Candlestick chart on computer screen.
Photo by M. B. M. on Unsplash

HELSINKI, Finland, September, 2019. – Euformatics has further developed its partnership with quality assessment bodies EMQN and the UK NEQAS for Molecular Genetics (now known as Genomics Quality Assessment, GenQA), which it started in 2015 with the development of the first unlimited external quality assessment technical scheme for NGS-based clinical testing. This autumn sees the next step in the evolution of this activity with the piloting of an extension of the EQA to incorporate copy number variation (CNV) data. This first will bring to the forefront essential discussion around the definition of CNV assessment and more broadly, harmonisation and consistency of data across the genomics field.

As the chosen and trusted partner of EMQN and GenQA for providing variant interpretation external quality assessments (EQA) using a bespoke version of omnomicsQ, Euformatics is ideally placed to help develop the first EQA for CNV data. As variant interpretation and reporting continues to grow and expand as an important part of genetic diagnostics and personalised healthcare, it is imperative that all those assessing CNV are doing so with the same definitions and understanding of standards.

Dr Sandi Deans, Director of GenQA explains that “The current NGS EQA which incorporates both germline and somatic testing has been expanded in response to participation demands and the widespread implementation of NGS detection of CNVs in the clinical setting. It is therefore important to standardise approaches to ensure high quality testing is delivered to patients, and EQA plays a fundamental role in this.”

Why are CNV assessments becoming more important?

Until recently, most variant interpretation and reporting solutions focused on single nucleotide variants (SNVs or SNPs) and small insertions/deletions (InDels). These types of variants are relatively easy to express in computer readable format and the conventions for doing so (e.g. VCF format standards) are available.

CNVs however, are changes in much larger portions of the genome, potentially covering large parts of a gene or even several genes, and which can delete or replicate entire protein coding regions several times over. While cytogenetic analysis and arrays have been studying CNVs for decades, it is only much more recently with NGS technology that we have been able to study the more detailed effects that such large genetic variations have on phenotype, and start to build stronger links between CNVs and disease. Contrary to the case with SNVs and InDels, it is much more complicated to formalise what constitutes as the same or different CNV because of the much wider genomic regions being affected, and a lack of sufficient biological understanding of precisely which regions potentially have the same function.

As more variant interpretation software comes to market which contains CNV calling and interpretation capabilities, its essential that we start to independently assess their performance and drive standardisation of the process. Ensuring this harmonisation will allow for better and more effective diagnostic judgments based on the data, to the benefit of patients. EMQN’s Managing Director, Simon Patton notes “NGS quality control is vital for ensuring successful and accurate NGS test results. This partnership has already delivered a world leading EQA scheme which is independent of testing context and scale, as well as being agnostic of test platform. The addition of CNV analysis is an exciting development and strengthens our approach to delivering a comprehensive EQA for NGS”.

Euformatics plays a central role

Euformatics is also further developing its CNV interpretation and reporting capabilities as part of its variant interpretation and reporting solution omnomicsNGS. Euformatics CTO Jussi Volanen notes that “CNV interpretation is quickly becoming one of the most sought after capabilities for software like ours, so it is imperative that we in the industry are all on the same page”. Building on its success as the provider of the quality assessment software used by EMQN and GenQA, “we look forward to being at the forefront of the development of European EQA for CNV as the demand for it continues to grow” adds Volanen.

For any questions regarding Euformatics’ role in the pilot, or any of their products mentioned in this piece, please get in touch at

– – –

About the organisations:

Euformatics is a Finnish software company that specialises in high standard bioinformatics tools for genomic data interpretation. Since 2010, Euformatics has been helping medical doctors and molecular genetics laboratories provide better precision medicine for cancer, common or rare disease diagnostics. At present, the most well known solutions include omnomicsNGS; for clinical analysis of patient NGS data, and omnomicsQ; for NGS data quality management.

EMQN is a not-for-profit organisation promoting quality in genetic testing by establishing, harmonising and disseminating best practice. EMQN provides accredited (ISO 17043) external quality assessment (EQA) to genomics labs worldwide in collaboration with many organisations including EuroGentestCF Network Genomic Quality Assessment (GenQA), Royal College of Pathologists of Australasia Quality Assurance Programs (RCPAQAP), QAP, Reference Institute for Bioanalytics (RfB), Swiss Centre for Quality Control (CSCQ) European Academy of Andrology (EAA) and the International Quality Network for Pathology (IQN Path).

Genomic Quality Assessment (GenQA) is a self-funding and not-for-profit organisation which is a member of the UK NEQAS Consortium. GenQA provides a broad, consistent and sustainable range of ISO 17043 accredited EQAs which covers the end to end processes of genomic testing from preanalytical, analytical, interpretation and reporting through to Clinical Genetics, at both the laboratory and the individual level. Advances in our understanding of genomic diseases has led to a revolution in testing technologies and GenQA is committed to providing external quality assessment in this rapidly evolving field.





Back to blog listing