Integrate Mutational Signatures into the cBioPortal

[jjgao]

@jjgao commented on Fri Dec 22 2017

Background: Signatures of mutational processes in human cancers can be inferred from somatic mutations data and have been detected in many cancers. For example, the signature below is associated with smoking. A list of 30 signatures is available on COSMIC.

Goal:

• Identify mutational signatures in each sample with mutations.
• Integrate identified mutational signatures into the database and web API.
• Build features for visualizing and analyzing mutational signatures in patient view, study view, and results page.

Note: In this project, we are not going to identify new signatures from a cohort, but rather to detect "known" signatures in individual samples.

Approach:

• Build a pipeline to identify mutational signatures from MAF. This project can be utilized here.
• Extended the cBioPortal data model (database schema) to incorporate the mutational signatures. For example, a molecular profile can be created for storing the data.
• On Patient View page, visualize the signatures identified in the samples from the patient. (note: multiple samples may exist)
• On Study View page, add a chart for signature analysis. For example, a table similar to Mutated Genes can be added.
• On Results page, implement an option to add mutational signatures into the OncoPrint, one signature per track.
• On Plots tab, add signatures as an option.
• Please propose other analysis features if you have any ideas.

Need skills: Javascript, ReactJS, Java, Python, MySQL, Web API

Possible mentors: [potential mentors please sign up here]

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[stale[bot]]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

[stale[bot]]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.