Best Practices for Variant Annotation and Filtration – Germline Variant Analysis

         January 14, 2025
Best Practices for Variant Annotation and Filtration - Germline Variant Analysis blog header

Golden Helix field application scientists curate a set of FAS templates that capture best practices for filtering, which we use when training and onboarding customers. In addition to the basic templates that come default with the software, these more fleshed-out templates are available upon request. This first blog in the series focuses on germline variant analysis.

Rare pathogenic variants

The main focus of the germline filtering strategy is to identify rare pathogenic variants. These are variants that would be classified as pathogenic or likely pathogenic when scored according to the ACMG guidelines. There is a lot of flexibility with this template for the user to customize the strategy to meet their specific requirements for variant quality or thresholds for what is, for example, considered rare. With this germline template approach, you can capture not only rare variants that may be well known and described by others but also novel likely pathogenic variants, for example, this variant that causes a LOF fulfilling PVS1 and that has never been seen before in widely used population databases and has not been previously reported or studied by anyone in the public domain.

Figure 1. Rare likely pathogenic variant identified in MT-CO3
Figure 1. Rare likely pathogenic variant identified in MT-CO3

Well-Known Pathogenic Variants

Our germline filter strategy is comprehensive in that it also allows users to capture well-known pathogenic variants that might have a higher-than-expected population frequency. In our standard approach described above, we typically focus on variants with high potential impacts, such as loss of function, missense mutations, and potential splice variants. The wider comprehensive strategy also allows users to identify those pathogenic needles in the haystack of non-coding or even synonymous variants that have already been well characterized and reported in the public domain, in databases like ClinVar, LOVD, ClinGen, or even the user’s internal database of variant assessments.

Our FAS template for germline variant analysis focuses on rare and impactful pathogenic variants, as well-known pathogenic variants that should not be missed because of frequency or variant class, and also helps users to triage variants of uncertain significance with disease association, and of course, secondary findings as desired. With this template, users also have the option to provide their own diagnostic inputs, like a virtual panel or filter variants based on phenotypic association. As always, these templates are a starting point, and any user is able to leverage the suggestions while maintaining the flexibility to update and modify the templates as best suit their standard operating procedures.

If you are interested in learning more, please visit our website here.

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