Many MAF files in tcga case

Question

[Beowulf]

Hi!

I've recently begun studying system biology and I'm now studying the TCGA database. As far as I know, files are collected into cases which describe a single tumor of a patient. I also know that MAF file contain information about genetic mutations in the patient's genome and they are built comparing a sample of the patient's tumor tissue and a sample from a healthy tissue. So, I was wondering why in almost every case there is more that one MAF file. Shouldn't there be just a single MAF file built from a sample of the tumor tissue? Are they different sample from the same tumor tissue or are they from different tissues? Same thing happens with files containing info about gene expression.

Many thanks in advance for your help!

Answer 1

[Zhenyu Zhang]

First, GDC analysis is at the aliquot level. If one patient has multiple aliquots, there are multiple analysis.

For MAF, you should look for ensemble masked maf. The rest are unfiltered maf or single caller maf that are really meant for expert to examine or filter themselves.

I will suggest you to read the GDC documentation. There are more details about what each files are for, and how they were generated.