Question: TCGA MAF (Mutations) data
gravatar for mario.zanfardino
6 months ago by
Naples (Italy)
mario.zanfardino150 wrote:

Hy everyone,

my question is: if a TCGA sample there is not in the MAF file for specific gene mutations (ex. KRAS), this means that patient not have KRAS mutations or that the patient was not analyzed in the corresponding pipeline?

Thank you!

snp tcga maf mutations gdc • 176 views
ADD COMMENTlink modified 6 months ago by Sean Davis21k • written 6 months ago by mario.zanfardino150

From where did you obtain the MAF file? - please be very specific. The TCGA samples were processed at different institutes / centres, and each would have produced a separate MAF file. If a patient's mutation data is not in one MAF file, it may be in another that you need to download.

ADD REPLYlink written 6 months ago by Kevin Blighe300
Answer: TCGA MAF (Mutations) data
gravatar for Sean Davis
6 months ago by
Sean Davis21k
United States
Sean Davis21k wrote:

MAF files contain only "positive" data. Lack of a mutation may mean that the patient did not have a mutation (true negative), was not tested for that mutation (panel did not cover the gene/location of interest), the mutation was "present" but filtered out in post-processing, or that the mutation was a false negative and not detected. Determining which of these cases applies can be challenging without information about read depth and potentially read counts for each allele at a "negative" site.

ADD COMMENTlink written 6 months ago by Sean Davis21k
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