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PLoS One. 2019 Apr 25;14(4):e0215618. doi: 10.1371/journal.pone.0215618. eCollection 2019.

VarWatch-A stand-alone software tool for variant matching.

Author information

1
Institute of Clinical Molecular Biology, Kiel University, University Hospital Schleswig-Holstein, Kiel, Germany.
2
Institute of Medical Informatics and Statistics, Kiel University, University Hospital Schleswig-Holstein, Kiel, Germany.
3
Humangenetische Praxis PD Dr. Pfeufer, München, Germany.
4
MVZ für Molekulardiagnostik GmbH, München, Germany.
5
Myriad GmbH, Martinsried, Germany.
6
TMF - Technologie- und Methodenplattform für die vernetzte medizinische Forschung e.V., Berlin, Germany.
7
Max Planck Institute for Molecular Genetics, Berlin, Germany.

Abstract

Massively parallel DNA sequencing of clinical samples holds great promise for the gene-based diagnosis of human inherited diseases because it allows rapid detection of putatively causative mutations at genome-wide level. Without additional evidence complementing their initial bioinformatics evaluation, however, the clinical relevance of such candidate genetic variants often remains unclear. In consequence, dedicated 'matching' services have been established in recent years that aim at the discovery of other, comparable case reports to facilitate individual diagnoses. However, legal concerns have been raised about the global sharing of genetic data, particularly in Europe where the recently enacted General Data Protection Regulation EU-2016/679 classifies genetic data as highly sensitive. Hence, unrestricted sharing of genetic data from clinical cases on platforms outside the national jurisdiction increasingly may be perceived as problematic. To allow collaborative data producers, particularly large consortia of diagnostic laboratories, to acknowledge these concerns while still practicing efficient case matching internally, novel tools are required. To this end, we developed VarWatch, an easy-to-deploy and highly scalable case matching software that provides users with comprehensive programmatic tools and a user-friendly interface to fulfil said purpose.

Conflict of interest statement

AP acknowledges support from Myriad GmbH, Planegg, Germany, and MZV für Molekulare Diagnostik, Munich, Germany. TB acknowledges support from MZV für. Molekulare Diagnostik, Munich, Germany. Myriad and MVZ provided support in the form of salaries for authors AP and TB. This does not alter our adherence to PLOS ONE policies on sharing data and materials.

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