The clinical information for each TCGA tumor sample is stored in a xml file. Patient ID, tumor and treatment info are entries of the xml file. These xml files have been preprocessed for further analysis.
Clinical data for tier 1 clinical variables are generated.
Table 1. Tier1 clinical variables
| Tumor.Feature | Date.Statistics |
|---|---|
| gender | dccuploaddate |
| primarysiteofdesease | dateofbirth |
| histologicaltype | dateofdeath |
| tumorstage | dateoflastfollowup |
| tumorgrade | dateoftumorrecurrence |
| patienttumorrecurrencestatus | dateofinitialpathologicdiagnosis |
| radiationtherapy | datelastknownalive |
| neoadjuvanttherapy | vitalstatus |
| pathologicspread(pt) | |
| pathologicspread(pn) | |
| karnofskyperformancescore |
Table 2. Statistics of selected clinical variables.
| Clinical.Variable | Statistics |
|---|---|
| age | mean: 65, std: 10 |
| vitalstatus | 578 living, 178 deceased |
| gender | 336 male, 420 female |
| histologicaltype | 482 lung adenocarcinoma- not otherwise specified (nos), 155 lung adenocarcinoma mixed subtype, 26 lung papillary adenocarcinoma, 6 lung mucinous adenocarcinoma, 15 mucinous (colloid) adenocarcinoma, 4 lung clear cell adenocarcinoma, 20 lung acinar adenocarcinoma, 32 lung bronchioloalveolar carcinoma nonmucinous, 6 lung bronchioloalveolar carcinoma mucinous, 4 lung solid pattern predominant adenocarcinoma, 6 lung micropapillary adenocarcinoma |
| tumorstage | 40 stage iv, 111 stage iiia, 217 stage ib, 184 stage ia, 20 stage iiib, 107 stage iib, 58 stage iia, 5 stage i |
| pathologicspread(pt) | 292 t2, 63 t3, 120 t1, 34 t4, 28 t2b, 57 t1b, 96 t2a, 59 t1a, 4 tx |
| pathologicspread(pn) | 114 n2, 467 n0, 149 n1, 2 n3, 19 nx |
Table 3. Get Full Table Illustration of the tier 1 data for three patients
| Clinical.Variable | Sample_1 | Sample_2 | Sample_3 |
|---|---|---|---|
| yearstobirth | 70 | 70 | 81 |
| daystodeath | NA | NA | NA |
| daystolastfollowup | 0 | 0 | 395 |
| vitalstatus | 0 | 0 | 0 |
| dccuploaddate | 31-8-2012 | 31-8-2012 | 31-8-2012 |
1. Each xml file is converted to a tab-delimited text file by our R package.
2. All text files are aggregated into one big table by the Clinical_Aggregate_Tier1 pipeline. The 1st column of the table is the entry name of the xml file and the rest columns are the associated data for samples.
3. Data for the tier 1 clinical variables are extracted by the Clinical_Picker_Tier1 pipeline.
Figure 1. Diagram that displays the work flow of processing clinical data. Clinical variables of interest and their associated values are marked in red and blue, respectively.
