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.
N1 - Funding Information:
DS Grosu, L Hague, M Chelliserry, KM Kruglyak, R Lenta, B Klotzle, J San, WM Goldstein, S Moturi, P Devers, E Lin and FS Ong are employees of Illumina, Inc. E Peters was a former employee of Illumina Inc. and is now an employee of Genentech, Inc. J Woolworth, B Elashoff, J Stoerker, DJ Wolff, KJ Friedman and WE Highsmith were in receipt of project funding from Illumina, Inc. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending or royalties.
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
UR - http://www.scopus.com/inward/record.url?scp=84901281950&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84901281950&partnerID=8YFLogxK
U2 - 10.1586/14737159.2014.916618
DO - 10.1586/14737159.2014.916618
M3 - Article
C2 - 24844137
AN - SCOPUS:84901281950
SN - 1473-7159
VL - 14
SP - 605
EP - 622
JO - Expert Review of Molecular Diagnostics
JF - Expert Review of Molecular Diagnostics
IS - 5
ER -