TY - JOUR
T1 - Clinical investigational studies for validation of a next-generation sequencing in vitro diagnostic device for cystic fibrosis testing
AU - Grosu, Daniel S.
AU - Hague, Lynda
AU - Chelliserry, Manjula
AU - Kruglyak, Kristina M.
AU - Lenta, Ross
AU - Klotzle, Brandy
AU - San, Jonathan
AU - Goldstein, Wendy M.
AU - Moturi, Sharmili
AU - Devers, Patricia
AU - Woolworth, Julie
AU - Peters, Eric
AU - Elashoff, Barbara
AU - Stoerker, Jay
AU - Wolff, Daynna J.
AU - Friedman, Kenneth J.
AU - Highsmith, W. Edward
AU - Lin, Erick
AU - Ong, Frank S.
PY - 2014/6
Y1 - 2014/6
N2 - Purpose: Clinical investigational studies were conducted to demonstrate the accuracy and reproducibility of the Illumina MiSeqDx CF System, a next-generation sequencing (NGS) in vitro diagnostic device for cystic fibrosis testing. Methods: Two NGS assays-a Clinical Sequencing Assay (Sequencing Assay) and a 139-Variant Assay (Variant Assay)-were evaluated in both an Accuracy Study and a Reproducibility Study, with comparison to bi-directional Sanger sequencing and PCR as reference methods. For each study, positive agreement (PA), negative agreement (NA), and overall agreement (OA) were evaluated. Results: In the Accuracy Study, the Sequencing Assay achieved PA of 99.7% including the polyTG/polyT region and PA of 100% excluding the region. The Variant Assay achieved PA of 100%. NA and OA were >99.99% for both Assays. In the Reproducibility Study, the Sequencing Assay achieved PA of 99.2%; NA and OA were both 99.7%. The Variant Assay achieved PA of 99.8%; NA and OA were both 99.9%. Sample pass rates were 99.7% in both studies for both assays. Conclusion: This is the first systematic evaluation of a NGS platform for broad clinical use as an in vitro diagnostic, including accuracy validation with multiple reference methods and reproducibility validation at multiple clinical sites. These NGS-based Assays had accurate and reproducible results which were comparable to or better than other methods currently in clinical use for clinical genetic testing of cystic fibrosis.
AB - Purpose: Clinical investigational studies were conducted to demonstrate the accuracy and reproducibility of the Illumina MiSeqDx CF System, a next-generation sequencing (NGS) in vitro diagnostic device for cystic fibrosis testing. Methods: Two NGS assays-a Clinical Sequencing Assay (Sequencing Assay) and a 139-Variant Assay (Variant Assay)-were evaluated in both an Accuracy Study and a Reproducibility Study, with comparison to bi-directional Sanger sequencing and PCR as reference methods. For each study, positive agreement (PA), negative agreement (NA), and overall agreement (OA) were evaluated. Results: In the Accuracy Study, the Sequencing Assay achieved PA of 99.7% including the polyTG/polyT region and PA of 100% excluding the region. The Variant Assay achieved PA of 100%. NA and OA were >99.99% for both Assays. In the Reproducibility Study, the Sequencing Assay achieved PA of 99.2%; NA and OA were both 99.7%. The Variant Assay achieved PA of 99.8%; NA and OA were both 99.9%. Sample pass rates were 99.7% in both studies for both assays. Conclusion: This is the first systematic evaluation of a NGS platform for broad clinical use as an in vitro diagnostic, including accuracy validation with multiple reference methods and reproducibility validation at multiple clinical sites. These NGS-based Assays had accurate and reproducible results which were comparable to or better than other methods currently in clinical use for clinical genetic testing of cystic fibrosis.
KW - Clinical validation
KW - Cystic fibrosis
KW - In vitro diagnostics
KW - Next-generation sequencing
KW - Sequencing-by-synthesis
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U2 - 10.1586/14737159.2014.916618
DO - 10.1586/14737159.2014.916618
M3 - Article
C2 - 24844137
AN - SCOPUS:84901281950
VL - 14
SP - 605
EP - 622
JO - Expert Review of Molecular Diagnostics
JF - Expert Review of Molecular Diagnostics
SN - 1473-7159
IS - 5
ER -