Integrating and visualizing circulating cell-free DNA (cfDNA) results

[jjgao]

Background: Circulating cell-free DNA (cfDNA) can act a noninvasive way to detect the presence of tumor in various cancer types. In the future, cfDNA can potentially provide an approach for real-time noninvasive monitoring of treatment response and cancer progression.

• Bettegowda et al. Detection of circulating tumor DNA in early- and late-stage human malignancies. Sci Transl Med. 2014.
• Eccles et al. Critical research gaps and translational priorities for the successful prevention and treatment of breast cancer, Sci Transl Med. 2015.

In the cBioPortal, we can visualize multiple samples with timeline data per patient, but cfDNA data poses a challenge because we need to deal with dozens of samples.

Goal: Implement alternative ways to integrate, visualize, and analyze cfDNA data. For example:

• Visualize cfDNA data over time -- similar to timeline (example).
• Visualize cfDNA data similar to OncoPrint but samples as rows and mutation events as columns.
• Compare genomics data in different samples, e.g. venn diagram.

Approach: Improve the current patient view to incorporate cfDNA.

Need skills: Javascript

Possible mentors: JJ Gao, Ino de Bruijn

[nikhilshagri]

Would knowledge of D3.js be required too for this project?

[jjgao]

@cynicaldevil: Javascript stills is required. Experience with D3.js or other JS visualization library would be helpful.

[katehara]

Hi, I have been working on Data Visualization using D3.js for while, have taken Biomedical Engineering Course at University level and am Interested in this project. How can I get started?

[jjgao]

@katehara: it would be a good start to get familiar with cBioPortal and its code base, especially the patient view (example). Here are a few tips. Once you understand the patient view, try to think about how to design a interface that can visualize, compare and analyze dozens of samples over time.

[pambot]

Hi JJ,

I think because cell-free DNA is essentially a "liquid biopsy", it makes sense to represent it in the timeline, along with the surgical biopsies. It would have its own numbered circle glyph, but with a different colour than yellow. The mutations and rearrangements (if tracked) could be appended to the Genomic Overview and Mutations of Interest boxes. It wouldn't have the same precedence as the yellow events, ultimately, because those represent actual treatments as well as measurements, so there's probably no need to modify the top header for the patient. If a venn diagram were to be implemented, I think it would have to incorporate the tissue sample mutation events too, and it would either be its own box or put underneath the variant allele frequency plot. What do you think? I can make a graphical mock-up for my proposal.

[pieterlukasse]

hi @pambot , not sure what the status is here, but I am still interested in seeing a graphical mock-up.

[jjgao]

@pambot

A "liquid biopsy" procedure is one event (one dot) we can put on the timeline. But we are more interested in visualizing mutations detected from the cfDNA over time. Being able to visualize the allele frequency of different mutation and see how change over time is the key. Also keep in mind that we may be dealing with hundreds of mutations, so visualizing all of them would be challenging.

Currently we model a liquid biopsy as sample, but when you have dozens of samples, the Mutations table does not work. We need better way to model / visualize the data.