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PLoS One. 2015 Oct 16;10(10):e0140712. doi: 10.1371/journal.pone.0140712. eCollection 2015.

Analytical and Clinical Validation of a Digital Sequencing Panel for Quantitative, Highly Accurate Evaluation of Cell-Free Circulating Tumor DNA.

Author information

1
Department of Medical Affairs, Guardant Health, Inc., Redwood City, California, United States of America.
2
Department of Research and Bioinformatics, Guardant Health, Inc., Redwood City, California, United States of America.
3
Rainier Hematology Oncology, Northwest Medical Specialties, Puyallup, Washington, United States of America.
4
Department of Medicine, University of California San Francisco School of Medicine, San Francisco, California, United States of America.
5
Genesis Cancer Center, Hot Springs, Arkansas, United States of America.
6
Department of Molecular Oncology, John Wayne Cancer Institute at Saint John's Health Center, Santa Monica, California, United States of America.
7
Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America.
8
Department of Medicine, Division of Hematology-Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.
9
Department of Hematology and Medical Oncology, University Cancer and Blood Center, Athens, Georgia, United States of America.
10
Administration, Guardant Health, Inc., Redwood City, California, United States of America.
11
Department of Research and Bioinformatics, Guardant Health, Inc., Redwood City, California, United States of America; Administration, Guardant Health, Inc., Redwood City, California, United States of America.

Abstract

Next-generation sequencing of cell-free circulating solid tumor DNA addresses two challenges in contemporary cancer care. First this method of massively parallel and deep sequencing enables assessment of a comprehensive panel of genomic targets from a single sample, and second, it obviates the need for repeat invasive tissue biopsies. Digital Sequencing™ is a novel method for high-quality sequencing of circulating tumor DNA simultaneously across a comprehensive panel of over 50 cancer-related genes with a simple blood test. Here we report the analytic and clinical validation of the gene panel. Analytic sensitivity down to 0.1% mutant allele fraction is demonstrated via serial dilution studies of known samples. Near-perfect analytic specificity (> 99.9999%) enables complete coverage of many genes without the false positives typically seen with traditional sequencing assays at mutant allele frequencies or fractions below 5%. We compared digital sequencing of plasma-derived cell-free DNA to tissue-based sequencing on 165 consecutive matched samples from five outside centers in patients with stage III-IV solid tumor cancers. Clinical sensitivity of plasma-derived NGS was 85.0%, comparable to 80.7% sensitivity for tissue. The assay success rate on 1,000 consecutive samples in clinical practice was 99.8%. Digital sequencing of plasma-derived DNA is indicated in advanced cancer patients to prevent repeated invasive biopsies when the initial biopsy is inadequate, unobtainable for genomic testing, or uninformative, or when the patient's cancer has progressed despite treatment. Its clinical utility is derived from reduction in the costs, complications and delays associated with invasive tissue biopsies for genomic testing.

PMID:
26474073
PMCID:
PMC4608804
DOI:
10.1371/journal.pone.0140712
[Indexed for MEDLINE]
Free PMC Article
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