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: 67, std: 13 |
| vitalstatus | 1101 living, 137 deceased |
| gender | 660 male, 578 female |
| histologicaltype | 774 colon adenocarcinoma, 119 colon mucinous adenocarcinoma, 299 rectal adenocarcinoma, 27 rectal mucinous adenocarcinoma |
| tumorstage | 326 stage iia, 149 stage iiib, 25 stage iib, 95 stage iiic, 113 stage iv, 204 stage i, 53 stage iva, 9 stage iic, 92 stage ii, 60 stage iii, 48 stage iiia, 2 stage ivb, 2 stage ia |
| pathologicspread(pt) | 849 t3, 18 t4b, 57 t4, 213 t2, 49 t4a, 39 t1, 2 t0, 2 tis |
| pathologicspread(pn) | 710 n0, 217 n1, 178 n2, 35 n1b, 31 n2b, 13 n2a, 36 n1a, 6 n1c, 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 | 45 | 45 | 85 |
| daystodeath | NA | NA | NA |
| daystolastfollowup | 423 | 423 | 648 |
| vitalstatus | 0 | 0 | 0 |
| dccuploaddate | 4-6-2012 | 4-6-2012 | 29-6-2012 |
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.
