Sequoia genetics Co. Ltd. announced the beginning of clinical trials of diagnostic system for severe hereditary diseases detection in newborns and carrier state in couples planning a family. The developed molecular genetic solution is based on next generation sequencing (NGS) technology and consists of reagents kits and specialized software. Since the solution is designed for the mutation detection in clinics a special attention has been given to the issue of traceability and unambiguity of sequencing results in order to ensure the accuracy and reproducibility of the assay. To provide extensive clinical trials Sequoia genetics established partnership with several European laboratories: Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP, Portugal), StabVida company (Portugal) and the Center for Genome Research at the University of Liverpool (UK).
The results of the "Neonatal NGS-based diagnostics" project will lead to the development and introduction into routine clinical practice of highly effective method of diagnostics of three congenital metabolic diseases: cystic fibrosis, phenylketonuria and galactosemia. Neonatal testing for these diseases is recommended by the World Health Organization (WHO) and is mandatory in Russian Federation and a number of developed countries in the framework of governmental screening programs. Genetic analysis component of diagnostic solution is being implemented on Ion PGM semiconductor sequencer (Life technologies). Target enrichment protocols and molecular bar-coding (up to 48 DNA samples per analysis) are used. Software and specialized database of pathogenic mutations have been created to analyze the sequencing data, visualize the results and generate medical report. Diagnostic solution is multi-ethnic and may be used in different parts of the world with equally effectiveness, depending on completeness description of mutations in local population and some method limitation. Usage of the suggested solution would give medical geneticists accurate and complete information on genetic markers of severe hereditary diseases in the newborn or their carrier state.
"Within the framework of the project "Neonatal NGS-gene diagnostics" we've performed all the steps necessary for creation of a fully functional prototype. And now we’re coming to the most important stage – evaluation of analytical and diagnostic properties of the test system –verification and validation steps. Verification is being conducted by comparing the DNA sequences received by the reference method (Sanger sequencing) and NGS. Thus we confirm that the analytical sensitivity and analytical specificity allow us reliably determine the primary sequence of DNA and the zygosity of the sample within the specified genome regions. Sample preparation and data analysis is being carried out in our laboratory, and Sanger sequencing itself - in a certified laboratory in Switzerland", says Alexander Pavlov, Sequoia genetics CEO.
Since NGS-based solutions for clinics is a new and fast-growing filed of molecular diagnostics and has not yet been introduced into a wide clinical practice there are no well-established approaches for validation of such solutions, as well as there are no standard guidelines for carrying out such investigations. "We created comprehensive validation plan and defined the requirements to the reference laboratories. First of all we have decided that the participants should be properly certified for conduction of such studies European laboratories which have a rich experience of using NGS sequencers in their routine practice for quite a long time", says Alexander Pavlov.
Validation is a comprehensive process aimed to determine the diagnostic properties of solution and assess the possibility of its usage in clinical practice. Investigations are being carried out in three reference laboratories on 576 DNA samples. All samples are characterized in terms of previously detected mutations and clinical status. The purpose of this study is to evaluate diagnostic sensitivity, diagnostic specificity, analytical performance, and also intra- and inter-laboratory reproducibility.
Alexander Pavlov:
«After the validation is completed in September we are going to prepare an article jointly with European colleagues where approaches underlying the investigation and its results will be described. We expect the results of our study to show strong evidence that the developed solution has significant diagnostic advantages. This by-turn will be a good basis for certification of the method and its introduction into routine clinical practice".
StabVida – www.stabvida.com
IPATIMUP – www.ipatimup.pt
Center for Genome Research at the University of Liverpool – www.liv.ac.uk/genomic-research