Mapping mutations to TCGA samples

Question

[esnolli]

Hello everyone,

I am interested in analyzing some data from TCGA, specifically the LAML project. From there I managed to download the HTSeq counts for the whole cohort, however I would like to map each sample to specific mutations for given set of genes in order to perform DE analysis between pools of samples with the same gene mutated.

I am struggling with this second part. I found a R package named RTCGAToolbox in which you can download the expression data and the Mutation data among others. Instead, what I am getting are the mutations present in the cohort rather than a table to map samples with their mutations. Is there any possibility to download this kind of metadata, or I have to manually check from MAF files for each sample? If I have to, how should I do it?

Thanks in advance to everyone,

Esteve

P.S: Checked before writing this post if there was any similar one, but I didn't find any. Apologies if it is a repeated question.

Answer 1

[Chris Miller]

I did a lot of the analysis for the TCGA AML paper. The simplest way to pull mutations is to go to the paper's supplemental site and pull Supplemental Table 6. Note that the variants are all on build 36, so liftover may be in order if you're working from a newer reference genome build.

[esnolli]

Thanks a lot, just right I was looking for!