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: 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
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 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
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.