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Interpreting Genomic Variation: Inherited Cancer Susceptibility

Explore how robust variant interpretation is needed to support patients with increased risk of cancer.

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Explore germline variation in cancer susceptibility genes

Germline genomic variation can increase the risk of developing cancer. It’s essential to use the best evidence available to decide if a genomic variant is likely to increase the chance of a person developing cancer. This allows us to offer at-risk individuals access to appropriate screening, prevention, and personalised treatments.

Learn how to interpret genes for susceptibility to cancer

On this course, you will consider how variant interpretation in cancer susceptibility genes has different considerations when compared with variant interpretation in rare paediatric disease.

You’ll explore the guidelines produced by the UK Cancer Variant Interpretation Group (CanVIG-UK) for variant interpretation and how these can be applied to the American College of Medical Genetics (ACMG) framework in the classification of germline variants in cancer susceptibility genes.

Study the CanVIG-UK guidelines in theory and practice

This course will provide you with patient examples to explore the complexities of variant interpretation in cancer genomics. You’ll also hear from experts in the field about how the CanVIG-UK guidance was created.

You’ll be encouraged to apply your learning through case-based exercises that illustrate both the strengths and weaknesses of the tools and guidelines available for cancer variant interpretation.

Study with world-leading genomic experts at St George’s

Learn from Professor Kate Tatton-Brown and Dr Katie Snape – renowned consultant Clinical Geneticists leading on variant interpretation for rare disease and cancer.

This course is part of a series with Interpreting Genomic Variation: Fundamental Principles.


  • Week 1

    Cancer susceptibility gene variant interpretation

    • Introduction to the course

      In this section, we welcome you to the course with more information about our course team and some key definitions.

    • Why is variant interpretation different in Cancer Susceptibility Genes (CSGs)?

      In this section, we look at why genomic variant interpretation is different in cancer susceptibility genes when compared with rare diseases.

    • Adapting the ACMG framework for CSGs

      In this section, we will explore the specialist CanVIG-UK guidance for variant interpretation.

    • Population data

      In this section, we begin to look at the different types of evidence available for variant interpretation in CSGs, starting with population data.

    • Computational and predictive data

      In this final section of the week, we will explore the next type of evidence which is computational and predictive data.

  • Week 2

    Cancer susceptibility gene variant interpretation

    • Introduction to Week 2

      In this section, we will introduce you to what to expect on the second week of the course.

    • Functional data

      In the section, we will take a detailed look at functional data use in CSG variant interpretation.

    • Allelic data

      In this section, we will examine the role of allelic data in cases of recessive disease and hear about a patients experience with genetic test.

    • Reputable sources

      In this section, we review one of the advantages of cancer being a common disease - the wealth of data available from a range of reputable sources.

    • Other data

      While phenotype data may be quite different to the dysmorphology considered in rare diseases, particular features of a tumour can give us a range of clues for variant interpretation.

    • Other considerations

      Having reviewed the different types of evidence towards pathogenicity, in this section, we will look at what happens when classifications clash, and when we have evidence to suggest a variant is benign.

    • Pulling it all together

      In this section, we find out Liz's mother's genetic test result and look at a useful resource that pulls together all of the different types of evidence available for CSG variant interpretation: CanVar-UK.

    • Putting it into practice

      It's your turn to practice working through variant interpretation in a range of CSGs, including a detailed review of the variant identified in Liz's mother.

    • The evolving landscape

      Cancer genomic is ever-changing - the more we learn about CSGs the more complex variant interpretation becomes. In this final section, we examining so key areas of development.

When would you like to start?

Start straight away and join a global classroom of learners. If the course hasn’t started yet you’ll see the future date listed below.

  • Available now

Learning on this course

On every step of the course you can meet other learners, share your ideas and join in with active discussions in the comments.

What will you achieve?

By the end of the course, you‘ll be able to...

  • Evaluate the variant interpretation tools (such as population databases, in silico tools, phenotype) and their application to the interpretation of cancer susceptibility genes.
  • Apply the American College of Medical Genetics (ACMG) framework to inherited cancer susceptibility and evaluate how the framework differs in the interpretation of severe paediatric disease and cancer susceptibility.
  • Compare constitutional and somatic genetic mechanisms of disease and their role in the development of rare disease and cancer.
  • Identify tumour specific mutational signatures and their role in the management of cancers.

Who is the course for?

This course would be suitable for:

• Clinical Genetics doctors (consultant and specialist registrars) • Clinical Scientists • Genetic Counsellors • Clinical Oncology doctors (consultants and specialist registrars) • Pathologists undertaking cancer MDTs • Specialist oncology nurses undertaking genetic testing

Who will you learn with?

I'm a consultant cancer geneticist at St George's University Hospitals NHS Foundation Trust. My research involved using next generation sequencing technology to identify genes associated with cancer.

I'm a Genetic Counsellor and Honorary Clinical Lecturer in Cancer Genomics.

Who developed the course?

St George's, University of London

St George’s is the UK’s only university dedicated to medical and health sciences education, training and research.

CanGene CanVar

CanGene CanVar is a five-year Cancer Research UK-funded research program which develops data resources, clinical and educational tools to leverage cancer susceptibility genetic for early detection and prevention of cancer.


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