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


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.

SUBMITTER: Lih CJ 

PROVIDER: S-EPMC5397672 | biostudies-literature | 2017 Mar

REPOSITORIES: biostudies-literature

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

Lih Chih-Jian CJ   Harrington Robin D RD   Sims David J DJ   Harper Kneshay N KN   Bouk Courtney H CH   Datta Vivekananda V   Yau Jonathan J   Singh Rajesh R RR   Routbort Mark J MJ   Luthra Rajyalakshmi R   Patel Keyur P KP   Mantha Geeta S GS   Krishnamurthy Savitri S   Ronski Karyn K   Walther Zenta Z   Finberg Karin E KE   Canosa Sandra S   Robinson Hayley H   Raymond Amelia A   Le Long P LP   McShane Lisa M LM   Polley Eric C EC   Conley Barbara A BA   Doroshow James H JH   Iafrate A John AJ   Sklar Jeffrey L JL   Hamilton Stanley R SR   Williams P Mickey PM  

The Journal of molecular diagnostics : JMD 20170207 2


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 ne  ...[more]

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