Broad/MC3 PTEN mutational frequency discrepancy

[alexjamesing]

Hi,
I am getting really different mutational frequencies in some genes, when looking at data from the Broad Firehose, compared to the MC3 source. I would expect some differences due to the documented differences in preprocessing, but this effect is quite extreme in some cases. For example, looking at the top 10 mutated genes in colon cancer for Broad and MC3:

Broad

MC3
If you look at the PTEN gene for example, this is mutated in over 40% of subjects in the Broad firehose data. This is way above its mutation rate in this cancer from the literature, including in the TCGA marker paper. Further, this gene is mutated in only 3% of cases in the MC3 data. Do you have an idea where such a large discrepancy could come from? Help here much appreciated!

[PoisonAlien]

Hi,
I can not really comment on these differences since I just used the MAF files as-is. However, in the MC3 article they do describe some of these discrepancies that might answer your question.
I checked cbioportal for PTEN in COAD, it seems the MC3 cohort has the same mutational load.