarian carcinoma.
In MetaGxOvarian: Transcriptomic Ovarian Cancer Datasets
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Description
A catalogue of molecular aberrations that cause ovarian cancer is critical for developing and deploying therapies that will improve patients' lives. The Cancer Genome Atlas project has analysed messenger RNA expression, microRNA expression, promoter methylation and DNA copy number in 489 high-grade serous ovarian adenocarcinomas and the DNA sequences of exons from coding genes in 316 of these tumours. Here we report that high-grade serous ovarian cancer is characterized by TP53 mutations in almost all tumours (96%); low prevalence but statistically recurrent somatic mutations in nine further genes including NF1, BRCA1, BRCA2, RB1 and CDK12; 113 significant focal DNA copy number aberrations; and promoter methylation events involving 168 genes. Analyses delineated four ovarian cancer transcriptional subtypes, three microRNA subtypes, four promoter methylation subtypes and a transcriptional signature associated with survival duration, and shed new light on the impact that tumours with BRCA1/2 (BRCA1 or BRCA2) and CCNE1 aberrations have on survival. Pathway analyses suggested that homologous recombination is defective in about half of the tumours analysed, and that NOTCH and FOXM1 signalling are involved in serous ovarian cancer pathophysiology.
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experimentData(eset):
Experiment data
Experimenter name: Integrated genomic analyses of ovarian carcinoma. Nature 2011, 474:609-615.
Laboratory: Cancer Genome Atlas Research Network 2011
Contact information:
Title: Integrated genomic analyses of ovarian carcinoma.
URL:
PMIDs: 21720365
Abstract: A 179 word abstract is available. Use 'abstract' method.
Information is available on: preprocessing
notes:
platform_title:
[RNASeqV2] Illumina HiSeq RNA sequencing
platform_shorttitle:
Illumina HiSeq RNA sequencing
platform_summary:
NA
platform_manufacturer:
Illumina
platform_distribution:
sequencing
platform_accession:
NA
platform_technology:
RNA sequencing
version:
2015-09-22 20:27:26
featureData(eset):
An object of class 'AnnotatedDataFrame'
featureNames: ?|100133144 ?|100134869 ... ZZZ3|26009 (20471 total)
varLabels: probeset gene EntrezGene.ID best_probe
varMetadata: labelDescription
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assayData: 20471 features, 261 samples
Platform type:
Overall survival time-to-event summary (in years):
Call: survfit(formula = Surv(time, cens) ~ -1)
5 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
256.00 143.00 3.62 3.19 4.03
---------------------------
Available sample meta-data:
---------------------------
alt_sample_name:
TCGA-04-1348-01A-01R-1565-13 TCGA-04-1357-01A-01R-1565-13
1 1
TCGA-04-1362-01A-01R-1565-13 TCGA-04-1364-01A-01R-1565-13
1 1
TCGA-04-1365-01A-01R-1565-13 TCGA-04-1514-01A-01R-1566-13
1 1
TCGA-04-1519-01A-01R-1565-13 TCGA-09-0364-01A-02R-1564-13
1 1
TCGA-09-0366-01A-01R-1564-13 TCGA-09-0367-01A-01R-1564-13
1 1
TCGA-09-0369-01A-01R-1564-13 TCGA-09-1662-01A-01R-1566-13
1 1
TCGA-09-1666-01A-01R-1566-13 TCGA-09-1667-01C-01R-1566-13
1 1
TCGA-09-1668-01B-01R-1566-13 TCGA-09-1669-01A-01R-1566-13
1 1
TCGA-09-1670-01A-01R-1566-13 TCGA-09-1673-01A-01R-1566-13
1 1
TCGA-09-1674-01A-01R-1566-13 TCGA-09-2044-01B-01R-1568-13
1 1
TCGA-09-2045-01A-01R-1568-13 TCGA-09-2048-01A-01R-1568-13
1 1
TCGA-09-2051-01A-01R-1568-13 TCGA-09-2054-01A-01R-1568-13
1 1
TCGA-09-2056-01B-01R-1568-13 TCGA-10-0928-01A-02R-1564-13
1 1
TCGA-10-0936-01A-01R-1564-13 TCGA-13-0730-01A-01R-1564-13
1 1
TCGA-13-0799-01A-01R-1564-13 TCGA-13-0800-01A-01R-1564-13
1 1
TCGA-13-0801-01A-01R-1564-13 TCGA-13-0890-01A-01R-1564-13
1 1
TCGA-13-0893-01B-01R-1565-13 TCGA-13-0897-01A-01R-1564-13
1 1
TCGA-13-0899-01A-01R-1564-13 TCGA-13-0913-01A-01R-1564-13
1 1
TCGA-13-0916-01A-01R-1564-13 TCGA-13-0920-01A-01R-1564-13
1 1
TCGA-13-0924-01A-01R-1564-13 TCGA-13-1403-01A-01R-1565-13
1 1
TCGA-13-1405-01A-01R-1565-13 TCGA-13-1410-01A-01R-1565-13
1 1
TCGA-13-1481-01A-01R-1565-13 TCGA-13-1497-01A-01R-1565-13
1 1
TCGA-13-1498-01A-01R-1565-13 TCGA-13-1505-01A-01R-1565-13
1 1
TCGA-13-1506-01A-01R-1565-13 TCGA-13-1507-01A-01R-1565-13
1 1
TCGA-13-1511-01A-01R-1565-13 TCGA-13-1512-01A-01R-1565-13
1 1
TCGA-13-2060-01A-01R-1568-13 TCGA-20-1682-01A-01R-1564-13
1 1
TCGA-20-1683-01A-01R-1566-13 TCGA-20-1684-01A-01R-1566-13
1 1
TCGA-20-1685-01A-01R-1566-13 TCGA-20-1687-01A-01R-1566-13
1 1
TCGA-23-1023-01A-02R-1564-13 TCGA-23-1026-01B-01R-1569-13
1 1
TCGA-23-1027-01A-02R-1564-13 TCGA-23-1029-01B-01R-1567-13
1 1
TCGA-23-1109-01A-01R-1564-13 TCGA-23-1111-01A-01R-1567-13
1 1
TCGA-23-1114-01B-01R-1566-13 TCGA-23-1120-01A-02R-1565-13
1 1
TCGA-23-1122-01A-01R-1565-13 TCGA-23-1123-01A-01R-1565-13
1 1
TCGA-23-1809-01A-01R-1566-13 TCGA-23-2077-01A-01R-1568-13
1 1
TCGA-23-2081-01A-01R-1568-13 TCGA-23-2084-01A-02R-1568-13
1 1
TCGA-24-0975-01A-02R-1565-13 TCGA-24-1103-01A-01R-1565-13
1 1
TCGA-24-1413-01A-01R-1565-13 TCGA-24-1416-01A-01R-1565-13
1 1
TCGA-24-1417-01A-01R-1565-13 TCGA-24-1418-01A-01R-1565-13
1 1
TCGA-24-1419-01A-01R-1565-13 TCGA-24-1423-01A-01R-1565-13
1 1
TCGA-24-1424-01A-01R-1565-13 TCGA-24-1427-01A-01R-1565-13
1 1
TCGA-24-1428-01A-01R-1564-13 TCGA-24-1430-01A-01R-1566-13
1 1
TCGA-24-1436-01A-01R-1566-13 TCGA-24-1467-01A-01R-1566-13
1 1
TCGA-24-1469-01A-01R-1566-13 TCGA-24-1474-01A-01R-1566-13
1 1
TCGA-24-1544-01A-01R-1566-13 TCGA-24-1548-01A-01R-1566-13
1 1
TCGA-24-1549-01A-01R-1566-13 TCGA-24-1550-01A-01R-1566-13
1 1
TCGA-24-1551-01A-01R-1566-13 TCGA-24-1552-01A-01R-1566-13
1 1
TCGA-24-1553-01A-01R-1566-13 TCGA-24-1555-01A-01R-1566-13
1 1
TCGA-24-1556-01A-01R-1566-13 TCGA-24-1557-01A-01R-1566-13
1 1
TCGA-24-1558-01A-01R-1566-13 TCGA-24-1560-01A-01R-1566-13
1 1
TCGA-24-1562-01A-01R-1566-13 (Other)
1 162
unique_patient_ID:
TCGA-04-1348 TCGA-04-1357 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1514
1 1 1 1 1 1
TCGA-04-1519 TCGA-09-0364 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-09-1662
1 1 1 1 1 1
TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1673
1 1 1 1 1 1
TCGA-09-1674 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2051 TCGA-09-2054
1 1 1 1 1 1
TCGA-09-2056 TCGA-10-0928 TCGA-10-0936 TCGA-13-0730 TCGA-13-0799 TCGA-13-0800
1 1 1 1 1 1
TCGA-13-0801 TCGA-13-0890 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0913
1 1 1 1 1 1
TCGA-13-0916 TCGA-13-0920 TCGA-13-0924 TCGA-13-1403 TCGA-13-1405 TCGA-13-1410
1 1 1 1 1 1
TCGA-13-1481 TCGA-13-1497 TCGA-13-1498 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507
1 1 1 1 1 1
TCGA-13-1511 TCGA-13-1512 TCGA-13-2060 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684
1 1 1 1 1 1
TCGA-20-1685 TCGA-20-1687 TCGA-23-1023 TCGA-23-1026 TCGA-23-1027 TCGA-23-1029
1 1 1 1 1 1
TCGA-23-1109 TCGA-23-1111 TCGA-23-1114 TCGA-23-1120 TCGA-23-1122 TCGA-23-1123
1 1 1 1 1 1
TCGA-23-1809 TCGA-23-2077 TCGA-23-2081 TCGA-23-2084 TCGA-24-0975 TCGA-24-1103
1 1 1 1 1 1
TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1423
1 1 1 1 1 1
TCGA-24-1424 TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1436 TCGA-24-1467
1 1 1 1 1 1
TCGA-24-1469 TCGA-24-1474 TCGA-24-1544 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550
1 1 1 1 1 1
TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557
1 1 1 1 1 1
TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 (Other)
1 1 1 162
sample_type:
tumor
261
histological_type:
ser
261
primarysite:
other ov
1 260
summarygrade:
high low NA's
226 29 6
summarystage:
early late NA's
18 242 1
tumorstage:
2 3 4 NA's
18 209 33 1
substage:
b c NA's
16 211 34
grade:
1 2 3 4 NA's
1 28 225 1 6
age_at_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
34.00 51.00 58.00 58.84 66.00 87.00
pltx:
n y NA's
17 215 29
tax:
n y NA's
17 215 29
neo:
n NA's
232 29
days_to_tumor_recurrence:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
9.0 225.0 426.5 585.3 755.0 5480.0 19
recurrence_status:
norecurrence recurrence
123 138
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
9.0 341.8 878.0 1018.0 1446.0 5480.0 5
vital_status:
deceased living NA's
143 114 4
site_of_tumor_first_recurrence:
locoregional metastasis NA's
82 56 123
primary_therapy_outcome_success:
completeresponse partialresponse progressivedisease stabledisease
147 30 15 15
NA's
54
debulking:
optimal suboptimal NA's
171 60 30
percent_normal_cells:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 0.000 0.000 2.066 0.000 55.000 5
percent_stromal_cells:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.00 5.00 10.00 11.43 15.00 70.00 4
percent_tumor_cells:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.00 77.00 85.00 82.07 90.00 100.00 4
uncurated_author_metadata:
age_at_initial_pathologic_diagnosis: 34///anatomic_organ_subdivision: Bilateral///bcr_patient_uuid: f9793a4b-c0e7-4475-bf80-69543b7ee2f6///days_to_birth: -12772///days_to_initial_pathologic_diagnosis: 0///ethnicity: NA///gender: FEMALE///gynecologic_figo_staging_system: NA///histological_type: Serous Cystadenocarcinoma///icd_10: NA///icd_o_3_histology: 8441/3///icd_o_3_site: C56.9///informed_consent_verified: YES///initial_pathologic_diagnosis_method: Tumor resection///jewish_origin: NA///lymphatic_invasion: NA///neoplasm_histologic_grade: G3///patient_id: 1416///pretreatment_history: NO///race: WHITE///residual_tumor: NA///tissue_source_site: 24///tumor_histologic_subtype: Cystadenocarcinoma///tumor_residual_disease: 1-10 mm///tumor_stage: IV///tumor_tissue_site: OVARY///venous_invasion: NA///year_of_initial_pathologic_diagnosis: 2008///additional_chemo_therapy: NO///additional_drug_therapy: NO///additional_immuno_therapy: NO///additional_pharmaceutical_therapy: NO///additional_radiation_therapy: NO///additional_surgery_locoregional_procedure: NA///additional_surgery_metastatic_procedure: NA///bcr_followup_uuid: cf7ad1d4-c805-41b7-8c74-2e09210bfd7e///chemo_therapy: YES///day_of_form_completion: 1///days_to_additional_surgery_locoregional_procedure: NA///days_to_additional_surgery_metastatic_procedure: NA///days_to_death: NA///days_to_last_followup: 194///days_to_new_tumor_event_after_initial_treatment: NA///days_to_tumor_progression: NA///days_to_tumor_recurrence: NA///eastern_cancer_oncology_group: NA///followup_case_report_form_submission_reason: NA///hormonal_therapy: NO///immuno_therapy: NO///karnofsky_performance_score: NA///month_of_form_completion: 4///performance_status_scale_timing: NA///person_neoplasm_cancer_status: TUMOR FREE///primary_therapy_outcome_success: Complete Response///progression_determined_by: NA///progression_determined_by_notes: NA///radiation_therapy: NO///site_of_tumor_first_recurrence: NA///targeted_molecular_therapy: NO///vital_status: LIVING///year_of_form_completion: 2009///Extract.Name: TCGA-24-1416-01A-01R-1565-13///unique_patient_id: TCGA-24-1416
1
age_at_initial_pathologic_diagnosis: 38///anatomic_organ_subdivision: Bilateral///bcr_patient_uuid: 1c0318d9-0472-4840-add4-46bb9f914a30///days_to_birth: -13894///days_to_initial_pathologic_diagnosis: 0///ethnicity: NOT HISPANIC OR LATINO///gender: FEMALE///gynecologic_figo_staging_system: NA///histological_type: Serous Cystadenocarcinoma///icd_10: NA///icd_o_3_histology: 8441/3///icd_o_3_site: C56.9///informed_consent_verified: YES///initial_pathologic_diagnosis_method: Excisional Biopsy///jewish_origin: NA///lymphatic_invasion: YES///neoplasm_histologic_grade: G1///patient_id: 1721///pretreatment_history: YES///race: WHITE///residual_tumor: NA///tissue_source_site: 61///tumor_histologic_subtype: Cystadenocarcinoma///tumor_residual_disease: NA///tumor_stage: IV///tumor_tissue_site: OVARY///venous_invasion: YES///year_of_initial_pathologic_diagnosis: 2008///additional_chemo_therapy: NO///additional_drug_therapy: NO///additional_immuno_therapy: NO///additional_pharmaceutical_therapy: NO///additional_radiation_therapy: NO///additional_surgery_locoregional_procedure: NA///additional_surgery_metastatic_procedure: NA///bcr_followup_uuid: 902be45d-0481-4e42-8dc7-10a185ca8ade///chemo_therapy: YES///day_of_form_completion: 2///days_to_additional_surgery_locoregional_procedure: NA///days_to_additional_surgery_metastatic_procedure: NA///days_to_death: NA///days_to_last_followup: 338///days_to_new_tumor_event_after_initial_treatment: NA///days_to_tumor_progression: NA///days_to_tumor_recurrence: NA///eastern_cancer_oncology_group: NA///followup_case_report_form_submission_reason: NA///hormonal_therapy: NO///immuno_therapy: NO///karnofsky_performance_score: NA///month_of_form_completion: 6///performance_status_scale_timing: NA///person_neoplasm_cancer_status: TUMOR FREE///primary_therapy_outcome_success: Complete Response///progression_determined_by: NA///progression_determined_by_notes: NA///radiation_therapy: NO///site_of_tumor_first_recurrence: NA///targeted_molecular_therapy: NO///vital_status: LIVING///year_of_form_completion: 2009///Extract.Name: TCGA-61-1721-01A-01R-1569-13///unique_patient_id: TCGA-61-1721
1
age_at_initial_pathologic_diagnosis: 38///anatomic_organ_subdivision: Bilateral///bcr_patient_uuid: 22178c3c-6b04-46d8-8041-dc83fa195029///days_to_birth: -14184///days_to_initial_pathologic_diagnosis: 0///ethnicity: NOT HISPANIC OR LATINO///gender: FEMALE///gynecologic_figo_staging_system: NA///histological_type: Serous Cystadenocarcinoma///icd_10: NA///icd_o_3_histology: 8441/3///icd_o_3_site: C56.9///informed_consent_verified: YES///initial_pathologic_diagnosis_method: Tumor resection///jewish_origin: NA///lymphatic_invasion: NA///neoplasm_histologic_grade: G3///patient_id: 2404///pretreatment_history: NO///race: AMERICAN INDIAN OR ALASKA NATIVE///residual_tumor: NA///tissue_source_site: 25///tumor_histologic_subtype: Cystadenocarcinoma///tumor_residual_disease: No Macroscopic disease///tumor_stage: IIIC///tumor_tissue_site: OVARY///venous_invasion: NA///year_of_initial_pathologic_diagnosis: 2005///additional_chemo_therapy: YES///additional_drug_therapy: NO///additional_immuno_therapy: NO///additional_pharmaceutical_therapy: NO///additional_radiation_therapy: NO///additional_surgery_locoregional_procedure: NO///additional_surgery_metastatic_procedure: NO///bcr_followup_uuid: 8b0b1002-3ed9-4317-ba15-982dc5522748///chemo_therapy: YES///day_of_form_completion: 5///days_to_additional_surgery_locoregional_procedure: NA///days_to_additional_surgery_metastatic_procedure: NA///days_to_death: 882///days_to_last_followup: 882///days_to_new_tumor_event_after_initial_treatment: NA///days_to_tumor_progression: NA///days_to_tumor_recurrence: 425///eastern_cancer_oncology_group: NA///followup_case_report_form_submission_reason: NA///hormonal_therapy: NO///immuno_therapy: NO///karnofsky_performance_score: NA///month_of_form_completion: 1///performance_status_scale_timing: NA///person_neoplasm_cancer_status: WITH TUMOR///primary_therapy_outcome_success: Complete Response///progression_determined_by: Imaging Study///progression_determined_by_notes: CT and Molecular Marker - CA125///radiation_therapy: NO///site_of_tumor_first_recurrence: Metastasis///targeted_molecular_therapy: NO///vital_status: DECEASED///year_of_form_completion: 2010///Extract.Name: TCGA-25-2404-01A-01R-1569-13///unique_patient_id: TCGA-25-2404
1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
age_at_initial_pathologic_diagnosis: 49///anatomic_organ_subdivision: Bilateral///bcr_patient_uuid: 41178cbc-db73-4007-b5d8-febebf7f578d///days_to_birth: -18161///days_to_initial_pathologic_diagnosis: 0///ethnicity: NOT HISPANIC OR LATINO///gender: FEMALE///gynecologic_figo_staging_system: NA///histological_type: Serous Cystadenocarcinoma///icd_10: NA///icd_o_3_histology: 8441/3///icd_o_3_site: C56.9///informed_consent_verified: YES///initial_pathologic_diagnosis_method: Tumor resection///jewish_origin: ASHKENAZI///lymphatic_invasion: YES///neoplasm_histologic_grade: G3///patient_id: 2081///pretreatment_history: NO///race: WHITE///residual_tumor: NA///tissue_source_site: 23///tumor_histologic_subtype: Cystadenocarcinoma///tumor_residual_disease: 1-10 mm///tumor_stage: IV///tumor_tissue_site: OVARY///venous_invasion: NA///year_of_initial_pathologic_diagnosis: 2000///additional_chemo_therapy: YES///additional_drug_therapy: NO///additional_immuno_therapy: NO///additional_pharmaceutical_therapy: NO///additional_radiation_therapy: NO///additional_surgery_locoregional_procedure: YES///additional_surgery_metastatic_procedure: NA///bcr_followup_uuid: 3bed5a01-64cb-41cf-9ed8-4d91eecc4adf///chemo_therapy: YES///day_of_form_completion: 20///days_to_additional_surgery_locoregional_procedure: 250///days_to_additional_surgery_metastatic_procedure: NA///days_to_death: 2342///days_to_last_followup: 2342///days_to_new_tumor_event_after_initial_treatment: NA///days_to_tumor_progression: NA///days_to_tumor_recurrence: NA///eastern_cancer_oncology_group: NA///followup_case_report_form_submission_reason: NA///hormonal_therapy: NO///immuno_therapy: NO///karnofsky_performance_score: NA///month_of_form_completion: 11///performance_status_scale_timing: NA///person_neoplasm_cancer_status: WITH TUMOR///primary_therapy_outcome_success: Progressive Disease///progression_determined_by: NA///progression_determined_by_notes: NA///radiation_therapy: NO///site_of_tumor_first_recurrence: NA///targeted_molecular_therapy: NO///vital_status: DECEASED///year_of_form_completion: 2009///Extract.Name: TCGA-23-2081-01A-01R-1568-13///unique_patient_id: TCGA-23-2081
1
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1
age_at_initial_pathologic_diagnosis: 49///anatomic_organ_subdivision: Bilateral///bcr_patient_uuid: 7dcc809b-e33a-4453-b92a-c00786f48cb0///days_to_birth: -17943///days_to_initial_pathologic_diagnosis: 0///ethnicity: NA///gender: FEMALE///gynecologic_figo_staging_system: NA///histological_type: Serous Cystadenocarcinoma///icd_10: NA///icd_o_3_histology: 8441/3///icd_o_3_site: C56.9///informed_consent_verified: YES///initial_pathologic_diagnosis_method: Tumor resection///jewish_origin: NA///lymphatic_invasion: NA///neoplasm_histologic_grade: G3///patient_id: 1557///pretreatment_history: NO///race: WHITE///residual_tumor: NA///tissue_source_site: 24///tumor_histologic_subtype: Cystadenocarcinoma///tumor_residual_disease: >20 mm///tumor_stage: IIIC///tumor_tissue_site: OVARY///venous_invasion: NA///year_of_initial_pathologic_diagnosis: 2000///additional_chemo_therapy: YES///additional_drug_therapy: NO///additional_immuno_therapy: NO///additional_pharmaceutical_therapy: YES///additional_radiation_therapy: NO///additional_surgery_locoregional_procedure: NA///additional_surgery_metastatic_procedure: NA///bcr_followup_uuid: 300786cc-f4e9-45c3-8987-c78cb62f21ea///chemo_therapy: YES///day_of_form_completion: 2///days_to_additional_surgery_locoregional_procedure: NA///days_to_additional_surgery_metastatic_procedure: NA///days_to_death: 1213///days_to_last_followup: 1213///days_to_new_tumor_event_after_initial_treatment: NA///days_to_tumor_progression: 447///days_to_tumor_recurrence: NA///eastern_cancer_oncology_group: NA///followup_case_report_form_submission_reason: NA///hormonal_therapy: NO///immuno_therapy: NO///karnofsky_performance_score: NA///month_of_form_completion: 6///performance_status_scale_timing: NA///person_neoplasm_cancer_status: WITH TUMOR///primary_therapy_outcome_success: Partial Response///progression_determined_by: Imaging Study///progression_determined_by_notes: Abdomin MIR;Molecular marker CA 125///radiation_therapy: NO///site_of_tumor_first_recurrence: Loco-Regional///targeted_molecular_therapy: NO///vital_status: DECEASED///year_of_form_completion: 2009///Extract.Name: TCGA-24-1557-01A-01R-1566-13///unique_patient_id: TCGA-24-1557
1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
age_at_initial_pathologic_diagnosis: 54///anatomic_organ_subdivision: Left///bcr_patient_uuid: 48f831b0-5d91-44ae-bc4e-db57ca84fe46///days_to_birth: -19775///days_to_initial_pathologic_diagnosis: 0///ethnicity: NA///gender: FEMALE///gynecologic_figo_staging_system: NA///histological_type: Serous Cystadenocarcinoma///icd_10: NA///icd_o_3_histology: 8441/3///icd_o_3_site: C56.9///informed_consent_verified: YES///initial_pathologic_diagnosis_method: Tumor resection///jewish_origin: NA///lymphatic_invasion: NA///neoplasm_histologic_grade: G3///patient_id: 1417///pretreatment_history: NO///race: WHITE///residual_tumor: NA///tissue_source_site: 24///tumor_histologic_subtype: Cystadenocarcinoma///tumor_residual_disease: 1-10 mm///tumor_stage: IV///tumor_tissue_site: OVARY///venous_invasion: NA///year_of_initial_pathologic_diagnosis: 2008///additional_chemo_therapy: NO///additional_drug_therapy: NO///additional_immuno_therapy: NO///additional_pharmaceutical_therapy: NO///additional_radiation_therapy: NO///additional_surgery_locoregional_procedure: NA///additional_surgery_metastatic_procedure: NA///bcr_followup_uuid: 6f2f5940-f189-4422-93fc-7571c6f994ba///chemo_therapy: YES///day_of_form_completion: 1///days_to_additional_surgery_locoregional_procedure: NA///days_to_additional_surgery_metastatic_procedure: NA///days_to_death: NA///days_to_last_followup: 238///days_to_new_tumor_event_after_initial_treatment: NA///days_to_tumor_progression: NA///days_to_tumor_recurrence: NA///eastern_cancer_oncology_group: NA///followup_case_report_form_submission_reason: NA///hormonal_therapy: NO///immuno_therapy: NO///karnofsky_performance_score: NA///month_of_form_completion: 4///performance_status_scale_timing: NA///person_neoplasm_cancer_status: TUMOR FREE///primary_therapy_outcome_success: Complete Response///progression_determined_by: NA///progression_determined_by_notes: NA///radiation_therapy: NO///site_of_tumor_first_recurrence: NA///targeted_molecular_therapy: NO///vital_status: LIVING///year_of_form_completion: 2009///Extract.Name: TCGA-24-1417-01A-01R-1565-13///unique_patient_id: TCGA-24-1417
1
age_at_initial_pathologic_diagnosis: 54///anatomic_organ_subdivision: NA///bcr_patient_uuid: 13319c20-02f6-4b5f-b24f-3d8f4084094c///days_to_birth: -19755///days_to_initial_pathologic_diagnosis: 0///ethnicity: NOT HISPANIC OR LATINO///gender: FEMALE///gynecologic_figo_staging_system: NA///histological_type: Serous Cystadenocarcinoma///icd_10: NA///icd_o_3_histology: 8441/3///icd_o_3_site: C56.9///informed_consent_verified: YES///initial_pathologic_diagnosis_method: NA///jewish_origin: NA///lymphatic_invasion: NA///neoplasm_histologic_grade: G3///patient_id: 1318///pretreatment_history: NO///race: WHITE///residual_tumor: NA///tissue_source_site: 25///tumor_histologic_subtype: Cystadenocarcinoma///tumor_residual_disease: 1-10 mm///tumor_stage: IIIC///tumor_tissue_site: OVARY///venous_invasion: NA///year_of_initial_pathologic_diagnosis: 2000///additional_chemo_therapy: YES///additional_drug_therapy: NO///additional_immuno_therapy: NO///additional_pharmaceutical_therapy: NO///additional_radiation_therapy: NO///additional_surgery_locoregional_procedure: NO///additional_surgery_metastatic_procedure: YES///bcr_followup_uuid: f632b553-5ecb-48ef-84bc-d5372657f82a///chemo_therapy: YES///day_of_form_completion: 27///days_to_additional_surgery_locoregional_procedure: NA///days_to_additional_surgery_metastatic_procedure: NA///days_to_death: 1064///days_to_last_followup: 1064///days_to_new_tumor_event_after_initial_treatment: NA///days_to_tumor_progression: NA///days_to_tumor_recurrence: 185///eastern_cancer_oncology_group: NA///followup_case_report_form_submission_reason: NA///hormonal_therapy: NO///immuno_therapy: NO///karnofsky_performance_score: NA///month_of_form_completion: 3///performance_status_scale_timing: NA///person_neoplasm_cancer_status: WITH TUMOR///primary_therapy_outcome_success: Partial Response///progression_determined_by: First Seen At Further Surgery///progression_determined_by_notes: NA///radiation_therapy: NO///site_of_tumor_first_recurrence: Metastasis///targeted_molecular_therapy: NO///vital_status: DECEASED///year_of_form_completion: 2009///Extract.Name: TCGA-25-1318-01A-01R-1565-13///unique_patient_id: TCGA-25-1318
1
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1
age_at_initial_pathologic_diagnosis: 54///anatomic_organ_subdivision: Right///bcr_patient_uuid: b1c90c69-6149-4105-8182-ab9212f196be///days_to_birth: -20052///days_to_initial_pathologic_diagnosis: 0///ethnicity: NOT HISPANIC OR LATINO///gender: FEMALE///gynecologic_figo_staging_system: NA///histological_type: Serous Cystadenocarcinoma///icd_10: NA///icd_o_3_histology: 8441/3///icd_o_3_site: C56.9///informed_consent_verified: YES///initial_pathologic_diagnosis_method: Tumor resection///jewish_origin: NA///lymphatic_invasion: NO///neoplasm_histologic_grade: G3///patient_id: 1669///pretreatment_history: NO///race: WHITE///residual_tumor: NA///tissue_source_site: 9///tumor_histologic_subtype: Cystadenocarcinoma///tumor_residual_disease: No Macroscopic disease///tumor_stage: IIIA///tumor_tissue_site: OVARY///venous_invasion: NO///year_of_initial_pathologic_diagnosis: 2004///additional_chemo_therapy: NO///additional_drug_therapy: NO///additional_immuno_therapy: NO///additional_pharmaceutical_therapy: NO///additional_radiation_therapy: NO///additional_surgery_locoregional_procedure: NA///additional_surgery_metastatic_procedure: NA///bcr_followup_uuid: be4d9604-3e6b-4bf2-bd2a-0be49751832a///chemo_therapy: YES///day_of_form_completion: 2///days_to_additional_surgery_locoregional_procedure: NA///days_to_additional_surgery_metastatic_procedure: NA///days_to_death: NA///days_to_last_followup: 927///days_to_new_tumor_event_after_initial_treatment: NA///days_to_tumor_progression: NA///days_to_tumor_recurrence: NA///eastern_cancer_oncology_group: NA///followup_case_report_form_submission_reason: NA///hormonal_therapy: NO///immuno_therapy: NO///karnofsky_performance_score: NA///month_of_form_completion: 6///performance_status_scale_timing: NA///person_neoplasm_cancer_status: WITH TUMOR///primary_therapy_outcome_success: Complete Response///progression_determined_by: NA///progression_determined_by_notes: NA///radiation_therapy: NO///site_of_tumor_first_recurrence: NA///targeted_molecular_therapy: NO///vital_status: LIVING///year_of_form_completion: 2009///Extract.Name: TCGA-09-1669-01A-01R-1566-13///unique_patient_id: TCGA-09-1669
1
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1
(Other)
162
Value
An expression set
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Description Format Details Value
Description
A catalogue of molecular aberrations that cause ovarian cancer is critical for developing and deploying therapies that will improve patients' lives. The Cancer Genome Atlas project has analysed messenger RNA expression, microRNA expression, promoter methylation and DNA copy number in 489 high-grade serous ovarian adenocarcinomas and the DNA sequences of exons from coding genes in 316 of these tumours. Here we report that high-grade serous ovarian cancer is characterized by TP53 mutations in almost all tumours (96%); low prevalence but statistically recurrent somatic mutations in nine further genes including NF1, BRCA1, BRCA2, RB1 and CDK12; 113 significant focal DNA copy number aberrations; and promoter methylation events involving 168 genes. Analyses delineated four ovarian cancer transcriptional subtypes, three microRNA subtypes, four promoter methylation subtypes and a transcriptional signature associated with survival duration, and shed new light on the impact that tumours with BRCA1/2 (BRCA1 or BRCA2) and CCNE1 aberrations have on survival. Pathway analyses suggested that homologous recombination is defective in about half of the tumours analysed, and that NOTCH and FOXM1 signalling are involved in serous ovarian cancer pathophysiology.
Format
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 | experimentData(eset):
Experiment data
Experimenter name: Integrated genomic analyses of ovarian carcinoma. Nature 2011, 474:609-615.
Laboratory: Cancer Genome Atlas Research Network 2011
Contact information:
Title: Integrated genomic analyses of ovarian carcinoma.
URL:
PMIDs: 21720365
Abstract: A 179 word abstract is available. Use 'abstract' method.
Information is available on: preprocessing
notes:
platform_title:
[RNASeqV2] Illumina HiSeq RNA sequencing
platform_shorttitle:
Illumina HiSeq RNA sequencing
platform_summary:
NA
platform_manufacturer:
Illumina
platform_distribution:
sequencing
platform_accession:
NA
platform_technology:
RNA sequencing
version:
2015-09-22 20:27:26
featureData(eset):
An object of class 'AnnotatedDataFrame'
featureNames: ?|100133144 ?|100134869 ... ZZZ3|26009 (20471 total)
varLabels: probeset gene EntrezGene.ID best_probe
varMetadata: labelDescription
|
Details
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 | assayData: 20471 features, 261 samples
Platform type:
Overall survival time-to-event summary (in years):
Call: survfit(formula = Surv(time, cens) ~ -1)
5 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
256.00 143.00 3.62 3.19 4.03
---------------------------
Available sample meta-data:
---------------------------
alt_sample_name:
TCGA-04-1348-01A-01R-1565-13 TCGA-04-1357-01A-01R-1565-13
1 1
TCGA-04-1362-01A-01R-1565-13 TCGA-04-1364-01A-01R-1565-13
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TCGA-04-1365-01A-01R-1565-13 TCGA-04-1514-01A-01R-1566-13
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TCGA-04-1519-01A-01R-1565-13 TCGA-09-0364-01A-02R-1564-13
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TCGA-09-0366-01A-01R-1564-13 TCGA-09-0367-01A-01R-1564-13
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TCGA-09-0369-01A-01R-1564-13 TCGA-09-1662-01A-01R-1566-13
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TCGA-09-1666-01A-01R-1566-13 TCGA-09-1667-01C-01R-1566-13
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TCGA-09-1668-01B-01R-1566-13 TCGA-09-1669-01A-01R-1566-13
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TCGA-09-1670-01A-01R-1566-13 TCGA-09-1673-01A-01R-1566-13
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TCGA-09-1674-01A-01R-1566-13 TCGA-09-2044-01B-01R-1568-13
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TCGA-09-2045-01A-01R-1568-13 TCGA-09-2048-01A-01R-1568-13
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TCGA-09-2051-01A-01R-1568-13 TCGA-09-2054-01A-01R-1568-13
1 1
TCGA-09-2056-01B-01R-1568-13 TCGA-10-0928-01A-02R-1564-13
1 1
TCGA-10-0936-01A-01R-1564-13 TCGA-13-0730-01A-01R-1564-13
1 1
TCGA-13-0799-01A-01R-1564-13 TCGA-13-0800-01A-01R-1564-13
1 1
TCGA-13-0801-01A-01R-1564-13 TCGA-13-0890-01A-01R-1564-13
1 1
TCGA-13-0893-01B-01R-1565-13 TCGA-13-0897-01A-01R-1564-13
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TCGA-13-0899-01A-01R-1564-13 TCGA-13-0913-01A-01R-1564-13
1 1
TCGA-13-0916-01A-01R-1564-13 TCGA-13-0920-01A-01R-1564-13
1 1
TCGA-13-0924-01A-01R-1564-13 TCGA-13-1403-01A-01R-1565-13
1 1
TCGA-13-1405-01A-01R-1565-13 TCGA-13-1410-01A-01R-1565-13
1 1
TCGA-13-1481-01A-01R-1565-13 TCGA-13-1497-01A-01R-1565-13
1 1
TCGA-13-1498-01A-01R-1565-13 TCGA-13-1505-01A-01R-1565-13
1 1
TCGA-13-1506-01A-01R-1565-13 TCGA-13-1507-01A-01R-1565-13
1 1
TCGA-13-1511-01A-01R-1565-13 TCGA-13-1512-01A-01R-1565-13
1 1
TCGA-13-2060-01A-01R-1568-13 TCGA-20-1682-01A-01R-1564-13
1 1
TCGA-20-1683-01A-01R-1566-13 TCGA-20-1684-01A-01R-1566-13
1 1
TCGA-20-1685-01A-01R-1566-13 TCGA-20-1687-01A-01R-1566-13
1 1
TCGA-23-1023-01A-02R-1564-13 TCGA-23-1026-01B-01R-1569-13
1 1
TCGA-23-1027-01A-02R-1564-13 TCGA-23-1029-01B-01R-1567-13
1 1
TCGA-23-1109-01A-01R-1564-13 TCGA-23-1111-01A-01R-1567-13
1 1
TCGA-23-1114-01B-01R-1566-13 TCGA-23-1120-01A-02R-1565-13
1 1
TCGA-23-1122-01A-01R-1565-13 TCGA-23-1123-01A-01R-1565-13
1 1
TCGA-23-1809-01A-01R-1566-13 TCGA-23-2077-01A-01R-1568-13
1 1
TCGA-23-2081-01A-01R-1568-13 TCGA-23-2084-01A-02R-1568-13
1 1
TCGA-24-0975-01A-02R-1565-13 TCGA-24-1103-01A-01R-1565-13
1 1
TCGA-24-1413-01A-01R-1565-13 TCGA-24-1416-01A-01R-1565-13
1 1
TCGA-24-1417-01A-01R-1565-13 TCGA-24-1418-01A-01R-1565-13
1 1
TCGA-24-1419-01A-01R-1565-13 TCGA-24-1423-01A-01R-1565-13
1 1
TCGA-24-1424-01A-01R-1565-13 TCGA-24-1427-01A-01R-1565-13
1 1
TCGA-24-1428-01A-01R-1564-13 TCGA-24-1430-01A-01R-1566-13
1 1
TCGA-24-1436-01A-01R-1566-13 TCGA-24-1467-01A-01R-1566-13
1 1
TCGA-24-1469-01A-01R-1566-13 TCGA-24-1474-01A-01R-1566-13
1 1
TCGA-24-1544-01A-01R-1566-13 TCGA-24-1548-01A-01R-1566-13
1 1
TCGA-24-1549-01A-01R-1566-13 TCGA-24-1550-01A-01R-1566-13
1 1
TCGA-24-1551-01A-01R-1566-13 TCGA-24-1552-01A-01R-1566-13
1 1
TCGA-24-1553-01A-01R-1566-13 TCGA-24-1555-01A-01R-1566-13
1 1
TCGA-24-1556-01A-01R-1566-13 TCGA-24-1557-01A-01R-1566-13
1 1
TCGA-24-1558-01A-01R-1566-13 TCGA-24-1560-01A-01R-1566-13
1 1
TCGA-24-1562-01A-01R-1566-13 (Other)
1 162
unique_patient_ID:
TCGA-04-1348 TCGA-04-1357 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1514
1 1 1 1 1 1
TCGA-04-1519 TCGA-09-0364 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-09-1662
1 1 1 1 1 1
TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1673
1 1 1 1 1 1
TCGA-09-1674 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2051 TCGA-09-2054
1 1 1 1 1 1
TCGA-09-2056 TCGA-10-0928 TCGA-10-0936 TCGA-13-0730 TCGA-13-0799 TCGA-13-0800
1 1 1 1 1 1
TCGA-13-0801 TCGA-13-0890 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0913
1 1 1 1 1 1
TCGA-13-0916 TCGA-13-0920 TCGA-13-0924 TCGA-13-1403 TCGA-13-1405 TCGA-13-1410
1 1 1 1 1 1
TCGA-13-1481 TCGA-13-1497 TCGA-13-1498 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507
1 1 1 1 1 1
TCGA-13-1511 TCGA-13-1512 TCGA-13-2060 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684
1 1 1 1 1 1
TCGA-20-1685 TCGA-20-1687 TCGA-23-1023 TCGA-23-1026 TCGA-23-1027 TCGA-23-1029
1 1 1 1 1 1
TCGA-23-1109 TCGA-23-1111 TCGA-23-1114 TCGA-23-1120 TCGA-23-1122 TCGA-23-1123
1 1 1 1 1 1
TCGA-23-1809 TCGA-23-2077 TCGA-23-2081 TCGA-23-2084 TCGA-24-0975 TCGA-24-1103
1 1 1 1 1 1
TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1423
1 1 1 1 1 1
TCGA-24-1424 TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1436 TCGA-24-1467
1 1 1 1 1 1
TCGA-24-1469 TCGA-24-1474 TCGA-24-1544 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550
1 1 1 1 1 1
TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557
1 1 1 1 1 1
TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 (Other)
1 1 1 162
sample_type:
tumor
261
histological_type:
ser
261
primarysite:
other ov
1 260
summarygrade:
high low NA's
226 29 6
summarystage:
early late NA's
18 242 1
tumorstage:
2 3 4 NA's
18 209 33 1
substage:
b c NA's
16 211 34
grade:
1 2 3 4 NA's
1 28 225 1 6
age_at_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
34.00 51.00 58.00 58.84 66.00 87.00
pltx:
n y NA's
17 215 29
tax:
n y NA's
17 215 29
neo:
n NA's
232 29
days_to_tumor_recurrence:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
9.0 225.0 426.5 585.3 755.0 5480.0 19
recurrence_status:
norecurrence recurrence
123 138
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
9.0 341.8 878.0 1018.0 1446.0 5480.0 5
vital_status:
deceased living NA's
143 114 4
site_of_tumor_first_recurrence:
locoregional metastasis NA's
82 56 123
primary_therapy_outcome_success:
completeresponse partialresponse progressivedisease stabledisease
147 30 15 15
NA's
54
debulking:
optimal suboptimal NA's
171 60 30
percent_normal_cells:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 0.000 0.000 2.066 0.000 55.000 5
percent_stromal_cells:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.00 5.00 10.00 11.43 15.00 70.00 4
percent_tumor_cells:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.00 77.00 85.00 82.07 90.00 100.00 4
uncurated_author_metadata:
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1
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1
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1
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1
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1
age_at_initial_pathologic_diagnosis: 40///anatomic_organ_subdivision: Bilateral///bcr_patient_uuid: 3ac45a71-c463-4f0f-b030-58c475a34418///days_to_birth: -14791///days_to_initial_pathologic_diagnosis: 0///ethnicity: NOT HISPANIC OR LATINO///gender: FEMALE///gynecologic_figo_staging_system: NA///histological_type: Serous Cystadenocarcinoma///icd_10: NA///icd_o_3_histology: 8441/3///icd_o_3_site: C56.9///informed_consent_verified: YES///initial_pathologic_diagnosis_method: Tumor resection///jewish_origin: NA///lymphatic_invasion: YES///neoplasm_histologic_grade: G2///patient_id: 2008///pretreatment_history: NO///race: ASIAN///residual_tumor: NA///tissue_source_site: 61///tumor_histologic_subtype: Cystadenocarcinoma///tumor_residual_disease: No Macroscopic disease///tumor_stage: IIC///tumor_tissue_site: OVARY///venous_invasion: YES///year_of_initial_pathologic_diagnosis: 2007///additional_chemo_therapy: YES///additional_drug_therapy: NO///additional_immuno_therapy: NO///additional_pharmaceutical_therapy: NO///additional_radiation_therapy: NO///additional_surgery_locoregional_procedure: YES///additional_surgery_metastatic_procedure: NA///bcr_followup_uuid: f45f3fe2-1f97-4e6f-afc7-d3abf0f3311a///chemo_therapy: YES///day_of_form_completion: 8///days_to_additional_surgery_locoregional_procedure: 827///days_to_additional_surgery_metastatic_procedure: NA///days_to_death: NA///days_to_last_followup: 931///days_to_new_tumor_event_after_initial_treatment: NA///days_to_tumor_progression: NA///days_to_tumor_recurrence: 817///eastern_cancer_oncology_group: NA///followup_case_report_form_submission_reason: NA///hormonal_therapy: NO///immuno_therapy: NO///karnofsky_performance_score: NA///month_of_form_completion: 12///performance_status_scale_timing: NA///person_neoplasm_cancer_status: WITH TUMOR///primary_therapy_outcome_success: Complete Response///progression_determined_by: Imaging Study///progression_determined_by_notes: CT///radiation_therapy: NO///site_of_tumor_first_recurrence: Loco-Regional///targeted_molecular_therapy: NO///vital_status: LIVING///year_of_form_completion: 2009///Extract.Name: TCGA-61-2008-01A-02R-1568-13///unique_patient_id: TCGA-61-2008
1
age_at_initial_pathologic_diagnosis: 40///anatomic_organ_subdivision: Bilateral///bcr_patient_uuid: a6eb0cd0-fe57-41b0-8593-776208684293///days_to_birth: -14782///days_to_initial_pathologic_diagnosis: 0///ethnicity: NOT HISPANIC OR LATINO///gender: FEMALE///gynecologic_figo_staging_system: NA///histological_type: Serous Cystadenocarcinoma///icd_10: NA///icd_o_3_histology: 8441/3///icd_o_3_site: C56.9///informed_consent_verified: YES///initial_pathologic_diagnosis_method: Tumor resection///jewish_origin: NA///lymphatic_invasion: YES///neoplasm_histologic_grade: G3///patient_id: 1725///pretreatment_history: NO///race: WHITE///residual_tumor: NA///tissue_source_site: 61///tumor_histologic_subtype: Cystadenocarcinoma///tumor_residual_disease: 11-20 mm///tumor_stage: IIIC///tumor_tissue_site: OVARY///venous_invasion: YES///year_of_initial_pathologic_diagnosis: 2007///additional_chemo_therapy: YES///additional_drug_therapy: NO///additional_immuno_therapy: NO///additional_pharmaceutical_therapy: NO///additional_radiation_therapy: NO///additional_surgery_locoregional_procedure: NA///additional_surgery_metastatic_procedure: NA///bcr_followup_uuid: 4795b469-2ea1-4e65-bb8f-5b401b6632d5///chemo_therapy: YES///day_of_form_completion: 2///days_to_additional_surgery_locoregional_procedure: NA///days_to_additional_surgery_metastatic_procedure: NA///days_to_death: NA///days_to_last_followup: 955///days_to_new_tumor_event_after_initial_treatment: NA///days_to_tumor_progression: NA///days_to_tumor_recurrence: 843///eastern_cancer_oncology_group: NA///followup_case_report_form_submission_reason: NA///hormonal_therapy: NO///immuno_therapy: NO///karnofsky_performance_score: NA///month_of_form_completion: 6///performance_status_scale_timing: NA///person_neoplasm_cancer_status: WITH TUMOR///primary_therapy_outcome_success: Stable Disease///progression_determined_by: Imaging Study///progression_determined_by_notes: CT Scan; Molecular marker-CA125///radiation_therapy: NO///site_of_tumor_first_recurrence: Metastasis///targeted_molecular_therapy: NO///vital_status: LIVING///year_of_form_completion: 2009///Extract.Name: TCGA-61-1725-01A-01R-1567-13///unique_patient_id: TCGA-61-1725
1
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1
age_at_initial_pathologic_diagnosis: 40///anatomic_organ_subdivision: Bilateral///bcr_patient_uuid: f4d95c8e-fb84-46ca-acc0-827015cc9d0a///days_to_birth: [Completed]///days_to_initial_pathologic_diagnosis: 0///ethnicity: NOT HISPANIC OR LATINO///gender: FEMALE///gynecologic_figo_staging_system: NA///histological_type: Serous Cystadenocarcinoma///icd_10: NA///icd_o_3_histology: 8441/3///icd_o_3_site: C56.9///informed_consent_verified: YES///initial_pathologic_diagnosis_method: Tumor resection///jewish_origin: NA///lymphatic_invasion: NO///neoplasm_histologic_grade: G3///patient_id: 2363///pretreatment_history: NO///race: ASIAN///residual_tumor: R0///tissue_source_site: 59///tumor_histologic_subtype: Cystadenocarcinoma///tumor_residual_disease: No Macroscopic disease///tumor_stage: IIIA///tumor_tissue_site: OVARY///venous_invasion: NO///year_of_initial_pathologic_diagnosis: 2007///additional_chemo_therapy: NO///additional_drug_therapy: NO///additional_immuno_therapy: NO///additional_pharmaceutical_therapy: NO///additional_radiation_therapy: NO///additional_surgery_locoregional_procedure: NA///additional_surgery_metastatic_procedure: NA///bcr_followup_uuid: b9fa6c71-a686-47cc-8b85-ba5cca27a399///chemo_therapy: YES///day_of_form_completion: 12///days_to_additional_surgery_locoregional_procedure: NA///days_to_additional_surgery_metastatic_procedure: NA///days_to_death: NA///days_to_last_followup: 164///days_to_new_tumor_event_after_initial_treatment: NA///days_to_tumor_progression: NA///days_to_tumor_recurrence: NA///eastern_cancer_oncology_group: NA///followup_case_report_form_submission_reason: NA///hormonal_therapy: NO///immuno_therapy: NO///karnofsky_performance_score: NA///month_of_form_completion: 2///performance_status_scale_timing: NA///person_neoplasm_cancer_status: TUMOR FREE///primary_therapy_outcome_success: Complete Response///progression_determined_by: NA///progression_determined_by_notes: NA///radiation_therapy: NO///site_of_tumor_first_recurrence: NA///targeted_molecular_therapy: NO///vital_status: LIVING///year_of_form_completion: 2010///Extract.Name: TCGA-59-2363-01A-01R-1569-13///unique_patient_id: TCGA-59-2363
1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
age_at_initial_pathologic_diagnosis: 50///anatomic_organ_subdivision: Bilateral///bcr_patient_uuid: 3768d34f-1527-40db-b116-cd80cee5ec3a///days_to_birth: -18285///days_to_initial_pathologic_diagnosis: 0///ethnicity: NOT HISPANIC OR LATINO///gender: FEMALE///gynecologic_figo_staging_system: NA///histological_type: Serous Cystadenocarcinoma///icd_10: NA///icd_o_3_histology: 8441/3///icd_o_3_site: C56.9///informed_consent_verified: YES///initial_pathologic_diagnosis_method: Tumor resection///jewish_origin: NA///lymphatic_invasion: YES///neoplasm_histologic_grade: G2///patient_id: 2045///pretreatment_history: NO///race: ASIAN///residual_tumor: NA///tissue_source_site: 9///tumor_histologic_subtype: Cystadenocarcinoma///tumor_residual_disease: 1-10 mm///tumor_stage: IV///tumor_tissue_site: OVARY///venous_invasion: YES///year_of_initial_pathologic_diagnosis: 1996///additional_chemo_therapy: YES///additional_drug_therapy: NO///additional_immuno_therapy: NO///additional_pharmaceutical_therapy: NO///additional_radiation_therapy: NO///additional_surgery_locoregional_procedure: NA///additional_surgery_metastatic_procedure: NA///bcr_followup_uuid: 0174cdfc-8808-4567-97bc-03c86ce40b50///chemo_therapy: YES///day_of_form_completion: 3///days_to_additional_surgery_locoregional_procedure: NA///days_to_additional_surgery_metastatic_procedure: NA///days_to_death: 1069///days_to_last_followup: 1069///days_to_new_tumor_event_after_initial_treatment: NA///days_to_tumor_progression: NA///days_to_tumor_recurrence: 631///eastern_cancer_oncology_group: NA///followup_case_report_form_submission_reason: NA///hormonal_therapy: NO///immuno_therapy: NO///karnofsky_performance_score: NA///month_of_form_completion: 11///performance_status_scale_timing: NA///person_neoplasm_cancer_status: WITH TUMOR///primary_therapy_outcome_success: Stable Disease///progression_determined_by: Physical Examination///progression_determined_by_notes: Image study and Other method was CA125///radiation_therapy: NO///site_of_tumor_first_recurrence: Loco-Regional///targeted_molecular_therapy: NO///vital_status: DECEASED///year_of_form_completion: 2009///Extract.Name: TCGA-09-2045-01A-01R-1568-13///unique_patient_id: TCGA-09-2045
1
age_at_initial_pathologic_diagnosis: 50///anatomic_organ_subdivision: Bilateral///bcr_patient_uuid: 4e6f88de-7624-4719-8234-4c9e5b2e2988///days_to_birth: -18599///days_to_initial_pathologic_diagnosis: 0///ethnicity: NOT HISPANIC OR LATINO///gender: FEMALE///gynecologic_figo_staging_system: NA///histological_type: Serous Cystadenocarcinoma///icd_10: NA///icd_o_3_histology: 8441/3///icd_o_3_site: C56.9///informed_consent_verified: YES///initial_pathologic_diagnosis_method: Tumor resection///jewish_origin: NA///lymphatic_invasion: YES///neoplasm_histologic_grade: G3///patient_id: 1673///pretreatment_history: NO///race: WHITE///residual_tumor: NA///tissue_source_site: 9///tumor_histologic_subtype: Cystadenocarcinoma///tumor_residual_disease: >20 mm///tumor_stage: IV///tumor_tissue_site: OVARY///venous_invasion: YES///year_of_initial_pathologic_diagnosis: 2008///additional_chemo_therapy: NO///additional_drug_therapy: NO///additional_immuno_therapy: NO///additional_pharmaceutical_therapy: NO///additional_radiation_therapy: NO///additional_surgery_locoregional_procedure: NA///additional_surgery_metastatic_procedure: NA///bcr_followup_uuid: 7596faa8-43be-4930-a899-cefee1f4f8c7///chemo_therapy: YES///day_of_form_completion: 2///days_to_additional_surgery_locoregional_procedure: NA///days_to_additional_surgery_metastatic_procedure: NA///days_to_death: NA///days_to_last_followup: 92///days_to_new_tumor_event_after_initial_treatment: NA///days_to_tumor_progression: NA///days_to_tumor_recurrence: NA///eastern_cancer_oncology_group: NA///followup_case_report_form_submission_reason: NA///hormonal_therapy: NO///immuno_therapy: NO///karnofsky_performance_score: NA///month_of_form_completion: 6///performance_status_scale_timing: NA///person_neoplasm_cancer_status: WITH TUMOR///primary_therapy_outcome_success: NA///progression_determined_by: NA///progression_determined_by_notes: NA///radiation_therapy: NO///site_of_tumor_first_recurrence: NA///targeted_molecular_therapy: NO///vital_status: LIVING///year_of_form_completion: 2009///Extract.Name: TCGA-09-1673-01A-01R-1566-13///unique_patient_id: TCGA-09-1673
1
age_at_initial_pathologic_diagnosis: 50///anatomic_organ_subdivision: Bilateral///bcr_patient_uuid: 5d36676e-4140-44b5-aa0e-b2af092b7dc0///days_to_birth: -18403///days_to_initial_pathologic_diagnosis: 0///ethnicity: NA///gender: FEMALE///gynecologic_figo_staging_system: NA///histological_type: Serous Cystadenocarcinoma///icd_10: NA///icd_o_3_histology: 8441/3///icd_o_3_site: C56.9///informed_consent_verified: YES///initial_pathologic_diagnosis_method: Tumor resection///jewish_origin: NA///lymphatic_invasion: NA///neoplasm_histologic_grade: G3///patient_id: 1555///pretreatment_history: NO///race: WHITE///residual_tumor: NA///tissue_source_site: 24///tumor_histologic_subtype: Cystadenocarcinoma///tumor_residual_disease: NA///tumor_stage: IIIC///tumor_tissue_site: OVARY///venous_invasion: NA///year_of_initial_pathologic_diagnosis: 1997///additional_chemo_therapy: YES///additional_drug_therapy: NO///additional_immuno_therapy: NO///additional_pharmaceutical_therapy: NO///additional_radiation_therapy: NO///additional_surgery_locoregional_procedure: NO///additional_surgery_metastatic_procedure: NO///bcr_followup_uuid: 5867b96d-991e-437a-9e0c-b4c7846721ad///chemo_therapy: YES///day_of_form_completion: 13///days_to_additional_surgery_locoregional_procedure: NA///days_to_additional_surgery_metastatic_procedure: NA///days_to_death: 2692///days_to_last_followup: 2692///days_to_new_tumor_event_after_initial_treatment: NA///days_to_tumor_progression: NA///days_to_tumor_recurrence: 1577///eastern_cancer_oncology_group: 0///followup_case_report_form_submission_reason: NA///hormonal_therapy: NO///immuno_therapy: NO///karnofsky_performance_score: NA///month_of_form_completion: 5///performance_status_scale_timing: Other///person_neoplasm_cancer_status: WITH TUMOR///primary_therapy_outcome_success: Complete Response///progression_determined_by: Imaging Study///progression_determined_by_notes: Abdomen CT scan; Moleular marker CA125///radiation_therapy: NO///site_of_tumor_first_recurrence: Loco-Regional///targeted_molecular_therapy: NO///vital_status: DECEASED///year_of_form_completion: 2009///Extract.Name: TCGA-24-1555-01A-01R-1566-13///unique_patient_id: TCGA-24-1555
1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
age_at_initial_pathologic_diagnosis: 54///anatomic_organ_subdivision: Right///bcr_patient_uuid: b1c90c69-6149-4105-8182-ab9212f196be///days_to_birth: -20052///days_to_initial_pathologic_diagnosis: 0///ethnicity: NOT HISPANIC OR LATINO///gender: FEMALE///gynecologic_figo_staging_system: NA///histological_type: Serous Cystadenocarcinoma///icd_10: NA///icd_o_3_histology: 8441/3///icd_o_3_site: C56.9///informed_consent_verified: YES///initial_pathologic_diagnosis_method: Tumor resection///jewish_origin: NA///lymphatic_invasion: NO///neoplasm_histologic_grade: G3///patient_id: 1669///pretreatment_history: NO///race: WHITE///residual_tumor: NA///tissue_source_site: 9///tumor_histologic_subtype: Cystadenocarcinoma///tumor_residual_disease: No Macroscopic disease///tumor_stage: IIIA///tumor_tissue_site: OVARY///venous_invasion: NO///year_of_initial_pathologic_diagnosis: 2004///additional_chemo_therapy: NO///additional_drug_therapy: NO///additional_immuno_therapy: NO///additional_pharmaceutical_therapy: NO///additional_radiation_therapy: NO///additional_surgery_locoregional_procedure: NA///additional_surgery_metastatic_procedure: NA///bcr_followup_uuid: be4d9604-3e6b-4bf2-bd2a-0be49751832a///chemo_therapy: YES///day_of_form_completion: 2///days_to_additional_surgery_locoregional_procedure: NA///days_to_additional_surgery_metastatic_procedure: NA///days_to_death: NA///days_to_last_followup: 927///days_to_new_tumor_event_after_initial_treatment: NA///days_to_tumor_progression: NA///days_to_tumor_recurrence: NA///eastern_cancer_oncology_group: NA///followup_case_report_form_submission_reason: NA///hormonal_therapy: NO///immuno_therapy: NO///karnofsky_performance_score: NA///month_of_form_completion: 6///performance_status_scale_timing: NA///person_neoplasm_cancer_status: WITH TUMOR///primary_therapy_outcome_success: Complete Response///progression_determined_by: NA///progression_determined_by_notes: NA///radiation_therapy: NO///site_of_tumor_first_recurrence: NA///targeted_molecular_therapy: NO///vital_status: LIVING///year_of_form_completion: 2009///Extract.Name: TCGA-09-1669-01A-01R-1566-13///unique_patient_id: TCGA-09-1669
1
age_at_initial_pathologic_diagnosis: 55///anatomic_organ_subdivision: Bilateral///bcr_patient_uuid: 23771dab-2aab-4d2b-95e2-9af7092cee6b///days_to_birth: -20440///days_to_initial_pathologic_diagnosis: 0///ethnicity: NA///gender: FEMALE///gynecologic_figo_staging_system: NA///histological_type: Serous Cystadenocarcinoma///icd_10: NA///icd_o_3_histology: 8441/3///icd_o_3_site: C56.9///informed_consent_verified: YES///initial_pathologic_diagnosis_method: Tumor resection///jewish_origin: NA///lymphatic_invasion: NO///neoplasm_histologic_grade: G3///patient_id: 366///pretreatment_history: NO///race: WHITE///residual_tumor: NA///tissue_source_site: 9///tumor_histologic_subtype: Cystadenocarcinoma///tumor_residual_disease: 1-10 mm///tumor_stage: IIIC///tumor_tissue_site: OVARY///venous_invasion: NO///year_of_initial_pathologic_diagnosis: 1999///additional_chemo_therapy: YES///additional_drug_therapy: NO///additional_immuno_therapy: NO///additional_pharmaceutical_therapy: NO///additional_radiation_therapy: NO///additional_surgery_locoregional_procedure: YES///additional_surgery_metastatic_procedure: NO///bcr_followup_uuid: 06ba5b59-0675-4fde-a4aa-237171de4442///chemo_therapy: YES///day_of_form_completion: 4///days_to_additional_surgery_locoregional_procedure: 189///days_to_additional_surgery_metastatic_procedure: NA///days_to_death: 1756///days_to_last_followup: 1756///days_to_new_tumor_event_after_initial_treatment: NA///days_to_tumor_progression: NA///days_to_tumor_recurrence: 189///eastern_cancer_oncology_group: NA///followup_case_report_form_submission_reason: NA///hormonal_therapy: NO///immuno_therapy: NO///karnofsky_performance_score: NA///month_of_form_completion: 3///performance_status_scale_timing: NA///person_neoplasm_cancer_status: WITH TUMOR///primary_therapy_outcome_success: Stable Disease///progression_determined_by: Imaging Study///progression_determined_by_notes: CT & CA125///radiation_therapy: NO///site_of_tumor_first_recurrence: Loco-Regional///targeted_molecular_therapy: NO///vital_status: DECEASED///year_of_form_completion: 2009///Extract.Name: TCGA-09-0366-01A-01R-1564-13///unique_patient_id: TCGA-09-0366
1
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Value
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