e-learning

Calculating CHEK2 variant effect scores from MAVE data with CountESS

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Abstract

Multiplexed assays of variant effect (MAVEs), including deep mutational scanning (DMS)

About This Material

This is a Hands-on Tutorial from the GTN which is usable either for individual self-study, or as a teaching material in a classroom.

Questions this will address

  • What is a multiplexed assay of variant effect?
  • How can variant frequencies before and after selection be transformed into functional scores?
  • How can a saved CountESS workflow be run in Galaxy?
  • How can calculated variant effect scores be visualized?

Learning Objectives

  • Explain how deep mutational scanning and MAVE experiments connect variant frequencies to functional effects.
  • Use CountESS in Galaxy to calculate RAD53 Complementation Scores for CHEK2 variants.
  • Compare calculated log-ratio scores with scores deposited in MaveDB.
  • Visualize the distribution of calculated CHEK2 RCS values.

Licence: Creative Commons Attribution 4.0 International

Keywords: DMS, MAVE, Variant Analysis, clinical genomics, functional genomics, variant effect

Competency level: • Beginner

Target audience: Students

Resource type: e-learning

Version: 1

Status: Active

Prerequisites:

  • Introduction to Galaxy Analyses
  • Mapping
  • Quality Control

Learning objectives:

  • Explain how deep mutational scanning and MAVE experiments connect variant frequencies to functional effects.
  • Use CountESS in Galaxy to calculate RAD53 Complementation Scores for CHEK2 variants.
  • Compare calculated log-ratio scores with scores deposited in MaveDB.
  • Visualize the distribution of calculated CHEK2 RCS values.

Date modified: 2026-07-30

Date published: 2026-07-30

Authors: Polina Polunina, Tristan Reynolds, Nick Moore, Alan Rubin

Scientific topics: Genetic variation

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