Implementing omnomicsQ in a Swiss University Hospital
Supporting ISO 17025 accreditation for Next Generation Sequencing (NGS)
Keeping within the high quality standards of their ISO 17025 accredited since 2001, the laboratory has been granted a Swiss Federal Authorization for Human Molecular Genetic Research (Lab-070041). The laboratory’s high quality standards were no different 2 years ago when NGS methods were introduced to perform somatic testing. While implementing the new technology, the goal was to ensure that:
- Good laboratory practices were implemented
- Laboratory protocols were relevant for somatic testing
- Methods could be validated
- Interpretation of results were correct
At the time, best practice guidelines still had to be developed. This made it very difficult to benchmark and validate different NGS methods and gene panels. The little data that did exist in publications were not reliable or sufficient. Furthermore there were no software available other than the limited QC software that came with the sequencer and which did not have any benchmarking capabilities.
In this context, Euformatics has developed omnomicsQ, a comprehensive NGS quality management software that can be integrated into in-house built pipelines and LIMSs or operated manually. The omnomicsQ was introduced in the Haematology Central Laboratory via a pilot phase to manage the different aspects of quality control in the NGS-based molecular tests. The piloting phase allowed the laboratory to improve the understanding of the value of the many quality parameters available as well as how accumulating quality data can be used to designing quality thresholds.
The laboratory’s ISO 17025 accreditation has extended to include NGS-based testing and the department now using the software on a regular basis to ensure high diagnostic quality and to provide protection against exceptions and slow quality drift in a much more automated fashion.
Although NGS technology started penetrating clinical diagnostics about 10 years ago, the standard guidelines from authoritative bodies like CLIA, CAP, and EuroGentest have not been available for more than the past 5 years. This delay reflects the complexity of the use of NGS in clinical diagnostics. Applications vary widely from haematological or solid cancer diagnostics to heritable or rare genetic disease testing, and so do the requirements and protocols used for these various diagnostic applications of NGS.
Moreover, the volume of generated data and its stochastic nature require a very active approach to QC. Labs need more than simple stand alone tools and spreadsheets for monitoring the quality data. They also need capabilities to manage standard operating procedures to achieve efficiency, quality output and uniformity of performance, while reducing miscommunication and failure to comply with good laboratory practice.
There are a wide array of commercial and lab developed genetic tests available on the market as well as a wide variety of extraction, library preparation and capture kits for different sequence and software platforms. Existing QC tools were not able to address the challenges of such variations but rather exacerbated the problem by adding an additional layer of complexity. Proper quality management could not be resolved easily, yet it was clear that the generated data from each sample tested could be used to drive the improvement of current and future tests.
The Inselspital occupies an important position as a university hospital in the Swiss healthcare system. They are a medical competence, high technology and knowledge centre with an international reputation as a meeting place for science and research.
The Molecular Diagnostics Laboratory of the Haematology Central Laboratory is the Swiss Reference Laboratory for the standardisation of the quantitative analysis of BCR-ABL1. The laboratory carries out gene tests for practising external physicians, hospitals of the Insel Gruppe AG and other hospitals as well as in clinical trials in Switzerland and abroad.
The essential services and tasks of the laboratory include molecular genetic studies in patients with leukaemia and lymphoma genotyping of thrombophilia risk factors. The laboratory, together with the Department for BioMedical Research at the University of Bern, has recently managed a European-wide proficiency pilot test among diagnostic laboratories involved in Next Generation Sequencing (NGS) -based testing for myeloproliferative neoplasms (MPNs).
Specialist for Genetics FAMH, Head of Molecular Diagnostics Molecular Diagnostics Department for Haematology Inselspital, University Hospital Bern
The Euformatics team, with expertise in IT, bioinformatics and genetics, was helpful in providing validation, technical support and NGS understanding. This is not something you can get from software alone.