Validation of NGS pipelines

Question 1

What do you need to validate an NGS pipeline?

Answer 1

• Samples with well characterised variants
• Samples with a variety of variants e.g. missense, nonsense, indels (frameshift/in-frame) and CNVs
• • Acceptance criteria
• …

Question 2

What sample sources could be used for validation?

Answer 2

GIAB (Genome in a Bottle) HapMap In-house samples, confirmed by Sanger sequencing

Question 3

What would be the differences between validation and re-validation?

Answer 3

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Question 4

What documentation is required?

Answer 4

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Question 5

What is the difference between verification and validation?

Answer 5

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Question 6

What do the ACGS guidelines say about validation?

Answer 6

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Question 7

What do the ACMG guidelines say about validation?

Answer 7

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Question 8

When would you carry out a full validation (wet-lab and bioinformatics processing)?

Answer 8

When any of the following have changed: - Instrumentation - Method of library preparation - Sequencing platform …

Question 9

In what circumstances would you only carry out a re-validation of the bioinformatics pipeline?

Answer 9

When any of the following have changed: - Software update/upgrade - …