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: 9 |
| vitalstatus | 112 deceased, 167 living |
| gender | 204 male, 75 female |
| histologicaltype | 269 lung squamous cell carcinoma- not otherwise specified (nos), 7 lung basaloid squamous cell carcinoma, 1 lung small cell squamous cell carcinoma, 1 lung papillary squamous cell caricnoma, 1 lung papillary squamous cell carcinoma |
| tumorstage | 43 stage ia, 100 stage ib, 35 stage iiia, 4 stage iv, 49 stage iib, 24 stage iia, 18 stage iiib, 1 stage ii, 1 stage i |
| pathologicspread(pt) | 39 t1, 132 t2, 26 t3, 17 t4, 31 t2a, 9 t2b, 19 t1b, 6 t1a |
| pathologicspread(pn) | 177 n0, 23 n2, 74 n1, 5 n3 |
Table 3. Get Full Table Illustration of the tier 1 data for three patients
| Clinical.Variable | Sample_1 | Sample_2 | Sample_3 |
|---|---|---|---|
| yearstobirth | 67 | 72 | 77 |
| daystodeath | 371 | 227 | NA |
| daystolastfollowup | 370 | 136 | 2466 |
| vitalstatus | 1 | 1 | 0 |
| dccuploaddate | 27-4-2012 | 27-4-2012 | 27-4-2012 |
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.
