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

View ORCID ProfileT. Simakova, A. Bragin, M. Zaytseva, C. Clemente, M. Lewicka, J.C. Machado, J.L. Costa, M. Hughes, C. Hertz-Fowler, N. Petrova, A. Polyakov, R. Zinchenko, E. Kondratyeva, A. Pavlov
doi: https://doi.org/10.1101/050419
T. Simakova
1Parseq Lab Company, Saint Petersburg, Russia
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A. Bragin
1Parseq Lab Company, Saint Petersburg, Russia
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M. Zaytseva
1Parseq Lab Company, Saint Petersburg, Russia
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C. Clemente
2Stab Vida Company, Caparica, Portugal
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M. Lewicka
2Stab Vida Company, Caparica, Portugal
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J.C. Machado
3Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal
4Institute of Molecular Pathology and Immunology (Ipatimup), University of Porto, Porto, Portugal
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J.L. Costa
3Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal
4Institute of Molecular Pathology and Immunology (Ipatimup), University of Porto, Porto, Portugal
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M. Hughes
5Centre for Genomic Research University of Liverpool, Liverpool, United Kingdom
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C. Hertz-Fowler
5Centre for Genomic Research University of Liverpool, Liverpool, United Kingdom
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N. Petrova
6Federal State Budgetary Institution “Research Centre for Medical Genetics”, Moscow, Russia
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A. Polyakov
6Federal State Budgetary Institution “Research Centre for Medical Genetics”, Moscow, Russia
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R. Zinchenko
6Federal State Budgetary Institution “Research Centre for Medical Genetics”, Moscow, Russia
7Pirogov Russian National Research Medical University, Moscow, Russia
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E. Kondratyeva
6Federal State Budgetary Institution “Research Centre for Medical Genetics”, Moscow, Russia
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A. Pavlov
1Parseq Lab Company, Saint Petersburg, Russia
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  • For correspondence: apavlov@parseq.pro
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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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Posted April 26, 2016.
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NGS-based assay for frequent newborn inherited diseases: from development to implementation
T. Simakova, A. Bragin, M. Zaytseva, C. Clemente, M. Lewicka, J.C. Machado, J.L. Costa, M. Hughes, C. Hertz-Fowler, N. Petrova, A. Polyakov, R. Zinchenko, E. Kondratyeva, A. Pavlov
bioRxiv 050419; doi: https://doi.org/10.1101/050419
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NGS-based assay for frequent newborn inherited diseases: from development to implementation
T. Simakova, A. Bragin, M. Zaytseva, C. Clemente, M. Lewicka, J.C. Machado, J.L. Costa, M. Hughes, C. Hertz-Fowler, N. Petrova, A. Polyakov, R. Zinchenko, E. Kondratyeva, A. Pavlov
bioRxiv 050419; doi: https://doi.org/10.1101/050419

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