Cited by 701Cancer Genomics and DiagnosticsPrenatal Screening and DiagnosticsBRCA gene mutations in cancer

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

Open access

Lanman, Richard B., Mortimer, Stefanie A., Zill, Oliver A., Sebisanovic, Dragan, Lopez, Rene, Blau, Sibel, Collisson, Eric A., Divers, Stephen G., Hoon, Dave S. B., Kopetz, E. Scott, Lee, Jeeyun, Nikolinakos, Petros G., Baca, Arthur M., Kermani, Bahram G., Eltoukhy, Helmy, Talasaz, AmirAli·2015·PLoS ONE

DOI 10.1371/journal.pone.0140712PMC PMC4608804

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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.

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Additional file 12 of A novel virtual barcode strategy for accurate panel-wide variant calling in circulating tumor DNA
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Additional file 14 of A novel virtual barcode strategy for accurate panel-wide variant calling in circulating tumor DNA
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Additional file 11 of A novel virtual barcode strategy for accurate panel-wide variant calling in circulating tumor DNA
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Additional file 10 of A novel virtual barcode strategy for accurate panel-wide variant calling in circulating tumor DNA
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Additional file 13 of A novel virtual barcode strategy for accurate panel-wide variant calling in circulating tumor DNA
Wu, L., Deng, Q., Xu, Z., Zhou, S., Li, C., & Li, Y. (2020) · Figshare · doi:10.6084/m9.figshare.12082254
Additional file 15 of A novel virtual barcode strategy for accurate panel-wide variant calling in circulating tumor DNA
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Additional file 5 of A novel virtual barcode strategy for accurate panel-wide variant calling in circulating tumor DNA
Wu, L., Deng, Q., Xu, Z., Zhou, S., Li, C., & Li, Y.-X. (2020) · Figshare · doi:10.6084/m9.figshare.12082278
Additional file 6 of A novel virtual barcode strategy for accurate panel-wide variant calling in circulating tumor DNA
Wu, L., Deng, Q., Xu, Z., Zhou, S., Li, C., & Li, Y.-X. (2020) · Figshare · doi:10.6084/m9.figshare.12082281
Additional file 16 of A novel virtual barcode strategy for accurate panel-wide variant calling in circulating tumor DNA
Wu, L., Deng, Q., Xu, Z., Zhou, S., Li, C., & Li, Y.-X. (2020) · Figshare · doi:10.6084/m9.figshare.12082263
Additional file 3 of A novel virtual barcode strategy for accurate panel-wide variant calling in circulating tumor DNA
Wu, L., Deng, Q., Xu, Z., Zhou, S., Li, C., & Li, Y.-X. (2020) · Figshare · doi:10.6084/m9.figshare.12082272
Additional file 9 of A novel virtual barcode strategy for accurate panel-wide variant calling in circulating tumor DNA
Wu, L., Deng, Q., Xu, Z., Zhou, S., Li, C., & Li, Y.-X. (2020) · Figshare · doi:10.6084/m9.figshare.12082290
Additional file 2 of A novel virtual barcode strategy for accurate panel-wide variant calling in circulating tumor DNA
Wu, L., Deng, Q., Xu, Z., Zhou, S., Li, C., & Li, Y.-X. (2020) · Figshare · doi:10.6084/m9.figshare.12082269
Additional file 1 of A novel virtual barcode strategy for accurate panel-wide variant calling in circulating tumor DNA
Wu, L., Deng, Q., Xu, Z., Zhou, S., Li, C., & Li, Y.-X. (2020) · Figshare · doi:10.6084/m9.figshare.12082266
Additional file 7 of A novel virtual barcode strategy for accurate panel-wide variant calling in circulating tumor DNA
Wu, L., Deng, Q., Xu, Z., Zhou, S., Li, C., & Li, Y.-X. (2020) · Figshare · doi:10.6084/m9.figshare.12082284
Additional file 4 of A novel virtual barcode strategy for accurate panel-wide variant calling in circulating tumor DNA
Wu, L., Deng, Q., Xu, Z., Zhou, S., Li, C., & Li, Y.-X. (2020) · Figshare · doi:10.6084/m9.figshare.12082275
Additional file 8 of A novel virtual barcode strategy for accurate panel-wide variant calling in circulating tumor DNA
Wu, L., Deng, Q., Xu, Z., Zhou, S., Li, C., & Li, Y.-X. (2020) · Figshare · doi:10.6084/m9.figshare.12082287
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Authors: Lanman, R. B., Mortimer, S. A., Zill, O. A., Sebisanovic, D., Lopez, R., Blau, S., Collisson, E. A., Divers, S. G., Hoon, D. S. B., Kopetz, E. S., Lee, J., Nikolinakos, P. G., Baca, A. M., Kermani, B. G., Eltoukhy, H., & Talasaz, A.
Affiliations: Guardant (United States) (US)
Northwest Medical Specialties (US)
University of California, San Francisco (US)
Saint John's Health Center (US)
Samsung Medical Center (KR)
University Cancer and Blood Center (US)
Corresponding author: Lanman, Richard B.
Talasaz, AmirAli
ORCID: Lanman, Richard B.
Mortimer, Stefanie A.
Zill, Oliver A.
Blau, Sibel
Collisson, Eric A.
Hoon, Dave S. B.
Lee, Jeeyun
Talasaz, AmirAli
Venue: PLoS ONE
Publisher: Public Library of Science (PLoS)
Published: 2015-10-16
Volume: 10
Issue: 10
Pages: e0140712
ISSN: 1932-6203 (ISSN-L)
DOI: 10.1371/journal.pone.0140712
PMC: PMC4608804
OpenAlex: W1864344361
Cited by: 695
References: 79
Citations by year: 2026: 24 · 2025: 46 · 2024: 40 · 2023: 66 · 2022: 57 · 2021: 60 · 2020: 82 · 2019: 92 · 2018: 102 · 2017: 91 · 2016: 31 · 2015: 3
FWCI: 25.02
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by
creativecommons.org/licenses/by/4.0/ (vor)
Locations: PLoS ONE (publishedVersion, cc-by)
Europe PMC (PubMed Central) (publishedVersion, cc-by)
PubMed Central (publishedVersion, cc-by)
PubMed (publishedVersion)
DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
eScholarship (California Digital Library) (submittedVersion, cc-by)
Figshare (submittedVersion, cc-by)
Funders: National Cancer Institute (P30CA016672)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
Health Sciences › Medicine › Pediatrics, Perinatology and Child Health › Prenatal Screening and Diagnostics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › BRCA gene mutations in cancer
Keywords: circulating tumor DNA, cell-free DNA, liquid biopsy, cancer gene panel, clinical validation, mutant allele fraction, solid tumors, biopsy alternative
MeSH terms: DNA, Neoplasm, Female, Humans, Male, Neoplasms, High-Throughput Nucleotide Sequencing

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

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