Body map showing locations of sequenced samples in patient view

Background: The cBioPortal Patient Viewer gives researchers an in-depth view of individual patients, providing a view of their specific gene alterations, CN alterations across the genome, as well as a clinical timeline of sequenced samples and other clinical events.

However, when analyzing a patient's clinical history, researchers must use their imagination to understand the context of where these sequenced samples have been biopsied from in the body.

To provide better clinical context, a visualization of the human body can be shown along side the patient timeline to highlight the region(s) of sequenced samples.

Goal: A visualization of the body map can be integrated along side the patient timeline. Overlaid on the body map would be markers of interest where a patient had a sample sequenced, biopsied, and/or had a surgical procedure. The markers on the body would have a hover-over feature that would provide metadata of the sample and highlight the corresponding marker shown on the patient timeline. The provided sample locations would be normalized to a set of anatomic locations, which is to be determined.

Below is a poorly photoshopped idea of what the result could be:

Screen Shot 2020-01-29 at 11 52 46 AM copy

Approach:

Create and embed a vectorized body map.
Create a mapping of normalized body locations to specific regions on the body map.
Overlay points of sequenced sites onto the body map.
Link points of sequenced sites to the patient timeline, make the points pop-up if mouse is hovered over the point on timeline or on body map.
Also provide metadata of sequenced sample/biopsy/surgery when hovering over point.
Create option to save bodymap with points of interest.
Create option to expand and compress the body map image for increased clarity.

Need skills: Javascript, HTML

Possible mentors: Co-mentor: @fongcj

cBioPortal / GSoC

Body map showing locations of sequenced samples in patient view #81