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

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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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Background
Detection of Circulating Tumor DNA in Early- and Late-Stage Human Malignancies
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Accurate whole human genome sequencing using reversible terminator chemistry
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Method
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“Perhaps a modification of these revolutionary techniques will provide the ultimate method for diagnosing and treating all cancers since they all may well be a result of the presence of vital oncogenes [187].”
Method
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Singh, A. P., Li, S., & Cheng, H. (2017) · Annals of Translational Medicine · doi:10.21037/atm.2017.07.10 · Cited by 31
“Another issue with tissue genotyping is potential poor yield of specimen for extensive molecular testing which may be circumvented by using ctDNA analysis (7,12,13).”
Background
Liquid biopsy for brain metastases and leptomeningeal disease in patients with breast cancer
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“Median age, years (range) 56 (25-84) Disease stage, n = 109 (%)a”
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“Guardant360 sequenced 74 cancer-associated genes to identify somatic alterations. cfDNA was extracted from plasma, enriched for targeted regions, and sequenced using the Illumina platform and hg19 as the reference genome as previously described (Lanman et al. 2015; Odegaard et al. 2018).”
Method
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Piotrowska, Z., Hazar-Rethinam, M. H., Rizzo, C., Nadres, B., Seventer, E. E. V., Shahzade, H. A., Lennes, I. T., Iafrate, A. J., Dias-Santagata, D. C., Leshchiner, I., et al. (2018) · JCO Precision Oncology · doi:10.1200/po.17.00263 · Cited by 28
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“Postsequencing bioinformatics matches the complementary strands of each barcoded DNA fragment to remove false-positive results.(19) The variant allele fraction (VAF; %ctDNA) is calculated as the number of mutated DNA molecules divided by the total number (mutated plus wild type) of DNA fragments at that allele.”
Background
Next generation sequencing of cell free circulating tumor DNA in blood samples of recurrent and metastatic head and neck cancer patients
Porter, A., Natsuhara, M., Daniels, G. A., Patel, S. P., Sacco, A. G., Bykowski, J., Banks, K. C., & Cohen, E. E. W. (2020) · Translational Cancer Research · doi:10.21037/tcr.2019.12.70 · Cited by 28
“At the time of this study, the Guardant panel utilized hybrid capture and NGS of critical exons of 70 genes, reporting point mutations for all genes and indels, fusions, and copy number amplifications for select genes (Figure S1) (5).”
Method
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Yoshinami, T., Kagara, N., Motooka, D., Nakamura, S., Miyake, T., Tanei, T., Naoi, Y., Shimoda, M., Shimazu, K., Kim, S. J., et al. (2020) · Translational Oncology · doi:10.1016/j.tranon.2020.100787 · Cited by 28
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“org Clin Cancer Res; 27(17) September 1, 2021 4809”
BackgroundMethodInfluential
Clinical Impact of Detecting Low-Frequency Variants in Cell-Free DNA on Treatment of Castration-Resistant Prostate Cancer
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Consensus Recommendations to Optimize Testing for New Targetable Alterations in Non-Small Cell Lung Cancer
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Integrating Artificial Intelligence for Advancing Multiple-Cancer Early Detection via Serum Biomarkers: A Narrative Review
Wang, H., Lin, W.-Y., Zhou, C., Yang, Z., Kalpana, S., & Lebowitz, M. (2024) · Cancers · doi:10.3390/cancers16050862 · Cited by 31
“Targeted sequencing approaches include the exome sequencing [60], CAncer Personalized Profiling by deep Sequencing (CAPP-Seq) [61], and digital sequencing [62].”
Method
CirculatingBRAFV600E Cell-Free DNA as a Biomarker in the Management of Anaplastic Thyroid Carcinoma
Iyer, P. C., Cote, G. J., Hai, T., Gule-Monroe, M. K., Bui, J. H., Williams, M. D., Hess, K. R., Hofmann, M.-C. C., Dadu, R., Zafereo, M., et al. (2018) · JCO Precision Oncology · doi:10.1200/po.18.00173 · Cited by 28
Advances in Circulating Tumor DNA Analysis
Perakis, S. O., Auer, M., Belic, J., & Heitzer, E. (2017) · Advances in clinical chemistry · doi:10.1016/bs.acc.2016.11.005 · Cited by 28
Study of Preanalytic and Analytic Variables for Clinical Next-Generation Sequencing of Circulating Cell-Free Nucleic Acid
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Cell-free DNA as a post-treatment surveillance strategy: current status
Burgener, J., Rostami, A., Carvalho, D. D. D., & Bratman, S. V. (2017) · Seminars in Oncology · doi:10.1053/j.seminoncol.2018.01.009 · Cited by 26
The role of circulating free DNA in the management of NSCLC
Abate, R. E., Pasquale, R., Fenizia, F., Rachiglio, A. M., Roma, C., Bergantino, F., Forgione, L., Lambiase, M., Sacco, A., Piccirillo, M. C., et al. (2018) · Expert Review of Anticancer Therapy · doi:10.1080/14737140.2019.1548938 · Cited by 26
Development and validation of a targeted gene sequencing panel for application to disparate cancers
McCabe, M. J., Gauthier, M.-E. A., Chan, C., Thompson, T. J., Sousa, S. M. C. D., Puttick, C., Grady, J. P., Gayevskiy, V., Tao, J., Ying, K., et al. (2019) · Scientific Reports · doi:10.1038/s41598-019-52000-3 · Cited by 27
Concordance between TP53 alterations in blood and tissue: impact of time interval, biopsy site, cancer type and circulating tumor DNA burden
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“Digital sequencing (54–73 genes) was performed by Guardant Health, Inc. (Redwood City, CA, USA; Guardant360, www.guardanthealth.com/guardant360/) (Lanman et al., 2015).”
Identification of Somatically Acquired BRCA1/2 Mutations by cfDNA Analysis in Patients with Metastatic Breast Cancer
Vidula, N., Dubash, T. D., Lawrence, M. S., Simoneau, A., Niemierko, A., Blouch, E. L., Nagy, B., Roh, W., Chirn, B., Reeves, B. A., et al. (2020) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-20-0638 · Cited by 27
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“After the isolation of ctDNA by hybrid capture, the assay was performed using molecular barcoding and proprietary bioinformatics algorithms with massively parallel sequencing on an Illumina Hi-Seq 2500 platform in a single laboratory (Guardant Health; Redwood City, CA, USA) [17,18].”
BackgroundMethod
Targeting the FGF/FGFR axis and its co-alteration allies
Uehara, Y., Ikeda, S., Kim, K. H., Lim, H. J., Adashek, J. J., Persha, H. E., Okamura, R., Lee, S., Sicklick, J. K., Kato, S., et al. (2022) · ESMO Open · doi:10.1016/j.esmoop.2022.100647 · Cited by 27
“Median age (range), year 61 (21-82) Sex, n (%) Men 6 (37.”
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Lim, M., Franses, J. W., Imperial, R. J. L., Majeed, U., Tsai, J., & Hsiehchen, D. (2023) · Gastroenterology · doi:10.1053/j.gastro.2023.01.023 · Cited by 26
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Maxwell, K. N., Soucier-Ernst, D., Tahirović, E., Troxel, A. B., Clark, C., Feldman, M. D., Colameco, C., Kakrecha, B., Langer, M., Lieberman, D. B., et al. (2017) · Breast Cancer Research and Treatment · doi:10.1007/s10549-017-4257-x · Cited by 26
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“That study used the Gardant360 gene panel, which took days to test and had a reported detection limit of 0.1% [33].”
MethodInfluential
Minimal Residual Disease using a Plasma-Only Circulating Tumor DNA Assay to Predict Recurrence of Metastatic Colorectal Cancer Following Curative Intent Treatment
Parikh, A. R., Chee, B. H., Tsai, J., Rich, T. A., Price, K. S., Patel, S. A., Zhang, L., Ibrahim, F., Esquivel, M., Seventer, E. E. V., et al. (2024) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-23-3660 · Cited by 25
“As per methods described previously, cell-free DNA (cfDNA) was extracted from plasma using the Qiagen circulating nucleic acid kit (32).”
Method
Clinical utility of circulating cell-free DNA in advanced colorectal cancer
Pereira, A. A. L., Morelli, M. P., Overman, M. J., Kee, B. K., Fogelman, D. R., Vilar, E., Shureiqi, I., Raghav, K. P. S., Eng, C., Manuel, S., et al. (2017) · PLoS ONE · doi:10.1371/journal.pone.0183949 · Cited by 25
Enrichment and Analysis of ctDNA
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Assessment of Circulating Nucleic Acids in Cancer: From Current Status to Future Perspectives and Potential Clinical Applications
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Genomic Landscape of Advanced Solid Tumors in Circulating Tumor DNA and Correlation With Tissue Sequencing: A Single Institution's Experience
Gerratana, L., Movarek, M., Wehbe, F., Katam, N., Mahalingam, D., Donahue, J., Shah, A. N., Chae, Y. K., Mulcahy, M. F., Tsarwhas, D., et al. (2022) · JCO Precision Oncology · doi:10.1200/po.21.00289 · Cited by 25
Clinical utility of liquid biopsy-based companion diagnostics in the non-small-cell lung cancer treatment
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“Improvement of highly accurate panel assay such as the implementation of the molecular barcoding method [8, 55] enables us to detect ctDNA with extremely high specificity and sensitivity.”
Highly sensitive detection of DNA hypermethylation in melanoma cancer cells
Nesvet, J. C., Rizzi, G., & Wang, S. X. (2018) · Biosensors and Bioelectronics · doi:10.1016/j.bios.2018.10.018 · Cited by 25
“1% variant allelic fractions (Lanman et al., 2015; Mehrotra et al., 2017), but these techniques are expensive, time consuming, and require high read depth to ensure detection of small ratios of methylated DNA (Aravanis et al.”
Background
Total Number of Alterations in Liquid Biopsies Is an Independent Predictor of Survival in Patients With Advanced Cancers
Vu, P., Khagi, Y., Riviere, P. J., Goodman, A. M., & Kurzrock, R. (2020) · JCO Precision Oncology · doi:10.1200/po.19.00204 · Cited by 25
“A strength of our study is that we used sequencing technology that allows for the detection of %ctDNA at a low level with high sensitivity and high specificity.(21,24) In comparison, some prior studies have used low-depth sequencing, which is less capable of detecting ctDNA.”
BackgroundMethod
Prognostic utility of pre- and postoperative circulating tumor DNA liquid biopsies in patients with peritoneal metastases
Baumgartner, J. M., Riviere, P., Lanman, R. B., Kelly, K. J., Veerapong, J., Lowy, A. M., & Kurzrock, R. (2020) · Annals of Surgical Oncology · doi:10.1245/s10434-020-08331-x · Cited by 25
D3S-001 in advanced solid tumors with KRASG12C mutations: a phase 1 trial
Cho, B. C., Lü, S., Lee, M. A., Song, Z., Park, J., Lim, S. M., Li, Z., Zhao, J., Richardson, G. E., Zhang, Y., et al. (2025) · Nature Medicine · doi:10.1038/s41591-025-03688-6 · Cited by 24
“Germline alterations were excluded as previously described 35,36 .”
Circulating stromal cells in resectable pancreatic cancer correlates to pathological stage and predicts for poor clinical outcomes
Gardner, K. P., Aldakkak, M., Tang, C., Tsai, S., & Adams, D. L. (2021) · npj Precision Oncology · doi:10.1038/s41698-021-00161-8 · Cited by 23
Duplex-Repair enables highly accurate sequencing, despite DNA damage
Xiong, K., Shea, D., Rhoades, J., Blewett, T., Liu, R., Bae, J. H., Nguyen, E., Makrigiorgos, G. M., Golub, T. R., & Adalsteinsson, V. A. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab855 · Cited by 25
“1–1% variant allele fraction, down to ‘single duplex’ resolution) is important for studying cancer evolution (8) and drug resistance (9), understanding somatic mosaicism (10) and clonal hematopoiesis (11), characterizing base editing technologies (12), evaluating the mutagenicity of chemical compounds (13), uncovering…”
Background
Clinical utility of plasma-based digital next-generation sequencing in oncogene-driven non-small-cell lung cancer patients with tyrosine kinase inhibitor resistance
Zugazagoitia, J., Gómez‐Rueda, A., Lewintre, E. J., Isla, D., Camps, C., Ramos, I., Trigo, J. M., Bernabé, R., Juan, Ó., Sánchez-Torres, J. M., et al. (2019) · Lung Cancer · doi:10.1016/j.lungcan.2019.05.032 · Cited by 25
Therapeutic Actionability of Circulating Cell-Free DNA Alterations in Carcinoma of Unknown Primary
Kato, S., Weipert, C. M., Gumas, S., Okamura, R., Lee, S., Sicklick, J. K., Saam, J. R., & Kurzrock, R. (2021) · JCO Precision Oncology · doi:10.1200/po.21.00011 · Cited by 24
Genomic Profiling of Blood-Derived Circulating Tumor DNA from Patients with Colorectal Cancer: Implications for Response and Resistance to Targeted Therapeutics
Choi, I. S., Kato, S., Fanta, P. T., Leichman, L., Okamura, R., Raymond, V. M., Lanman, R. B., Lippman, S. M., & Kurzrock, R. (2019) · Molecular Cancer Therapeutics · doi:10.1158/1535-7163.mct-18-0965 · Cited by 23
“ctDNA was extracted from whole blood collected in 10mL Streck tubes, and 5–30 ng of ctDNA was prepared for sequencing as described previously (23).”
Method
Can integrative biomarker approaches improve prediction of platinum and PARP inhibitor response in ovarian cancer?
Funingana, I.-G., Reinius, M. A. V., Petrillo, A., Ang, J. E., & Brenton, J. D. (2021) · Seminars in Cancer Biology · doi:10.1016/j.semcancer.2021.02.008 · Cited by 23
Ultrasensitive Circulating Tumor DNA Pilot Study Distinguishes Complete Response and Partial Response With Immunotherapy in Patients With Metastatic Renal Cell Carcinoma
Chehrazi‐Raffle, A., Muddasani, R., Dizman, N., Hsu, J., Meza, L., Zengin, Z. B., Malhotra, J., Chawla, N. S., Dorff, T. B., Contente‐Cuomo, T., et al. (2023) · JCO Precision Oncology · doi:10.1200/po.22.00543 · Cited by 23
“8% of patients,(21) commensurate to rates seen in other tumor types.(22) Using TARDIS, a targeted tumor-informed approach, yielded higher assay sensitivity and specificity.”
Result
Ultra-short cell-free DNA fragments enhance cancer early detection in a multi-analyte blood test combining mutation, protein and fragmentomics
Wang, F., Li, X., Li, M., Liu, W., Lu, L., Li, Y., Chen, X., Yang, S., Liu, T., Cheng, W., et al. (2023) · Clinical Chemistry and Laboratory Medicine (CCLM) · doi:10.1515/cclm-2023-0541 · Cited by 23
“Circulating tumor DNA (ctDNA) carrying cancer speci ﬁ c mutations has proven to be a remarkable biomarker for cancer treatment selection, cancerprognosisandmonitoring[9 – 12].”
Background
High-Throughput and Sensitive Quantification of Circulating Tumor DNA by Microfluidic-Based Multiplex PCR and Next-Generation Sequencing
Guan, Y., Mayba, O., Sandmann, T., Lu, S., Choi, Y., Darbonne, W. C., Lévêque, V., Ryner, L. C., Humke, E. W., Tam, N. W. R., et al. (2017) · Journal of Molecular Diagnostics · doi:10.1016/j.jmoldx.2017.08.001 · Cited by 24
Circulating Tumor DNA in Non–Small-Cell Lung Cancer: A Primer for the Clinician
Singh, A. P., Cheng, H., Guo, X., Levy, B. P., & Halmos, B. (2017) · JCO Precision Oncology · doi:10.1200/po.17.00054 · Cited by 23
Multiplex Gene Profiling of Cell-Free DNA in Patients With Metastatic Melanoma for Monitoring Disease
Lin, S. Y., Huang, S. K., Huynh, K. T., Salomon, M. P., Chang, S., Marzese, D. M., Lanman, R. B., Talasaz, A. H., & Hoon, D. S. �. (2018) · JCO Precision Oncology · doi:10.1200/po.17.00225 · Cited by 23
Analysis of solid tumor mutation profiles in liquid biopsy
Andugulapati, S. B., Shanmugam, A., Chougule, A., Sridharan, S., Prabhash, K., Arya, A., Chaubey, A., Hariharan, A. K., Kolekar, P. S., Sen, M., et al. (2018) · Cancer Medicine · doi:10.1002/cam4.1791 · Cited by 22
Toward liquid biopsies in cancer treatment: application of circulating tumor DNA
Ahlborn, L. B., & Østrup, O. (2019) · Apmis · doi:10.1111/apm.12912 · Cited by 25
Clinical Application of Next-Generation Sequencing as A Liquid Biopsy Technique in Advanced Colorectal Cancer: A Trick or A Treat?
Kastrisiou, M., Zarkavelis, G., Pentheroudakis, G. E., & Magklara, A. (2019) · Cancers · doi:10.3390/cancers11101573 · Cited by 23
“The more recently launched Guardant360 digital sequencing technology, also used in a number of studies, has been strategically developed solely as a liquid assay since the beginning [43].”
Method
Correlation of Somatic Genomic Alterations Between Tissue Genomics and ctDNA Employing Next-Generation Sequencing: Analysis of Lung and Gastrointestinal Cancers
Toor, O. M., Ahmed, Z., Bahaj, W., Boda, U., Cummings, L. S., McNally, M. E., Kennedy, K. F., Pluard, T., Hussain, A., Subramanian, J., et al. (2018) · Molecular Cancer Therapeutics · doi:10.1158/1535-7163.mct-17-1015 · Cited by 22
Cabozantinib and Panitumumab for RAS Wild-Type Metastatic Colorectal Cancer
Strickler, J. H., Rushing, C. N., Uronis, H. E., Morse, M. A., Niedzwiecki, D., Blobe, G. C., Moyer, A. N., Bolch, E. K., Webb, R., Haley, S. T., et al. (2021) · The Oncologist · doi:10.1002/onco.13678 · Cited by 24
“Plasma-EDTA was collected from 24 evaluable patients prior to treatment and quantitatively evaluated using a digital next generation sequencing panel (Guardant360) [37].”
Method
Use of Circulating Cell-Free DNA to Guide Precision Medicine in Patients with Colorectal Cancer
Morris, V. K., & Strickler, J. H. (2021) · Annual Review of Medicine · doi:10.1146/annurev-med-070119-120448 · Cited by 23
Implementation of a Molecular Tumor Registry to Support the Adoption of Precision Oncology Within an Academic Medical Center: The Duke University Experience
Green, M. F., Bell, J. L., Hubbard, C. B., McCall, S. J., McKinney, M. S., Riedel, J., Menendez, C. S., Abbruzzese, J. L., Strickler, J. H., & Datto, M. (2021) · JCO Precision Oncology · doi:10.1200/po.21.00030 · Cited by 24
“Tumor tissue 6 (3-45) Time between MTB meeting and therapy change, days”
Background
Analytical and clinical validation of an amplicon-based next generation sequencing assay for ultrasensitive detection of circulating tumor DNA
Poh, J., Ngeow, K. C., Pek, M., Tan, K.-H., Lim, J. S., Chen, H., Ong, C. K., Lim, J. S., Lim, S. T., Lim, C. M., et al. (2022) · PLoS ONE · doi:10.1371/journal.pone.0267389 · Cited by 22
Integrating Biomarkers and Targeted Therapy Into Colorectal Cancer Management
Lieu, C. H., Corcoran, R. B., & Overman, M. J. (2019) · American Society of Clinical Oncology Educational Book · doi:10.1200/edbk_240839 · Cited by 22
Liquid Biopsy by Next-Generation Sequencing: a Multimodality Test for Management of Cancer
Achi, H. E., Khoury, J. D., & Loghavi, S. (2019) · Current Hematologic Malignancy Reports · doi:10.1007/s11899-019-00532-w · Cited by 22
血中遊離DNAにおける低頻度変異検出が去勢抵抗性前立腺癌の治療に与える影響
Mizuno, K. (2022) · Institutional Repositories DataBase (IRDB) · doi:10.14989/doctor.k23772 · Cited by 22
Cell-Free Tumor DNA Dominant Clone Allele Frequency Is Associated With Poor Outcomes in Advanced Biliary Cancers Treated With Platinum-Based Chemotherapy
Usón, P. L. S., Majeed, U., Yin, J., Botrus, G., Sonbol, M. B., Ahn, D. H., Starr, J. S., Jones, J. C., Babiker, H. M., Inabinett, S. R., et al. (2022) · JCO Precision Oncology · doi:10.1200/po.21.00274 · Cited by 21
“Analytical information, bioinformatics analysis, and Guardant360 database have been previously described.(15,16) Outcomes Assessments regarding response to therapy (complete response [CR], partial response [PR], stable disease, and disease progression) were retrospectively collected by review of patient’s charts.”
Method
Clonal evolution and expansion associated with therapy resistance and relapse of colorectal cancer
Anupriya, S., Chakraborty, A., & Patnaik, S. (2022) · Mutation Research/Reviews in Mutation Research · doi:10.1016/j.mrrev.2022.108445 · Cited by 22
Rechallenge with anti-EGFR therapy to extend the continuum of care in patients with metastatic colorectal cancer
Cremolini, C., Montagut, C. O., Ronga, P., Venturini, F., Yamaguchi, K., Stintzing, S., & Sobrero, A. F. (2023) · Frontiers in Oncology · doi:10.3389/fonc.2022.946850 · Cited by 22
Sequence-Based Platforms for Discovering Biomarkers in Liquid Biopsy of Non-Small-Cell Lung Cancer
Brockley, L. J., Souza, V. G. P., Forder, A., Pewarchuk, M. E., Erkan, M., Telkar, N., Benard, K., Trejo, J., Stewart, M. D., Stewart, G. L., et al. (2023) · Cancers · doi:10.3390/cancers15082275 · Cited by 22
Deep Learning-Based, Multiclass Approach to Cancer Classification on Liquid Biopsy Data
Jopek, M. A., Pastuszak, K., Cygert, S., Best, M. G., Wurdinger, T. D., Jassem, J., Zaczek, A. J., & Supernat, A. M. (2024) · IEEE Journal of Translational Engineering in Health and Medicine · doi:10.1109/jtehm.2024.3360865 · Cited by 21
The Pursuit of Noninvasive Diagnosis of Lung Cancer
Atwater, T., Cook, C., & Massion, P. P. (2016) · Seminars in Respiratory and Critical Care Medicine · doi:10.1055/s-0036-1592314 · Cited by 20
Duplex Proximity Sequencing (Pro-Seq): A method to improve DNA sequencing accuracy without the cost of molecular barcoding redundancy
Pel, J., Choi, W. W. Y., Leung, A. O., Shibahara, G., Gelinas, L., Despotovic, M., Ung, W. L., & Marziali, A. (2018) · PLoS ONE · doi:10.1371/journal.pone.0204265 · Cited by 21
The Role of ctDNA and Liquid Biopsy in the Diagnosis and Monitoring of Head and Neck Cancer: Towards Precision Medicine
Nassar, S. I., Suk, A., Nguyen, S. A., Adilbay, D., Pang, J., & Nathan, C. O. (2024) · Cancers · doi:10.3390/cancers16183129 · Cited by 21
“In addition to NGS of plasma having a higher sensitivity in the detection of genetic mutations than NGS of tumor tissue, it is also less invasive [108,109].”
Background
Detection of Circulating Tumor DNA in Liquid Biopsy: Current Techniques and Potential Applications in Melanoma
Martínez-Vila, C., Teixidó, C., Aya, F., Martín, R., González‐Navarro, E. A., Alós, L., de Anta, N. C., & Arance, A. M. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms26020861 · Cited by 22
“Guardant360 ® CDx utilizes cfDNA from plasma of peripheral whole blood collected in two 10 mL streck cfDNA blood collection tubes [58].”
Circulating Cell-Free Tumor DNA in Advanced Pancreatic Adenocarcinoma Identifies Patients With Worse Overall Survival
Botrus, G., Usón, P. L. S., Raman, P., Kaufman, A. E., Kosiorek, H., Yin, J., Fu, Y., Majeed, U., Sonbol, M. B., Ahn, D. H., et al. (2022) · Frontiers in Oncology · doi:10.3389/fonc.2021.794009 · Cited by 20
Identification of KRASG12C Mutations in Circulating Tumor DNA in Patients With Cancer
Thein, K. Z., Biter, A. B., Banks, K. C., Duda, A. W., Saam, J. R., Roszik, J., Jankú, F., Skoulidis, F., Heymach, J. V., Kopetz, S., et al. (2022) · JCO Precision Oncology · doi:10.1200/po.21.00547 · Cited by 20
“ctDNA Analysis The Guardant360 assay, which has been certified by Clinical Laboratory Improvement Amendments, the College of American Pathology, and the state of New York, was performed on plasma as previously described.(19,20) Over the time frame of this analysis, multiple iterations of the test were used, and all it…”
Method
Tepotinib in patients with non-small cell lung cancer with high-level MET amplification detected by liquid biopsy: VISION Cohort B
Le, X., Paz-Ares, L. G., van Meerbeeck, J. P., Viteri, S., Galvez, C. C., Smit, E. F., Garassino, M. C., Veillon, R., Baz, D. V., Pradera, J. F., et al. (2023) · Cell Reports Medicine · doi:10.1016/j.xcrm.2023.101280 · Cited by 20
“48,49 Therefore, ctDNA-based analysis may select a poorer prognostic group of patients compared with tissue-based screening.”
Background
New insights in non-small-cell lung cancer: circulating tumor cells and cell-free DNA
Duréndez-Saéz, E., Azkárate, A., Meri-Abad, M., Fariñas, S. C., Aguilar-Gallardo, C., Blasco, A., Lewintre, E. J., & Camps, C. (2017) · Journal of Thoracic Disease · doi:10.21037/jtd.2017.06.112 · Cited by 19
“Another NGS technique is digital sequencing, in where each strand of a double-stranded cfDNA molecule is individually tagged, to allow custom software to compare the two complementary strands and to minimize the errors that occur during library preparation or in the sequencing phase (68).”
Method
Detection of somatic variants and EGFR mutations in cell-free DNA from non-small cell lung cancer patients by ultra-deep sequencing using the ion ampliseq cancer hotspot panel and droplet digital polymerase chain reaction
Sung, J. S., Chong, H., Kwon, N., Kim, H. M., Lee, J. W., Kim, B., Lee, S. B., Park, C. W., Choi, J. Y., Chang, W. J., et al. (2017) · Oncotarget · doi:10.18632/oncotarget.22456 · Cited by 20
Detection of ERBB2 (HER2) Gene Amplification Events in Cell-Free DNA and Response to Anti-HER2 Agents in a Large Asian Cancer Patient Cohort
Lee, J., Franovic, A., Shiotsu, Y., Kim, S. T., Kim, K.-M., Banks, K. C., Raymond, V. M., & Lanman, R. B. (2019) · Frontiers in Oncology · doi:10.3389/fonc.2019.00212 · Cited by 22
“Analytic and clinical validation of the assay has been previously reported (18, 19).”
BackgroundMethod
Analytical validation of the Target Selector ctDNA platform featuring single copy detection sensitivity for clinically actionable EGFR, BRAF, and KRAS mutations
Poole, J. C., Wu, S., Lu, T. T., Vibat, C. R. T., Pham, A., Samuëlsz, E., Patel, M., Chen, J. W., Daher, T., Singh, V., et al. (2019) · PLoS ONE · doi:10.1371/journal.pone.0223112 · Cited by 19
Cell-Free Circulating Tumour DNA Blood Testing to Detect EGFR T790M Mutation in People With Advanced Non-Small Cell Lung Cancer: A Health Technology Assessment.
(2020) · PubMed Central · Cited by 20
Erratum to: Comparative clinical utility of tumor genomic testing and cell-free DNA in metastatic breast cancer
Maxwell, K. N., Soucier-Ernst, D., Tahirović, E., Troxel, A. B., Clark, C., Feldman, M. D., Colameco, C., Kakrecha, B., Langer, M., Lieberman, D. B., et al. (2017) · Breast Cancer Research and Treatment · doi:10.1007/s10549-017-4339-9 · Cited by 20
Comprehensive targeted super-deep next generation sequencing enhances differential diagnosis of solitary pulmonary nodules
Ye, M., Li, S., Huang, W., Wang, C., Liu, L., Liu, J., Liu, J., Pan, H., Deng, Q., Tang, H., et al. (2018) · Journal of Thoracic Disease · doi:10.21037/jtd.2018.04.09 · Cited by 19
CLAmp‐seq: A Novel Amplicon‐Based NGS Assay with Concatemer Error Correction for Improved Detection of Actionable Mutations in Plasma cfDNA from Patients with NSCLC
Wang, L., Hu, X., Guo, Q., Huang, X., Lin, C., Chen, X., Li, M., Yao, Q., Zhou, Q., Wang, J., et al. (2019) · Small Methods · doi:10.1002/smtd.201900357 · Cited by 19
Clinical and biological determinants of circulating tumor DNA detection and prognostication using a next-generation sequencing panel assay
Hsiehchen, D., Espinoza, M., Gerber, D. E., & Beg, M. S. (2021) · Cancer Biology & Therapy · doi:10.1080/15384047.2021.1963166 · Cited by 19
Elevated serum CEA is associated with liver metastasis and distinctive circulating tumor DNA alterations in patients with castration‐resistant prostate cancer
Bray, A. W., Duan, R., Malalur, P. G., Drusbosky, L. M., Gourdin, T. S., Hill, E. G., & Lilly, M. B. (2022) · The Prostate · doi:10.1002/pros.24400 · Cited by 19
“While genetic profiling of individual cancers is conventionally performed via solid tissue biopsy, this technique is subject to sampling bias and may fail to capture the predominant driver mutations in clonally diverse cancers.(7) To circumvent this issue, we utilized circulating tumor DNA (ctDNA) analysis that is an…”
Method
Feasibility and clinical value of circulating tumor DNA testing in patients with gastric adenocarcinomas
Iqbal, M., Roberts, A., Starr, J. S., Mody, K., & Kasi, P. M. (2019) · Journal of Gastrointestinal Oncology · doi:10.21037/jgo.2019.01.14 · Cited by 18
“Analytic and clinical validation has been previously reported (7).”
BackgroundMethod
Identification of osimertinib-resistant EGFR L792 mutations by cfDNA sequencing: oncogenic activity assessment and prevalence in large cfDNA cohort
Fairclough, S. R., Kiedrowski, L. A., Lin, J. J., Zelichov, O., Tarcic, G., Stinchcombe, T. E., Odegaard, J. I., Lanman, R. B., Shaw, A. T., & Nagy, R. J. (2019) · Experimental Hematology and Oncology · doi:10.1186/s40164-019-0148-7 · Cited by 19
Technological considerations for genome-guided diagnosis and management of cancer
Lennon, N. J., Adalsteinsson, V. A., & Gabriel, S. (2016) · Genome Medicine · doi:10.1186/s13073-016-0370-4 · Cited by 19
“For liquid biopsies, these tests are commonly run at far greater read depths (>5000× mean coverage) and require use of molecular barcodes to achieve acceptable sensitivity and specificity for samples with low (<5 %) tumor purity [5, 35].”
BackgroundMethod
A Phase II Study Investigating Cabozantinib in Patients with Refractory Metastatic Colorectal Cancer (AGICC 17CRC01)
Scott, A. J., Basu Mallick, A., Dotan, E., Cohen, S. J., Gold, P. J., Hochster, H. S., Subramaniam, S., Barzi, A., Watts, G. S., Blatchford, P. J., et al. (2022) · Cancer Research Communications · doi:10.1158/2767-9764.crc-22-0169 · Cited by 18
“While there are several blood-based assays commercially available to molecularly characterize tumors and monitor response via ctDNA, data on how to utilize these technologies as a predictive tool are limited (37).”
Background
Prevalence and Spectrum of AR Ligand-Binding Domain Mutations Detected in Circulating-Tumor DNA Across Disease States in Men With Metastatic Castration-Resistant Prostate Cancer
Antonarakis, E. S., Zhang, N. J., Saha, J., Nevalaita, L., Ikonen, T., Tsai, J., Garratt, C., & Fizazi, K. S. (2024) · JCO Precision Oncology · doi:10.1200/po.23.00330 · Cited by 18
“28,29 The Guardant360 assay reports a targeted gene panel of up to 83 genes during the study period.”
Accuracy of analysis of cfDNA for detection of single nucleotide variants and copy number variants in breast cancer
Yang, X., Zhang, K., Zhang, C., Peng, R., & Sun, C. (2019) · BMC Cancer · doi:10.1186/s12885-019-5698-x · Cited by 18
“many disadvantages in this method, since it is invasive and repeated biopsies often yield variable results owing to intra-tumor heterogeneity [19].”
Background
eVIDENCE: a practical variant filtering for low-frequency variants detection in cell-free DNA
Mizuno, K., Akamatsu, S., Sumiyoshi, T., Wong, J. H., Fujita, M., Maejima, K., Nakano, K., Ono, A., Aikata, H., Ueno, M., et al. (2019) · Scientific Reports · doi:10.1038/s41598-019-51459-4 · Cited by 17
Circulating tumour DNA characterisation of invasive lobular carcinoma in patients with metastatic breast cancer
Davis, A. A., Gerratana, L., Clifton, K., Medford, A. J., Velimirovic, M., Hensing, W. L., Bucheit, L. A., Shah, A. N., D’Amico, P., Reduzzi, C., et al. (2022) · EBioMedicine · doi:10.1016/j.ebiom.2022.104316 · Cited by 18
Cyclin-Dependent Kinase 4/6 Inhibitors Beyond Progression in Metastatic Breast Cancer: A Retrospective Real-World Biomarker Analysis
Gerratana, L., Davis, A. A., Velimirovic, M., Reduzzi, C., Clifton, K., Bucheit, L. A., Hensing, W. L., Shah, A. N., Pivetta, T., Dai, C. S., et al. (2023) · JCO Precision Oncology · doi:10.1200/po.22.00531 · Cited by 18
Efficient diagnosis of cancer using biosensing of circulating tumor DNAs(ctDNA): Recent progress and challenges
Farshchi, F., & Hasanzadeh, M. (2023) · Microchemical Journal · doi:10.1016/j.microc.2023.109076 · Cited by 18
Use of Low-Frequency Driver Mutations Detected by Cell-Free Circulating Tumor DNA to Guide Targeted Therapy in Non–Small-Cell Lung Cancer: A Multicenter Case Series
Jacobs, M. T., Mohindra, N. A., Shantzer, L., Chen, I. L., Phull, H. S., Mitchell, W., Raymond, V. M., Banks, K. C., Nagy, R. J., Lanman, R. B., et al. (2018) · JCO Precision Oncology · doi:10.1200/po.17.00318 · Cited by 18
IL-6 predicts CDK4/6 inhibitor resistance, identifying STAT3 as a target in HR + /HER2-negative metastatic breast cancer
Kettner, N. M., Bui, T. N., Navarro-Yepes, J., Ghotbaldini, S., Quintela, B., Luo, C. K., Lam, N., Rao, X., Raghavendra, A. S., Wang, Y., et al. (2025) · npj Precision Oncology · doi:10.1038/s41698-025-01041-1 · Cited by 21
Genetic features and therapeutic relevance of emergent circulating tumor DNA alterations in refractory non-colorectal gastrointestinal cancers
Hsiehchen, D., Bucheit, L. A., Yang, D., Beg, M. S., Lim, M., Lee, S. S., Kasi, P. M., Kaseb, A. O., & Zhu, H. (2022) · Nature Communications · doi:10.1038/s41467-022-35144-1 · Cited by 18
Targeted Next-Generation Sequencing in Men with Metastatic Prostate Cancer: a Pilot Study
Barata, P. C., Mendiratta, P., Heald, B., Klek, S., Grivas, P. D., Sohal, D. P. S., & Garcia, J. A. (2018) · Targeted Oncology · doi:10.1007/s11523-018-0576-z · Cited by 17

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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