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: 65, std: 10
vitalstatus 246 living, 87 deceased
gender 150 male, 183 female
histologicaltype 205 lung adenocarcinoma- not otherwise specified (nos), 74 lung adenocarcinoma mixed subtype, 13 lung papillary adenocarcinoma, 2 lung mucinous adenocarcinoma, 5 mucinous (colloid) adenocarcinoma, 2 lung clear cell adenocarcinoma, 10 lung acinar adenocarcinoma, 14 lung bronchioloalveolar carcinoma nonmucinous, 3 lung bronchioloalveolar carcinoma mucinous, 2 lung solid pattern predominant adenocarcinoma, 3 lung micropapillary adenocarcinoma
tumorstage 18 stage iv, 53 stage iiia, 95 stage ib, 76 stage ia, 10 stage iiib, 48 stage iib, 25 stage iia, 2 stage i
pathologicspread(pt) 141 t2, 26 t3, 54 t1, 17 t4, 13 t2b, 21 t1b, 37 t2a, 21 t1a, 2 tx
pathologicspread(pn) 54 n2, 200 n0, 68 n1, 1 n3, 8 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 70 81 67
daystodeath NA NA NA
daystolastfollowup 0 395 1158
vitalstatus 0 0 0
dccuploaddate 31-8-2012 31-8-2012 31-8-2012
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.