question about mutation data from TCGA

Question

[tujuchuanli]

I want to download and analyze the mutation data of TCGA. I find that the mutation data is controlled on original download source (https://portal.gdc.cancer.gov/repository). I search on net and find another source to download the data (http://gdac.broadinstitute.org/runs/stddata__2016_01_28/). This source are from a thread (https://www.biostars.org/p/189418/).

Taking BRCA as example, this is data related to mutation “gdac.broadinstitute.org_BRCA.Mutation_Packager_Calls.Level_3.2016012800.0.0.tar.gz”. I download and unzip it. There are 982 files and one file for one sample.

I find that there are no more than 100 genes with mutations in each file. Why are there so few mutations in each sample?

Where can I download a relative comprehensive mutation dataset of TCGA?

[tujuchuanli]

Thanks again, Kevin I realized that I made a mistake. Unlike the expression and methylation data, the separate mutation data are controlled but the merged MAF files are open.

[Ram]

Hi tujuchuanli ,

This reply is better suited as a comment on Kevin's answer. Could you make the appropriate change please? That would involve the following steps:

1. Copy the contents of your reply from this answer (you can edit this answer (Ctrl/Cmd + click the link to open it in a new tab) and do a Select All -> Copy there).
2. Click on Add Comment on Kevin's post here: A: question about mutation data from TCGA
3. Paste the copied text
4. Click on the green Add Comment button
5. Click on moderate back in your answer here: A: question about mutation data from TCGA
6. Choose Delete Post
7. Click on the blue Submit button.

Thank you!

[tujuchuanli]

Dear RamRS, I know I should add comment instead of simple adding my reply at the end of this thread. But there is nothing happened when I pressed the "Add Comment" button on the Kevin's post. I saw there should be a pop-down text input dialog when pressing "Add Comment" on my friend's computer. I don`t know why it does not appear on my computer!

[Ram]

Your browser is probably blocking javascript on the site. Users from China have faced similar problems but since you're saying your friend is able to see the Add Comment dialog, that's probably not the case. I'll move your comment myself now, but I can only move it to the top-level post, not to Kevin's answer. Please try enabling Javascript on your browser (See: How to enable javascript)

Answer 1

[Kevin Blighe]

GDC

At the Genomic Data Commons (GDC), the open access mutation data is available as Mutation Annotation Format (MAF). Here is a search configured for breast cancer (BRCA): https://portal.gdc.cancer.gov/repository?facetTab=cases&f...

Broad Institute

At the Broad Institute, there are many more files listed that contain mutation data. You happened to download just the first in the listing (alphabetically).

Xena

As per Igor in the other thread, the Xena Browser data appears to be quite neatly arranged. Take a look at GDC TCGA Breast Cancer (BRCA) (18 datasets) at https://xenabrowser.net/datapages/

Kevin