Questions about cBioPortal

[Victoria Tomaz]

Hi everyone

My name is Victoria Tomaz and I am a PhD student at Hospital Israelita Albert Einstein at São Paulo - Brazil

I am using cBioPortal to develop my PhD project. I have already watched your tutorials, but I still have some questions. They are below:

1. In addition to the API as a tool to access your data, is it possible for me to create my own data tables on your website and work online?

2. When I download all the patients/samples that have a mutation in a gene X from the "Mutations" tab, there is a column referring to the OncoKB classification. When I use your API, I am unable to download this information about the OncoKB classification for each of the variants. Could you help me with this problem?

3. Furthermore, I would like to know how you treat benign variants in the samples, since the tables I download only show oncogenic variants, probably oncogenic and of uncertain significance (according to the OncoKB classification). How can I find out the number and benign variants found in each patient in the studies?

If we can schedule a meeting to talk about the platform, it would be very helpful!

If you have any courses available on cBioPortal, I would like to take one too! To learn about all the tools available on the site and how I can manage my data and analyze it there.

Thank you in advance and I look forward to hearing from you!

Best Regards

Victória Tomaz

Biomédica, Doutorada em Ciências da Saúde

Instituto Israelita de Ensino e Pesquisa Albert Einstein 

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[Tali Mazor]

Hi Victoria,

Thanks for reaching out. I will try to address all your questions.

1) If you want to supplement an existing study with additional data, you can do so using the Custom Data option in the Charts menu in study view. This allows you to add sample or patient level attributes to an existing study (see screenshot below). Note that you will have to log in to the site in order to take advantage of this feature.

If you have your own complete dataset, you can set up your own instance of cBioPortal locally or utilize our OncoPrint & MutationMapper: https://www.cbioportal.org/visualize

2) You can use the OncoKB API or the OncoKB Annotator (https://www.oncokb.org/api-access) to annotate data with OncoKB classification.

3) There are some mutation types (eg synonymous mutations, see https://docs.cbioportal.org/file-formats/#variant-classification-filter) which are not imported into cBioPortal, but beyond that all variants are treated the same. cBioPortal ingests variants as they were called in the original publication and it's always possible that the original publication had some filtering steps -- in which case I'd suggest referring back to the methods section of the original publication for your study of interest.

-Tali

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