How to download clinical information of TCGA tumor patients with GDC

How to use GDC to download the clinical information of TCGA tumor patients, I believe that many inexperienced people do not know what to do. Therefore, this paper summarizes the causes and solutions of the problem. Through this article, I hope you can solve this problem.

In GDC, the clinical information of tumor patients is standardized and divided into the following seven categories

Demographic

Diagnosis

Exposure

Family History

Follow Up

Molecular Test

Treatment

Of these, 20 items of clinical information are required, as shown below

In GDC, the download of clinical information is similar to ordinary files. In Repository, the data type is Clinical, as shown below.

Of course, you can filter according to the attributes of Cases. After filtering, you can see the list of files on the right, as shown below.

It can be seen that the original clinical information is stored in XML format, and the information saved in the modified file is more comprehensive. Add the corresponding file to Cart and download it, as shown below

If you need to download the original file, you can download the manifest file by clicking Download, and download it through gdc-client. To do so, you need to read the information in the XML file later and sort it out.

For clinical information, the download formats of TSV and JSON are also provided. The TSV format is particularly friendly and can be viewed by opening it with Excel, as shown below.

There are more columns, and only some of them are intercepted here. It should be noted that this approach produces a little less clinical information than XML files, but is sufficient for common scenarios such as survival analysis.

After reading the above, have you mastered the method of how to download the clinical information of TCGA tumor patients with GDC? If you want to learn more skills or want to know more about it, you are welcome to follow the industry information channel, thank you for reading!