NGS-based assay for frequent newborn inherited diseases: from development to implementation

Tamara Simakova; Anton Bragin; Maria Zaytseva; Carla Clemente; Magdalena Lewicka; Jose Machado; Jose Costa; Margaret Hughes; Christiane Hertz-Fowler; Nika Petrova; Alexander Polyakov; Rena Zinchenko; Elena Kondratyeva; Alexander Pavlov

doi:10.1101/050419

bioRxiv · 10.1101/050419

NGS-based assay for frequent newborn inherited diseases: from development to implementation

Tamara Simakova·Anton Bragin·Maria Zaytseva·Carla Clemente·Magdalena Lewicka·Jose Machado·Jose Costa·Margaret Hughes·Christiane Hertz-Fowler·Nika Petrova·Alexander Polyakov·Rena Zinchenko·Elena Kondratyeva·Alexander Pavlov

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Abstract

NGS is a powerful tool for the diagnostics of inherited diseases. A number of studies devoted to the development and validation of targeted NGS panels are published. Here we present not only development and validation of an assay, but report our experience on introduction of a new approach into the real clinical practice. The assay is intended for the diagnostics of frequent newborn inherited diseases: cystic fibrosis, phenylketonuria and galactosemia. The analysis is performed on the Ion PGM sequencing platform and allows the detection of single-nucleotide variations as well as copy number variants. We developed the software performing data quality control, providing decision-support variant annotation and generating the medical report that enables clinical application of the assay. Analytical validation of the assay was performed by bi-directional Sanger sequencing of the most part of the targeted region. Clinical validation was performed by multicenter blind testing of clinical and control samples. Sensitivity and specificity of the assay are above 99%. We have developed statements for test ordering, test acquisition form and practical recommendations for the results interpretation. The test has been successfully applied for the confirmatory diagnostics in a clinical laboratory during a year. Thus, the developed assay is a comprehensive ready-to-use CE-IVD solution for clinical diagnostics.

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Tamara Simakova, Anton Bragin, Maria Zaytseva, Carla Clemente, Magdalena Lewicka, Jose Machado, Jose Costa, Margaret Hughes, Christiane Hertz-Fowler, Nika Petrova, Alexander Polyakov, Rena Zinchenko, Elena Kondratyeva, Alexander Pavlov. 2016-04-26. NGS-based assay for frequent newborn inherited diseases: from development to implementation. https://doi.org/10.1101/050419

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