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Introduction to Clinical Interpretation of Somatic Cancer Variants

This course was created from this GitHub template.

This course was created with Bookdown and introduces best practices and tools for clinical interpretation of somatic cancer variants.

You can see the bookdown rendered course material here (GitHub pages site) or the leanpub course here.

About this course

This course will introduce background concepts, tools, resources, and relevant standard operating procedures and guidelines for the clinical interpretation of somatic cancer variants.

Learning Objectives

This course will teach learners to:

  • Understand key concepts of somatic cancer variant interpretation
  • Introduce ClinGen Somatic Cancer efforts
  • Introduce key SOPs and guidelines for classifying the clinical relevance and oncogenicity of somatic cancer variants
  • Introduce CIViC as a curation platform for somatic variant interpretation

Encountering problems?

If you are encountering any problems with this course, please file a GitHub issue or contact us at CIViC help.

How to contribute to this course

There are extensive instructions available in the OTTR documentation. Here are basic instructions/reminders:

  1. Clone the repo.
  2. Create and checkout a new branch.
  3. Add new chapters by copying and modifying one of the existing Rmd chapter files. Add an appropriate entry in the _bookdown.yml file.
  4. Add images to this Google Slide deck, copy the slide link, and embed in chapters following example code in existing chapters.
  5. Add references in BibTex format to the book.bib file. BibTex entries can be obtained with doi2bib.org. Cite references inline using @key where key is the citation key in the first line of the BibTex entry.
  6. Once new/revised content is ready, commit and push from the branch, and create a pull request.
  7. Go to pull requests and make sure all checks passing.
  8. Correct any reported errors. Any words incorrectly reported as spelling mistakes can be added to resources/dictionary.txt. Commit and push to re-run PR checks.
  9. Have someone review and approve the pull request.
  10. Merge the PR and delete the branch.
  11. Make sure all build Actions complete successfully.
  12. Review the bookdown build at github pages site.
  13. Have the leanpub course admin Preview and then Publish a new version of the course.

Creative Commons License
All materials in this course are licensed under a Creative Commons Attribution 4.0 International License unless noted otherwise.