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 | 206 living, 86 deceased |
| gender | 133 male, 159 female |
| histologicaltype | 187 lung adenocarcinoma- not otherwise specified (nos), 65 lung adenocarcinoma mixed subtype, 10 lung papillary adenocarcinoma, 2 lung mucinous adenocarcinoma, 4 mucinous (colloid) adenocarcinoma, 2 lung clear cell adenocarcinoma, 6 lung acinar adenocarcinoma, 3 lung bronchioloalveolar carcinoma mucinous, 9 lung bronchioloalveolar carcinoma nonmucinous, 3 lung micropapillary adenocarcinoma, 1 lung solid pattern predominant adenocarcinoma |
| tumorstage | 17 stage iv, 50 stage iiia, 84 stage ib, 65 stage ia, 8 stage iiib, 41 stage iib, 21 stage iia, 1 stage i |
| pathologicspread(pt) | 137 t2, 23 t3, 51 t1, 15 t4, 8 t2b, 17 t1b, 26 t2a, 13 t1a, 1 tx |
| pathologicspread(pn) | 52 n2, 172 n0, 60 n1, 1 n3, 6 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 | 81 | 67 |
| daystodeath | NA | NA | NA |
| daystolastfollowup | 0 | 395 | 1158 |
| vitalstatus | 0 | 0 | 0 |
| dccuploaddate | 28-6-2012 | 28-6-2012 | 28-6-2012 |
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.
