Preprocessing of clinical data
Overview
Introduction

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.

Summary

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
Results
Tier 1 Data Statistics

Table 2.  Statistics of selected clinical variables.

Clinical.Variable Statistics
age mean: 61, std: 12
vitalstatus 697 living, 321 deceased
gender 669 male, 349 female
histologicaltype 1018 kidney clear cell renal carcinoma
tumorstage 499 stage i, 106 stage ii, 250 stage iii, 163 stage iv
pathologicspread(pt) 211 t1b, 104 t3b, 44 t1, 111 t2, 252 t1a, 11 t2a, 242 t3a, 9 t3, 22 t4, 4 t3c, 8 t2b
pathologicspread(pn) 476 n0, 506 nx, 36 n1
Tier 1 Data

Table 3.  Get Full Table Illustration of the tier 1 data for three patients

Clinical.Variable Sample_1 Sample_2 Sample_3
yearstobirth 67 67 66
daystodeath NA NA NA
daystolastfollowup 1120 1120 1436
vitalstatus 0 0 0
dccuploaddate 25-7-2012 25-7-2012 25-7-2012
Methods & Data
Work Flow

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.

Diagram of Clinical Data Dicer

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.