RT Journal Article
SR Electronic
T1 NGS-based assay for frequent newborn inherited diseases: from development to implementation
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 050419
DO 10.1101/050419
A1 T. Simakova
A1 A. Bragin
A1 M. Zaytseva
A1 C. Clemente
A1 M. Lewicka
A1 J.C. Machado
A1 J.L. Costa
A1 M. Hughes
A1 C. Hertz-Fowler
A1 N. Petrova
A1 A. Polyakov
A1 R. Zinchenko
A1 E. Kondratyeva
A1 A. Pavlov
YR 2016
UL http://biorxiv.org/content/early/2016/04/26/050419.abstract
AB 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.