HELSINKI, Finland, November, 2019. – Euformatics’ work with the European Molecular Genetics Network (EMQN) and the Genetic Quality Association (GenQA) to create the first NGS data external quality assessment (EQA) has been showcased in article co-written by two of the Euformatics team and their colleagues in the partner organisations. The article entitled “One byte at a time: evidencing the quality of clinical service next-generation sequencing for germline and somatic variants” has been published in the renowned European Journal of Human Genetics, and is the culmination of 3 years work to put together a strong case for an NGS data quality assessment to drive top-quality data using a technology which is becoming ever more important to clinical molecular diagnostics.
The article discusses in detail the development and execution of the EQA, including the kinds of reference material used, and the use of Euformatics’ world-leading omnomicsQ quality control and validation software as the data collection, storage and analysis tool. Of particular interest was the creation of consensus truth sets (one for germline and one for somatic) as defined by participant data submitted as part of the EQA in 2016. These consensus truth sets were established based on two criteria being fulfilled, namely that at least 7 participants had studied a a region of interest, and at least 75% of those had called a variant in the same position.
The benefit of using this consensus based truth set method instead of an off-the-shelf truth set is that as the EQA needs to be agnostic and able to test all setups and kits, the results of the truth set should not be known beforehand ensuring that all participants can test the same sample and none know what results they should be aiming for from the outset. This technique reduces the possibility of result fabrication, while also enabling all lab setups to supply their results to be compared against each other.
Furthermore, it highlights the importance of EQA for NGS data as it becomes an every more important part of the molecular diagnostics toolkit. The authors conclude on the positive declaration that over the 3 years of EQA development, it has become clear that “clinical diagnostic laboratories are providing an increasingly high-quality NGS service”, suggesting a bright outlook for the future of NGS in the field, and better outcomes for personalised patient treatment. Finally, the article pointed out some of the challenges in expanding EQA capabilities to cope with the development trajectory of the NGS field, although some work towards this has already started in the form of the first pilot of a CNV EQA for NGS data which opened for submissions last month, and is also being run by EMQN, GenQA and Euformatics.
The article can be accessed freely online by clicking on the following link https://doi.org/10.1038/s41431-019-0515-1
For more information on the EQA or any of the points brought up in the article, please get in touch with either Christophe Roos or Jukka Matilainen, using the email format firstname.lastname@example.org