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Visser E, de Kock R, Genet S, Borne BVD, Soud MYE, Belderbos H, Stege G, de Saegher M, ’t Westeinde SV, Broeren M, Eduati F, Deiman B, Scharnhorst V. Up-front mutation detection in circulating tumor DNA by droplet digital PCR has added diagnostic value in lung cancer. Transl Oncol 2022; 27:101589. [PMID: 36413862 PMCID: PMC9679361 DOI: 10.1016/j.tranon.2022.101589] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/28/2022] [Accepted: 11/11/2022] [Indexed: 11/21/2022] Open
Abstract
Identification of actionable mutations in advanced stage non-squamous non-small-cell lung cancer (NSCLC) patients is recommended by guidelines as it enables treatment with targeted therapies. In current practice, mutations are identified by next-generation sequencing of tumor DNA (tDNA-NGS), which requires tissue biopsies of sufficient quality. Alternatively, circulating tumor DNA (ctDNA) could be used for mutation analysis. This prospective, multicenter study establishes the diagnostic value of ctDNA analysis by droplet digital PCR (ctDNA-ddPCR) in patients with primary lung cancer. CtDNA from 458 primary lung cancer patients was analyzed using a panel of multiplex ddPCRs for EGFR (Ex19Del, G719S, L858R, L861Q and S768I), KRAS G12/G13 and BRAF V600 mutations. For 142 of 175 advanced stage non-squamous NSCLC patients tDNA-NGS results were available to compare to ctDNA-ddPCR. tDNA-NGS identified 98 mutations, of which ctDNA-ddPCR found 53 mutations (54%), including 32 of 45 (71%) targetable driver mutations. In 2 of these 142 patients, a mutation was found by ctDNA-ddPCR only. In 33 advanced stage patients lacking tDNA-NGS results, ctDNA-ddPCR detected 15 additional mutations, of which 7 targetable. Overall, ctDNA-ddPCR detected 70 mutations and tDNA-NGS 98 mutations in 175 advanced NSCLC patients. Using an up-front ctDNA-ddPCR strategy, followed by tDNA-NGS only if ctDNA-ddPCR analysis is negative, increases the number of mutations found from 98 to 115 (17%). At the same time, up-front ctDNA-ddPCR reduces tDNA-NGS analyses by 40%, decreasing the need to perform (additional) biopsies.
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Affiliation(s)
- Esther Visser
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands,Catharina Hospital Eindhoven, Eindhoven, the Netherlands,Máxima Medical Center, Eindhoven, Veldhoven, the Netherlands,Expert Center Clinical Chemistry Eindhoven, Eindhoven, the Netherlands,Corresponding author at: Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands.
| | - Remco de Kock
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands,Catharina Hospital Eindhoven, Eindhoven, the Netherlands,Máxima Medical Center, Eindhoven, Veldhoven, the Netherlands,Expert Center Clinical Chemistry Eindhoven, Eindhoven, the Netherlands
| | - Sylvia Genet
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands,Catharina Hospital Eindhoven, Eindhoven, the Netherlands,Expert Center Clinical Chemistry Eindhoven, Eindhoven, the Netherlands,Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, the Netherlands
| | | | | | | | | | | | | | - Maarten Broeren
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands,Máxima Medical Center, Eindhoven, Veldhoven, the Netherlands,Expert Center Clinical Chemistry Eindhoven, Eindhoven, the Netherlands
| | - Federica Eduati
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands,Expert Center Clinical Chemistry Eindhoven, Eindhoven, the Netherlands,Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, the Netherlands,Eindhoven Artificial Intelligence Systems Institute, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Birgit Deiman
- Catharina Hospital Eindhoven, Eindhoven, the Netherlands,Expert Center Clinical Chemistry Eindhoven, Eindhoven, the Netherlands
| | - Volkher Scharnhorst
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands,Catharina Hospital Eindhoven, Eindhoven, the Netherlands,Expert Center Clinical Chemistry Eindhoven, Eindhoven, the Netherlands,Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, the Netherlands,Eindhoven Artificial Intelligence Systems Institute, Eindhoven University of Technology, Eindhoven, the Netherlands
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Ren Y, Cao L, You M, Ji J, Gong Y, Ren H, Xu F, Guo H, Hu J, Li Z. “SMART” digital nucleic acid amplification technologies for lung cancer monitoring from early to advanced stages. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Riudavets M, Lamberts V, Vasseur D, Auclin E, Aldea M, Jovelet C, Naltet C, Lavaud P, Gazzah A, Aboubakar F, Dorta M, Remon J, Rouleau E, Ngocamus M, Nicotra C, Lacroix L, Besse B, Mezquita L, Planchard D. Clinical utility and outcomes impact of crystal digital PCR of sensitizing and resistance EGFR mutations in patients with advanced non-small cell lung cancer. Clin Lung Cancer 2022; 23:e377-e383. [DOI: 10.1016/j.cllc.2022.05.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 04/05/2022] [Accepted: 05/02/2022] [Indexed: 11/03/2022]
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Tan LL, Loganathan N, Agarwalla S, Yang C, Yuan W, Zeng J, Wu R, Wang W, Duraiswamy S. Current commercial dPCR platforms: technology and market review. Crit Rev Biotechnol 2022; 43:433-464. [PMID: 35291902 DOI: 10.1080/07388551.2022.2037503] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Digital polymerase chain reaction (dPCR) technology has provided a new technique for molecular diagnostics, with superior advantages, such as higher sensitivity, precision, and specificity over quantitative real-time PCRs (qPCR). Eight companies have offered commercial dPCR instruments: Fluidigm Corporation, Bio-Rad, RainDance Technologies, Life Technologies, Qiagen, JN MedSys Clarity, Optolane, and Stilla Technologies Naica. This paper discusses the working principle of each offered dPCR device and compares the associated: technical aspects, usability, costs, and current applications of each dPCR device. Lastly, up-and-coming dPCR technologies are also presented, as anticipation of how the dPCR device landscape may likely morph in the next few years.
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Affiliation(s)
- Li Ling Tan
- Singapore Institute of Manufacturing Technology, Singapore, Singapore.,Materials Science and Engineering School, Nanyang Technological University, Singapore, Singapore
| | - Nitin Loganathan
- Singapore Institute of Manufacturing Technology, Singapore, Singapore
| | - Sushama Agarwalla
- Department of Chemical Engineering, Indian Institute of Technology Hyderabad, Hyderabad, India
| | - Chun Yang
- Mechanical and Aerospace Engineering School, Nanyang Technological University, Singapore, Singapore
| | - Weiyong Yuan
- Faculty of Materials & Energy, Institute for Clean Energy and Advanced Materials, Southwest University, Chongqing, China.,Chongqing Key Laboratory for Advanced Materials and Technologies of Clean Energies, Chongqing, China
| | - Jasmine Zeng
- Singapore Institute of Manufacturing Technology, Singapore, Singapore
| | - Ruige Wu
- Singapore Institute of Manufacturing Technology, Singapore, Singapore
| | - Wei Wang
- Singapore Institute of Manufacturing Technology, Singapore, Singapore
| | - Suhanya Duraiswamy
- Department of Chemical Engineering, Indian Institute of Technology Hyderabad, Hyderabad, India
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Agulnik JS, Papadakis AI, Pepe C, Sakr L, Small D, Wang H, Kasymjanova G, Spatz A, Cohen V. Cell-Free Tumor DNA (ctDNA) Utility in Detection of Original Sensitizing and Resistant EGFR Mutations in Non-Small Cell Lung Cancer (NSCLC). Curr Oncol 2022; 29:1107-1116. [PMID: 35200593 PMCID: PMC8871000 DOI: 10.3390/curroncol29020094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/17/2022] [Accepted: 02/10/2022] [Indexed: 11/16/2022] Open
Abstract
Background: Recent studies have demonstrated the utility of cell-free tumor DNA (ctDNA) from plasma as an alternative source of genomic material for detection of sensitizing and resistance mutations in NSCLC. We hypothesized that the plasma level of ctDNA is an effective biomarker to provide a non-invasive and thus a less risky method to determine new resistance mutations and to monitor response to treatment and tumor progression in lung cancer patients. Methods: This prospective cohort study was approved and conducted at the Peter Brojde Lung Cancer Centre, Montreal. Blood was collected in STRECK tubes at four time points. DNA was extracted from plasma, and ctDNA was analyzed for the presence of mutations in the EGFR gene using the COBAS® EGFR v2 qPCR (Roche) test. Results: Overall, 75 pts were enrolled in the study. In total, 23 pts were TKI-naïve, and 52 were already receiving first-line TKI treatment. ctDNA detected the original mutations (OM) in 35/75 (48%) patients. Significantly higher detection rates were observed in TKI-naïve patients compared to the TKI-treated group, 70% versus 37%, respectively (p = 0.012). The detection of the original mutation at the study baseline was a negative predictor of progression-free survival (PFS) and overall survival (OS). The resistance mutation (T790M) was detected in 32/74 (43%) patients. In 27/32 (84%), the T790M was detected during treatment with TKI: in 25/27 patients, T790M was detected at the time of radiologic progression, in one patient, T790M was detected before radiologic progression, and in one patient, T790M was detected four weeks after starting systemic chemotherapy post progression on TKI. At the time of progression, the detection of T790M significantly correlates with the re-appearance of OM (p = 0.001). Conclusion: Plasma ctDNA is a noninvasive patient-friendly test that can be used to monitor response to treatment, early progression, and detection of acquired resistant mutations. Monitoring of clearance and re-emergence of driver mutations during TKI treatment effectively identifies progression of the disease. As larger NGS panels are available for ctDNA testing, these findings may also have implications for other biomarkers. The results from ongoing and prospective studies will further determine the utility of plasma testing to diagnose, monitor for disease progression, and guide treatment decisions in NSCLC.
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Affiliation(s)
- Jason S. Agulnik
- Peter Brojde Lung Cancer Centre, Jewish General Hospital, McGill University, Montreal, QC H3T 1E2, Canada; (J.S.A.); (C.P.); (L.S.); (D.S.); (V.C.)
| | - Andreas I. Papadakis
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC H3T 1E2, Canada;
| | - Carmela Pepe
- Peter Brojde Lung Cancer Centre, Jewish General Hospital, McGill University, Montreal, QC H3T 1E2, Canada; (J.S.A.); (C.P.); (L.S.); (D.S.); (V.C.)
| | - Lama Sakr
- Peter Brojde Lung Cancer Centre, Jewish General Hospital, McGill University, Montreal, QC H3T 1E2, Canada; (J.S.A.); (C.P.); (L.S.); (D.S.); (V.C.)
| | - David Small
- Peter Brojde Lung Cancer Centre, Jewish General Hospital, McGill University, Montreal, QC H3T 1E2, Canada; (J.S.A.); (C.P.); (L.S.); (D.S.); (V.C.)
| | - Hangjun Wang
- Department of Pathology, Jewish General Hospital, Montreal, QC H3T 1E2, Canada;
| | - Goulnar Kasymjanova
- Peter Brojde Lung Cancer Centre, Jewish General Hospital, McGill University, Montreal, QC H3T 1E2, Canada; (J.S.A.); (C.P.); (L.S.); (D.S.); (V.C.)
- Correspondence:
| | - Alan Spatz
- OPTILAB-Montreal MUHC & Department of Laboratory Medicine, McGill University Health Center, Montreal, QC H3T 1E2, Canada;
| | - Victor Cohen
- Peter Brojde Lung Cancer Centre, Jewish General Hospital, McGill University, Montreal, QC H3T 1E2, Canada; (J.S.A.); (C.P.); (L.S.); (D.S.); (V.C.)
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Olmedillas-López S, Olivera-Salazar R, García-Arranz M, García-Olmo D. Current and Emerging Applications of Droplet Digital PCR in Oncology: An Updated Review. Mol Diagn Ther 2021; 26:61-87. [PMID: 34773243 DOI: 10.1007/s40291-021-00562-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/17/2021] [Indexed: 12/14/2022]
Abstract
In the era of personalized medicine and targeted therapies for the management of patients with cancer, ultrasensitive detection methods for tumor genotyping, such as next-generation sequencing or droplet digital polymerase chain reaction (ddPCR), play a significant role. In the search for less invasive strategies for diagnosis, prognosis and disease monitoring, the number of publications regarding liquid biopsy approaches using ddPCR has increased substantially in recent years. There is a long list of malignancies in which ddPCR provides a reliable and accurate tool for detection of nucleic acid-based markers derived from cell-free DNA, cell-free RNA, circulating tumor cells, extracellular vesicles or exosomes when isolated from whole blood, plasma and serum, helping to anticipate tumor relapse or unveil intratumor heterogeneity and clonal evolution in response to treatment. This updated review describes recent developments in ddPCR platforms and provides a general overview about the major applications of liquid biopsy in blood, including its utility for molecular response and minimal residual disease monitoring in hematological malignancies or the therapeutic management of patients with colorectal or lung cancer, particularly for the selection and monitoring of treatment with tyrosine kinase inhibitors. Although plasma is the main source of genetic material for tumor genomic profiling, liquid biopsy by ddPCR is being investigated in a wide variety of biologic fluids, such as cerebrospinal fluid, urine, stool, ocular fluids, sputum, saliva, bronchoalveolar lavage, pleural effusion, mucin, peritoneal fluid, fine needle aspirate, bile or pancreatic juice. The present review focuses on these "alternative" sources of genetic material and their analysis by ddPCR in different kinds of cancers.
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Affiliation(s)
- Susana Olmedillas-López
- New Therapies Laboratory, Health Research Institute-Fundación Jiménez Díaz University Hospital (IIS-FJD), Avda. Reyes Católicos, 2, 28040, Madrid, Spain.
| | - Rocío Olivera-Salazar
- New Therapies Laboratory, Health Research Institute-Fundación Jiménez Díaz University Hospital (IIS-FJD), Avda. Reyes Católicos, 2, 28040, Madrid, Spain
| | - Mariano García-Arranz
- New Therapies Laboratory, Health Research Institute-Fundación Jiménez Díaz University Hospital (IIS-FJD), Avda. Reyes Católicos, 2, 28040, Madrid, Spain.,Department of Surgery, School of Medicine, Universidad Autónoma de Madrid (UAM), 28029, Madrid, Spain
| | - Damián García-Olmo
- New Therapies Laboratory, Health Research Institute-Fundación Jiménez Díaz University Hospital (IIS-FJD), Avda. Reyes Católicos, 2, 28040, Madrid, Spain.,Department of Surgery, School of Medicine, Universidad Autónoma de Madrid (UAM), 28029, Madrid, Spain.,Department of Surgery, Fundación Jiménez Díaz University Hospital (FJD), 28040, Madrid, Spain
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Liquid Biopsy for Biomarker Testing in Non-Small Cell Lung Cancer: A European Perspective. JOURNAL OF MOLECULAR PATHOLOGY 2021. [DOI: 10.3390/jmp2030022] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The development of targeted therapies has improved survival rates for patients with advanced non-small cell lung cancer (NSCLC). However, tissue biopsy is unfeasible or inadequate in many patients, limiting biomarker testing and access to targeted therapies. The increasing numbers of established and emerging biomarkers with available targeted treatments highlights the challenges associated with sequential single-gene testing and limited tissue availability. Multiplex next-generation sequencing (NGS) offers an attractive alternative and represents a logical next step, and in cases where the tumour is inaccessible, tissue biopsy yields insufficient tumour content, or when the patient’s performance status does not allow a tissue biopsy, liquid biopsy can provide valuable material for molecular diagnosis. Here, we explore the role of liquid biopsy (i.e., circulating cell-free DNA analysis) in Europe. Liquid biopsies could be used as a complementary approach to increase rates of molecular diagnosis, with the ultimate aim of improving patient access to appropriate targeted therapies. Expert opinion is also provided on potential future applications of liquid biopsy in NSCLC, including for cancer prevention, detection of early stage and minimum residual disease, monitoring of response to therapy, selection of patients for immunotherapy, and monitoring of tumour evolution to enable optimal adaptation/combination of drug therapies.
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Ntzifa A, Kotsakis A, Georgoulias V, Lianidou E. Detection of EGFR Mutations in Plasma cfDNA and Paired CTCs of NSCLC Patients before and after Osimertinib Therapy Using Crystal Digital PCR. Cancers (Basel) 2021; 13:2736. [PMID: 34073111 PMCID: PMC8197887 DOI: 10.3390/cancers13112736] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 05/13/2021] [Accepted: 05/27/2021] [Indexed: 12/23/2022] Open
Abstract
Circulating tumor DNA (ctDNA) analysis has clinical utility in EGFR mutant NSCLC. Circulating tumor cells (CTCs) consist a unique source of information at the cellular level. Digital PCR (dPCR) is a valuable tool for accurate and valid analysis of gene mutations in liquid biopsy analysis. In the present study we detected EGFR mutations in ctDNA and paired CTCs under osimertinib therapy at two time points using crystal dPCR and the naica® system (Stilla Technologies). We quantified mutation allele frequencies (MAF) of EGFR mutations in 91 plasma cfDNA samples of 48 EGFR mutant NSCLC patients and in 64 matched CTC-derived genomic DNA samples, and the FDA-cleared cobas® EGFR mutation test in 80 identical plasma samples. Direct comparison between crystal dPCR and the cobas EGFR assay revealed a high concordance for all EGFR mutations. Our comparison of crystal dPCR results in ctDNA with the corresponding primary tissue has shown a strong correlation. EGFR mutations analysis in paired CTC-derived gDNA revealed a high heterogeneity. Crystal dPCR offers the unique advantages of high analytical sensitivity, precision, and accuracy for detecting and quantifying multiple EGFR mutations in plasma cfDNA and CTCs of NSCLC patients.
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Affiliation(s)
- Aliki Ntzifa
- Analysis of Circulating Tumor Cells Lab, Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece;
| | - Athanasios Kotsakis
- Department of Medical Oncology, General University Hospital of Larissa, 41110 Larissa, Greece;
| | | | - Evi Lianidou
- Analysis of Circulating Tumor Cells Lab, Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece;
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Therapy Monitoring of EGFR-Positive Non–Small-Cell Lung Cancer Patients Using ddPCR Multiplex Assays. J Mol Diagn 2021; 23:495-505. [DOI: 10.1016/j.jmoldx.2021.01.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 10/30/2020] [Accepted: 01/12/2021] [Indexed: 12/18/2022] Open
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Chiou CC, Wang CL, Luo JD, Liu CY, Ko HW, Yang CT. Targeted Sequencing of Circulating Cell Free DNA Can Be Used to Monitor Therapeutic Efficacy of Tyrosine Kinase Inhibitors in Non-small Cell Lung Cancer Patients. Cancer Genomics Proteomics 2021; 17:417-423. [PMID: 32576586 DOI: 10.21873/cgp.20200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 03/13/2020] [Accepted: 03/14/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND/AIM Circulating tumor DNA (ctDNA) bears specific mutations derived from tumor cells. The amount of mutant ctDNA may reflect tumor burden. In this study, we detected epidermal growth factor receptor (EGFR) mutations in ctDNA as a monitoring marker for the response of non-small cell lung cancer (NSCLC) patients to tyrosine kinase inhibitors (TKIs). PATIENTS AND METHODS Serial plasma samples from eight NSCLC patients during TKI treatment were collected. Libraries with barcoded adapters were constructed from ctDNA of these plasma samples using a PCR-based targeted DNA panel. The libraries were then sequenced for measuring EGFR mutations. In addition, carcinoembryonic antigen (CEA) was also measured in these patients. RESULTS In six patients who suffered disease progression (PD), five had elevated EGFR mutation reads before PD. In the two patients who did not develop PD, EGFR mutations remained undetectable in their plasma. The CEA levels were higher than the cutoff value in most samples and had a poor correlation with disease status. CONCLUSION The mutation count of tumor-specific mutations can be a monitoring marker of TKI treatment in NSCLC patients.
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Affiliation(s)
- Chiuan-Chian Chiou
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan, R.O.C.,Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan, R.O.C.,Department of Thoracic Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan, R.O.C
| | - Chih-Liang Wang
- Department of Thoracic Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan, R.O.C.,Department of Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan, R.O.C
| | - Ji-Dung Luo
- Bioinformatics Resource Center, The Rockefeller University, New York, NY, U.S.A
| | - Chien-Ying Liu
- Department of Thoracic Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan, R.O.C.,Department of Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan, R.O.C
| | - How-Wen Ko
- Department of Thoracic Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan, R.O.C
| | - Cheng-Ta Yang
- Department of Thoracic Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan, R.O.C. .,Department of Respiratory Therapy, College of Medicine, Chang Gung University, Taoyuan, Taiwan, R.O.C
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Abstract
Response evaluation for cancer treatment consists primarily of clinical and radiological assessments. In addition, a limited number of serum biomarkers that assess treatment response are available for a small subset of malignancies. Through recent technological innovations, new methods for measuring tumor burden and treatment response are becoming available. By utilization of highly sensitive techniques, tumor-specific mutations in circulating DNA can be detected and circulating tumor DNA (ctDNA) can be quantified. These so-called liquid biopsies provide both molecular information about the genomic composition of the tumor and opportunities to evaluate tumor response during therapy. Quantification of tumor-specific mutations in plasma correlates well with tumor burden. Moreover, with liquid biopsies, it is also possible to detect mutations causing secondary resistance during treatment. This review focuses on the clinical utility of ctDNA as a response and follow-up marker in patients with non-small cell lung cancer, melanoma, colorectal cancer, and breast cancer. Relevant studies were retrieved from a literature search using PubMed database. An overview of the available literature is provided and the relevance of ctDNA as a response marker in anti-cancer therapy for clinical practice is discussed. We conclude that the use of plasma-derived ctDNA is a promising tool for treatment decision-making based on predictive testing, detection of resistance mechanisms, and monitoring tumor response. Necessary steps for translation to daily practice and future perspectives are discussed.
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Duan J, Xu J, Wang Z, Bai H, Cheng Y, An T, Gao H, Wang K, Zhou Q, Hu Y, Song Y, Ding C, Peng F, Liang L, Hu Y, Huang C, Zhou C, Shi Y, Han J, Wang D, Tian Y, Yang Z, Zhang L, Chuai S, Ye J, Zhu G, Zhao J, Wu YL, Wang J. Refined Stratification Based on Baseline Concomitant Mutations and Longitudinal Circulating Tumor DNA Monitoring in Advanced EGFR-Mutant Lung Adenocarcinoma Under Gefitinib Treatment. J Thorac Oncol 2020; 15:1857-1870. [PMID: 32916309 DOI: 10.1016/j.jtho.2020.08.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 07/16/2020] [Accepted: 08/04/2020] [Indexed: 02/05/2023]
Abstract
INTRODUCTION The optimal treatment for EGFR-mutant lung adenocarcinoma (LUAD) remains challenging because of intratumor heterogeneity. We aimed to explore a refined stratification model based on the integrated analysis of circulating tumor DNA (ctDNA) tracking. METHODS ctDNA was prospectively collected at baseline and at every 8 weeks in patients with advanced treatment-naive EGFR-mutant LUAD under gefitinib treatment enrolled in a phase 2 trial and analyzed using next-generation sequencing of a 168-gene panel. RESULTS Three subgroups categorized by baseline comutations-EGFR-sensitizing mutations (59, 32.8%), EGFR-sensitizing mutations with tumor suppressor mutations (97, 53.9%), and EGFR-sensitizing mutations with other driver mutations (24, 13.3%)-exhibited distinct progression-free survival (13.2 [11.3-15.2] versus 9.3 [7.6-10.5] versus 4.0 [2.4-9.3] months) and overall survival (32.0 [29.2-41.5] versus 21.7 [19.3-27.0] versus 15.5 [10.5-33.7] months, respectively), providing evidence for initial stratification. A total of 63.7% of the patients achieved week 8 ctDNA clearance, with significant difference noted among the three subgroups (74.5% versus 64.0% versus 29.4%, respectively, p = 0.004, Fisher's exact test). Patients without week 8 ctDNA clearance had worse progression-free survival (clearance versus nonclearance 11.2 [9.9-13.2] versus 7.4 [5.6-9.6] months, p = 0.016, Cox regression], especially in the second subgroup [5.8 (5.6-11.5) months], suggesting the necessity of adaptive stratification during treatment. During follow-up, 56.0% and 20.8% of the patients eventually harbored p.T790M and non-p.T790M mutations, respectively, with a significant difference in non-p.T790M mutations among the three subgroups (7.5% versus 15.7% versus 80.0%, respectively, p < 0.001, Fisher's exact test), giving clues to postline treatment. CONCLUSIONS The patients with baseline comutations and ctDNA nonclearance at first visit might require combined therapy because of the limited survival benefit of EGFR tyrosine kinase inhibitor monotherapy. We proposed a refined stratification mode for the whole-course management of EGFR-mutant LUAD.
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Affiliation(s)
- Jianchun Duan
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - JiaChen Xu
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Zhijie Wang
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Hua Bai
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Ying Cheng
- Division of Thoracic Oncology, Jilin Cancer Hospital, Jilin Province Cancer Hospital, Changchun, People's Republic of China
| | - Tongtong An
- Department of Thoracic Medical Oncology, Peking University School of Oncology, Beijing Cancer Hospital and Institute, Beijing, People's Republic of China
| | - Hongjun Gao
- The 307th Hospital of Chinese People's Liberation Army, Beijing, People's Republic of China
| | - Kai Wang
- Department of Respiratory Medicine, Second Affiliated Hospital Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Qing Zhou
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, People's Republic of China
| | - Yanping Hu
- Department of Oncology, Hubei Cancer Hospital, Hubei, People's Republic of China
| | - Yong Song
- Nanjing General Hospital of Nanjing Military Command and PLA Bayi Hospital, Nanjing, People's Republic of China
| | - Cuimin Ding
- Department of Respiratory Medicine, The Fourth Hospital of Hebei Medical University, Hebei, People's Republic of China
| | - Feng Peng
- Department of Thoracic Oncology, Cancer Center, West China Hospital, Medical School, Sichuan University, Chengdu, People's Republic of China
| | - Li Liang
- Peking University Third Hospital, Beijing, People's Republic of China
| | - Yi Hu
- Chinese People's Liberation Army General Hospital, Beijing, People's Republic of China
| | - Cheng Huang
- Department of Medical Oncology, Fujian Provincial Cancer Hospital, Teaching Hospital of Fujian University of Traditional Chinese Medicine, Teaching Hospital of Fujian Medical University, Fuzhou, People's Republic of China
| | - Caicun Zhou
- Shanghai Pulmonary Hospital, Tongji University, Shanghai, People's Republic of China
| | - Yuankai Shi
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Jiefei Han
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Di Wang
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Yanhua Tian
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Zhenlin Yang
- Department of Thoracic Surgery, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Li Zhang
- Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China
| | - Shaokun Chuai
- Burning Rock Biotech, Guangdong, People's Republic of China
| | - Junyi Ye
- Burning Rock Biotech, Guangdong, People's Republic of China
| | - Guanshan Zhu
- Amoy Diagnostics, Xiamen, People's Republic of China
| | - Junhui Zhao
- Department of Medical Oncology, Affiliated Hospital of Qinghai University, Qinghai, People's Republic of China
| | - Yi-Long Wu
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, People's Republic of China
| | - Jie Wang
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China.
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13
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Álvarez-Alegret R, Rojo Todo F, Garrido P, Bellosillo B, Rodríguez-Lescure Á, Rodríguez-Peralto JL, Vera R, de Álava E, García-Campelo R, Remon J. [Liquid biopsy in oncology: A consensus statement of the Spanish Society of Pathology and the Spanish Society of Medical Oncology]. REVISTA ESPAÑOLA DE PATOLOGÍA : PUBLICACIÓN OFICIAL DE LA SOCIEDAD ESPAÑOLA DE ANATOMÍA PATOLÓGICA Y DE LA SOCIEDAD ESPAÑOLA DE CITOLOGÍA 2020; 53:234-245. [PMID: 33012494 DOI: 10.1016/j.patol.2019.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/27/2019] [Accepted: 12/09/2019] [Indexed: 11/18/2022]
Abstract
The proportion of cancer patients with tumours that harbour a potentially targetable genomic alteration is increasing considerably. The diagnosis of these genomic alterations can lead to tailoring of treatment, at the onset of disease or during progression, as well as providing additional, predictive information on the efficacy of immunotherapy. However, in up to 25% of cases, the initial tissue biopsy is inadequate for precision oncology and, in many cases, tumour genomic profiling at progression is not possible due to technical limitations of obtaining new tumour tissue specimens. Efficient diagnostic alternatives are therefore required for molecular stratification, such as liquid biopsy. This technique enables the evaluation of the tumour genomic profile dynamically and as well as capturing intra-patient genomic heterogeneity. To date, there are several diagnostic techniques available for use in liquid biopsy, each with different precision and performance levels. The objective of this consensus statement of the Spanish Society of Pathology (SEAP) and the Spanish Society of Medical Oncology (SEOM) is to evaluate the viability and effectiveness of the different methodological approaches of liquid biopsy in cancer patients, and the potential application of this method to current clinical practice. The experts contributing to this consensus statement agree that, according to current evidence, liquid biopsy is an acceptable alternative to tumour tissue biopsy for the study of biomarkers in various clinical settings. It is therefore important to standardise pre-analytical and analytical procedures to ensure reproducibility and to generate structured and accessible clinical reports. It is essential to appoint multidisciplinary tumour molecular committees to oversee these processes and to enable the most suitable therapeutic decisions for each patient according to the genomic profile.
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Affiliation(s)
| | - Federico Rojo Todo
- Departamento de Patología, Fundación Universitaria Jiménez Díaz, CIBERONC, Madrid, España
| | - Pilar Garrido
- Universidad de Alcalá; Departamento de Oncología Médica, IRYCIS, Hospital Universitario Ramón y Cajal, CIBERONC, Madrid, España
| | - Beatriz Bellosillo
- Departamento de Patología, Hospital del Mar, CIBERONC, Barcelona, España
| | - Álvaro Rodríguez-Lescure
- Departamento de Oncología Médica, Hospital General Universitario de Elche y Vega Baja, GEICAM, Elche, España
| | | | - Ruth Vera
- Departamento de Oncología Médica, Complejo Hospitalario de Navarra, Navarra Institute for health research (IdiSNA), Pamplona, España
| | - Enrique de Álava
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, CIBERONC, Departamento de Citología e Histología Normal y Patológica, Sevilla, España
| | - Rosario García-Campelo
- Departamento de Oncología Médica, Complexo Hospitalario Universitario A Coruña, A Coruña, España
| | - Jordi Remon
- Departamento de Oncología Médica, Centro Integral Oncológico Clara Campal Barcelona (CIOCCB), HM Delfos, Barcelona, España
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14
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Fang QQ, Huang WJ, Li XY, Cheng YH, Tan MJ, Liu J, Wei HJ, Meng Y, Wang DY. Effectiveness of favipiravir (T-705) against wild-type and oseltamivir-resistant influenza B virus in mice. Virology 2020; 545:1-9. [PMID: 32174453 DOI: 10.1016/j.virol.2020.02.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 02/21/2020] [Accepted: 02/21/2020] [Indexed: 10/24/2022]
Abstract
The emergence of resistant mutants to the wildly used neuraminidase inhibitors (NAIs) makes the development of novel drugs necessary. Favipiravir (T-705) is one of the RNA-dependent RNA polymerase (RdRp) inhibitors developed in recent years. To examine the efficacy of T-705 against influenza B virus infections in vivo, C57BL/6 mice infected with wild-type or oseltamivir-resistant influenza B/Memphis/20/96 viruses were treated with T-705. Starting 2 h post inoculation (hpi), T-705 was orally administered to mice BID at dosages of 50, 150, or 300 mg/kg/day for 5 days. Oseltamivir was used as control. Here, we showed that T-705 protected mice from lethal infection in a dose-dependent manner. T-705 administration also significantly reduced viral loads and suppressed pulmonary pathology. In addition, phenotypic assays demonstrated that no T-705-resistant viruses emerged after T-705 treatment. In conclusion, T-705 can be effective to protect mice from lethal infection with both wild-type and oseltamivir-resistant influenza B viruses.
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Affiliation(s)
- Qiong-Qiong Fang
- Chinese National Influenza Center, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, WHO Collaborating Center for Reference and Research on Influenza, Beijing, 102206, China.
| | - Wei-Juan Huang
- Chinese National Influenza Center, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, WHO Collaborating Center for Reference and Research on Influenza, Beijing, 102206, China
| | - Xi-Yan Li
- Chinese National Influenza Center, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, WHO Collaborating Center for Reference and Research on Influenza, Beijing, 102206, China
| | - Yan-Hui Cheng
- Chinese National Influenza Center, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, WHO Collaborating Center for Reference and Research on Influenza, Beijing, 102206, China
| | - Min-Ju Tan
- Chinese National Influenza Center, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, WHO Collaborating Center for Reference and Research on Influenza, Beijing, 102206, China
| | - Jia Liu
- Chinese National Influenza Center, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, WHO Collaborating Center for Reference and Research on Influenza, Beijing, 102206, China
| | - He-Jiang Wei
- Chinese National Influenza Center, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, WHO Collaborating Center for Reference and Research on Influenza, Beijing, 102206, China
| | - Yao Meng
- Shaanxi Provincial Center for Disease Control and Prevention, Xi'an, 710054, China
| | - Da-Yan Wang
- Chinese National Influenza Center, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, WHO Collaborating Center for Reference and Research on Influenza, Beijing, 102206, China.
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15
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Abstract
ctDNA provided by liquid biopsy offers a promising alternative to tumor biopsy as it gives a non-invasive and «real-time» access to the cancer genome and reflects tumor intra and extra heterogeneity. ctDNA has shown growing clinical interest for cancer diagnosis, prognosis, theragnostics, therapeutic monitoring, and clonal evolution tracking. A major technical limit for ctDNA analysis from body fluids is the extremely low proportion of ctDNA compared to non-malignant cell-free DNA, underscoring the need for highly sensitive and specific detection techniques. The control of pre-analytical procedures appears essential for optimal ctDNA analysis and need to be standardized for clinical research applications. This chapter provides insights into major current technologies for ctDNA detection. Overall, PCR-based techniques are able to detect limited molecular alterations and have a high sensitivity suitable for monitoring purposes while NGS-based approaches are broad range molecular screening assays more specifically indicated for treatment selection. We briefly reviewed new technical innovations that are now available for ctDNA detection.
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Affiliation(s)
- Pauline Gilson
- Université de Lorraine, CNRS UMR 7039 CRAN, Institut de Cancérologie de Lorraine, Service de Biopathologie, 54000, Nancy, France.
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16
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Remon J, Steuer CE, Ramalingam SS, Felip E. Osimertinib and other third-generation EGFR TKI in EGFR-mutant NSCLC patients. Ann Oncol 2019; 29:i20-i27. [PMID: 29462255 DOI: 10.1093/annonc/mdx704] [Citation(s) in RCA: 157] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Osimertinib was the first third-generation epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor (TKI) to receive FDA and EMA approval for metastatic EGFR-mutant non-small-cell lung cancer (NSCLC) patients that have acquired the EGFR T790M resistance mutation. Clinical trials have demonstrated the efficacy of osimertinib in this patient population and clinical trials of other third-generation EGFR TKI are currently under way. Additional challenges in this patient population, such as the upfront efficacy of osimertinib, validation of T790M in liquid biopsies as a dynamic predictive marker of efficacy, along with combination with immune checkpoint inhibitors are being explored, representing an extraordinary time of development for EGFR-mutant NSCLC.
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Affiliation(s)
- J Remon
- Medical Oncologist Department, Thoracic Tumor Unit, Vall d'Hebron University Hospital, Barcelona.,Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - C E Steuer
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, USA
| | - S S Ramalingam
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, USA
| | - E Felip
- Medical Oncologist Department, Thoracic Tumor Unit, Vall d'Hebron University Hospital, Barcelona.,Vall d'Hebron Institute of Oncology, Barcelona, Spain
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17
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Liquid biopsy in oncology: a consensus statement of the Spanish Society of Pathology and the Spanish Society of Medical Oncology. Clin Transl Oncol 2019; 22:823-834. [PMID: 31559582 PMCID: PMC7854395 DOI: 10.1007/s12094-019-02211-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 09/13/2019] [Indexed: 02/06/2023]
Abstract
The proportion of cancer patients with tumours that harbour a potentially targetable genomic alteration is growing considerably. The diagnosis of these genomic alterations can lead to tailored treatment at the onset of disease or on progression and to obtaining additional predictive information on immunotherapy efficacy. However, in up to 25% of cases, the initial tissue biopsy is inadequate for precision oncology and, in many cases, tumour genomic profiling at progression is not possible due to technical limitations of obtaining new tumour tissue specimens. Efficient diagnostic alternatives are therefore required for molecular stratification, which includes liquid biopsy. This technique enables the evaluation of the tumour genomic profile dynamically and captures intra-patient genomic heterogeneity as well. To date, there are several diagnostic techniques available for use in liquid biopsy, each one of them with different precision and performance levels. The objective of this consensus statement of the Spanish Society of Pathology and the Spanish Society of Medical Oncology is to evaluate the viability and effectiveness of the different methodological approaches in liquid biopsy in cancer patients and the potential application of this method to current clinical practice. The experts contributing to this consensus statement agree that, according to current evidence, liquid biopsy is an acceptable alternative to tumour tissue biopsy for the study of biomarkers in various clinical settings. It is therefore important to standardise pre-analytical and analytical procedures, to ensure reproducibility and generate structured and accessible clinical reports. It is essential to appoint multidisciplinary tumour molecular boards to oversee these processes and to enable the most suitable therapeutic decisions for each patient according to the genomic profile.
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18
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Cervena K, Vodicka P, Vymetalkova V. Diagnostic and prognostic impact of cell-free DNA in human cancers: Systematic review. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2019; 781:100-129. [DOI: 10.1016/j.mrrev.2019.05.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 05/03/2019] [Accepted: 05/07/2019] [Indexed: 02/06/2023]
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19
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Franczak C, Filhine-Tresarrieu P, Gilson P, Merlin JL, Au L, Harlé A. Technical considerations for circulating tumor DNA detection in oncology. Expert Rev Mol Diagn 2019; 19:121-135. [DOI: 10.1080/14737159.2019.1568873] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Claire Franczak
- Service de Biopathologie, Institut de Cancérologie de Lorraine, Vandoeuvre les Nancy, France
| | | | - Pauline Gilson
- Service de Biopathologie, Institut de Cancérologie de Lorraine, Université de Lorraine, CNRS UMR 7039 CRAN, Nancy, France
| | - Jean-Louis Merlin
- Service de Biopathologie, Institut de Cancérologie de Lorraine, Université de Lorraine, CNRS UMR 7039 CRAN, Nancy, France
| | - Lewis Au
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Alexandre Harlé
- Service de Biopathologie, Institut de Cancérologie de Lorraine, Université de Lorraine, CNRS UMR 7039 CRAN, Nancy, France
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20
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Yen GS, Fujimoto BS, Schneider T, Kreutz JE, Chiu DT. Statistical Analysis of Nonuniform Volume Distributions for Droplet-Based Digital PCR Assays. J Am Chem Soc 2019; 141:1515-1525. [PMID: 30605325 DOI: 10.1021/jacs.8b09073] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We present a method to determine the concentration of nucleic acids in a sample by partitioning it into droplets with a nonuniform volume distribution. This digital PCR method requires no special equipment for partitioning, unlike other methods that require nearly identical volumes. Droplets are generated by vortexing a sample in an immiscible oil to create an emulsion. PCR is performed, and droplets in the emulsion are imaged. Droplets with one or more copies of a nucleic acid are identified, and the nucleic acid concentration of the sample is determined. Numerical simulations of droplet distributions were used to estimate measurement error and dynamic range and to examine the effects of the total volume of droplets imaged and the shape of the droplet size distribution on measurement accuracy. The ability of the method to resolve 1.5- and 3-fold differences in concentration was assessed by using simulations of statistical power. The method was validated experimentally; droplet shrinkage and fusion during amplification were also assessed experimentally and showed negligible effects on measured concentration.
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Affiliation(s)
- Gloria S Yen
- Department of Chemistry , University of Washington , Seattle , Washington 98195-1700 , United States
| | - Bryant S Fujimoto
- Department of Chemistry , University of Washington , Seattle , Washington 98195-1700 , United States
| | - Thomas Schneider
- Department of Chemistry , University of Washington , Seattle , Washington 98195-1700 , United States
| | - Jason E Kreutz
- Department of Chemistry , University of Washington , Seattle , Washington 98195-1700 , United States
| | - Daniel T Chiu
- Department of Chemistry , University of Washington , Seattle , Washington 98195-1700 , United States
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21
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Zhu K, Chi J, Zhang D, Ma B, Dong X, Yang J, Zhao C, Liu H. Bio-inspired photonic crystals for naked eye quantification of nucleic acids. Analyst 2019; 144:5413-5419. [DOI: 10.1039/c9an01042d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The quantitative detection of nucleic acids by the naked eye was achieved based on structural color.
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Affiliation(s)
- Ke Zhu
- State Key Laboratory of Bioelectronics
- School of Biological Science and Medical Engineering
- Southeast University
- Nanjing 210096
- China
| | - Junjie Chi
- State Key Laboratory of Bioelectronics
- School of Biological Science and Medical Engineering
- Southeast University
- Nanjing 210096
- China
| | - Dagan Zhang
- State Key Laboratory of Bioelectronics
- School of Biological Science and Medical Engineering
- Southeast University
- Nanjing 210096
- China
| | - Biao Ma
- State Key Laboratory of Bioelectronics
- School of Biological Science and Medical Engineering
- Southeast University
- Nanjing 210096
- China
| | - Xing Dong
- State Key Laboratory of Bioelectronics
- School of Biological Science and Medical Engineering
- Southeast University
- Nanjing 210096
- China
| | - Jun Yang
- Nanjing Institute for Food and Drug Control
- Nanjing
- PR China
| | - Chao Zhao
- State Key Laboratory of Bioelectronics
- School of Biological Science and Medical Engineering
- Southeast University
- Nanjing 210096
- China
| | - Hong Liu
- State Key Laboratory of Bioelectronics
- School of Biological Science and Medical Engineering
- Southeast University
- Nanjing 210096
- China
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22
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Malic L, Daoud J, Geissler M, Boutin A, Lukic L, Janta M, Elmanzalawy A, Veres T. Epigenetic subtyping of white blood cells using a thermoplastic elastomer-based microfluidic emulsification device for multiplexed, methylation-specific digital droplet PCR. Analyst 2019; 144:6541-6553. [DOI: 10.1039/c9an01316d] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Digital droplet PCR for epigenetic leukocyte subtyping from clinically relevant samples is implemented using a thermoplastic elastomer microfluidic droplet generator as a first step towards an economical, customizable and easily deployable system.
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Affiliation(s)
- Lidija Malic
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
| | - Jamal Daoud
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
| | - Matthias Geissler
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
| | - Alex Boutin
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
| | - Ljuboje Lukic
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
| | - Mojra Janta
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
| | | | - Teodor Veres
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
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23
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Madic J, Jovelet C, Lopez J, André B, Fatien J, Miran I, Honoré A, Mezquita L, Besse B, Lacroix L, Droniou M. EGFR C797S, EGFR T790M and EGFR sensitizing mutations in non-small cell lung cancer revealed by six-color crystal digital PCR. Oncotarget 2018; 9:37393-37406. [PMID: 30647840 PMCID: PMC6324771 DOI: 10.18632/oncotarget.26446] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 11/26/2018] [Indexed: 12/31/2022] Open
Abstract
Background Detection of EGFR sensitizing and p.T790M and p.C797S resistance mutations is particularly important for non-small cell lung cancer (NSCLC) patient therapy management. Non-invasive blood-based monitoring of these mutations may pave the way to a fine-tuned personalized treatment. Digital PCR has emerged as an extremely sensitive method to detect rare mutations, however its major limitation is the number of hotspots that can be simultaneously differentiated. Methods We developed a 6-color digital PCR assay for the detection and quantification of 19 most prevalent EGFR sensitizing and resistance mutations and evaluated this assay on 82 tumor and plasma samples from NSLC patients. Results Limits of detection (LOD) for the 6-color digital PCR assay were assessed on serial dilutions of DNA standards. We found that the 6-color assay enabled detection of mutant fractions as low as 1 mutant in 1025 wild-type molecules, depending on the mutation targeted, when assayed in a background of 10 000 wild-type DNA copies. EGFR mutant allelic fraction was also measured on tumor and plasma samples by 6-color digital PCR, and displayed a highly significant correlation with next generation sequencing and 3-color digital PCR. Lastly, the 6-color digital PCR assay was performed on several longitudinal plasma samples from four patients and revealed levels of sensitizing and resistance EGFR mutations that reflected well the course of the disease. Conclusion This 6-color Crystal digital PCR assay could represent a robust solution using digital PCR for the monitoring of EGFR mutations.
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Affiliation(s)
- Jordan Madic
- Stilla Technologies, 1 Mail du Professeur Georges Mathé, Villejuif, France
| | - Cécile Jovelet
- Plateforme de Génomique, Module de Biopathologie Moléculaire et Centre de Ressources Biologiques, AMMICa, INSERM US23/CNRS UMS3655, Gustave Roussy, Villejuif, France
| | - Julien Lopez
- Stilla Technologies, 1 Mail du Professeur Georges Mathé, Villejuif, France
| | - Barbara André
- Stilla Technologies, 1 Mail du Professeur Georges Mathé, Villejuif, France
| | - Jean Fatien
- Ecole Polytechnique, Route de Saclay, Palaiseau, France
| | - Isabelle Miran
- Plateforme de Génomique, Module de Biopathologie Moléculaire et Centre de Ressources Biologiques, AMMICa, INSERM US23/CNRS UMS3655, Gustave Roussy, Villejuif, France
| | - Aurélie Honoré
- Plateforme de Génomique, Module de Biopathologie Moléculaire et Centre de Ressources Biologiques, AMMICa, INSERM US23/CNRS UMS3655, Gustave Roussy, Villejuif, France
| | - Laura Mezquita
- Département d'Oncologie Médicale, Gustave Roussy, Villejuif, France
| | - Benjamin Besse
- Département d'Oncologie Médicale, Gustave Roussy, Villejuif, France
| | - Ludovic Lacroix
- Plateforme de Génomique, Module de Biopathologie Moléculaire et Centre de Ressources Biologiques, AMMICa, INSERM US23/CNRS UMS3655, Gustave Roussy, Villejuif, France.,Département de Biologie et Pathologie Médicales, Institut Gustave Roussy, Villejuif, France
| | - Magali Droniou
- Stilla Technologies, 1 Mail du Professeur Georges Mathé, Villejuif, France
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24
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Khatami F, Tavangar SM. Circulating tumor DNA (ctDNA) in the era of personalized cancer therapy. J Diabetes Metab Disord 2018; 17:19-30. [PMID: 30288382 PMCID: PMC6154523 DOI: 10.1007/s40200-018-0334-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 01/17/2018] [Indexed: 02/07/2023]
Abstract
The heterogeneity of tumor is considered as a major difficulty to victorious personalized cancer medicine. There is an extremeneed of consistent response evaluation for in vivo tumor heterogeneity anditscoupledconflict mechanisms. In this occasion researchers will be able to keep pace withpredictive, preventive, personalized, and Participatory (P4) medicine for cancer managements. In fact tumor heterogeneity is a central part of cancer evolution,soin order to progress in understanding of the dynamics within a tumor some diagnostic apparatus should be improved. Latest molecular techniques like Next generation Sequencing (NGS) and ultra-deep sequencing could disclose some clones within a liquid tumor biopsy which mainly responsible of treatment resistance. Circulating tumor DNA (ctDNA) as a main component of liquid biopsy is agifted biomarker for cancer mutation tracking as well as profiling. Personalized medicine facilitate learning regarding to genetic pools of tumor and their possible respond to treatment which could be much easier by using of ctDNA.With this information, cliniciansarelooking forward to find the best strategies for prevention, screening, and treatment in the way of precision medicine. Currently, numerous clinical efficacy of such informative improved treatment are in hand. Here we represent the review of plasma-derived ctDNA studies use in personalized cancer managements.
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Affiliation(s)
- Fatemeh Khatami
- Chronic Diseases Research Center, Endocrinology and Metabolism Population Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Seyed Mohammad Tavangar
- Chronic Diseases Research Center, Endocrinology and Metabolism Population Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
- Departments of Pathology, Doctor Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
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25
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A photosensitive liposome with NIR light triggered doxorubicin release as a combined photodynamic-chemo therapy system. J Control Release 2018; 277:114-125. [DOI: 10.1016/j.jconrel.2018.02.001] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 01/08/2018] [Accepted: 02/02/2018] [Indexed: 01/19/2023]
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26
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Goldman JW, Noor ZS, Remon J, Besse B, Rosenfeld N. Are liquid biopsies a surrogate for tissue EGFR testing? Ann Oncol 2018; 29:i38-i46. [PMID: 29462257 DOI: 10.1093/annonc/mdx706] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Molecular profiling has changed the treatment landscape in advanced non-small-cell lung cancer. Accurately identifying the tumours that harbour sensitizing EGFR mutations, the most common targetable molecular alteration, as well as those with acquired resistance mutations (e.g. T790M) on treatment is a high clinical priority. The current clinical gold standard is genotyping of tumour specimens. However, the practical utility of this approach is limited by the lack of available tissue and the potential complications associated with biopsies. With the advent of newer sequencing assays, it has become feasible to assess tumour genomics via a blood sample, termed a 'liquid biopsy'. In this review, we summarize the available techniques for liquid biopsies and their applicability for detecting sensitizing and resistance EGFR mutations and how these results may be used for making treatment decisions.
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Affiliation(s)
- J W Goldman
- David Geffen School of Medicine at University of California Los Angeles, Los Angeles, USA
| | - Z S Noor
- David Geffen School of Medicine at University of California Los Angeles, Los Angeles, USA
| | - J Remon
- Department of Oncology Medicine, Gustave Roussy, Villejuif
| | - B Besse
- Department of Oncology Medicine, Gustave Roussy, Villejuif
- University Paris-Sud, Orsay, France
| | - N Rosenfeld
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge
- Cancer Research UK Major Centre - Cambridge, Cambridge, UK
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