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J Mol Diagn. 2017 Mar;19(2):313-327. doi: 10.1016/j.jmoldx.2016.10.007. Epub 2017 Feb 7.

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

Author information

1
Molecular Characterization and Clinical Assay Development Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland.
2
Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas.
3
Department of Pathology, School of Medicine, Yale University, New Haven, Connecticut.
4
Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts.
5
Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland.
6
Molecular Characterization and Clinical Assay Development Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland. Electronic address: mickey.williams@nih.gov.

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.

PMID:
28188106
PMCID:
PMC5397672
DOI:
10.1016/j.jmoldx.2016.10.007
[Indexed for MEDLINE]
Free PMC Article

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