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Fu X, Yang M, Zhang H, Wang Q, Fu Y, Liu Q. Microfluidic bead-based biosensor: Ultrasensitive ctDNA detection based on duplex-functional split-DNAzyme and dendritic enzyme-free signal amplification. Anal Biochem 2024; 687:115457. [PMID: 38184137 DOI: 10.1016/j.ab.2024.115457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/20/2023] [Accepted: 01/01/2024] [Indexed: 01/08/2024]
Abstract
Circulating tumor DNA (ctDNA) is a crucial cancer biomarker for early or noninvasive monitoring, which is essential for developing ultrasensitive and selective assays in cancer diagnosis and treatment. Herein, a cascade signal amplification of duplex-functional split-DNAzyme and dendritic probes was proposed for ultrasensitive and specific detection of nasopharyngeal carcinoma-associated Epstein-Barr virus (EBV) DNA on microfluidic microbead array chips. With the assistance of Pb2+, the duplex-functional split-DNAzyme recognizes EBV DNA and then rapidly cleaves the substrate strand. Subsequently, the released target could be recycled, and its exposed capture probe, triggered the dendritic enzyme-free signal amplification. As the enhanced mass transfer capability, target recycling, and dendritic DNA structure signal amplification inherent to microfluidic bead arrays were integrated, it achieved an excellent detection limit of 0.36 fM and a wide linear range of 1 fM∼103 fM. Further, it was applied to content detect simulated samples of EBV DNA, recovery ranged from 97.2 % to 108.1 %, and relative standard deviation (RSD) from 3.3 % to 5.9 %, exhibiting satisfactory recovery results. The developed microfluidic biosensor was a high-sensitivity and anti-interference system for ctDNA analysis, with minimal reagent volumes (microlitres) required. Thus, it is a promising platform for ctDNA at the lowest level at their earliest incidence.
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Affiliation(s)
- Xin Fu
- Hunan Provincial Key Laboratory of Environmental Catalysis and Waste Recycling, College of Materials and Chemical Engineering, Hunan Institute of Engineering, Xiangtan, 411104, China
| | - Mei Yang
- Hunan Provincial Key Laboratory of Environmental Catalysis and Waste Recycling, College of Materials and Chemical Engineering, Hunan Institute of Engineering, Xiangtan, 411104, China
| | - He Zhang
- Hunan Provincial Key Laboratory of Environmental Catalysis and Waste Recycling, College of Materials and Chemical Engineering, Hunan Institute of Engineering, Xiangtan, 411104, China.
| | - Qing Wang
- Hunan Provincial Key Laboratory of Environmental Catalysis and Waste Recycling, College of Materials and Chemical Engineering, Hunan Institute of Engineering, Xiangtan, 411104, China
| | - Yu Fu
- Hunan Provincial Key Laboratory of Environmental Catalysis and Waste Recycling, College of Materials and Chemical Engineering, Hunan Institute of Engineering, Xiangtan, 411104, China
| | - Qiong Liu
- Hunan Provincial Key Laboratory of Environmental Catalysis and Waste Recycling, College of Materials and Chemical Engineering, Hunan Institute of Engineering, Xiangtan, 411104, China
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2
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Chen M, Shen MC, Chang SP, Ma GC, Lee DJ, Yan A. De Novo Noninversion Variants Implicated in Sporadic Hemophilia A: A Variant Origin and Timing Study. Int J Mol Sci 2024; 25:1763. [PMID: 38339041 PMCID: PMC10855912 DOI: 10.3390/ijms25031763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/26/2024] [Accepted: 01/26/2024] [Indexed: 02/12/2024] Open
Abstract
Sporadic hemophilia A (HA) enables the persistence of HA in the population. F8 gene inversion originates mainly in male germ cells during meiosis. To date, no studies have shown the origin and timing of HA sporadic noninversion variants (NIVs); herein, we assume that HA-sporadic NIVs are generated as a de novo variant. Of the 125 registered families with HA, 22 were eligible for inclusion. We conducted a linkage analysis using F8 gene markers and amplification refractory mutation system-quantitative polymerase chain reaction to confirm the origin of the sporadic NIVs (~0% mutant cells) or the presence of a mosaic variant, which requires further confirmation of the origin in the parent. Nine mothers, four maternal grandmothers, and six maternal grandfathers were confirmed to be the origin of sporadic NIVs, which most likely occurred in the zygote within the first few cell divisions and in single sperm cells, respectively. Three mothers had mosaic variants, which most likely occurred early in postzygotic embryogenesis. All maternal grandparents were free from sporadic NIV. In conclusion, F8 NIVs in sporadic HA were found to be caused primarily by de novo variants. Our studies are essential for understanding the genetic pathogenesis of HA and improving current genetic counseling.
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Affiliation(s)
- Ming Chen
- Department of Genomic Medicine, Changhua Christian Hospital, Changhua 500, Taiwan; (M.C.); (S.-P.C.); (G.-C.M.); (D.-J.L.); (A.Y.)
- Department of Obstetrics and Gynecology, Changhua Christian Hospital, Changhua 500, Taiwan
- Department of Medical Genetics National Taiwan University Hospital, Taipei 100, Taiwan
- Department of Obstetrics and Gynecology, National Taiwan University Hospital, Taipei 100, Taiwan
| | - Ming-Ching Shen
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei 100, Taiwan
- Department of Internal Medicine, National Taiwan University Hospital, Taipei 100, Taiwan
- Hemophilia Treatment and Thrombosis Center, Department of Internal Medicine, Changhua Christian Hospital, Changhua 500, Taiwan
| | - Shun-Ping Chang
- Department of Genomic Medicine, Changhua Christian Hospital, Changhua 500, Taiwan; (M.C.); (S.-P.C.); (G.-C.M.); (D.-J.L.); (A.Y.)
| | - Gwo-Chin Ma
- Department of Genomic Medicine, Changhua Christian Hospital, Changhua 500, Taiwan; (M.C.); (S.-P.C.); (G.-C.M.); (D.-J.L.); (A.Y.)
| | - Dong-Jay Lee
- Department of Genomic Medicine, Changhua Christian Hospital, Changhua 500, Taiwan; (M.C.); (S.-P.C.); (G.-C.M.); (D.-J.L.); (A.Y.)
| | - Adeline Yan
- Department of Genomic Medicine, Changhua Christian Hospital, Changhua 500, Taiwan; (M.C.); (S.-P.C.); (G.-C.M.); (D.-J.L.); (A.Y.)
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3
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Long J, Chen M, Yu Y, Wu Q, Yang X. Triple-recognition strategy for one-pot detection of single nucleotide variants by aligner-mediated cleavage-triggered exponential amplification. Anal Chim Acta 2023; 1276:341617. [PMID: 37573107 DOI: 10.1016/j.aca.2023.341617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/06/2023] [Accepted: 07/12/2023] [Indexed: 08/14/2023]
Abstract
The detection of single nucleotide variants (SNVs) is important for the diagnosis and treatment of cancer. To date, researchers have devised several methods to detect SNVs, but most of them are complex and time-consuming. To improve SNVs detection specificity and sensitivity, we developed a triple-recognition strategy, which facilitates aligner-mediated cleavage-triggered exponential amplification (Trec-AMC-EXPAR) for the rapid, specific, and one-pot detection of SNV. Under optimized conditions, Trec-AMC-EXPAR detected two clinically significant SNVs, PIK3CAH1047R and EGFR L858R within 80 min, with a reliable detection of 0.1% SNV in the wide type, which is lower than that of allele-specific PCR (AS-PCR) for detecting SNV. Finally, by spiking into normal human serum samples, mutants mixed with the wild-type targets in different ratios were analyzed, resulting in the relative standard deviation (RSD) of recovery ratios <3%. The findings suggested the potential application of Trec-AMC-EXPAR in clinical disease diagnosis. In summary, the proposed Trec-AMC-EXPAR technique provides a novel fast and convenient method for one-pot detection of SNV with high sensitivity and specificity.
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Affiliation(s)
- Jinyan Long
- Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Mengqi Chen
- Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Yang Yu
- Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Qiaomin Wu
- Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Xiaolan Yang
- Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China.
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Dao J, Conway PJ, Subramani B, Meyyappan D, Russell S, Mahadevan D. Using cfDNA and ctDNA as Oncologic Markers: A Path to Clinical Validation. Int J Mol Sci 2023; 24:13219. [PMID: 37686024 PMCID: PMC10487653 DOI: 10.3390/ijms241713219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 08/21/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
The detection of circulating tumor DNA (ctDNA) in liquid biopsy samples as an oncological marker is being used in clinical trials at every step of clinical management. As ctDNA-based liquid biopsy kits are developed and used in clinics, companies work towards increased convenience, accuracy, and cost over solid biopsies and other oncological markers. The technology used to differentiate ctDNA and cell-free DNA (cfDNA) continues to improve with new tests and methodologies being able to detect down to mutant allele frequencies of 0.001% or 1/100,000 copies. Recognizing this development in technology, the FDA has recently given pre-market approval and breakthrough device designations to multiple companies. The purpose of this review is to look at the utility of measuring total cfDNA, techniques used to differentiate ctDNA from cfDNA, and the utility of different ctDNA-based liquid biopsy kits using relevant articles from PubMed, clinicaltrials.gov, FDA approvals, and company newsletters. Measuring total cfDNA could be a cost-effective, viable prognostic marker, but various factors do not favor it as a monitoring tool during chemotherapy. While there may be a place in the clinic for measuring total cfDNA in the future, the lack of standardization means that it is difficult to move forward with large-scale clinical validation studies currently. While the detection of ctDNA has promising standardized liquid biopsy kits from various companies with large clinical trials ongoing, their applications in screening and minimal residual disease can suffer from lower sensitivity. However, researchers are working towards solutions to these issues with innovations in technology, multi-omics, and sampling. With great promise, further research is needed before liquid biopsies can be recommended for everyday clinical management.
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Affiliation(s)
- Jonathan Dao
- Long School of Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Patrick J. Conway
- Mays Cancer Center, University of Texas Health, San Antonio, TX 78229, USA
- Graduate School of Biomedical Sciences, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Baskaran Subramani
- Mays Cancer Center, University of Texas Health, San Antonio, TX 78229, USA
- Graduate School of Biomedical Sciences, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Devi Meyyappan
- Mays Cancer Center, University of Texas Health, San Antonio, TX 78229, USA
| | - Sammy Russell
- Long School of Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Daruka Mahadevan
- Long School of Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA
- Mays Cancer Center, University of Texas Health, San Antonio, TX 78229, USA
- Graduate School of Biomedical Sciences, University of Texas Health San Antonio, San Antonio, TX 78229, USA
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5
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Site-specific insertion of endonuclease recognition sites into amplicons to improve post-PCR analysis sensitivity of gene mutation. Biosens Bioelectron 2022; 208:114191. [PMID: 35366426 DOI: 10.1016/j.bios.2022.114191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/01/2022] [Accepted: 03/14/2022] [Indexed: 12/31/2022]
Abstract
Precise detection of low-frequency gene mutations surrounded by excess wild-type DNA is important in many aspects of medical fields. Most hybridization-based methods for high-resolution mutant allele analysis are hindered by competition of the complementary strand with single-strand probes for the target strand. Here, we demonstrate that site-specific insertion of endonuclease recognition sites into amplicons allows post-PCR generation of short dsDNA or ssDNA, whereby improves the sensitivity of both melting temperature analysis (MTA) and end-point detection following up. Using a three-staged PCR protocol, enrichment of target gene and incorporation of specific restriction sites in amplicons were ensued with hardly any loss in amplification efficiency and specificity. It enables simultaneous discrimination among a panel of totally 11 EGFR 19 exon deletion mutations via MTA after post-PCR digestion by either FokI only or cooperated with CRISPR-Cas12a, using SYBR green I. By replacement of one double-strand cleavage site with a nickase binding domain post-PCR generation of ssDNA of interest via strand displacement amplification (termed as iSDA) is realized. Our preliminary investigation shows that iSDA permits analysis of single nucleotide variants down to 0.1% allelic-frequency using end-point detection. Given the good compatibility with the majority of mutant-enrich PCR methods, we envision it would advance the current gene profiling technologies to a large extent.
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6
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Qiao X, Gao Y, Li J, Wang Z, Qiao H, Qi H. Sensitive analysis of single nucleotide variation by Cas13d orthologs, EsCas13d and RspCas13d. Biotechnol Bioeng 2021; 118:3037-3045. [PMID: 33964175 DOI: 10.1002/bit.27813] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/28/2021] [Accepted: 04/30/2021] [Indexed: 12/26/2022]
Abstract
RNA-guided CRISPR (RNA-targeting clustered regularly interspaced short palindromic repeats) effector Cas13d is the smallest Class II subtype VI proteins identified so far. Here, two recently identified Cas13d effectors from Eubacterium siraeum (Es) and Ruminococcus sp. (Rsp) were characterized and applied for sensitive nucleic acid detection. We demonstrated that the special target triggered collateral cleavage of these two Cas13d orthologs could provide rapid target RNA detection in picomolar range and then the tolerance for mismatch between crRNA and target RNA was characterized as well. Finally, an additional single mismatch was introduced into crRNA to enhance the two Cas13d orthologs mediated detection of low variant allele fraction, 0.1% T790M. Overall, this study demonstrated that both EsCas13d and RspCas13d could robustly detect target RNA carrying special single-nucleotide variation with high specificity and sensitivity, thereby providing newly qualified machinery in toolbox for efficient molecular diagnostics.
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Affiliation(s)
- Xin Qiao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
| | - Yanmin Gao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
| | - Jiaojiao Li
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
| | - Zhaoguan Wang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
| | - Hongyan Qiao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
| | - Hao Qi
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
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7
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Wang YH, Song Z, Hu XY, Wang HS. Circulating tumor DNA analysis for tumor diagnosis. Talanta 2021; 228:122220. [PMID: 33773726 DOI: 10.1016/j.talanta.2021.122220] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 02/05/2021] [Accepted: 02/13/2021] [Indexed: 01/10/2023]
Abstract
Tumor is a kind of abnormal organism generated by the proliferation and differentiation of cells in the body under the action of various initiating and promoting factors, which seriously threatens human life and health. Tumorigenesis is a gradual process that involves multistage reactions and the accumulation of mutations. Gene mutation usually occurs during tumorigenesis, and can be used for tumor diagnosis. Early diagnosis is the most effective way to improve the cure rate and reduce the mortality rate. Among the peripheral blood circulating tumor DNA (ctDNA), gene mutation in keeping with tumor cells can be detected, which can potentially replace tumor tissue section for early diagnosis. It has been considered as a liquid biopsy marker with good clinical application prospect. However, the high fragmentation and low concentration of ctDNA in blood result in the difficulty of tumor stage determination. Therefore, high sensitive and specific mutation detection methods have been developed to detect trace mutant ctDNA. At present, the approaches include digital PCR (dPCR), Bead, Emulsion, Amplification and Magnetic (BEAMing), Next Generation Sequencing (NGS), Amplification Refractory Mutation System (ARMS), etc. In this paper, the principle, characteristics, latest progress and application prospects of these methods are reviewed, which will facilitate researchers to choose appropriate ctDNA detection approaches.
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Affiliation(s)
- Yi-Hui Wang
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), China Pharmaceutical University, Nanjing, 210009, China; Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, 210009, China
| | - Zhen Song
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), China Pharmaceutical University, Nanjing, 210009, China; Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, 210009, China
| | - Xin-Yuan Hu
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), China Pharmaceutical University, Nanjing, 210009, China; Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, 210009, China
| | - Huai-Song Wang
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), China Pharmaceutical University, Nanjing, 210009, China; Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, 210009, China.
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8
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Bai S, Xu B, Zhang Y, Zhang Y, Dang H, Yang S, Zuo C, Zhang L, Li J, Xie G. Tuning the specificity of DNA probes using bulge-loops for low-abundance SNV detection. Biosens Bioelectron 2020; 154:112092. [DOI: 10.1016/j.bios.2020.112092] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 02/05/2020] [Accepted: 02/11/2020] [Indexed: 12/15/2022]
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9
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SLAM-MS: Mutation scanning of stem-loop amplicons with TaqMan probes by quantitative DNA melting analysis. Sci Rep 2020; 10:5476. [PMID: 32214156 PMCID: PMC7096437 DOI: 10.1038/s41598-020-62173-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Accepted: 03/09/2020] [Indexed: 12/30/2022] Open
Abstract
DNA Melting Analysis (DMA) with a TaqMan probe covering the mutation “hot spot” is a simple, sensitive, and “closed tube” method of mutation detection. However, DMA requires asymmetric PCR to produce single-stranded amplicons capable of interacting with TaqMan probes. This makes quantitative analysis impossible owing to low amplification efficiency. Moreover, bi-strand mutation detection necessitates two independent PCRs. The SLAM-MS (Stem-Loop AMplicon Mutation Scanning) assay, in which symmetric PCR is performed using primers with 5'-universal primer sequence (UPS), has been developed to detect KRAS mutations. Some of the resulting amplicons, sense and antisense, adopt single-stranded stem-loop conformation and become unable to renature, but able to hybridize with TaqMan probes. Hybrids of stem-loops and complementary TaqMan probes are suitable for melting analysis and simultaneous bi-strand mutation scanning. In addition, the areas under the melting peaks are determined by the PeakFit software, a non-linear iterative curve fitting program, to evaluate the wild-type/mutant allele ratio. Thus, the SLAM-MS assay permits quantification of both the number of copies of the target sequence and the percentage of mutant alleles. For mutant enrichment, the SLAM-MS assay uses TaqMan probes as PCR blocking agents allowing an ~10 times higher mutation detection sensitivity than High Resolution Melting (HRM) assay.
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10
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Wood-Bouwens CM, Haslem D, Moulton B, Almeda AF, Lee H, Heestand GM, Nadauld LD, Ji HP. Therapeutic Monitoring of Circulating DNA Mutations in Metastatic Cancer with Personalized Digital PCR. J Mol Diagn 2020; 22:247-261. [PMID: 31837432 PMCID: PMC7031679 DOI: 10.1016/j.jmoldx.2019.10.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 09/09/2019] [Accepted: 10/17/2019] [Indexed: 02/06/2023] Open
Abstract
As a high-performance solution for longitudinal monitoring of patients being treated for metastatic cancer, a single-color digital PCR (dPCR) assay that detects and quantifies specific cancer mutations present in circulating tumor DNA (ctDNA) was developed. This customizable assay has a high sensitivity of detection. One can detect a mutation allelic fraction of 0.1%, equivalent to three mutation-bearing DNA molecules among 3000 genome equivalents. The objective of this study was to validate the use of personalized dPCR mutation assays to monitor patients with metastatic cancer. The dPCR results were compared with serum biomarkers indicating disease progression or response. Patients had metastatic colorectal, biliary, breast, lung, and melanoma cancers. Mutations occurred in essential cancer drivers such as BRAF, KRAS, and PIK3CA. Patients were monitored over multiple cycles of treatment for up to a year. All patients had detectable ctDNA mutations. The results correlated with serum markers of metastatic cancer burden, including carcinoembryonic antigen, CA-19-9, and CA-15-3, and qualitatively corresponding to imaging studies. Corresponding trends were observed among these patients receiving active treatment with chemotherapy or targeted agents. For example, in one patient under active treatment, increasing quantities of ctDNA molecules were detected over time, indicating recurrence of tumor. This study demonstrates that personalized dPCR enables longitudinal monitoring of patients with metastatic cancer and may be a useful indicator for treatment response.
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Affiliation(s)
- Christina M Wood-Bouwens
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Derrick Haslem
- Precision Genomics, Intermountain Healthcare, St. George, Utah
| | - Bryce Moulton
- Precision Genomics, Intermountain Healthcare, St. George, Utah
| | - Alison F Almeda
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Hojoon Lee
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Gregory M Heestand
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, California
| | | | - Hanlee P Ji
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, California; Stanford Genome Technology Center, Stanford University, Palo Alto, California.
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11
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Herbreteau G, Charpentier S, Vallée A, Denis MG. Use of circulating tumoral DNA to guide treatment for metastatic melanoma. Pharmacogenomics 2019; 20:1259-1270. [DOI: 10.2217/pgs-2019-0097] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The management of metastatic cutaneous melanoma is conditioned by the identification of BRAF-activating mutations in tumor DNA. Tumor genotyping is usually performed on DNA extracted from tissue samples. However, these invasive samples are rarely repeated during follow-up, and their analysis requires a sample pre-treatment which may take several weeks. Circulating tumor DNA (ctDNA), released into blood by cancer cells, is a good alternative to tissue sampling. ctDNA is not subject to tumor heterogeneity, and can be analyzed rapidly, making possible the detection of mutations in emergency or in patients whose tumor cannot be sampled. ctDNA can also be analyzed repeatedly during follow-up, for postresection minimal residual disease assessment, for therapeutic response monitoring and for early relapse detection.
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Affiliation(s)
- Guillaume Herbreteau
- Laboratoire de Biochimie et Plateforme de Génétique Moléculaire des Cancers, CHU Nantes, Nantes, France
- Centre de Recherche en Cancérologie et Immunologie, CRCINA, INSERM U1232, Nantes, France
| | - Sandrine Charpentier
- Laboratoire de Biochimie et Plateforme de Génétique Moléculaire des Cancers, CHU Nantes, Nantes, France
- Centre de Recherche en Cancérologie et Immunologie, CRCINA, INSERM U1232, Nantes, France
| | - Audrey Vallée
- Laboratoire de Biochimie et Plateforme de Génétique Moléculaire des Cancers, CHU Nantes, Nantes, France
- Centre de Recherche en Cancérologie et Immunologie, CRCINA, INSERM U1232, Nantes, France
| | - Marc G Denis
- Laboratoire de Biochimie et Plateforme de Génétique Moléculaire des Cancers, CHU Nantes, Nantes, France
- Centre de Recherche en Cancérologie et Immunologie, CRCINA, INSERM U1232, Nantes, France
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12
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Tuaeva NO, Falzone L, Porozov YB, Nosyrev AE, Trukhan VM, Kovatsi L, Spandidos DA, Drakoulis N, Kalogeraki A, Mamoulakis C, Tzanakakis G, Libra M, Tsatsakis A. Translational Application of Circulating DNA in Oncology: Review of the Last Decades Achievements. Cells 2019; 8:E1251. [PMID: 31615102 PMCID: PMC6829588 DOI: 10.3390/cells8101251] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 09/30/2019] [Accepted: 10/12/2019] [Indexed: 02/06/2023] Open
Abstract
In recent years, the introduction of new molecular techniques in experimental and clinical settings has allowed researchers and clinicians to propose circulating-tumor DNA (ctDNA) analysis and liquid biopsy as novel promising strategies for the early diagnosis of cancer and for the definition of patients' prognosis. It was widely demonstrated that through the non-invasive analysis of ctDNA, it is possible to identify and characterize the mutational status of tumors while avoiding invasive diagnostic strategies. Although a number of studies on ctDNA in patients' samples significantly contributed to the improvement of oncology practice, some investigations generated conflicting data about the diagnostic and prognostic significance of ctDNA. Hence, to highlight the relevant achievements obtained so far in this field, a clearer description of the current methodologies used, as well as the obtained results, are strongly needed. On these bases, this review discusses the most relevant studies on ctDNA analysis in cancer, as well as the future directions and applications of liquid biopsy. In particular, special attention was paid to the early diagnosis of primary cancer, to the diagnosis of tumors with an unknown primary location, and finally to the prognosis of cancer patients. Furthermore, the current limitations of ctDNA-based approaches and possible strategies to overcome these limitations are presented.
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Affiliation(s)
- Natalia O Tuaeva
- I.M. Sechenov First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia.
| | - Luca Falzone
- Department of Biomedical and Biotechnlogical Sciences, University of Catania, 95123 Catania, Italy.
- Epidemiology Unit, IRCCS Istituto Nazionale Tumori "Fondazione G. Pascale", 80131 Naples, Italy.
| | - Yuri B Porozov
- I.M. Sechenov First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia.
- ITMO University, Saint Petersburg 197101, Russia.
| | - Alexander E Nosyrev
- I.M. Sechenov First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia.
| | - Vladimir M Trukhan
- I.M. Sechenov First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia.
| | - Leda Kovatsi
- Laboratory of Forensic Medicine and Toxicology, School of Medicine, Aristotle University of Thessaloniki, 54248 Thessaloniki, Greece.
| | - Demetrios A Spandidos
- Laboratory of Clinical Virology, Medical School, University of Crete, Heraklion, 70013 Crete, Greece.
| | - Nikolaos Drakoulis
- Research Group of Clinical Pharmacology and Pharmacogenomics, Faculty of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, 15771 Zografou, Greece.
| | - Alexandra Kalogeraki
- Department of Pathology-Cytopathology, Medical School, University of Crete, Heraklion, 70013 Crete, Greece.
| | - Charalampos Mamoulakis
- Department of Urology, University General Hospital of Heraklion, University of Crete, Medical School, Heraklion, 70013 Crete, Greece.
| | - George Tzanakakis
- Laboratory of Anatomy-Histology-Embryology, Medical School, University of Crete, Heraklion, 70013 Crete, Greece.
| | - Massimo Libra
- Department of Biomedical and Biotechnlogical Sciences, University of Catania, 95123 Catania, Italy.
- Research Center for Prevention, Diagnosis and Treatment of Cancer, University of Catania, 95123 Catania, Italy.
| | - Aristides Tsatsakis
- I.M. Sechenov First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia.
- Department of Forensic Sciences and Toxicology, Faculty of Medicine, University of Crete, Heraklion, 71003 Crete, Greece.
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Schmidt H, Kulasinghe A, Allcock RJN, Tan LY, Mokany E, Kenny L, Punyadeera C. A Pilot Study to Non-Invasively Track PIK3CA Mutation in Head and Neck Cancer. Diagnostics (Basel) 2018; 8:diagnostics8040079. [PMID: 30501041 PMCID: PMC6315660 DOI: 10.3390/diagnostics8040079] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 11/21/2018] [Accepted: 11/26/2018] [Indexed: 12/21/2022] Open
Abstract
Background: PIK3CA pathways are the most frequently mutated oncogenic pathway in head and neck squamous cell carcinoma (HNSCC), including virally driven HNCs. PIK3CA is involved in the PI3K-PTEN-mTOR signalling pathway. PIK3CA has been implicated in HNSCC progression and PIK3CA mutations may serve as predictive biomarkers for therapy selection. Circulating tumour DNA (ctDNA) derived from necrotic and apoptotic tumour cells are thought to harbour tumour-specific genetic alterations. As such, the detection of PIK3CA alterations detected by ctDNA holds promise as a potential biomarker in HNSCC. Methods: Blood samples from treatment naïve HNSCC patients (n = 29) were interrogated for a commonly mutated PIK3CA hotspot mutation using low cost allele-specific Plex-PCRTM technology. Results: In this pilot, cross sectional study, PIK3CA E545K mutation was detected in the plasma samples of 9/29 HNSCC patients using the Plex-PCRTM technology. Conclusion: The results of this pilot study support the notion of using allele-specific technologies for cost-effective testing of ctDNA, and further assert the potential utility of ctDNA in HNSCC.
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Affiliation(s)
- Henri Schmidt
- The School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove 4059, Queensland, Australia.
- Translational Research Institute, Queensland University of Technology, Woolloongabba 4102, Queensland, Australia.
| | - Arutha Kulasinghe
- The School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove 4059, Queensland, Australia.
- Translational Research Institute, Queensland University of Technology, Woolloongabba 4102, Queensland, Australia.
| | - Richard J N Allcock
- School of Biomedical sciences, The University of Western Australia, Nedlands 6009, Western Australia, Australia.
- Pathwest Laboratory Medicine WA, Nedlands 6009, Western Australia, Australia.
| | - Lit Yeen Tan
- SpeeDx Pty. Ltd., National Innovation Centre, Australian Technology Park, Eveleigh Sydney 2015, New South Wales, Australia.
| | - Elisa Mokany
- SpeeDx Pty. Ltd., National Innovation Centre, Australian Technology Park, Eveleigh Sydney 2015, New South Wales, Australia.
| | - Liz Kenny
- Central Integrated Regional Cancer Service, Royal Brisbane and Women's Hospital, Herston 4029, Queensland, Australia.
| | - Chamindie Punyadeera
- The School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove 4059, Queensland, Australia.
- Translational Research Institute, Queensland University of Technology, Woolloongabba 4102, Queensland, Australia.
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14
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Lu W, Burton L, Larkin J, Chapman PB, Ascierto PA, Ribas A, Robert C, Sosman JA, McArthur GA, Chang I, Caro I, Penuel E, Yan Y, Wongchenko MJ. Elevated Levels of BRAFV600 Mutant Circulating Tumor DNA and Circulating Hepatocyte Growth Factor Are Associated With Poor Prognosis in Patients With Metastatic Melanoma. JCO Precis Oncol 2018; 2:1-17. [DOI: 10.1200/po.17.00168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Purpose We performed a retrospective exploratory analysis to evaluate the prognostic and predictive effect of two circulating biomarkers, BRAFV600 mutant circulating tumor DNA (ctDNA) and circulating hepatocyte growth factor (cHGF), in metastatic melanoma. Materials and Methods This study evaluated patients from BRIM-3, a phase III trial comparing vemurafenib and dacarbazine in 675 patients with BRAFV600 mutated advanced melanoma. ctDNA was measured using droplet digital polymerase chain reaction, and cHGF was measured by enzyme-linked immunosorbent assay. Overall survival (OS) was estimated using the Kaplan-Meier method, and hazard ratios (HRs) were estimated using Cox proportional hazards modeling. Partitioning analysis was used to group patients into risk categories. Results Patients with elevated levels of baseline BRAFV600 ctDNA had significantly shorter median OS than those with undetectable levels of ctDNA (vemurafenib arm, 9.9 v 21.4 months, respectively, and dacarbazine arm: 6.1 v 21.0 months, respectively). Median OS was also shorter in patients with high levels of cHGF compared with those with low cHGF (vemurafenib arm, 11.9 v 17.3 months, respectively, and dacarbazine arm, 6.1 v 14.4 months, respectively). In a multivariable proportional hazards model with adjustment for lactate dehydrogenase, Eastern Cooperative Oncology Group status, disease stage, and treatment, ctDNA and cHGF were both independent prognostic factors for OS, (HR, 1.75; 95% CI, 1.35 to 2.28 for high v undetectable ctDNA; HR, 1.24; 95% CI, 1.00 to 1.53 for high v low cHGF). Using partitioning analysis, we found that patients with elevated ctDNA combined with elevated cHGF constituted the highest risk group with significantly shorter OS. Conclusion Here, we report that BRIM-3 patients with high levels of ctDNA and cHGF have worse OS regardless of treatment and that these factors are independent prognostic markers for metastatic melanoma.
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Affiliation(s)
- William Lu
- William Lu, Luciana Burton, Ilsung Chang, Ivor Caro, Elicia Penuel, Yibing Yan, and Matthew J. Wongchenko, Genentech, South San Francisco; Antoni Ribas, The Jonsson Comprehensive Cancer Center at University of California, Los Angeles, CA; James Larkin, The Royal Marsden NHS Foundation Trust, London, United Kingdom; Paul B. Chapman, Memorial Sloan Kettering Cancer Center, New York, NY; Paolo A. Ascierto, Istituto Nazionale Tumori Fondazione G. Pascale, Naples, Italy; Caroline Robert, Institut Gustave
| | - Luciana Burton
- William Lu, Luciana Burton, Ilsung Chang, Ivor Caro, Elicia Penuel, Yibing Yan, and Matthew J. Wongchenko, Genentech, South San Francisco; Antoni Ribas, The Jonsson Comprehensive Cancer Center at University of California, Los Angeles, CA; James Larkin, The Royal Marsden NHS Foundation Trust, London, United Kingdom; Paul B. Chapman, Memorial Sloan Kettering Cancer Center, New York, NY; Paolo A. Ascierto, Istituto Nazionale Tumori Fondazione G. Pascale, Naples, Italy; Caroline Robert, Institut Gustave
| | - James Larkin
- William Lu, Luciana Burton, Ilsung Chang, Ivor Caro, Elicia Penuel, Yibing Yan, and Matthew J. Wongchenko, Genentech, South San Francisco; Antoni Ribas, The Jonsson Comprehensive Cancer Center at University of California, Los Angeles, CA; James Larkin, The Royal Marsden NHS Foundation Trust, London, United Kingdom; Paul B. Chapman, Memorial Sloan Kettering Cancer Center, New York, NY; Paolo A. Ascierto, Istituto Nazionale Tumori Fondazione G. Pascale, Naples, Italy; Caroline Robert, Institut Gustave
| | - Paul B. Chapman
- William Lu, Luciana Burton, Ilsung Chang, Ivor Caro, Elicia Penuel, Yibing Yan, and Matthew J. Wongchenko, Genentech, South San Francisco; Antoni Ribas, The Jonsson Comprehensive Cancer Center at University of California, Los Angeles, CA; James Larkin, The Royal Marsden NHS Foundation Trust, London, United Kingdom; Paul B. Chapman, Memorial Sloan Kettering Cancer Center, New York, NY; Paolo A. Ascierto, Istituto Nazionale Tumori Fondazione G. Pascale, Naples, Italy; Caroline Robert, Institut Gustave
| | - Paolo A. Ascierto
- William Lu, Luciana Burton, Ilsung Chang, Ivor Caro, Elicia Penuel, Yibing Yan, and Matthew J. Wongchenko, Genentech, South San Francisco; Antoni Ribas, The Jonsson Comprehensive Cancer Center at University of California, Los Angeles, CA; James Larkin, The Royal Marsden NHS Foundation Trust, London, United Kingdom; Paul B. Chapman, Memorial Sloan Kettering Cancer Center, New York, NY; Paolo A. Ascierto, Istituto Nazionale Tumori Fondazione G. Pascale, Naples, Italy; Caroline Robert, Institut Gustave
| | - Antoni Ribas
- William Lu, Luciana Burton, Ilsung Chang, Ivor Caro, Elicia Penuel, Yibing Yan, and Matthew J. Wongchenko, Genentech, South San Francisco; Antoni Ribas, The Jonsson Comprehensive Cancer Center at University of California, Los Angeles, CA; James Larkin, The Royal Marsden NHS Foundation Trust, London, United Kingdom; Paul B. Chapman, Memorial Sloan Kettering Cancer Center, New York, NY; Paolo A. Ascierto, Istituto Nazionale Tumori Fondazione G. Pascale, Naples, Italy; Caroline Robert, Institut Gustave
| | - Caroline Robert
- William Lu, Luciana Burton, Ilsung Chang, Ivor Caro, Elicia Penuel, Yibing Yan, and Matthew J. Wongchenko, Genentech, South San Francisco; Antoni Ribas, The Jonsson Comprehensive Cancer Center at University of California, Los Angeles, CA; James Larkin, The Royal Marsden NHS Foundation Trust, London, United Kingdom; Paul B. Chapman, Memorial Sloan Kettering Cancer Center, New York, NY; Paolo A. Ascierto, Istituto Nazionale Tumori Fondazione G. Pascale, Naples, Italy; Caroline Robert, Institut Gustave
| | - Jeffrey A. Sosman
- William Lu, Luciana Burton, Ilsung Chang, Ivor Caro, Elicia Penuel, Yibing Yan, and Matthew J. Wongchenko, Genentech, South San Francisco; Antoni Ribas, The Jonsson Comprehensive Cancer Center at University of California, Los Angeles, CA; James Larkin, The Royal Marsden NHS Foundation Trust, London, United Kingdom; Paul B. Chapman, Memorial Sloan Kettering Cancer Center, New York, NY; Paolo A. Ascierto, Istituto Nazionale Tumori Fondazione G. Pascale, Naples, Italy; Caroline Robert, Institut Gustave
| | - Grant A. McArthur
- William Lu, Luciana Burton, Ilsung Chang, Ivor Caro, Elicia Penuel, Yibing Yan, and Matthew J. Wongchenko, Genentech, South San Francisco; Antoni Ribas, The Jonsson Comprehensive Cancer Center at University of California, Los Angeles, CA; James Larkin, The Royal Marsden NHS Foundation Trust, London, United Kingdom; Paul B. Chapman, Memorial Sloan Kettering Cancer Center, New York, NY; Paolo A. Ascierto, Istituto Nazionale Tumori Fondazione G. Pascale, Naples, Italy; Caroline Robert, Institut Gustave
| | - Ilsung Chang
- William Lu, Luciana Burton, Ilsung Chang, Ivor Caro, Elicia Penuel, Yibing Yan, and Matthew J. Wongchenko, Genentech, South San Francisco; Antoni Ribas, The Jonsson Comprehensive Cancer Center at University of California, Los Angeles, CA; James Larkin, The Royal Marsden NHS Foundation Trust, London, United Kingdom; Paul B. Chapman, Memorial Sloan Kettering Cancer Center, New York, NY; Paolo A. Ascierto, Istituto Nazionale Tumori Fondazione G. Pascale, Naples, Italy; Caroline Robert, Institut Gustave
| | - Ivor Caro
- William Lu, Luciana Burton, Ilsung Chang, Ivor Caro, Elicia Penuel, Yibing Yan, and Matthew J. Wongchenko, Genentech, South San Francisco; Antoni Ribas, The Jonsson Comprehensive Cancer Center at University of California, Los Angeles, CA; James Larkin, The Royal Marsden NHS Foundation Trust, London, United Kingdom; Paul B. Chapman, Memorial Sloan Kettering Cancer Center, New York, NY; Paolo A. Ascierto, Istituto Nazionale Tumori Fondazione G. Pascale, Naples, Italy; Caroline Robert, Institut Gustave
| | - Elicia Penuel
- William Lu, Luciana Burton, Ilsung Chang, Ivor Caro, Elicia Penuel, Yibing Yan, and Matthew J. Wongchenko, Genentech, South San Francisco; Antoni Ribas, The Jonsson Comprehensive Cancer Center at University of California, Los Angeles, CA; James Larkin, The Royal Marsden NHS Foundation Trust, London, United Kingdom; Paul B. Chapman, Memorial Sloan Kettering Cancer Center, New York, NY; Paolo A. Ascierto, Istituto Nazionale Tumori Fondazione G. Pascale, Naples, Italy; Caroline Robert, Institut Gustave
| | - Yibing Yan
- William Lu, Luciana Burton, Ilsung Chang, Ivor Caro, Elicia Penuel, Yibing Yan, and Matthew J. Wongchenko, Genentech, South San Francisco; Antoni Ribas, The Jonsson Comprehensive Cancer Center at University of California, Los Angeles, CA; James Larkin, The Royal Marsden NHS Foundation Trust, London, United Kingdom; Paul B. Chapman, Memorial Sloan Kettering Cancer Center, New York, NY; Paolo A. Ascierto, Istituto Nazionale Tumori Fondazione G. Pascale, Naples, Italy; Caroline Robert, Institut Gustave
| | - Matthew J. Wongchenko
- William Lu, Luciana Burton, Ilsung Chang, Ivor Caro, Elicia Penuel, Yibing Yan, and Matthew J. Wongchenko, Genentech, South San Francisco; Antoni Ribas, The Jonsson Comprehensive Cancer Center at University of California, Los Angeles, CA; James Larkin, The Royal Marsden NHS Foundation Trust, London, United Kingdom; Paul B. Chapman, Memorial Sloan Kettering Cancer Center, New York, NY; Paolo A. Ascierto, Istituto Nazionale Tumori Fondazione G. Pascale, Naples, Italy; Caroline Robert, Institut Gustave
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15
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Gorgannezhad L, Umer M, Islam MN, Nguyen NT, Shiddiky MJA. Circulating tumor DNA and liquid biopsy: opportunities, challenges, and recent advances in detection technologies. LAB ON A CHIP 2018; 18:1174-1196. [PMID: 29569666 DOI: 10.1039/c8lc00100f] [Citation(s) in RCA: 184] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Cell-free DNA (cfDNA) refers to short fragments of acellular nucleic acids detectable in almost all body fluids, including blood, and is involved in various physiological and pathological phenomena such as immunity, coagulation, aging, and cancer. In cancer patients, a fraction of hematogenous cfDNA originates from tumors, termed circulating tumor DNA (ctDNA), and may carry the same mutations and genetic alterations as those of a primary tumor. Thus, ctDNA potentially provides an opportunity for noninvasive assessment of cancer. Recent advances in ctDNA analysis methods will potentially lead to the development of a liquid biopsy tool for the diagnosis, prognosis, therapy response monitoring, and tracking the rise of new mutant sub-clones in cancer patients. Over the past few decades, cancer-specific mutations in ctDNA have been detected using a variety of untargeted methods such as digital karyotyping, personalized analysis of rearranged ends (PARE), whole-genome sequencing of ctDNA, and targeted approaches such as conventional and digital PCR-based methods and deep sequencing-based technologies. More recently, several chip-based electrochemical sensors have been developed for the analysis of ctDNA in patient samples. This paper aims to comprehensively review the diagnostic, prognostic, and predictive potential of ctDNA as a minimally invasive liquid biopsy for cancer patients. We also present an overview of current advances in the analytical sensitivity and accuracy of ctDNA analysis methods as well as biological and technical challenges, which need to be resolved for the integration of ctDNA analysis into routine clinical practice.
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Affiliation(s)
- Lena Gorgannezhad
- School of Environment and Science, Griffith University, Nathan Campus, QLD 4111, Australia. and Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan Campus, QLD 4111, Australia
| | - Muhammad Umer
- Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan Campus, QLD 4111, Australia
| | - Md Nazmul Islam
- School of Environment and Science, Griffith University, Nathan Campus, QLD 4111, Australia. and Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan Campus, QLD 4111, Australia
| | - Nam-Trung Nguyen
- Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan Campus, QLD 4111, Australia
| | - Muhammad J A Shiddiky
- School of Environment and Science, Griffith University, Nathan Campus, QLD 4111, Australia. and Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan Campus, QLD 4111, Australia
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16
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Rodda AE, Parker BJ, Spencer A, Corrie SR. Extending Circulating Tumor DNA Analysis to Ultralow Abundance Mutations: Techniques and Challenges. ACS Sens 2018; 3:540-560. [PMID: 29441780 DOI: 10.1021/acssensors.7b00953] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Liquid biopsies that analyze circulating tumor DNA (ctDNA) hold great promise in the guidance of clinical treatment for various cancers. However, the innate characteristics of ctDNA make it a difficult target: ctDNA is highly fragmented, and found at very low concentrations, both in absolute terms and relative to wildtype species. Clinically relevant target sequences often differ from the wildtype species by a single DNA base pair. These characteristics make analyzing mutant ctDNA a uniquely difficult process. Despite this, techniques have recently emerged for analyzing ctDNA, and have been used in pilot studies that showed promising results. These techniques each have various drawbacks, either in their analytical capabilities or in practical considerations, which restrict their application to many clinical situations. Many of the most promising potential applications of ctDNA require assay characteristics that are not currently available, and new techniques with these properties could have benefits in companion diagnostics, monitoring response to treatment and early detection. Here we review the current state of the art in ctDNA detection, with critical comparison of the analytical techniques themselves. We also examine the improvements required to expand ctDNA diagnostics to more advanced applications and discuss the most likely pathways for these improvements.
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Affiliation(s)
| | | | - Andrew Spencer
- Myeloma Research Group, Australian Center for Blood Diseases, Monash University, Melbourne, Victoria 3004, Australia
- Malignant Haematology & Stem Cell Transplantation Service, Alfred Hospital, Melbourne, Victoria 3004, Australia
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17
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Wu T, Chen W, Yang Z, Tan H, Wang J, Xiao X, Li M, Zhao M. DNA terminal structure-mediated enzymatic reaction for ultra-sensitive discrimination of single nucleotide variations in circulating cell-free DNA. Nucleic Acids Res 2018; 46:e24. [PMID: 29190359 PMCID: PMC5829738 DOI: 10.1093/nar/gkx1218] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Revised: 11/08/2017] [Accepted: 11/23/2017] [Indexed: 12/18/2022] Open
Abstract
Sensitive detection of the single nucleotide variants in cell-free DNA (cfDNA) may provide great opportunity for minimally invasive diagnosis and prognosis of cancer and other related diseases. Here, we demonstrate a facile new strategy for quantitative measurement of cfDNA mutations at low abundance in the cancer patients' plasma samples. The method takes advantage of a novel property of lambda exonuclease which effectively digests a 5'-fluorophore modified dsDNA with a 2-nt overhang structure and sensitively responds to the presence of mismatched base pairs in the duplex. It achieves a limit of detection as low as 0.02% (percentage of the mutant type) for BRAFV600E mutation, NRASQ61R mutation and three types of EGFR mutations (G719S, T790M and L858R). The method enabled identification of BRAFV600E and EGFRL858R mutations in the plasma of different cancer patients within only 3.5 h. Moreover, the terminal structure-dependent reaction greatly simplifies the probe design and reduces the cost, and the assay only requires a regular real-time PCR machine. This new method may serve as a practical tool for quantitative measurement of low-abundance mutations in clinical samples for providing genetic mutation information with prognostic or therapeutic implications.
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Affiliation(s)
- Tongbo Wu
- Beijing National Laboratory for Molecular Sciences and MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Wei Chen
- Beijing National Laboratory for Molecular Sciences and MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Ziyu Yang
- Beijing National Laboratory for Molecular Sciences and MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Haocheng Tan
- Beijing National Laboratory for Molecular Sciences and MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jiayu Wang
- Beijing National Laboratory for Molecular Sciences and MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xianjin Xiao
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Mengyuan Li
- Beijing National Laboratory for Molecular Sciences and MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Meiping Zhao
- Beijing National Laboratory for Molecular Sciences and MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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18
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Zou Z, Qi P, Qing Z, Zheng J, Yang S, Chen W, Yang R. Technologies for analysis of circulating tumour DNA: Progress and promise. Trends Analyt Chem 2017. [DOI: 10.1016/j.trac.2017.08.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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19
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Single-Color Digital PCR Provides High-Performance Detection of Cancer Mutations from Circulating DNA. J Mol Diagn 2017; 19:697-710. [PMID: 28818432 PMCID: PMC6593258 DOI: 10.1016/j.jmoldx.2017.05.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 05/05/2017] [Accepted: 05/09/2017] [Indexed: 02/02/2023] Open
Abstract
We describe a single-color digital PCR assay that detects and quantifies cancer mutations directly from circulating DNA collected from the plasma of cancer patients. This approach relies on a double-stranded DNA intercalator dye and paired allele-specific DNA primer sets to determine an absolute count of both the mutation and wild-type–bearing DNA molecules present in the sample. The cell-free DNA assay uses an input of 1 ng of nonamplified DNA, approximately 300 genome equivalents, and has a molecular limit of detection of three mutation DNA genome-equivalent molecules per assay reaction. When using more genome equivalents as input, we demonstrated a sensitivity of 0.10% for detecting the BRAF V600E and KRAS G12D mutations. We developed several mutation assays specific to the cancer driver mutations of patients' tumors and detected these same mutations directly from the nonamplified, circulating cell-free DNA. This rapid and high-performance digital PCR assay can be configured to detect specific cancer mutations unique to an individual cancer, making it a potentially valuable method for patient-specific longitudinal monitoring.
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20
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Liquid Biopsies for Cancer: Coming to a Patient near You. J Clin Med 2017; 6:jcm6010003. [PMID: 28054963 PMCID: PMC5294956 DOI: 10.3390/jcm6010003] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 12/15/2016] [Accepted: 12/18/2016] [Indexed: 12/14/2022] Open
Abstract
The use of circulating tumor DNA (ctDNA) as a novel and non-invasive test for the diagnosis and surveillance of cancer is a rapidly growing area of interest, with sequencing of ctDNA acting as a potential surrogate for tissue biopsy. Circulating tumor DNA has been detected incidentally during noninvasive prenatal testing and additionally in more than 75% of known cancer patients participating in ctDNA studies evaluating its sensitivity. In the setting of mutation-based targeted tumor therapy, it shows a concordance rate >80% when compared with gold-standard tissue biopsies. Through ctDNA detection and sequencing, a simple blood test becomes a liquid biopsy for cancer, surveying a patient’s entire circulation with the goal of early detection, prognostic information, personalized therapy options, and tracking for recurrence or resistance, all with fewer or no tissue biopsies. Given the recent first-ever FDA approval of a liquid biopsy, it is important for clinicians to be aware of the rapid advancements likely to bring these tests into our practices soon. Here we review the biology, clinical implications, and recent advances in circulating tumor DNA analysis.
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21
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Perakis S, Auer M, Belic J, Heitzer E. Advances in Circulating Tumor DNA Analysis. Adv Clin Chem 2017; 80:73-153. [PMID: 28431643 DOI: 10.1016/bs.acc.2016.11.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The analysis of cell-free circulating tumor DNA (ctDNA) is a very promising tool and might revolutionize cancer care with respect to early detection, identification of minimal residual disease, assessment of treatment response, and monitoring tumor evolution. ctDNA analysis, often referred to as "liquid biopsy" offers what tissue biopsies cannot-a continuous monitoring of tumor-specific changes during the entire course of the disease. Owing to technological improvements, efforts for the establishment of preanalytical and analytical benchmark, and the inclusion of ctDNA analyses in clinical trial, an actual clinical implementation has come within easy reach. In this chapter, recent advances of the analysis of ctDNA are summarized starting from the discovery of cell-free DNA, to methodological approaches and the clinical applicability.
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Affiliation(s)
- Samantha Perakis
- Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Martina Auer
- Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Jelena Belic
- Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Ellen Heitzer
- Institute of Human Genetics, Medical University of Graz, Graz, Austria.
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22
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Neueste technologische Entwicklungen für die Analyse von zirkulierender Tumor-DNA. MED GENET-BERLIN 2016. [DOI: 10.1007/s11825-016-0089-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Zusammenfassung
Die Analyse von zirkulierender Tumor-DNA, zusammen mit der Analyse von zirkulierenden Tumorzellen auch oft Liquid Biopsy genannt, ist ein sich rasch entwickelndes Feld in der medizinischen Forschung. Obwohl es von der Entdeckung der zellfreien DNA bis hin zur Erkenntnis, dass sie sich als Biomarker eignet, Jahrzehnte gedauert hat, wurde der klinische Nutzen der ctDNA hinsichtlich der Überwachung des Therapieansprechens, der Identifizierung von Resistenzmechanismen und neu aufkommenden Therapiezielen sowie der Detektion von minimaler Resterkrankung mittlerweile in unzähligen Studien bewiesen.
Aufgrund der hohen Variabilität, mit der ctDNA in der Zirkulation vorkommt, sowie der starken Fragmentierung, stellt die ctDNA aber einen schwierigen Analyten dar. In den letzten Jahren haben erhebliche technologische Fortschritte dazu beigetragen, dass eine Routineanwendung der ctDNA-Analysen tatsächlich realisierbar wird, sofern eine Reihe von regulatorischen Hürden überwunden wird.
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23
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Biosensors for liquid biopsy: circulating nucleic acids to diagnose and treat cancer. Anal Bioanal Chem 2016; 408:7255-64. [PMID: 27497966 DOI: 10.1007/s00216-016-9806-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 07/05/2016] [Accepted: 07/18/2016] [Indexed: 01/05/2023]
Abstract
The detection of cancer biomarkers freely circulating in blood offers new opportunities for cancer early diagnosis, patient follow-up, and therapy efficacy assessment based on liquid biopsy. In particular, circulating cell-free nucleic acids released from tumor cells have recently attracted great attention also because they become detectable in blood before the appearance of other circulating biomarkers, such as circulating tumor cells. The detection of circulating nucleic acids poses several technical challenges that arise from their low concentration and relatively small size. Here, possibilities offered by innovative biosensing approaches for the detection of circulating DNA in peripheral blood and blood-derived products such as plasma and serum blood are discussed. Different transduction principles are used to detect circulating DNAs and great advantages are derived from the combined use of nanostructured materials.
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