Colon/Rectal Adenocarcinoma: Preprocessing of clinical data
Maintained by TCGA GDAC Team (Broad Institute/Dana-Farber Cancer Institute/Harvard Medical School)
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 | 525 living, 66 deceased
gender | 318 male, 273 female
histologicaltype | 364 colon adenocarcinoma, 56 colon mucinous adenocarcinoma, 149 rectal adenocarcinoma, 13 rectal mucinous adenocarcinoma
tumorstage | 155 stage iia, 72 stage iiib, 11 stage iib, 45 stage iiic, 55 stage iv, 100 stage i, 26 stage iva, 4 stage iic, 44 stage ii, 28 stage iii, 24 stage iiia, 1 stage ivb, 1 stage ia
pathologicspread(pt) | 402 t3, 8 t4b, 28 t4, 105 t2, 24 t4a, 19 t1, 1 t0, 1 tis
pathologicspread(pn) | 339 n0, 104 n1, 84 n2, 17 n1b, 15 n2b, 7 n2a, 17 n1a, 3 n1c, 3 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 | 85 | 82
daystodeath | NA | NA | NA
daystolastfollowup | 423 | 648 | 503
vitalstatus | 0 | 0 | 0
dccuploaddate | 4-6-2012 | 29-6-2012 | 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.

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

Copyright © 2012 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
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