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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 accessAbstract
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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“Moreover, ctDNA is readily detectable in lung cancer patient blood (20, 27, 29, 30), and sensitivity of variant detection was recently shown to be higher in ctDNA than CTCs (25).”
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Cites
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“This efficiency at 10ng input is at least double the theoretical efficiency of amplicon-based methods (e.g., BEAMing [78], TAM-Seq [27], etc) and at least 5 to greater than 10-fold the reported 3–13% efficiencies of ligation-based (e.g. highly optimized off-the-shelf next-generation sequencing kits [79]) genetic analy…”
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Intratumor Heterogeneity: Evolution through Space and Time
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“Temporal heterogeneity may occur by linear evolution or by competition between different subclones in the same tumor that compete with each other for dominance during the disease course or under pressure from targeted therapies [11].”
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“3-fold or longer compared to their previous line of therapy in 27% (95% CI, 17% to 38%) of tested patients [64].”
BackgroundCirculating Tumor Cells and Response to Chemotherapy in Metastatic Breast Cancer: SWOG S0500
Smerage, J. B., Barlow, W. E., Hortobágyi, G. N., Winer, E. P., Leyland-Jones, B. R., Srkalović, G., Tejwani, S., Schott, A. F., O’Rourke, M. A., Lew, D. L., et al. (2014) · Journal of Clinical Oncology · doi:10.1200/jco.2014.56.2561 · Cited by 649
Clonal competition with alternating dominance in multiple myeloma
Keats, J. J., Chesi, M., Egan, J. B., Garbitt, V. M., Palmer, S. E., Braggio, E., Wier, S. V., Blackburn, P. R., Baker, A. S., Dispenzieri, A. A., et al. (2012) · Blood · doi:10.1182/blood-2012-01-405985 · Cited by 636 · cited 1×
“that the initial biopsy genomics did not reveal the tumor subclone that ultimately drove mortality (secondary plasma cell leukemia) [63].”
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BackgroundPersonalized Medicine in a Phase I Clinical Trials Program: The MD Anderson Cancer Center Initiative
Tsimberidou, A. M., Iskander, N. G., Hong, D. S., Wheler, J. J., Falchook, G. S., Fu, S., Piha-Paul, S. A., Naing, A., Jankú, F., Luthra, R., et al. (2012) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-12-1627 · Cited by 538
Resistance to anti-EGFR therapy in colorectal cancer: From heterogeneity to convergent evolution
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BackgroundBEAMing: single-molecule PCR on microparticles in water-in-oil emulsions
Diehl, F., Li, M., He, Y., Kinzler, K. W., Vogelstein, B., & Dressman, D. C. (2006) · Nature Methods · doi:10.1038/nmeth898 · Cited by 496 · cited 2×
“This efficiency at 10ng input is at least double the theoretical efficiency of amplicon-based methods (e.g., BEAMing [78], TAM-Seq [27], etc) and at least 5 to greater than 10-fold the reported 3–13% efficiencies of ligation-based (e.g. highly optimized off-the-shelf next-generation sequencing kits [79]) genetic analy…”
BackgroundAssuring the quality of next-generation sequencing in clinical laboratory practice
Gargis, A. S., Kalman, L. V., Berry, M. W., Bick, D. P., Dimmock, D., Hambuch, T. M., Lu, F., Lyon, E., Voelkerding, K. V., Zehnbauer, B. A., et al. (2012) · Nature Biotechnology · doi:10.1038/nbt.2403 · Cited by 460
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“This figure is comparable to a previous study of a hotspot cfDNA assay for EGFRmutation in NSCLC—19% of invasive biopsy tissue samples were unusable because they were QNS or there was some technical problem [69].”
ResultDETECTION OF CIRCULATING TUMOR DNA IN EARLY AND LATE STAGE HUMAN MALIGNANCIES
Bettegowda, C., Sausen, M., Leary, R. J., Kinde, I., Agrawal, N., Bartlett, B. R., Wang, H., Luber, B. S., Kinzler, K. W., Vogelstein, B., et al. (2014) · Neuro-Oncology · doi:10.1093/neuonc/nou206.24 · Cited by 441
Amir, E., Miller, N., Geddie, W., Freedman, O., Kassam, F., Simmons, C., Oldfield, M., Dranitsaris, G., Tomlinson, G., Laupacis, A., et al. (2012) · Journal of Clinical Oncology · doi:10.1200/jco.2010.33.5232 · Cited by 434 · cited 1×
“In a study of advanced breast cancer, yield for molecular testing was even lower (36%) for biopsy samples from bone, the most common site of breast cancer metastasis [9].”
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“In metastatic breast cancer changing HER2 (coded by ERBB2 gene) status may occur in 24% of initially HER2 positive tumors which escape trastuzumab by mutating to HER2 negative [50].”
BackgroundIsolation and characterization of DNA from the plasma of cancer patients
Stroun, M., Anker, P., Lyautey, J., Lederrey, C., & Maurice, P. A. (1987) · European Journal of Cancer and Clinical Oncology · doi:10.1016/0277-5379(87)90266-5 · Cited by 373
The Implications of Clonal Genome Evolution for Cancer Medicine
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“With high sensitivity and the ultra-high specificity required to comprehensively sequence cfDNA, the Guardant360 test has the potential to evaluate the multiple genomic alterations cited in NCCN guidelines, to act as a “summary” of the different tumor clones in patients with tumor heterogeneity [34], to interrogate al…”
BackgroundTumor clone dynamics in lethal prostate cancer
Carreira, S., Romanel, A., GOODALL, J. C., Grist, E., Ferraldeschi, R., Miranda, S., Prandi, D., Lorente, D., Frenel, J., Pezaro, C. J., et al. (2014) · Science Translational Medicine · doi:10.1126/scitranslmed.3009448 · Cited by 344 · cited 1×
“Tumor sampling errors can occur because of genomically different sub-clones within the same primary tumor, between the primary tumor and its metastases, or between metastatic lesions [11,12].”
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Gazdar, A. F., Kurvari, V., Virmani, A. K., Gollahon, L., Sakaguchi, M., Westerfield, M., Kodagoda, D., Stasny, V., Cunningham, H. T., Wistuba, I. I., et al. (1998) · International Journal of Cancer · doi:10.1002/(sici)1097-0215(19981209)78:6 · Cited by 336
Use of Research Biopsies in Clinical Trials: Are Risks and Benefits Adequately Discussed?
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Cell-free DNA next-generation sequencing in pancreatobiliary carcinomas
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“In addition, this external validation study showed that 90% of mutations detected in tumor biopsies were also detected in cfDNA and that diagnostic test performance was consistent or better than reported here with cfDNA sensitivity of 92%, specificity 100% and diagnostic accuracy of 98% across five informative genes […”
ResultDrilon, A., Wang, L., Arcila, M. E., Balasubramanian, S., Greenbowe, J. R., Ross, J. S., Stephens, P., Lipson, D., Miller, V. A., Kris, M. G., et al. (2015) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-14-2683 · Cited by 274
Meta-analysis of multiple outcomes by regression with random effects
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Clinical next‐generation sequencing in patients with non–small cell lung cancer
Hagemann, I. S., Devarakonda, S. H. K., Lockwood, C. M., Spencer, D. H., Guebert, K., Bredemeyer, A. J., Al‐Kateb, H., Nguyen, T. T., Duncavage, E. J., Cottrell, C. E., et al. (2014) · Cancer · doi:10.1002/cncr.29089 · Cited by 232
Tsimberidou, A. M., Wen, S., Hong, D. S., Wheler, J. J., Falchook, G. S., Fu, S., Piha-Paul, S. A., Naing, A., Jankú, F., Aldape, K., et al. (2014) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-14-0603 · Cited by 210 · cited 1×
“8%, had a genomic alteration, which they attributed to the use of NGS to sequence a broader panel of genes [66].”
BackgroundUltrasound-Guided Liver Biopsy for Parenchymal Liver Disease (An Economic Analysis)
Younossi, Z. M., Teran, J. C., Ganiats, T. G., & Carey, W. D. (1998) · Digestive Diseases and Sciences · doi:10.1023/a:1018815802500 · Cited by 208 · cited 1×
“Unfortunately, invasive needle biopsies of visceral metastases are accompanied by complications including a 1–2% risk of hospitalization for hemorrhage after liver biopsy [56], or a 6.”
BackgroundValidation of Biomarker-based risk prediction models
Taylor, J. M. G., Ankerst, D., & Andridge, R. (2008) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-07-4534 · Cited by 207 · cited 1×
“These results are consistent with those of the current study and add a high level of evidence for clinical validity because in these two studies Guardant Health was blind to the external laboratories’ results [72].”
ResultBidard, F., Madic, J., Mariani, P., Piperno-Neumann, S., Rampanou, A., Servois, V., Cassoux, N., Desjardins, L., Milder, M., Vaucher, I., et al. (2013) · International Journal of Cancer · doi:10.1002/ijc.28436 · Cited by 202
Molecular Tumor Board: The University of California San Diego Moores Cancer Center Experience
Schwaederle, M. C., Parker, B. A., Schwab, R. B., Fanta, P. T., Boles, S. G., Daniels, G. A., Bazhenova, L. A., Subramanian, R., Coutinho, A., Ojeda‐Fournier, H., et al. (2014) · The Oncologist · doi:10.1634/theoncologist.2013-0405 · Cited by 196 · cited 1×
“In addition, this cfDNA panel dramatically reduces the total time from initial evaluation to treatment (TTT) of advanced cancer patients, by eliminating the time lost waiting for an invasive biopsy to be scheduled and performed, and for pathological material to be reviewed and qualified before NGS can be conducted [67…”
BackgroundGradishar, W. J., Anderson, B. O., Blair, S. L., Burstein, H. J., Cyr, A. E., ELIAS, A. D., Farrar, W. B., Forero, A., Giordano, S. H., Goldstein, L. J., et al. (2014) · Journal of the National Comprehensive Cancer Network · doi:10.6004/jnccn.2014.0058 · Cited by 187 · cited 1×
“The evolution of resistance and importance of adaptively managing treatment to changing genomic status has led to recommendation for repeat tissue biopsies when new metastatic and/or recurrent disease occurs in several cancers, including breast [53], non-small cell lung [1], colorectal [54] and melanoma [55].”
BackgroundKRAS and BRAF oncogenic mutations in MSS colorectal carcinoma progression
Oliveíra, C., Velho, S., Moutinho, C., Ferreira, A. M., Preto, A., Domingo, E., Capelinha, A. F., Duval, A., Hamelin, R., Machado, J. C., et al. (2006) · Oncogene · doi:10.1038/sj.onc.1209758 · Cited by 176 · cited 1×
“In colorectal cancer KRAS exons 12 and 13 mutations drive de novo or acquired resistance to anti-EGFR therapy [48] and KRAS and/or BRAF status may change with time between primary and metastatic lesions in colorectal cancer in 17% of patients [49].”
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“(11-105240), the Danish Council for Strategic Research (1309-00006B), the Novo Nordisk”
Background
Metadata
- 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
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2015-10-16
- Volume
- 10
- Issue
- 10
- Pages
- e0140712
- ISSN
- 1932-6203 (ISSN-L)
- 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
- 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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