Re-analysis of Next Generation Sequencing (NGS) data using the varvis® software

Ever wondered how many additional cases could be solved by re-analyzing old data? A team from the University of Leipzig published the results of re-analyzing 1000 whole exome cases.

Several recent studies [1,2,3] have shown the importance of data reanalysis when it comes to NGS data. The push for re-sequencing using a different platform or methodology is not always warranted and does not necessarily mean a positive result. Reanalysis as a first step, especially after a considerable lapse of time, seems the best way forward as it enables use of the rapidly generated data points during this time.

In particular, the team of the Prof. Jamra from the Institute for Human Genetics at the University of Leipzig published an article [1], presenting the impressive results of their study on cohort-wide re-analysis of more than 1000 exome data sets, in which the varvis® Software played a central role. They have documented and shared the filtering strategy they used (Fig.1). In the cascade, they filter for morbid genes, variants with high Human Phenotype Ontology similarity score (varvis® HPOSimScore) and finally filtering them down further with the inheritance filters.

Fig.1 Filter cascade to be used in the workflow of the clinical routine.

The study demonstrates how the re-analysis of non-diagnostic exome sequencing may increase diagnostic yields significantly, and therefore should become part of daily lab routines.

In this article we will show how the varvis® Software and its features help with data reanalysis becoming a crucial part of the data analysis workflow:

1. HPO similarity score

One of the fundamental steps employed by Jamra’s team involves utilizing the HPOSimScore within the varvis® platform. This is a matrix that can be used to efficiently prioritize genes and variants based on the clinical information entered for the patient. It is an indispensable initial filter, assessing the association between genes and patient phenotypes while considering the specificity, similarity, and relevance of HPO terms. This is far superior to considering string matches that would not consider similar terms as a match. A detailed course in the varvis® Academy explains how the HPOSimscore works in the software.

2. Share and Aggregate Data

The varvis® software facilitates the sharing and aggregation of data, enabling integration of updated information through the allexes® platform. The reference data network allexes® does not only deliver the most recent versions of public databases, but also provides access to aggregated genomic reference data from all our users compliant with HIPAA and EU regulations. Since then, the allexes® database contains information about more than 40,000,000 unique variants from more than 150,000 cases and accelerates in growth. Users may opt-in to leverage aggregated data across all users comprising valuable information about every single variant like frequency, technical metadata, associated phenotypes and previous classifications. Most importantly, both the data capture as well as the data sharing are automated, and data is continuously updated.

This GDPR-compliant large-scale data sharing between private and public institutions alike is not only technically feasible but also enhances the data analysis of every individual patient.

3. Annotation Update Integration

Annotation sources, such as ClinVar, are regularly updated in specific releases to keep pace with mounting evidence from studies. Recognizing the dynamic nature of the annotation sources, the varvis® platform integrates workflows for effortless updates. This feature ensures that re-analyzed cases reflect the most recent information, aiding in the identification and classification of pathogenic genes and variants.

The varvis® annotation update feature is designed for simple usage, allowing users to incorporate the latest data with just a single click, without re-submitting the case. This streamlines the process of keeping analyses current, eliminating complexities, and saving time. Moreover, the automated variant alerts for individual patients play a crucial role because they ensure that clinicians are promptly informed about pertinent updates specific to their patients’ genetic profiles. This proactive approach aids in maintaining up-to-date reports, a fundamental aspect of providing optimal patient care.

4. Classification Alerts

Newly published information about a variant may change its significance. The varvis® platform is also equipped with alert systems that notifies users about changes in classification helping them to stay updated with the evolving knowledge landscape or about new evidence for variants that have not been considered before in cases reported as negative. The varvis® “Classification alerts” feature allows you to cross-reference any updates in ClinVar between the current and the last ClinVar release and your own variant database. These alerts assist in reanalysis by highlighting alterations in variant significance and classification status.

And we have many more ideas to improve genetic diagnostics. Stay tuned!

About the varvis® Software

The varvis® software is a clinical decision support system designed by Limbus Medical Technologies GmbH, a medical device manufacturer and software development company. The cloud-based genomics platform is tailored to support the entire NGS workflow, from raw data processing to genomics data management and variant interpretation. Automated CNV and SNV analysis are completely integrated into the NGS workflow and clinically validated for panels of all sizes including WES. Our services comprise first class support, training, automated quality control and validation compliant with relevant international guidelines. The varvis® software is a registered CE-IVD device and specifically made to aid in the diagnosis of patients.

See for yourself

If you want to learn more about the varvis® software and how it can help you navigating, please get in touch with us to schedule your personal varvis® software demo or check our varvis® Academy courses.

References

1. Halfmeyer, I.; Bartolomaeus, T.; Popp, B.; Radtke, M.; Helms, T.; Hentschel, J.; Popp, D.; Jamra, R.A. Approach to Cohort-Wide Re-Analysis of Exome Data in 1000 Individuals with Neurodevelopmental Disorders. Genes 2023, 14, 30.
2. Bartolomaeus, T., Hentschel, J., Jamra, R.A. et al. Re-evaluation and re-analysis of 152 research exomes five years after the initial report reveals clinically relevant changes in 18%. Eur J Hum Genet 31, 1154–1164 (2023).
3. Henkel, J., Laner, A., Locher, M. et al. Diagnostic yield and clinical relevance of expanded germline genetic testing for nearly 7000 suspected HBOC patients. Eur J Hum Genet 31, 925–930 (2023).
4. Deignan, J.L.; Chung, W.K.; Kearney, H.M.; Monaghan, K.G.; Rehder, C.W.; Chao, E.C. Points to Consider in the Reevaluation and Reanalysis of Genomic Test Results: A Statement of the American College of Medical Genetics and Genomics (ACMG). Genet. Med. 2019, 21, 1267–1270.
5. Dai, P.; Honda, A.; Ewans, L.; McGaughran, J.; Burnett, L.; Law, M.; Phan, T.G. Recommendations for next Generation Sequencing Data Reanalysis of Unsolved Cases with Suspected Mendelian Disorders: A Systematic Review and Meta-Analysis. Genet. Med. 2022, 24, 1618–1629.