VarWatch-A stand-alone software tool for variant matching

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

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology / instrumentation*
  • Datasets as Topic
  • Genetic Diseases, Inborn / diagnosis*
  • Genetic Diseases, Inborn / genetics
  • Genetic Testing / instrumentation*
  • Genetic Variation
  • Genomics / instrumentation*
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Sequence Analysis, DNA
  • Software*

Grant support

Funding was provided by Bundesministerium für Bildung und Forschung (grant no. 01EK1506) to MK and AF. AF acknowledges support from DFG-funded Excellence Cluster "Inflammation at Interfaces". 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, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the ‘author contributions’ section. All authors gratefully acknowledge support from TMF eV., Berlin, Germany, a non-profit platform for the sharing of methods and technologies in networked medical research (http://www.tmf-ev.de). TMF e.V. actively supported the development of VarWatch by hosting stake-holder meetings and by promoting the tool among its members. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.