Analytical Validation of the Next-Generation Sequencing Assay for a Nationwide Signal-Finding Clinical Trial: Molecular Analysis for Therapy Choice Clinical Trial

Chih Jian Lih, Robin D. Harrington, David J. Sims, Kneshay N. Harper, Courtney H. Bouk, Vivekananda Datta, Jonathan Yau, Rajesh R. Singh, Mark J. Routbort, Rajyalakshmi Luthra, Keyur P. Patel, Geeta S. Mantha, Savitri Krishnamurthy, Karyn Ronski, Zenta Walther, Karin E. Finberg, Sandra Canosa, Hayley Robinson, Amelia Raymond, Long P. LeLisa M. McShane, Eric Polley, Barbara A. Conley, James H. Doroshow, A. John Iafrate, Jeffrey L. Sklar, Stanley R. Hamilton, P. Mickey Williams

Research output: Contribution to journalArticle

44 Scopus citations

Abstract

The National Cancer Institute–Molecular Analysis for Therapy Choice (NCI-MATCH) trial is a national signal-finding precision medicine study that relies on genomic assays to screen and enroll patients with relapsed or refractory cancer after standard treatments. We report the analytical validation processes for the next-generation sequencing (NGS) assay that was tailored for regulatory compliant use in the trial. The Oncomine Cancer Panel assay and the Personal Genome Machine were used in four networked laboratories accredited for the Clinical Laboratory Improvement Amendments. Using formalin-fixed paraffin-embedded clinical specimens and cell lines, we found that the assay achieved overall sensitivity of 96.98% for 265 known mutations and 99.99% specificity. High reproducibility in detecting all reportable variants was observed, with a 99.99% mean interoperator pairwise concordance across the four laboratories. The limit of detection for each variant type was 2.8% for single-nucleotide variants, 10.5% for insertion/deletions, 6.8% for large insertion/deletions (gap ≥4 bp), and four copies for gene amplification. The assay system from biopsy collection through reporting was tested and found to be fully fit for purpose. Our results indicate that the NCI-MATCH NGS assay met the criteria for the intended clinical use and that high reproducibility of a complex NGS assay is achievable across multiple clinical laboratories. Our validation approaches can serve as a template for development and validation of other NGS assays for precision medicine.

Original languageEnglish (US)
Pages (from-to)313-327
Number of pages15
JournalJournal of Molecular Diagnostics
Volume19
Issue number2
DOIs
StatePublished - Mar 1 2017
Externally publishedYes

ASJC Scopus subject areas

  • Pathology and Forensic Medicine
  • Molecular Medicine

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    Lih, C. J., Harrington, R. D., Sims, D. J., Harper, K. N., Bouk, C. H., Datta, V., Yau, J., Singh, R. R., Routbort, M. J., Luthra, R., Patel, K. P., Mantha, G. S., Krishnamurthy, S., Ronski, K., Walther, Z., Finberg, K. E., Canosa, S., Robinson, H., Raymond, A., ... Williams, P. M. (2017). Analytical Validation of the Next-Generation Sequencing Assay for a Nationwide Signal-Finding Clinical Trial: Molecular Analysis for Therapy Choice Clinical Trial. Journal of Molecular Diagnostics, 19(2), 313-327. https://doi.org/10.1016/j.jmoldx.2016.10.007