Show Variant Allele Frequency on the Plots Tab and OncoPrint

[inodb]

Background:

The cBioPortal is an open-access, open-source resource for interactive exploration of multidimensional cancer genomics data sets, which are collected from a multitude of sources such as published research papers, publicly available data repositories, and private data sets. Please refer to the cBioPortal home page for an overview.

The cBioPortal can show mutations in a cohort of patients on various pages, but in most places it only shows the mutation type (missense, truncating, etc). Another attribute of a mutation is the "variant allele frequency (VAF)", in how many reads of sequenced DNA a mutation occurs in all of the sequenced DNA at that position in the genome.

Plots Tab

One can currently plot e.g. the cancer type vs the number of mutations in a sample (see here):

It is, however, not possible to plot e.g. the VAF of a particular gene across the different cancer types (or stages of the tumor), one can only choose categorical values:

OncoPrint

The OncoPrint currently only shows the type of mutations on the Results View. See e.g. here:

We can add a new feature to allow users to plot the VAF of each individual mutation in a separate track. Similar to what's possible on the patient view:

---

Goal:

1. Add Variant Allele Frequency in the Plots Tab

2. Add Variant Allele Frequency in the OncoPrint on the Restuls View

Approach:

Add VAF to the Plots Tab:

1. Get familiar with the plots tab codebase
2. Update the axis selection interface to allow a user to select the VAF of a specific Gene
3. Implement and collaborate with other devs

For OncoPrint:

1. Get familiar with the oncoprint codebase
2. Update the toolbox interface to allow a user to select the VAF
3. Implement and collaborate with other devs

For a medium project (175h), one could do only the Plots Tab. For a large project (350h), one could implement both. An additional way to expand scope would be to add the cancer cell fraction of a mutation, which is available for a subset of studies.

---

Needed skills:

• Javascript, TypeScript, React
• General good programming skills and willingness to learn.

Possible mentors:

@onursumer
@mlizchap
@gblaih
@fuzhaoyuan

[DeepamJha]

Hello Mentors @onursumer @mlizchap ,

I’m Deepam Jha, a sophomore from GGSIPU, and I’m excited to contribute to cBioPortal. I’ve started familiarizing myself with the Plots Tab and OncoPrint codebase to explore how VAF can be integrated.

Before finalizing an approach, I have a few questions:

Does the API already expose VAF data, or would adjustments be needed?
Would VAF be better as an overlay in OncoPrint or a separate track?
Any UX considerations for adding VAF selection in the Plots Tab?

I’ll be outlining a plan soon and would love any feedback. Looking forward to your insights!