In January 2014 Sequoia genetics (Saint-Petersburg, Russia) announced that the development of diagnostic solution intended for diagnostics of inherited diseases in newborns based on the next-generation sequencing (NGS) technology has been completed. The solution named VariFind Neonatal assay based on Ion PGM (Life Technologies, US) sequencing platform and consists of reagents kits, protocols and specialized software. The assay is designed for diagnostics of three inborn metabolic abnormalities: cystic fibrosis, phenylketonuria and galactosemia. Solution is intended to detect up to 360 clinically-significant and novel mutations lying within three genes associated with the named diseases. Diagnostics of these disorders is strongly recommended by the World Healthcare Organization (WHO) and is included in national newborns screening program in many countries.
The assay development lasted 18 months. In summer 2013 Sequoia genetics carried out independent clinical trials (validation) of the VariFind Neonatal assay in three European laboratories: in the Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP, Portugal), in Stab Vida company (Portugal) and in the Centre for Genomic Research University of Liverpool (CGR, UK). These organizations have the authorization for conducting such investigations as well as the extensive experience of working with NGS technology. The solution verification, i.e. approval of analytical characteristics of the assay, was based on Sanger resequencing and carried out in certified laboratory of Microsynth AG (Switzerland). Results of verification and validation revealed the important characteristics of the assay: analytical sensitivity, analytical specificity, overall accuracy, diagnostic sensitivity, diagnostic specificity, analytical performance, inter- and intra-laboratory reproducibility.
Alexander Pavlov, Sequoia genetics CEO, comments the obtained results: “The parameters and values defined during studies allowed us to establish diagnostic characteristics of the assay and assess their eligibility for clinical grade diagnostics. Now we can conclude that parameters are acceptable and analytical and diagnostic characteristics are suitable for routine clinical practice. Results and detailed report on performed studies will be published in scientific literature in the nearest future. One of the main challenges of the development stage was the creation of a complete solution directed to use by medical geneticist. The goal was to make completely bioinformatician-free analysis workflow”.
Anton Bragin, the head of the Sequoia genetics bioinformatics department, says:
“Despite the wide availability of genomic data analysis software on the market, its application in diagnostics is limited since the presence of essential requirements for genetic data analysis in clinics. The main goal is to provide the way for simple visualization of complex genetic data taking into account the essential subject area features. During the assay development we have formulated our own vision of clinical grade diagnostic test system requirements. Software in diagnostic solution should be integrated with other components of the assay. In case of highly throughput methods, such as NGS, the software also has a great contribution to proper data analysis and interpretation”.
Sequoia genetics specialists have already reported results to Russian key medical genetic associations and scientific society: the Research Centre of Medical Genetics of the Russian Academy of Medical Sciences (Moscow, Russia) and the Research Institute of Medical Genetics of the Russian Academy of Medical Sciences (Tomsk, Russia). Results were also reported on the conference “Actual problems of clinical genetics of orphan diseases” (5-6 December 2013, Moscow, Russia). Moreover Sequoia genetics in partnership with Khimexpert company (Moscow, Russia) conducted training session for Russian medical geneticists, where theoretical and practical aspects of using new technology in clinics were considered. During the classes physicians used Sequoia’s software for variant detection in complicated clinical samples. Over 50 medical geneticists and genetic counselors from all over Russia have attended the training session.
“Scientific and medical societies were enthusiastic about the idea of introduction this new technology in routine molecular diagnostics within the framework of newborn screening. Now our goal is to rationale the expediency and effectiveness of the new approach for newborn screening program. We assume these tasks to be worked out during the pilot clinical approbation, which is going to be launched in 2014 and last half a year. This extensive investigation will include testing of all newborns in selected federal district using current protocol simultaneously with the developed approach. Second stage of unselective screening will be carried out by NGS sequencing of positive samples from the first stage. We expect that the investigation will affect approximately 170 000 newborns and results on using the alternative scheme will be available by the end of 2014. It will be shown whether there are diagnostic advantages and economical profit from the introduction of new scheme to the newborn screening program or not. After completing the investigation we will discuss possibilities of using new protocol of screening within the framework of federal screening program in Russia”, says Alexander Pavlov.
To be included in routine clinical practice the diagnostic solution should have appropriate certification, therefore Sequoia genetics has already applied for an CE-mark which expected to be gained till the end of the 2013 year. Thus VariFind Neonatal assay will be the first certified diagnostic test based on the semiconductor sequencing technology. Today the assay is offered for confirmatory diagnostics and is available on the Russian market.
“In addition to Russia and CIS we are interested in launching the product on foreign markets. Our solution is multiethnic and can be efficiently applied to different populations. After certification in EU the assay will be available on the European market. Latin America is of special interest for us due to its genetically heterogeneous population and ongoing screening programs. We are also interested in being represented in the US though it has strict marketing policy. Therefore we are open to partnering with foreign companies interested in promoting of our solution on their territory”, says Alexander Pavlov.
Completion of development of a diagnostic solution, and its successful verification and validation, show us that NGS technology can be applied in clinical practice. It seems to be a powerful tool for solving wide range of diagnostic issues. However, it should be always taken into account that any technologies have their own limitations. High-performance methods for genome analysis should be used in clinics only in the scope of reasonability, effectiveness and presence of the evidence base.