Looking For Frequncies Of Mutations In Set Of Genes In Different Cancers

Question

[aparkhitko]

Hi, I recently found very helpful http://cancergenome.broadinstitute.org/ portal to find out which gene is mutated in which cancer, frequencies and vice versa. But I can't find out how to determine frequencies for the combinations of genes. For example, based on data from this portal PTEN is mutated in 7% of all cancers and in 30% of gliobastomas. Rb is mutated in 3% of all patients and in 8% of glioblastomas. But what will be the easiest way for non bioinformatician to find out the frequency of patients with both Pten and Rb mutation in general population, in glioblastomas and in other cancers?

Thanks for your help! Andrey

Answer 1

[Malachi Griffith]

You can get at this kind of information using the cBioPortal for Cancer Genomics.

To get a relevant visualization:

1. Go to http://www.cbioportal.org/public-portal/
2. Enter your gene names using their official HUGO designations: PTEN, RB1. One per line.
3. If you are only interested in mutations, select the 'Only Mutation' option
4. Hit the submit button
5. Hover your mouse over the bar for your cancer type of interest and select 'click to view details'
6. This will bring you to an 'OncoPrint' that shows which cases have mutations in: PTEN, RB1, both, neither
7. Also check out the additional tabs of this view to explore the data for these two genes further. You can also refine your query using the 'Modify Query' section.

Here is an example query for: RB1 and PTEN in GBM

In this example, 31% have PTEN mutations, 9% have RB1 mutations, and 5% have both. According to the 'mutual exclusivity' tab there is a highly significant tendency tendency toward co-occurrence of mutations in these mutations (odds ratio: 3.875, p-value: 0.001463)

[frida.danielsson]

Do you know any way to do this for a larger group of genes? I have a list of 700 genes that I would like to retrieve this information for..

Answer 2

[Shicheng Guo]

Here, click each cancer and then you can find the most frequent mutated genes for each cancer:

https://icgc.org/

Answer 3

[aparkhitko]

Thanks a lot for your help! It is very helpful resource and I am going to read their tutorials. It is said that the combined changes in Pten and Rb genes are occurred in 69.2% of Uterine Corpus Endometrial Carcinoma. How can I determine which other mutations/alterations of genes and their frequencies most often co-occur with Pten+Rb? Thanks! Andrey