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: 61, std: 13 |
| vitalstatus | 3398 living, 1512 deceased |
| gender | 1826 male, 3074 female |
| histologicaltype | 363 colon adenocarcinoma, 56 colon mucinous adenocarcinoma, 543 untreated primary (de novo) gbm, 20 treated primary gbm, 255 head & neck squamous cell carcinoma, 502 kidney clear cell renal carcinoma, 84 kidney papillary renal cell carcinoma, 49 astrocytoma, 58 oligodendroglioma, 33 oligoastrocytoma, 178 lung adenocarcinoma- not otherwise specified (nos), 61 lung adenocarcinoma mixed subtype, 10 lung papillary adenocarcinoma, 2 lung mucinous adenocarcinoma, 3 mucinous (colloid) adenocarcinoma, 2 lung clear cell adenocarcinoma, 4 lung acinar adenocarcinoma, 3 lung bronchioloalveolar carcinoma mucinous, 8 lung bronchioloalveolar carcinoma nonmucinous, 2 lung micropapillary adenocarcinoma, 1 lung solid pattern predominant adenocarcinoma, 264 lung squamous cell carcinoma- not otherwise specified (nos), 6 lung basaloid squamous cell carcinoma, 1 lung papillary squamous cell caricnoma, 1 lung papillary squamous cell carcinoma, 570 serous cystadenocarcinoma, 149 rectal adenocarcinoma, 13 rectal mucinous adenocarcinoma, 13 stomach adenocarcinoma - diffuse type, 85 stomach adenocarcinoma - not otherwise specified (nos), 10 stomach intestinal adenocarcinoma - tubular type, 3 stomach intestinal adenocarcinoma - papillary type, 27 stomach intestinal adenocarcinoma - type not otherwise specified (nos), 6 stomach intestinal adenocarcinoma - mucinous type, 70 uterine serous endometrial adenocarcinoma, 143 endometrioid endometrial adenocarcinoma (grade 3), 104 endometrioid endometrial adenocarcinoma (grade 1 or 2), 17 mixed serous and endometrioid, 57 endometrioid endometrial adenocarcinoma (grade 2), 34 endometrioid endometrial adenocarcinoma (grade 1) |
| patienttumorrecurrencestatus | 4627 without recurrence, 283 with recurrence |
| tumorgrade | 637 g3, 286 g2, 33 g1, 13 gx, 1 g4, 1 gb, 197 grade 3, 106 grade 2, 89 grade 1, 33 high grade |
| pathologicspread(pt) | 582 t3, 12 t4b, 82 t4, 533 t2, 116 t4a, 155 t1, 1 t0, 1 tis, 23 tx, 143 t1b, 60 t3b, 168 t1a, 68 t2a, 137 t3a, 2 t3c, 33 t2b |
| pathologicspread(pn) | 353 n1, 188 n2, 1067 n0, 17 n1b, 62 n2b, 13 n2a, 17 n1a, 3 n1c, 341 nx, 30 n2c, 22 n3, 1 n3a |
Table 3. Get Full Table Illustration of the tier 1 data for three patients
| Clinical.Variable | Sample_ID | Sample_ID | Sample_ID |
|---|---|---|---|
| yearstobirth | sample_1 | sample_2 | sample_3 |
| daystodeath | NA | 223 | 81 |
| daystolastfollowup | 389 | 223 | 81 |
| vitalstatus | 0 | 1 | 1 |
| dccuploaddate | 22-12-2011 | 22-12-2011 | 22-12-2011 |
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.
